--- /dev/null
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
--- /dev/null
+language: c
+os: linux
+arch: ppc64le
+
+# use the containers for a faster build
+sudo: false
+
+env:
+ - PYTHON_VERSION=3.7 NUMPY_VERSION=1.16
+
+before_install:
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+ wget http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+ else
+ if [[ "$TRAVIS_CPU_ARCH" == "ppc64le" ]]; then
+ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh -O miniconda.sh;
+ else
+ wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+ fi
+ fi
+ - chmod +x miniconda.sh
+ - ./miniconda.sh -b -p $HOME/miniconda
+ - export PATH=$HOME/miniconda/bin:$PATH
+ - conda update --yes conda
+ - wget https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-3.49.tar.gz
+ - tar -xzvf cfitsio-3.49.tar.gz
+ - (cd cfitsio-3.49; ./configure --disable-shared --prefix=$HOME/cfitsio-static-install; make install -j 4)
+
+install:
+ - conda create --yes -n test python=$PYTHON_VERSION
+ - source activate test
+ - conda install --yes numpy=$NUMPY_VERSION nose cython
+ - if [ $PYTHON_VERSION == 2.6 ]; then conda install --yes argparse; fi
+
+script:
+ - FITSIO_INSTALL_DIR=$HOME/fitsio-temp-install
+ - export PYTHONPATH=$FITSIO_INSTALL_DIR/lib/python$PYTHON_VERSION/site-packages:$PYTHONPATH
+ - mkdir -p $FITSIO_INSTALL_DIR/lib/python$PYTHON_VERSION/site-packages
+
+ - export INSTALLFLAGS="--prefix=$FITSIO_INSTALL_DIR --single-version-externally-managed --record rec.txt"
+ - python setup.py install $INSTALLFLAGS
+
+ - pushd /tmp
+ - SKIP_BZIP_TEST=true python -c "import fitsio; fitsio.test.test()"
+ - popd
+ - rm -rf $FITSIO_INSTALL_DIR
+
+ - python setup.py clean -a
+ - mkdir -p $FITSIO_INSTALL_DIR/lib/python$PYTHON_VERSION/site-packages
+ - python setup.py install $INSTALLFLAGS build_ext --use-system-fitsio --system-fitsio-includedir=$HOME/cfitsio-static-install/include --system-fitsio-libdir=$HOME/cfitsio-static-install/lib
+
+ - pushd /tmp
+ - SKIP_BZIP_TEST=true SKIP_HCOMPRESS_U2_TEST=true python -c "import fitsio; fitsio.test.test()"
+ - popd
+ - rm -rf $FITSIO_INSTALL_DIR
+
+ - python setup.py clean -a
+ - python setup.py build
+ - python setup.py clean -a
+ - python setup.py build_ext
+
+#notifications:
+# email: false
--- /dev/null
+version 1.1.4
+---------------------------------
+
+New Features
+
+ - Moved most testing to GitHub actions (linux, osx).
+ - Added testing on ppc64le w/ TravisCI (thanks @asellappen)
+
+Bug Fixes
+
+ - Don't remove BLANK keywords in header clean
+ - Preserve order of comments in header
+
+Compatibility changes
+
+ - moved to sing `bool` rather than `np.bool` to be compativle
+ with numpy 1.2
+
+version 1.1.3
+---------------------------------
+
+This release moves to cfitsio 3.49, which has bug fixes and now properly
+supports reading certain classes of lossless compressed files
+
+New Features
+
+ - Added keywords to control compression
+ - qlevel control the quantization level
+ - qmethod set the quantization method
+ - hcomp_scale, hcomp_smooth HCOMPRESS specific settings
+
+ A nice result of this is that one can do lossless gzip compression
+ (setting qlevel=0) and
+ - Work around some types of garbage characters that might appear
+ in headers
+
+BACKWARDS INCOMPATIBLE CHANGES
+
+ - non-ascii junk in headers is replaced by ascii characters to
+ avoid segmentation faults in the python standard library
+ when non-unicode characters are detected. This will cause
+ codes that check for consistency between copied headers
+ to fail, since the header data is modified.
+
+Bug Fixes
+
+ - Write integer keywords using the long long support rather than long
+ - Fix bug where a new file is started and the user can access a
+ fictional HDU, causing book keeping problems
+ - Return zero length result when requested rows have
+ zero length (rainwoodman)
+
+version 1.1.2
+---------------------------------
+
+Bug Fixes
+
+ - Fixed deprecation warnings for extra keyword arguments.
+ - Fixed SyntaxWarning: "is" with a literal (Michka Popoff)
+
+version 1.1.1
+---------------------------------
+
+Bug Fixes
+
+ - Fix bug in drvrnet.c in printf statement, causing compile
+ issues on some systems.
+
+version 1.1.0
+---------------------------------
+
+Bumping the minor version due to the update of the cfitsio version
+
+This reverts to the behavior that compression settings are set as a toggle,
+which is the cfitsio convention. The user needs to turn compression on and off
+selectively. The alternative behavior, introduced in 1.0.1, broke the mode
+where compression is set in the filename, as well as breaking with convention.
+
+New Features
+
+ - Updated to cfitsio version 3.470 (#261)
+ - Add ability to stride (step value) when slicing (Dustin Jenkins)
+ - Add feature to flip along axis when slicing (Dustin Jenkins)
+ - Feature to ignore image scaling (Dustin Jenkins)
+
+Bug Fixes
+
+ - Fix error reading with an empty rows argument (rainwoodman)
+ - Fix bug when reading slice with step, but no start/stop (Mike Jarvis)
+ - Fix bug with clobber when compression is sent in filename
+
+
+Deprecations
+
+ - Removed the use of `**kwargs` in various read/write routines. This
+ pattern was causing silent bugs. All functions now use explicit
+ keyword arguments. A warning will be raised in any keyword arguments
+ are passed. In version `1.2`, this warning will become an error.
+
+version 1.0.5
+---------------------------------
+
+Bug Fixes
+
+ - fixed bug getting `None` keywords
+ - fixed bug writing 64 bit images (#256, #257)
+ - fixed HISTORY card value not being read
+
+version 1.0.4
+---------------------------------
+
+New Features
+
+ - support for empty keywords in header, which are supported
+ by the standard and are used for cosmetic comments
+
+Bug Fixes
+
+ - Fix for inserting bit columns and appending data with bitcols
+ - deal with non-standard header values such as NAN
+ [by returning as strings
+ - fixed many bugs reading headers; these were a casualty of
+ the header reading optimizations put in for 1.0.1
+
+version 1.0.3
+---------------------------------
+
+This is a bug fix release
+
+Bug Fixes
+
+ - The new header reading code did not deal properly with some
+ HIERARCH non-standard header key values.
+
+version 1.0.2
+---------------------------------
+
+This is a bug fix release
+
+Bug Fixes
+
+ - the read_header function was not treating the case_sensitive
+ keyword properly (Stephen Bailey)
+
+version 1.0.1
+---------------------------------
+
+Backwards Incompatible Changes
+
+ - Support for python 3 strings.
+ - Support for proper string null termination. This means you can read back exactly
+ what you wrote. However this departs from previous fitsio which used
+ the non-standard cfitsio convention of padding strings with spaces.
+ - Scalar indexing of FITS objects now returns a scalar, consistent
+ with numpy indexing rules (rainwoodman)
+
+New Features
+
+ - Installation moved to setuptools from distutils.
+ - Bundling of cfitsio now done with patches against the upstream
+ version instead of direct edits to the upstream code.
+ - Speed improvements for the read_header conveniance function, and
+ reading of headers in general.
+
+Bug Fixes
+
+ - CONTINUE in headers are now properly read. Note there is a corner
+ case that is mis-handled by the underlying cfitsio library. A bug
+ report has been sent. (thanks for help with Alex Drlica-Wagner
+ identifying and testing this issue)
+ - Fixed bug where some long strings were not properly written to headers
+ - Fixed bug where compression settings for an open FITS object was inherited
+ from the previous HDU by a new HDU
+ - Fixed bug where comment strings were lost when setting the value in
+ a FITSHDR entry
+ - Fixed bug where get_comment was raising ValueError rather than KeyError
+ - For py3 need to ensure by hand that strings sizes are greater than 0
+
+Deprecations
+
+ - removed `convert` keyword in `FITSRecord` and `FITSHDR` classes.
+
+version 0.9.12
+---------------------------------
+
+New Features
+
+ - Deal properly with undefined value header entries
+ - can delete rows from a table
+ - can insert rows with resize()
+ - can create empty HDU extension for extensions beyond 0 (Felipe Menanteau)
+ - sanitize string input for py3
+ - GZIP_2 compression support (Felipe Menanteau)
+ - Improvements to python packaging for easier installation.
+ - Using cfitsio 3.430 now with patches for known bugs
+ - Now support reading and writing bit columns (Eli Rykoff)
+ - Can now read CONTINUE keywords in headers. It is currently
+ treated as a comment; full implementation to come. (Alex Drlica-Wagner)
+ - Can now use a standard key dict when writing a header key using
+ the write_key method via `**`, e.g. `write_key(**key_dict)`
+ (Alex Drlica-Wagner)
+ - Delete row sets and row ranges using the delete_rows() method
+ for tables
+ - Resize tables, adding or removing rows, using the resize() method for
+ tables
+ - make write_key usable with standard dictionary using the `**keydict`
+ style
+ - allow writing empty HDUs after the first one using
+ ignore_empty=True to the FITS constructor or
+ the write convenience function (Felipe Menanteau)
+ We might make this the default in the future if
+ it is found to be benign
+
+Bug Fixes
+
+ - Only raise exception when PLIO u4/u8 is selected now that u1/u2 is supported
+ in cfitsio (Eli Rykoff)
+ - link curl library if cfitsio linked to it
+ - don't require numpy to run setup (Simon Conseil)
+ - strings with understores in headers, such as `1_000_000` are now not converted to numbers in py3
+ - check that the input fields names for tables are unique after converting
+ to upper case
+ - link against libm explicitly for compatibility on some systems
+
+
+version 0.9.11
+---------------------------------
+
+New Features
+
+ - Added trim_strings option to constructor and as keyword for read methods.
+ If trim_strings=True is set, white space is trimmed from the end
+ of all string columns upon reading. This was introduced because
+ cfitsio internally pads strings out with spaces to the full column
+ width when writing, against the FITS standard.
+
+ - Added read_raw() method to the FITS class, to read the raw underlying data
+ from the file (Dustin Lang)
+
+Bug Fixes
+
+ - Fix bug reading hierarch keywords. recent changes to keyword parsing had
+ broken reading of hierarch keywords
+ - Fix for strings that look like expressions, e.g. '3-4' which were
+ being evaluated rather than returned as strings.
+ - Fix bug for missing key in FITSHDR object using the hdr[key]
+ notation. Also raise KeyError rather than ValueError
+
+version 0.9.10
+---------------
+
+Bug Fixes
+
+ - Fix variable length string column copying in python 3
+ - Fix bug checking for max size in a variable length table column.
+ - Raise an exception when writing to a table with data
+ that has shape ()
+ - exit test suite with non-zero exit code if a test fails
+
+Continuous integration
+
+ - the travis ci now runs unit tests, ignoring those that may fail
+ when certain libraries/headers are not installed on the users system (for
+ now this is only bzip2 support)
+ - only particular pairs of python version/numpy version are tested
+
+python3 compatibility
+
+ - the compatibility is now built into the code rather than
+ using 2to3 to modify code at install time.
+
+Workarounds
+
+ - It turns out that when python, numpy etc. are compiled with gcc 4*
+ and fitsio is compiled with gcc 5* there is a problem, in some cases,
+ reading from an array with not aligned memory. This has to do with using
+ the -O3 optimization flag when compiling cfitsio. For replacing -O3 with
+ -O2 fixes the issue. This was an issue on linux in both anaconda python2
+ and python3.
+
+
+version 0.9.9.1
+----------------------------------
+
+New tag so that pypi will accept the updated version
+
+version 0.9.9
+----------------------------------
+
+New Features
+
+ - header_start, data_start, data_end now available in the
+ info dictionary, as well as the new get_offsets() method
+ to access these in a new dict.
+ (thanks Dimitri Muna for the initial version of this)
+
+Bug Fixes
+
+ - Fix bug when writing new COMMENT fields (thanks Alex Drlica-Wagner for
+ initial fix)
+ - deal correctly with aligned data in some scenarios
+ (thanks Ole Streicher)
+ - use correct data type long for tile_dims_fits in
+ the set_compression C code. This avoids a crash
+ on 32 but systems. (thanks Ole Streicher)
+ - use correct data type npy_int64 for pointer in
+ get_long_slices (this function is not not correctly
+ named). Avoids crash on some 32 bit systems.
+ (thanks Ole Streicher)
+ - use correct data type npy_int64 for pointer in
+ PyFITSObject_create_image_hdu, rather than npy_intp.
+ (thanks Ole Streicher)
+
+version 0.9.8
+----------------------------------
+
+New Features
+
+ - added read_scamp_head function to read the .head files output
+ by SCAMP and return a FITSHDR object
+ - reserved header space when creating image and table extensions
+ and a header is being written. This can improve performance
+ substantially, especially on distributed file systems.
+ - When possible write image data at HDU creation. This can
+ be a big performance improvement, especially on distributed file
+ systems.
+ - Support for reading bzipped FITS files. (Dustin Lang)
+
+ - Added option to use the system CFITSIO instead of the bundled one,
+ by sending --use-system-fitsio. Strongly recommend only use cfitsio
+ that are as new as the bundled one. Also note the bundled cfitsio
+ sometimes contains patches that are not yet upstream in an
+ official cfitsio release
+ - proper support for reading unsigned images compressed with PLIO.
+ This is a patch directly on the cfitsio code base. The same
+ code is in the upstream, but not yet released.
+ - New method reshape(dims) for images
+ - When writing into an existing image HDU, and larger dimensions
+ are required, the image is automatically expanded.
+
+Bug Fixes
+
+ - Fixed broken boolean fields in new versions of numpy (rainwoodman) Fixed
+ - bug when image was None (for creating empty first HDU) removed -iarch in
+ - setup.py for mac OS X. This should
+ work for versions Mavericks and Snow Leapard (Christopher Bonnett)
+ - Reading a single string column was failing in some cases, this
+ has been fixed
+ - When creating a TableColumnSubset using [cols], the existence
+ of the columns is checked immediately, rather than waiting for the
+ check in the read()
+ - make sure to convert correct endianness when writing during image HDU
+ creation
+ - Corrected the repr for single column subsets
+ - only clean bzero,bscale,bunit from headers for TableHDU
+
+Dev features
+
+ - added travis ci
+
+version 0.9.7
+----------------------------------
+
+New Features
+
+ - python 3 compatibility
+ - Adding a new HDU is now near constant time
+ - Can now create an empty image extension using create_image_hdu
+ and sending the dims= and dtype= keywords
+ - Can now write into a sub-section of an existing image using the
+ start= keyword.
+ - Can now use a scalar slice for reading images, e.g.
+ hdu[row1:row2, col]
+ although this still currently retains the extra dimension
+ - Use warnings instead of printing to stdout
+ - IOError is now used to indicate a number of errors that
+ were previously ValueError
+
+
+version 0.9.6
+--------------
+
+New Features
+
+ - use cfitsio 3370 to support new tile compression features
+ - FITSRecord class to encapsulate all the ways one can represent header
+ records. This is now used internally in the FITSHDR class instead of raw
+ dicts, but as FITSRecord inherits from dict this should be transparent.
+ - FITSCard class; inherits from FITSRecord and is a special case for header
+ card strings
+ - One can directly add a fits header card string to the FITSHDR object
+ using add_record
+
+Bug Fixes
+
+ - use literal_eval instead of eval for evaluating header values (D. Lang)
+ - If input to write_keys is a FITSHDR, just use it instead of creating a
+ new FITSHDR object. (D. Lang)
+ - update existing keys when adding records to FITSHDR, except for
+ comment and history fields.
+ - fixed bug with empty string in header card
+ - deal with cfitsio treating first 4 comments specially
+
+version 0.9.5
+--------------------------------
+
+Note the version 0.9.4 was skipped because some people had been using the
+master branch in production, which had version 0.9.4 set. This will allow
+automatic version detection to work. In the future master will not have
+the next version set until release.
+
+New Features
+
+ - Re-factored code to use sub-classes for each HDU type. These are called
+ ImageHDU, TableHDU, and AsciiTableHDU.
+ - Write and read 32-bit and 64-bit complex table columns
+ - Write and read boolean table columns (contributed by Dustin Lang)
+ - Specify tile dimensions for compressed images.
+ - write_comment and write_history methods added.
+ - is_compressed() for image HDUs, True if tile compressed.
+ - added `**keys` to the image hdu reading routines to provide a more uniform
+ interface for all hdu types
+
+Bug Fixes
+
+ - Correct appending to COMMENT and HISTORY fields when writing a full
+ header object.
+ - Correct conversion of boolean keywords, writing and reading.
+ - Strip out compression related reserved keywords when writing a
+ user-provided header.
+ - Simplified reading string columns in ascii tables so that certain
+ incorrectly formatted tables from CASUTools are now read accurately.
+ The change was minimal and did not affect reading well formatted tables,
+ so seemed worth it.
+ - Support non-standard TSHORT and TFLOAT columns in ascii tables as
+ generated by CASUTools. They are non-standard but supporting them
+ does not seem to break anything (pulled from Simon Walker).
+
+All changes E. Sheldon except where noted.
+
+version 0.9.3
+--------------------------
+New Features
+
+ - Can write lists of arrays and dictionaries of arrays
+ to fits tables.
+ - Added iteration over HDUs in FITS class
+ - Added iteration to the FITSHDU object
+ - Added iteration to the FITSHDR header object
+ - added checking that a hdu exists in the file, either
+ by extension number or name, using the "in" syntax. e.g.
+ fits=fitsio.FITS(filename)
+ if 'name' in fits:
+ data=fits['name'].read()
+ - added `**keys` to the read_header function
+ - added get_exttype() to the FITSHDU class
+ 'BINARY_TBL' 'ASCII_TBL' 'IMAGE_HDU'
+ - added get_nrows() for binary tables
+ - added get_colnames()
+ - added get_filename()
+ - added get_info()
+ - added get_nrows()
+ - added get_vstorage()
+ - added is_compressed()
+ - added get_ext()
+
+minor changes
+
+ - raise error on malformed TDIM
+
+Backwards incompatible changes
+
+ - renamed some attributes; use the getters instead
+ - `colnames` -> `_colnames`
+ - `info` -> `_info`
+ - `filename` -> `_filename`
+ - `ext` -> `_ext`
+ - `vstorage` -> `_vstorage`
+ - `is_comparessed` -> `_is_compressed`
+ ( use the getter )
+
+Bug Fixes
+
+ - newer numpys (1.6.2) were barfing adding a python float to u4 arrays.
+ - Give a more clear error message for malformed TDIM header keywords
+ - fixed bug displaying column info for string array columns in tables
+ - got cfitsio patch to deal with very large compressed images, which were
+ not read properly. This is now in the latest cfitsio.
+ - implemented workaround for bug where numpy declareds 'i8' arrays as type
+ npy_longlong, which is not correct.
+ - fixed bug in order of iteration of HDUs
+
+version 0.9.2
+--------------------------
+
+New Features
+
+ - Much faster writing to tables when there are many columns.
+ - Header object now has a setitem feature
+ h['item'] = value
+ - Header stores values now instead of the string rep
+ - You can force names of fields read from tables to upper
+ or lower case, either during construction of the FITS object
+ using or at read time using the lower= and upper= keywords.
+
+bug fixes
+ - more sensible data structure for header keywords. Now works in all known
+ cases when reading and rewriting string fields.
+
+version 0.9.1
+-------------------------
+
+New features
+
+ - Added reading of image slices, e.g. `f[ext][2:25, 10:100]`
+ - Added insert_column(name, data, colnum=) method for HDUs., 2011-11-14 ESS
+ - Added a verify_checksum() method for HDU objects. 2011-10-24, ESS
+ - Headers are cleaned of required keyword before writing. E.g. if you have
+ with fitsio.FITS(file,'rw') as fits:
+ fits.write(data, header=h)
+ Keywords like NAXIS, TTYPE* etc are removed. This allows you to read
+ a header from a fits file and write it to another without clobbering
+ the required keywords.
+
+ - when accessing a column subset object, more metadata are shown
+ `f[ext][name]`
+ - can write None as an image for extension 0, as supported by
+ the spirit standard. Similarly reading gives None in that case.
+ - the setup.py is now set up for registering versions to pypi.
+
+bug fixes
+
+ - Fixed bug that occured sometimes when reading individual columns where a
+ few bytes were not read. Now using the internal cfitsio buffers more
+ carefully.
+
+ - Using fits_read_tblbytes when reading full rows fixes a bug that showed
+ up in a particular file.
+
+ - required header keywords are stripped from input header objects before
+ writing.
+
+version 0.9.0 (2011-10-21)
+-------------------------
+
+This is the first "official" release. A patched version of cfitsio 3.28 is now
+bundled. This will make it easier for folks to install, and provide a
+consistent code base with which to develop. Thanks to Eli Rykoff for
+suggesting a bundle. Thanks to Eli and Martin White for helping extensively
+with testing.
+
+On OS X, we now link properly with universal binaries on intel. Thanks to Eli
+Rykoff for help with OS X testing and bug fixes.
+
+New features
+
+
+ - Write and read variable length columns. When writing a table, any fields
+ declared "object" ("O" type char) in the input array will be written to a
+ variable length column. For numbers, this means vectors of varying
+ length. For strings, it means varying length strings.
+
+ When reading, there are two options. 1) By default the data are read
+ into fixed length fields with padding to the maximum size in the table
+ column. This is a "least surprise" approach, since fancy indexing and
+ other array ops will work as expectd. 2) To save memory, construct the
+ FITS object with vstorage='object' to store the data as objects. This
+ storage can also be written back out to a new FITS file with variable
+ length columns. You can also over-ride the default vstorage when calling
+ read functions.
+
+ - Write and read ascii tables. cfitsio supports writing scalar 2- and
+ 4-byte integers, floats and doubles. But for reading only 4-byte integers
+ and doubles are supported, presumably because of the ambiguity in the
+ tform fields. Scalar strings are fully supported in both reading and
+ writing. No array fields are supported for ascii.
+
+ - Append rows to an existing table using the append method.
+ >>> fits.write_table(data1)
+ >>> fits[-1].append(data2)
+
+ - Using the new "where" method, you can select rows in a table where an
+ input expression evaluates to true. The table is scanned row by row
+ without a large read. This is surprisingly fast, and useful for figuring
+ out what sections of a large file you want to extract. only requires
+ enough memory to hold the row indices.
+
+ >>> w=fits[ext].where('x > 3 && y < 25')
+ >>> data=fits[ext].read(rows=w)
+ >>> data=fits[ext][w]
+
+ - You can now read rows and columns from a table HDU using slice notation. e.g.
+ to read row subsets from extension 1
+ >>> fits=fitsio.FITS(filename)
+ >>> data=fits[1][:]
+ >>> data=fits[1][10:30]
+ >>> data=fits[1][10:30:2]
+
+ You can also specify a list of rows
+ >>> rows=[3,8,25]
+ >>> data=fits[1][rows]
+
+ This is equivalent to
+ >>> data=fits[1].read(rows=rows)
+
+ To get columns subsets, the notation is similar. The data are read
+ when the rows are specified. If a sequence of columns is entered,
+ a recarray is returned, otherwise a simple array.
+ >>> data=fits[1]['x'][:]
+ >>> data=fits[1]['x','y'][3:20]
+ >>> data=fits[1][column_list][row_list]
+
+
+ - Added support for EXTVER header keywords. When choosing an HDU by name,
+ this allows one to select among HDUs that have the same name. Thanks to
+ Eli Rykoff for suggesting this feature and helping with testing.
+
+ - Name matching for table columns and extension names is not
+ case-insensitive by default. You can turn on case sensitivity by
+ constructing the FITS object with case_sensitive=True, or sending
+ that keyword to the convenience functions read and read_header.
+
+ - Added write_checksum method to the FITSHDU class, which computes the
+ checksum for the HDU, both the data portion alone (DATASUM keyword)
+ and the checksum complement for the entire HDU (CHECKSUM).
+
+ - Added an extensive test suite. Use this to run the tests
+ fitsio.test.test()
+
+ - Added fitsio.cfitsio_version() function, returns the cfitsio
+ version as a string.
+
+ - added read_slice method, which is used to implement the slice
+ notation introduced above.
+
+significant code changes
+
+ - Now using fits_read_tblbytes when reading all rows and columns. This
+ is just as fast but does not bypass, and thus confuse, the read buffers.
+ - Removed many direct uses of the internal cfitsio struct objects,
+ preferring to use provided access functions. This allowed compilation
+ on older cfitsio that had different struct representations.
+
+bug fixes
+
+ - too many to list in this early release.
--- /dev/null
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
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+\f
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+
+ If you develop a new program, and you want it to be of the greatest
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+free software which everyone can redistribute and change under these terms.
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+
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+ This is free software, and you are welcome to redistribute it
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+
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+
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+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
--- /dev/null
+include *.txt
+include README.md
+recursive-include cfitsio3490 *
+recursive-include patches *
+recursive-include fitsio/test_images *
--- /dev/null
+Metadata-Version: 2.1
+Name: fitsio
+Version: 1.1.4
+Summary: A full featured python library to read from and write to FITS files.
+Home-page: https://github.com/esheldon/fitsio
+Author: Erin Scott Sheldon
+Author-email: erin.sheldon@gmail.com
+License: GPL
+Description: A python library to read from and write to FITS files.
+
+ [](https://travis-ci.com/esheldon/fitsio)
+ [](https://github.com/esheldon/fitsio/actions?query=workflow%3Atests)
+
+ ## Description
+
+ This is a python extension written in c and python. Data are read into
+ numerical python arrays.
+
+ A version of cfitsio is bundled with this package, there is no need to install
+ your own, nor will this conflict with a version you have installed.
+
+
+ ## Some Features
+
+ - Read from and write to image, binary, and ascii table extensions.
+ - Read arbitrary subsets of table columns and rows without loading all the data
+ to memory.
+ - Read image subsets without reading the whole image. Write subsets to existing images.
+ - Write and read variable length table columns.
+ - Read images and tables using slice notation similar to numpy arrays. This is like a more
+ powerful memmap, since it is column-aware for tables.
+ - Append rows to an existing table. Delete row sets and row ranges. Resize tables,
+ or insert rows.
+ - Query the columns and rows in a table.
+ - Read and write header keywords.
+ - Read and write images in tile-compressed format (RICE,GZIP,PLIO,HCOMPRESS).
+ - Read/write gzip files directly. Read unix compress (.Z,.zip) and bzip2 (.bz2) files.
+ - TDIM information is used to return array columns in the correct shape.
+ - Write and read string table columns, including array columns of arbitrary
+ shape.
+ - Read and write complex, bool (logical), unsigned integer, signed bytes types.
+ - Write checksums into the header and verify them.
+ - Insert new columns into tables in-place.
+ - Iterate over rows in a table. Data are buffered for efficiency.
+ - python 3 support, including python 3 strings
+
+
+ ## Examples
+
+ ```python
+ import fitsio
+ from fitsio import FITS,FITSHDR
+
+ # Often you just want to quickly read or write data without bothering to
+ # create a FITS object. In that case, you can use the read and write
+ # convienience functions.
+
+ # read all data from the first hdu that has data
+ filename='data.fits'
+ data = fitsio.read(filename)
+
+ # read a subset of rows and columns from a table
+ data = fitsio.read(filename, rows=[35,1001], columns=['x','y'], ext=2)
+
+ # read the header
+ h = fitsio.read_header(filename)
+ # read both data and header
+ data,h = fitsio.read(filename, header=True)
+
+ # open the file and write a new binary table extension with the data
+ # array, which is a numpy array with fields, or "recarray".
+
+ data = np.zeros(10, dtype=[('id','i8'),('ra','f8'),('dec','f8')])
+ fitsio.write(filename, data)
+
+ # Write an image to the same file. By default a new extension is
+ # added to the file. use clobber=True to overwrite an existing file
+ # instead. To append rows to an existing table, see below.
+
+ fitsio.write(filename, image)
+
+ # NOTE when reading row subsets, the data must still be read from disk.
+ # This is most efficient if the data are read in the order they appear in
+ # the file. For this reason, the rows are always returned in row-sorted
+ # order.
+
+ #
+ # the FITS class gives the you the ability to explore the data, and gives
+ # more control
+ #
+
+ # open a FITS file for reading and explore
+ fits=fitsio.FITS('data.fits')
+
+ # see what is in here; the FITS object prints itself
+ print(fits)
+
+ file: data.fits
+ mode: READONLY
+ extnum hdutype hduname
+ 0 IMAGE_HDU
+ 1 BINARY_TBL mytable
+
+ # at the python or ipython prompt the fits object will
+ # print itself
+ >>> fits
+ file: data.fits
+ ... etc
+
+ # explore the extensions, either by extension number or
+ # extension name if available
+ >>> fits[0]
+
+ file: data.fits
+ extension: 0
+ type: IMAGE_HDU
+ image info:
+ data type: f8
+ dims: [4096,2048]
+
+ # by name; can also use fits[1]
+ >>> fits['mytable']
+
+ file: data.fits
+ extension: 1
+ type: BINARY_TBL
+ extname: mytable
+ rows: 4328342
+ column info:
+ i1scalar u1
+ f f4
+ fvec f4 array[2]
+ darr f8 array[3,2]
+ dvarr f8 varray[10]
+ s S5
+ svec S6 array[3]
+ svar S0 vstring[8]
+ sarr S2 array[4,3]
+
+ # See bottom for how to get more information for an extension
+
+ # [-1] to refers the last HDU
+ >>> fits[-1]
+ ...
+
+ # if there are multiple HDUs with the same name, and an EXTVER
+ # is set, you can use it. Here extver=2
+ # fits['mytable',2]
+
+
+ # read the image from extension zero
+ img = fits[0].read()
+ img = fits[0][:,:]
+
+ # read a subset of the image without reading the whole image
+ img = fits[0][25:35, 45:55]
+
+
+ # read all rows and columns from a binary table extension
+ data = fits[1].read()
+ data = fits['mytable'].read()
+ data = fits[1][:]
+
+ # read a subset of rows and columns. By default uses a case-insensitive
+ # match. The result retains the names with original case. If columns is a
+ # sequence, a numpy array with fields, or recarray is returned
+ data = fits[1].read(rows=[1,5], columns=['index','x','y'])
+
+ # Similar but using slice notation
+ # row subsets
+ data = fits[1][10:20]
+ data = fits[1][10:20:2]
+ data = fits[1][[1,5,18]]
+
+ # Using EXTNAME and EXTVER values
+ data = fits['SCI',2][10:20]
+
+ # Slicing with reverse (flipped) striding
+ data = fits[1][40:25]
+ data = fits[1][40:25:-5]
+
+ # all rows of column 'x'
+ data = fits[1]['x'][:]
+
+ # Read a few columns at once. This is more efficient than separate read for
+ # each column
+ data = fits[1]['x','y'][:]
+
+ # General column and row subsets. As noted above, the data are returned
+ # in row sorted order for efficiency reasons.
+ columns=['index','x','y']
+ rows=[1,5]
+ data = fits[1][columns][rows]
+
+ # iterate over rows in a table hdu
+ # faster if we buffer some rows, let's buffer 1000 at a time
+ fits=fitsio.FITS(filename,iter_row_buffer=1000)
+ for row in fits[1]:
+ print(row)
+
+ # iterate over HDUs in a FITS object
+ for hdu in fits:
+ data=hdu.read()
+
+ # Note dvarr shows type varray[10] and svar shows type vstring[8]. These
+ # are variable length columns and the number specified is the maximum size.
+ # By default they are read into fixed-length fields in the output array.
+ # You can over-ride this by constructing the FITS object with the vstorage
+ # keyword or specifying vstorage when reading. Sending vstorage='object'
+ # will store the data in variable size object fields to save memory; the
+ # default is vstorage='fixed'. Object fields can also be written out to a
+ # new FITS file as variable length to save disk space.
+
+ fits = fitsio.FITS(filename,vstorage='object')
+ # OR
+ data = fits[1].read(vstorage='object')
+ print(data['dvarr'].dtype)
+ dtype('object')
+
+
+ # you can grab a FITS HDU object to simplify notation
+ hdu1 = fits[1]
+ data = hdu1['x','y'][35:50]
+
+ # get rows that satisfy the input expression. See "Row Filtering
+ # Specification" in the cfitsio manual (note no temporary table is
+ # created in this case, contrary to the cfitsio docs)
+ w=fits[1].where("x > 0.25 && y < 35.0")
+ data = fits[1][w]
+
+ # read the header
+ h = fits[0].read_header()
+ print(h['BITPIX'])
+ -64
+
+ fits.close()
+
+
+ # now write some data
+ fits = FITS('test.fits','rw')
+
+
+ # create a rec array. Note vstr
+ # is a variable length string
+ nrows=35
+ data = np.zeros(nrows, dtype=[('index','i4'),('vstr','O'),('x','f8'),
+ ('arr','f4',(3,4))])
+ data['index'] = np.arange(nrows,dtype='i4')
+ data['x'] = np.random.random(nrows)
+ data['vstr'] = [str(i) for i in xrange(nrows)]
+ data['arr'] = np.arange(nrows*3*4,dtype='f4').reshape(nrows,3,4)
+
+ # create a new table extension and write the data
+ fits.write(data)
+
+ # can also be a list of ordinary arrays if you send the names
+ array_list=[xarray,yarray,namearray]
+ names=['x','y','name']
+ fits.write(array_list, names=names)
+
+ # similarly a dict of arrays
+ fits.write(dict_of_arrays)
+ fits.write(dict_of_arrays, names=names) # control name order
+
+ # append more rows to the table. The fields in data2 should match columns
+ # in the table. missing columns will be filled with zeros
+ fits[-1].append(data2)
+
+ # insert a new column into a table
+ fits[-1].insert_column('newcol', data)
+
+ # insert with a specific colnum
+ fits[-1].insert_column('newcol', data, colnum=2)
+
+ # overwrite rows
+ fits[-1].write(data)
+
+ # overwrite starting at a particular row. The table will grow if needed
+ fits[-1].write(data, firstrow=350)
+
+
+ # create an image
+ img=np.arange(2*3,dtype='i4').reshape(2,3)
+
+ # write an image in a new HDU (if this is a new file, the primary HDU)
+ fits.write(img)
+
+ # write an image with rice compression
+ fits.write(img, compress='rice')
+
+ # control the compression
+ fimg=np.random.normal(size=2*3).reshape(2, 3)
+ fits.write(img, compress='rice', qlevel=16, qmethod='SUBTRACTIVE_DITHER_2')
+
+ # lossless gzip compression for integers or floating point
+ fits.write(img, compress='gzip', qlevel=None)
+ fits.write(fimg, compress='gzip', qlevel=None)
+
+ # overwrite the image
+ fits[ext].write(img2)
+
+ # write into an existing image, starting at the location [300,400]
+ # the image will be expanded if needed
+ fits[ext].write(img3, start=[300,400])
+
+ # change the shape of the image on disk
+ fits[ext].reshape([250,100])
+
+ # add checksums for the data
+ fits[-1].write_checksum()
+
+ # can later verify data integridy
+ fits[-1].verify_checksum()
+
+ # you can also write a header at the same time. The header can be
+ # - a simple dict (no comments)
+ # - a list of dicts with 'name','value','comment' fields
+ # - a FITSHDR object
+
+ hdict = {'somekey': 35, 'location': 'kitt peak'}
+ fits.write(data, header=hdict)
+ hlist = [{'name':'observer', 'value':'ES', 'comment':'who'},
+ {'name':'location','value':'CTIO'},
+ {'name':'photometric','value':True}]
+ fits.write(data, header=hlist)
+ hdr=FITSHDR(hlist)
+ fits.write(data, header=hdr)
+
+ # you can add individual keys to an existing HDU
+ fits[1].write_key(name, value, comment="my comment")
+
+ # Write multiple header keys to an existing HDU. Here records
+ # is the same as sent with header= above
+ fits[1].write_keys(records)
+
+ # write special COMMENT fields
+ fits[1].write_comment("observer JS")
+ fits[1].write_comment("we had good weather")
+
+ # write special history fields
+ fits[1].write_history("processed with software X")
+ fits[1].write_history("re-processed with software Y")
+
+ fits.close()
+
+ # using a context, the file is closed automatically after leaving the block
+ with FITS('path/to/file') as fits:
+ data = fits[ext].read()
+
+ # you can check if a header exists using "in":
+ if 'blah' in fits:
+ data=fits['blah'].read()
+ if 2 in f:
+ data=fits[2].read()
+
+ # methods to get more information about extension. For extension 1:
+ f[1].get_info() # lots of info about the extension
+ f[1].has_data() # returns True if data is present in extension
+ f[1].get_extname()
+ f[1].get_extver()
+ f[1].get_extnum() # return zero-offset extension number
+ f[1].get_exttype() # 'BINARY_TBL' or 'ASCII_TBL' or 'IMAGE_HDU'
+ f[1].get_offsets() # byte offsets (header_start, data_start, data_end)
+ f[1].is_compressed() # for images. True if tile-compressed
+ f[1].get_colnames() # for tables
+ f[1].get_colname(colnum) # for tables find the name from column number
+ f[1].get_nrows() # for tables
+ f[1].get_rec_dtype() # for tables
+ f[1].get_rec_column_descr() # for tables
+ f[1].get_vstorage() # for tables, storage mechanism for variable
+ # length columns
+
+ # public attributes you can feel free to change as needed
+ f[1].lower # If True, lower case colnames on output
+ f[1].upper # If True, upper case colnames on output
+ f[1].case_sensitive # if True, names are matched case sensitive
+ ```
+
+
+ ## Installation
+
+ The easiest way is using pip or conda. To get the latest release
+
+ pip install fitsio
+
+ # update fitsio (and everything else)
+ pip install fitsio --upgrade
+
+ # if pip refuses to update to a newer version
+ pip install fitsio --upgrade --ignore-installed
+
+ # if you only want to upgrade fitsio
+ pip install fitsio --no-deps --upgrade --ignore-installed
+
+ # for conda, use conda-forge
+ conda install -c conda-forge fitsio
+
+ You can also get the latest source tarball release from
+
+ https://pypi.python.org/pypi/fitsio
+
+ or the bleeding edge source from github or use git. To check out
+ the code for the first time
+
+ git clone https://github.com/esheldon/fitsio.git
+
+ Or at a later time to update to the latest
+
+ cd fitsio
+ git update
+
+ Use tar xvfz to untar the file, enter the fitsio directory and type
+
+ python setup.py install
+
+ optionally with a prefix
+
+ python setup.py install --prefix=/some/path
+
+ ## Requirements
+
+ - python 2 or python 3
+ - a C compiler and build tools like `make`, `patch`, etc.
+ - numpy (See the note below. Generally, numpy 1.11 or later is better.)
+
+
+ ### Do not use numpy 1.10.0 or 1.10.1
+
+ There is a serious performance regression in numpy 1.10 that results
+ in fitsio running tens to hundreds of times slower. A fix may be
+ forthcoming in a later release. Please comment here if this
+ has already impacted your work https://github.com/numpy/numpy/issues/6467
+
+
+ ## Tests
+
+ The unit tests should all pass for full support.
+
+ ```bash
+ python -c "import fitsio; fitsio.test.test()"
+ ```
+
+ Some tests may fail if certain libraries are not available, such
+ as bzip2. This failure only implies that bzipped files cannot
+ be read, without affecting other functionality.
+
+ ## Notes on Usage and Features
+
+ ### cfitsio bundling
+
+ We bundle cfitsio partly because many deployed versions of cfitsio in the
+ wild do not have support for interesting features like tiled image compression.
+ Bundling a version that meets our needs is a safe alternative.
+
+ ### array ordering
+
+ Since numpy uses C order, FITS uses fortran order, we have to write the TDIM
+ and image dimensions in reverse order, but write the data as is. Then we need
+ to also reverse the dims as read from the header when creating the numpy dtype,
+ but read as is.
+
+ ### `distutils` vs `setuptools`
+
+ As of version `1.0.0`, `fitsio` has been transitioned to `setuptools` for packaging
+ and installation. There are many reasons to do this (and to not do this). However,
+ at a practical level, what this means for you is that you may have trouble uninstalling
+ older versions with `pip` via `pip uninstall fitsio`. If you do, the best thing to do is
+ to manually remove the files manually. See this [stackoverflow question](https://stackoverflow.com/questions/402359/how-do-you-uninstall-a-python-package-that-was-installed-using-distutils)
+ for example.
+
+ ### python 3 strings
+
+ As of version `1.0.0`, fitsio now supports Python 3 strings natively. This support
+ means that for Python 3, native strings are read from and written correctly to
+ FITS files. All byte string columns are treated as ASCII-encoded unicode strings
+ as well. For FITS files written with a previous version of fitsio, the data
+ in Python 3 will now come back as a string and not a byte string. Note that this
+ support is not the same as full unicode support. Internally, fitsio only supports
+ the ASCII character set.
+
+ ## TODO
+
+ - HDU groups: does anyone use these? If so open an issue!
+
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License (GPL)
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Intended Audience :: Science/Research
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
--- /dev/null
+A python library to read from and write to FITS files.
+
+[](https://travis-ci.com/esheldon/fitsio)
+[](https://github.com/esheldon/fitsio/actions?query=workflow%3Atests)
+
+## Description
+
+This is a python extension written in c and python. Data are read into
+numerical python arrays.
+
+A version of cfitsio is bundled with this package, there is no need to install
+your own, nor will this conflict with a version you have installed.
+
+
+## Some Features
+
+- Read from and write to image, binary, and ascii table extensions.
+- Read arbitrary subsets of table columns and rows without loading all the data
+ to memory.
+- Read image subsets without reading the whole image. Write subsets to existing images.
+- Write and read variable length table columns.
+- Read images and tables using slice notation similar to numpy arrays. This is like a more
+ powerful memmap, since it is column-aware for tables.
+- Append rows to an existing table. Delete row sets and row ranges. Resize tables,
+ or insert rows.
+- Query the columns and rows in a table.
+- Read and write header keywords.
+- Read and write images in tile-compressed format (RICE,GZIP,PLIO,HCOMPRESS).
+- Read/write gzip files directly. Read unix compress (.Z,.zip) and bzip2 (.bz2) files.
+- TDIM information is used to return array columns in the correct shape.
+- Write and read string table columns, including array columns of arbitrary
+ shape.
+- Read and write complex, bool (logical), unsigned integer, signed bytes types.
+- Write checksums into the header and verify them.
+- Insert new columns into tables in-place.
+- Iterate over rows in a table. Data are buffered for efficiency.
+- python 3 support, including python 3 strings
+
+
+## Examples
+
+```python
+import fitsio
+from fitsio import FITS,FITSHDR
+
+# Often you just want to quickly read or write data without bothering to
+# create a FITS object. In that case, you can use the read and write
+# convienience functions.
+
+# read all data from the first hdu that has data
+filename='data.fits'
+data = fitsio.read(filename)
+
+# read a subset of rows and columns from a table
+data = fitsio.read(filename, rows=[35,1001], columns=['x','y'], ext=2)
+
+# read the header
+h = fitsio.read_header(filename)
+# read both data and header
+data,h = fitsio.read(filename, header=True)
+
+# open the file and write a new binary table extension with the data
+# array, which is a numpy array with fields, or "recarray".
+
+data = np.zeros(10, dtype=[('id','i8'),('ra','f8'),('dec','f8')])
+fitsio.write(filename, data)
+
+# Write an image to the same file. By default a new extension is
+# added to the file. use clobber=True to overwrite an existing file
+# instead. To append rows to an existing table, see below.
+
+fitsio.write(filename, image)
+
+# NOTE when reading row subsets, the data must still be read from disk.
+# This is most efficient if the data are read in the order they appear in
+# the file. For this reason, the rows are always returned in row-sorted
+# order.
+
+#
+# the FITS class gives the you the ability to explore the data, and gives
+# more control
+#
+
+# open a FITS file for reading and explore
+fits=fitsio.FITS('data.fits')
+
+# see what is in here; the FITS object prints itself
+print(fits)
+
+file: data.fits
+mode: READONLY
+extnum hdutype hduname
+0 IMAGE_HDU
+1 BINARY_TBL mytable
+
+# at the python or ipython prompt the fits object will
+# print itself
+>>> fits
+file: data.fits
+... etc
+
+# explore the extensions, either by extension number or
+# extension name if available
+>>> fits[0]
+
+file: data.fits
+extension: 0
+type: IMAGE_HDU
+image info:
+ data type: f8
+ dims: [4096,2048]
+
+# by name; can also use fits[1]
+>>> fits['mytable']
+
+file: data.fits
+extension: 1
+type: BINARY_TBL
+extname: mytable
+rows: 4328342
+column info:
+ i1scalar u1
+ f f4
+ fvec f4 array[2]
+ darr f8 array[3,2]
+ dvarr f8 varray[10]
+ s S5
+ svec S6 array[3]
+ svar S0 vstring[8]
+ sarr S2 array[4,3]
+
+# See bottom for how to get more information for an extension
+
+# [-1] to refers the last HDU
+>>> fits[-1]
+...
+
+# if there are multiple HDUs with the same name, and an EXTVER
+# is set, you can use it. Here extver=2
+# fits['mytable',2]
+
+
+# read the image from extension zero
+img = fits[0].read()
+img = fits[0][:,:]
+
+# read a subset of the image without reading the whole image
+img = fits[0][25:35, 45:55]
+
+
+# read all rows and columns from a binary table extension
+data = fits[1].read()
+data = fits['mytable'].read()
+data = fits[1][:]
+
+# read a subset of rows and columns. By default uses a case-insensitive
+# match. The result retains the names with original case. If columns is a
+# sequence, a numpy array with fields, or recarray is returned
+data = fits[1].read(rows=[1,5], columns=['index','x','y'])
+
+# Similar but using slice notation
+# row subsets
+data = fits[1][10:20]
+data = fits[1][10:20:2]
+data = fits[1][[1,5,18]]
+
+# Using EXTNAME and EXTVER values
+data = fits['SCI',2][10:20]
+
+# Slicing with reverse (flipped) striding
+data = fits[1][40:25]
+data = fits[1][40:25:-5]
+
+# all rows of column 'x'
+data = fits[1]['x'][:]
+
+# Read a few columns at once. This is more efficient than separate read for
+# each column
+data = fits[1]['x','y'][:]
+
+# General column and row subsets. As noted above, the data are returned
+# in row sorted order for efficiency reasons.
+columns=['index','x','y']
+rows=[1,5]
+data = fits[1][columns][rows]
+
+# iterate over rows in a table hdu
+# faster if we buffer some rows, let's buffer 1000 at a time
+fits=fitsio.FITS(filename,iter_row_buffer=1000)
+for row in fits[1]:
+ print(row)
+
+# iterate over HDUs in a FITS object
+for hdu in fits:
+ data=hdu.read()
+
+# Note dvarr shows type varray[10] and svar shows type vstring[8]. These
+# are variable length columns and the number specified is the maximum size.
+# By default they are read into fixed-length fields in the output array.
+# You can over-ride this by constructing the FITS object with the vstorage
+# keyword or specifying vstorage when reading. Sending vstorage='object'
+# will store the data in variable size object fields to save memory; the
+# default is vstorage='fixed'. Object fields can also be written out to a
+# new FITS file as variable length to save disk space.
+
+fits = fitsio.FITS(filename,vstorage='object')
+# OR
+data = fits[1].read(vstorage='object')
+print(data['dvarr'].dtype)
+ dtype('object')
+
+
+# you can grab a FITS HDU object to simplify notation
+hdu1 = fits[1]
+data = hdu1['x','y'][35:50]
+
+# get rows that satisfy the input expression. See "Row Filtering
+# Specification" in the cfitsio manual (note no temporary table is
+# created in this case, contrary to the cfitsio docs)
+w=fits[1].where("x > 0.25 && y < 35.0")
+data = fits[1][w]
+
+# read the header
+h = fits[0].read_header()
+print(h['BITPIX'])
+ -64
+
+fits.close()
+
+
+# now write some data
+fits = FITS('test.fits','rw')
+
+
+# create a rec array. Note vstr
+# is a variable length string
+nrows=35
+data = np.zeros(nrows, dtype=[('index','i4'),('vstr','O'),('x','f8'),
+ ('arr','f4',(3,4))])
+data['index'] = np.arange(nrows,dtype='i4')
+data['x'] = np.random.random(nrows)
+data['vstr'] = [str(i) for i in xrange(nrows)]
+data['arr'] = np.arange(nrows*3*4,dtype='f4').reshape(nrows,3,4)
+
+# create a new table extension and write the data
+fits.write(data)
+
+# can also be a list of ordinary arrays if you send the names
+array_list=[xarray,yarray,namearray]
+names=['x','y','name']
+fits.write(array_list, names=names)
+
+# similarly a dict of arrays
+fits.write(dict_of_arrays)
+fits.write(dict_of_arrays, names=names) # control name order
+
+# append more rows to the table. The fields in data2 should match columns
+# in the table. missing columns will be filled with zeros
+fits[-1].append(data2)
+
+# insert a new column into a table
+fits[-1].insert_column('newcol', data)
+
+# insert with a specific colnum
+fits[-1].insert_column('newcol', data, colnum=2)
+
+# overwrite rows
+fits[-1].write(data)
+
+# overwrite starting at a particular row. The table will grow if needed
+fits[-1].write(data, firstrow=350)
+
+
+# create an image
+img=np.arange(2*3,dtype='i4').reshape(2,3)
+
+# write an image in a new HDU (if this is a new file, the primary HDU)
+fits.write(img)
+
+# write an image with rice compression
+fits.write(img, compress='rice')
+
+# control the compression
+fimg=np.random.normal(size=2*3).reshape(2, 3)
+fits.write(img, compress='rice', qlevel=16, qmethod='SUBTRACTIVE_DITHER_2')
+
+# lossless gzip compression for integers or floating point
+fits.write(img, compress='gzip', qlevel=None)
+fits.write(fimg, compress='gzip', qlevel=None)
+
+# overwrite the image
+fits[ext].write(img2)
+
+# write into an existing image, starting at the location [300,400]
+# the image will be expanded if needed
+fits[ext].write(img3, start=[300,400])
+
+# change the shape of the image on disk
+fits[ext].reshape([250,100])
+
+# add checksums for the data
+fits[-1].write_checksum()
+
+# can later verify data integridy
+fits[-1].verify_checksum()
+
+# you can also write a header at the same time. The header can be
+# - a simple dict (no comments)
+# - a list of dicts with 'name','value','comment' fields
+# - a FITSHDR object
+
+hdict = {'somekey': 35, 'location': 'kitt peak'}
+fits.write(data, header=hdict)
+hlist = [{'name':'observer', 'value':'ES', 'comment':'who'},
+ {'name':'location','value':'CTIO'},
+ {'name':'photometric','value':True}]
+fits.write(data, header=hlist)
+hdr=FITSHDR(hlist)
+fits.write(data, header=hdr)
+
+# you can add individual keys to an existing HDU
+fits[1].write_key(name, value, comment="my comment")
+
+# Write multiple header keys to an existing HDU. Here records
+# is the same as sent with header= above
+fits[1].write_keys(records)
+
+# write special COMMENT fields
+fits[1].write_comment("observer JS")
+fits[1].write_comment("we had good weather")
+
+# write special history fields
+fits[1].write_history("processed with software X")
+fits[1].write_history("re-processed with software Y")
+
+fits.close()
+
+# using a context, the file is closed automatically after leaving the block
+with FITS('path/to/file') as fits:
+ data = fits[ext].read()
+
+ # you can check if a header exists using "in":
+ if 'blah' in fits:
+ data=fits['blah'].read()
+ if 2 in f:
+ data=fits[2].read()
+
+# methods to get more information about extension. For extension 1:
+f[1].get_info() # lots of info about the extension
+f[1].has_data() # returns True if data is present in extension
+f[1].get_extname()
+f[1].get_extver()
+f[1].get_extnum() # return zero-offset extension number
+f[1].get_exttype() # 'BINARY_TBL' or 'ASCII_TBL' or 'IMAGE_HDU'
+f[1].get_offsets() # byte offsets (header_start, data_start, data_end)
+f[1].is_compressed() # for images. True if tile-compressed
+f[1].get_colnames() # for tables
+f[1].get_colname(colnum) # for tables find the name from column number
+f[1].get_nrows() # for tables
+f[1].get_rec_dtype() # for tables
+f[1].get_rec_column_descr() # for tables
+f[1].get_vstorage() # for tables, storage mechanism for variable
+ # length columns
+
+# public attributes you can feel free to change as needed
+f[1].lower # If True, lower case colnames on output
+f[1].upper # If True, upper case colnames on output
+f[1].case_sensitive # if True, names are matched case sensitive
+```
+
+
+## Installation
+
+The easiest way is using pip or conda. To get the latest release
+
+ pip install fitsio
+
+ # update fitsio (and everything else)
+ pip install fitsio --upgrade
+
+ # if pip refuses to update to a newer version
+ pip install fitsio --upgrade --ignore-installed
+
+ # if you only want to upgrade fitsio
+ pip install fitsio --no-deps --upgrade --ignore-installed
+
+ # for conda, use conda-forge
+ conda install -c conda-forge fitsio
+
+You can also get the latest source tarball release from
+
+ https://pypi.python.org/pypi/fitsio
+
+or the bleeding edge source from github or use git. To check out
+the code for the first time
+
+ git clone https://github.com/esheldon/fitsio.git
+
+Or at a later time to update to the latest
+
+ cd fitsio
+ git update
+
+Use tar xvfz to untar the file, enter the fitsio directory and type
+
+ python setup.py install
+
+optionally with a prefix
+
+ python setup.py install --prefix=/some/path
+
+## Requirements
+
+- python 2 or python 3
+- a C compiler and build tools like `make`, `patch`, etc.
+- numpy (See the note below. Generally, numpy 1.11 or later is better.)
+
+
+### Do not use numpy 1.10.0 or 1.10.1
+
+There is a serious performance regression in numpy 1.10 that results
+in fitsio running tens to hundreds of times slower. A fix may be
+forthcoming in a later release. Please comment here if this
+has already impacted your work https://github.com/numpy/numpy/issues/6467
+
+
+## Tests
+
+The unit tests should all pass for full support.
+
+```bash
+python -c "import fitsio; fitsio.test.test()"
+```
+
+Some tests may fail if certain libraries are not available, such
+as bzip2. This failure only implies that bzipped files cannot
+be read, without affecting other functionality.
+
+## Notes on Usage and Features
+
+### cfitsio bundling
+
+We bundle cfitsio partly because many deployed versions of cfitsio in the
+wild do not have support for interesting features like tiled image compression.
+Bundling a version that meets our needs is a safe alternative.
+
+### array ordering
+
+Since numpy uses C order, FITS uses fortran order, we have to write the TDIM
+and image dimensions in reverse order, but write the data as is. Then we need
+to also reverse the dims as read from the header when creating the numpy dtype,
+but read as is.
+
+### `distutils` vs `setuptools`
+
+As of version `1.0.0`, `fitsio` has been transitioned to `setuptools` for packaging
+and installation. There are many reasons to do this (and to not do this). However,
+at a practical level, what this means for you is that you may have trouble uninstalling
+older versions with `pip` via `pip uninstall fitsio`. If you do, the best thing to do is
+to manually remove the files manually. See this [stackoverflow question](https://stackoverflow.com/questions/402359/how-do-you-uninstall-a-python-package-that-was-installed-using-distutils)
+for example.
+
+### python 3 strings
+
+As of version `1.0.0`, fitsio now supports Python 3 strings natively. This support
+means that for Python 3, native strings are read from and written correctly to
+FITS files. All byte string columns are treated as ASCII-encoded unicode strings
+as well. For FITS files written with a previous version of fitsio, the data
+in Python 3 will now come back as a string and not a byte string. Note that this
+support is not the same as full unicode support. Internally, fitsio only supports
+the ASCII character set.
+
+## TODO
+
+- HDU groups: does anyone use these? If so open an issue!
--- /dev/null
+Metadata-Version: 2.1
+Name: fitsio
+Version: 1.1.4
+Summary: A full featured python library to read from and write to FITS files.
+Home-page: https://github.com/esheldon/fitsio
+Author: Erin Scott Sheldon
+Author-email: erin.sheldon@gmail.com
+License: GPL
+Description: A python library to read from and write to FITS files.
+
+ [](https://travis-ci.com/esheldon/fitsio)
+ [](https://github.com/esheldon/fitsio/actions?query=workflow%3Atests)
+
+ ## Description
+
+ This is a python extension written in c and python. Data are read into
+ numerical python arrays.
+
+ A version of cfitsio is bundled with this package, there is no need to install
+ your own, nor will this conflict with a version you have installed.
+
+
+ ## Some Features
+
+ - Read from and write to image, binary, and ascii table extensions.
+ - Read arbitrary subsets of table columns and rows without loading all the data
+ to memory.
+ - Read image subsets without reading the whole image. Write subsets to existing images.
+ - Write and read variable length table columns.
+ - Read images and tables using slice notation similar to numpy arrays. This is like a more
+ powerful memmap, since it is column-aware for tables.
+ - Append rows to an existing table. Delete row sets and row ranges. Resize tables,
+ or insert rows.
+ - Query the columns and rows in a table.
+ - Read and write header keywords.
+ - Read and write images in tile-compressed format (RICE,GZIP,PLIO,HCOMPRESS).
+ - Read/write gzip files directly. Read unix compress (.Z,.zip) and bzip2 (.bz2) files.
+ - TDIM information is used to return array columns in the correct shape.
+ - Write and read string table columns, including array columns of arbitrary
+ shape.
+ - Read and write complex, bool (logical), unsigned integer, signed bytes types.
+ - Write checksums into the header and verify them.
+ - Insert new columns into tables in-place.
+ - Iterate over rows in a table. Data are buffered for efficiency.
+ - python 3 support, including python 3 strings
+
+
+ ## Examples
+
+ ```python
+ import fitsio
+ from fitsio import FITS,FITSHDR
+
+ # Often you just want to quickly read or write data without bothering to
+ # create a FITS object. In that case, you can use the read and write
+ # convienience functions.
+
+ # read all data from the first hdu that has data
+ filename='data.fits'
+ data = fitsio.read(filename)
+
+ # read a subset of rows and columns from a table
+ data = fitsio.read(filename, rows=[35,1001], columns=['x','y'], ext=2)
+
+ # read the header
+ h = fitsio.read_header(filename)
+ # read both data and header
+ data,h = fitsio.read(filename, header=True)
+
+ # open the file and write a new binary table extension with the data
+ # array, which is a numpy array with fields, or "recarray".
+
+ data = np.zeros(10, dtype=[('id','i8'),('ra','f8'),('dec','f8')])
+ fitsio.write(filename, data)
+
+ # Write an image to the same file. By default a new extension is
+ # added to the file. use clobber=True to overwrite an existing file
+ # instead. To append rows to an existing table, see below.
+
+ fitsio.write(filename, image)
+
+ # NOTE when reading row subsets, the data must still be read from disk.
+ # This is most efficient if the data are read in the order they appear in
+ # the file. For this reason, the rows are always returned in row-sorted
+ # order.
+
+ #
+ # the FITS class gives the you the ability to explore the data, and gives
+ # more control
+ #
+
+ # open a FITS file for reading and explore
+ fits=fitsio.FITS('data.fits')
+
+ # see what is in here; the FITS object prints itself
+ print(fits)
+
+ file: data.fits
+ mode: READONLY
+ extnum hdutype hduname
+ 0 IMAGE_HDU
+ 1 BINARY_TBL mytable
+
+ # at the python or ipython prompt the fits object will
+ # print itself
+ >>> fits
+ file: data.fits
+ ... etc
+
+ # explore the extensions, either by extension number or
+ # extension name if available
+ >>> fits[0]
+
+ file: data.fits
+ extension: 0
+ type: IMAGE_HDU
+ image info:
+ data type: f8
+ dims: [4096,2048]
+
+ # by name; can also use fits[1]
+ >>> fits['mytable']
+
+ file: data.fits
+ extension: 1
+ type: BINARY_TBL
+ extname: mytable
+ rows: 4328342
+ column info:
+ i1scalar u1
+ f f4
+ fvec f4 array[2]
+ darr f8 array[3,2]
+ dvarr f8 varray[10]
+ s S5
+ svec S6 array[3]
+ svar S0 vstring[8]
+ sarr S2 array[4,3]
+
+ # See bottom for how to get more information for an extension
+
+ # [-1] to refers the last HDU
+ >>> fits[-1]
+ ...
+
+ # if there are multiple HDUs with the same name, and an EXTVER
+ # is set, you can use it. Here extver=2
+ # fits['mytable',2]
+
+
+ # read the image from extension zero
+ img = fits[0].read()
+ img = fits[0][:,:]
+
+ # read a subset of the image without reading the whole image
+ img = fits[0][25:35, 45:55]
+
+
+ # read all rows and columns from a binary table extension
+ data = fits[1].read()
+ data = fits['mytable'].read()
+ data = fits[1][:]
+
+ # read a subset of rows and columns. By default uses a case-insensitive
+ # match. The result retains the names with original case. If columns is a
+ # sequence, a numpy array with fields, or recarray is returned
+ data = fits[1].read(rows=[1,5], columns=['index','x','y'])
+
+ # Similar but using slice notation
+ # row subsets
+ data = fits[1][10:20]
+ data = fits[1][10:20:2]
+ data = fits[1][[1,5,18]]
+
+ # Using EXTNAME and EXTVER values
+ data = fits['SCI',2][10:20]
+
+ # Slicing with reverse (flipped) striding
+ data = fits[1][40:25]
+ data = fits[1][40:25:-5]
+
+ # all rows of column 'x'
+ data = fits[1]['x'][:]
+
+ # Read a few columns at once. This is more efficient than separate read for
+ # each column
+ data = fits[1]['x','y'][:]
+
+ # General column and row subsets. As noted above, the data are returned
+ # in row sorted order for efficiency reasons.
+ columns=['index','x','y']
+ rows=[1,5]
+ data = fits[1][columns][rows]
+
+ # iterate over rows in a table hdu
+ # faster if we buffer some rows, let's buffer 1000 at a time
+ fits=fitsio.FITS(filename,iter_row_buffer=1000)
+ for row in fits[1]:
+ print(row)
+
+ # iterate over HDUs in a FITS object
+ for hdu in fits:
+ data=hdu.read()
+
+ # Note dvarr shows type varray[10] and svar shows type vstring[8]. These
+ # are variable length columns and the number specified is the maximum size.
+ # By default they are read into fixed-length fields in the output array.
+ # You can over-ride this by constructing the FITS object with the vstorage
+ # keyword or specifying vstorage when reading. Sending vstorage='object'
+ # will store the data in variable size object fields to save memory; the
+ # default is vstorage='fixed'. Object fields can also be written out to a
+ # new FITS file as variable length to save disk space.
+
+ fits = fitsio.FITS(filename,vstorage='object')
+ # OR
+ data = fits[1].read(vstorage='object')
+ print(data['dvarr'].dtype)
+ dtype('object')
+
+
+ # you can grab a FITS HDU object to simplify notation
+ hdu1 = fits[1]
+ data = hdu1['x','y'][35:50]
+
+ # get rows that satisfy the input expression. See "Row Filtering
+ # Specification" in the cfitsio manual (note no temporary table is
+ # created in this case, contrary to the cfitsio docs)
+ w=fits[1].where("x > 0.25 && y < 35.0")
+ data = fits[1][w]
+
+ # read the header
+ h = fits[0].read_header()
+ print(h['BITPIX'])
+ -64
+
+ fits.close()
+
+
+ # now write some data
+ fits = FITS('test.fits','rw')
+
+
+ # create a rec array. Note vstr
+ # is a variable length string
+ nrows=35
+ data = np.zeros(nrows, dtype=[('index','i4'),('vstr','O'),('x','f8'),
+ ('arr','f4',(3,4))])
+ data['index'] = np.arange(nrows,dtype='i4')
+ data['x'] = np.random.random(nrows)
+ data['vstr'] = [str(i) for i in xrange(nrows)]
+ data['arr'] = np.arange(nrows*3*4,dtype='f4').reshape(nrows,3,4)
+
+ # create a new table extension and write the data
+ fits.write(data)
+
+ # can also be a list of ordinary arrays if you send the names
+ array_list=[xarray,yarray,namearray]
+ names=['x','y','name']
+ fits.write(array_list, names=names)
+
+ # similarly a dict of arrays
+ fits.write(dict_of_arrays)
+ fits.write(dict_of_arrays, names=names) # control name order
+
+ # append more rows to the table. The fields in data2 should match columns
+ # in the table. missing columns will be filled with zeros
+ fits[-1].append(data2)
+
+ # insert a new column into a table
+ fits[-1].insert_column('newcol', data)
+
+ # insert with a specific colnum
+ fits[-1].insert_column('newcol', data, colnum=2)
+
+ # overwrite rows
+ fits[-1].write(data)
+
+ # overwrite starting at a particular row. The table will grow if needed
+ fits[-1].write(data, firstrow=350)
+
+
+ # create an image
+ img=np.arange(2*3,dtype='i4').reshape(2,3)
+
+ # write an image in a new HDU (if this is a new file, the primary HDU)
+ fits.write(img)
+
+ # write an image with rice compression
+ fits.write(img, compress='rice')
+
+ # control the compression
+ fimg=np.random.normal(size=2*3).reshape(2, 3)
+ fits.write(img, compress='rice', qlevel=16, qmethod='SUBTRACTIVE_DITHER_2')
+
+ # lossless gzip compression for integers or floating point
+ fits.write(img, compress='gzip', qlevel=None)
+ fits.write(fimg, compress='gzip', qlevel=None)
+
+ # overwrite the image
+ fits[ext].write(img2)
+
+ # write into an existing image, starting at the location [300,400]
+ # the image will be expanded if needed
+ fits[ext].write(img3, start=[300,400])
+
+ # change the shape of the image on disk
+ fits[ext].reshape([250,100])
+
+ # add checksums for the data
+ fits[-1].write_checksum()
+
+ # can later verify data integridy
+ fits[-1].verify_checksum()
+
+ # you can also write a header at the same time. The header can be
+ # - a simple dict (no comments)
+ # - a list of dicts with 'name','value','comment' fields
+ # - a FITSHDR object
+
+ hdict = {'somekey': 35, 'location': 'kitt peak'}
+ fits.write(data, header=hdict)
+ hlist = [{'name':'observer', 'value':'ES', 'comment':'who'},
+ {'name':'location','value':'CTIO'},
+ {'name':'photometric','value':True}]
+ fits.write(data, header=hlist)
+ hdr=FITSHDR(hlist)
+ fits.write(data, header=hdr)
+
+ # you can add individual keys to an existing HDU
+ fits[1].write_key(name, value, comment="my comment")
+
+ # Write multiple header keys to an existing HDU. Here records
+ # is the same as sent with header= above
+ fits[1].write_keys(records)
+
+ # write special COMMENT fields
+ fits[1].write_comment("observer JS")
+ fits[1].write_comment("we had good weather")
+
+ # write special history fields
+ fits[1].write_history("processed with software X")
+ fits[1].write_history("re-processed with software Y")
+
+ fits.close()
+
+ # using a context, the file is closed automatically after leaving the block
+ with FITS('path/to/file') as fits:
+ data = fits[ext].read()
+
+ # you can check if a header exists using "in":
+ if 'blah' in fits:
+ data=fits['blah'].read()
+ if 2 in f:
+ data=fits[2].read()
+
+ # methods to get more information about extension. For extension 1:
+ f[1].get_info() # lots of info about the extension
+ f[1].has_data() # returns True if data is present in extension
+ f[1].get_extname()
+ f[1].get_extver()
+ f[1].get_extnum() # return zero-offset extension number
+ f[1].get_exttype() # 'BINARY_TBL' or 'ASCII_TBL' or 'IMAGE_HDU'
+ f[1].get_offsets() # byte offsets (header_start, data_start, data_end)
+ f[1].is_compressed() # for images. True if tile-compressed
+ f[1].get_colnames() # for tables
+ f[1].get_colname(colnum) # for tables find the name from column number
+ f[1].get_nrows() # for tables
+ f[1].get_rec_dtype() # for tables
+ f[1].get_rec_column_descr() # for tables
+ f[1].get_vstorage() # for tables, storage mechanism for variable
+ # length columns
+
+ # public attributes you can feel free to change as needed
+ f[1].lower # If True, lower case colnames on output
+ f[1].upper # If True, upper case colnames on output
+ f[1].case_sensitive # if True, names are matched case sensitive
+ ```
+
+
+ ## Installation
+
+ The easiest way is using pip or conda. To get the latest release
+
+ pip install fitsio
+
+ # update fitsio (and everything else)
+ pip install fitsio --upgrade
+
+ # if pip refuses to update to a newer version
+ pip install fitsio --upgrade --ignore-installed
+
+ # if you only want to upgrade fitsio
+ pip install fitsio --no-deps --upgrade --ignore-installed
+
+ # for conda, use conda-forge
+ conda install -c conda-forge fitsio
+
+ You can also get the latest source tarball release from
+
+ https://pypi.python.org/pypi/fitsio
+
+ or the bleeding edge source from github or use git. To check out
+ the code for the first time
+
+ git clone https://github.com/esheldon/fitsio.git
+
+ Or at a later time to update to the latest
+
+ cd fitsio
+ git update
+
+ Use tar xvfz to untar the file, enter the fitsio directory and type
+
+ python setup.py install
+
+ optionally with a prefix
+
+ python setup.py install --prefix=/some/path
+
+ ## Requirements
+
+ - python 2 or python 3
+ - a C compiler and build tools like `make`, `patch`, etc.
+ - numpy (See the note below. Generally, numpy 1.11 or later is better.)
+
+
+ ### Do not use numpy 1.10.0 or 1.10.1
+
+ There is a serious performance regression in numpy 1.10 that results
+ in fitsio running tens to hundreds of times slower. A fix may be
+ forthcoming in a later release. Please comment here if this
+ has already impacted your work https://github.com/numpy/numpy/issues/6467
+
+
+ ## Tests
+
+ The unit tests should all pass for full support.
+
+ ```bash
+ python -c "import fitsio; fitsio.test.test()"
+ ```
+
+ Some tests may fail if certain libraries are not available, such
+ as bzip2. This failure only implies that bzipped files cannot
+ be read, without affecting other functionality.
+
+ ## Notes on Usage and Features
+
+ ### cfitsio bundling
+
+ We bundle cfitsio partly because many deployed versions of cfitsio in the
+ wild do not have support for interesting features like tiled image compression.
+ Bundling a version that meets our needs is a safe alternative.
+
+ ### array ordering
+
+ Since numpy uses C order, FITS uses fortran order, we have to write the TDIM
+ and image dimensions in reverse order, but write the data as is. Then we need
+ to also reverse the dims as read from the header when creating the numpy dtype,
+ but read as is.
+
+ ### `distutils` vs `setuptools`
+
+ As of version `1.0.0`, `fitsio` has been transitioned to `setuptools` for packaging
+ and installation. There are many reasons to do this (and to not do this). However,
+ at a practical level, what this means for you is that you may have trouble uninstalling
+ older versions with `pip` via `pip uninstall fitsio`. If you do, the best thing to do is
+ to manually remove the files manually. See this [stackoverflow question](https://stackoverflow.com/questions/402359/how-do-you-uninstall-a-python-package-that-was-installed-using-distutils)
+ for example.
+
+ ### python 3 strings
+
+ As of version `1.0.0`, fitsio now supports Python 3 strings natively. This support
+ means that for Python 3, native strings are read from and written correctly to
+ FITS files. All byte string columns are treated as ASCII-encoded unicode strings
+ as well. For FITS files written with a previous version of fitsio, the data
+ in Python 3 will now come back as a string and not a byte string. Note that this
+ support is not the same as full unicode support. Internally, fitsio only supports
+ the ASCII character set.
+
+ ## TODO
+
+ - HDU groups: does anyone use these? If so open an issue!
+
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License (GPL)
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Intended Audience :: Science/Research
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
--- /dev/null
+.gitignore
+.travis.yml
+CHANGES.md
+LICENSE.txt
+MANIFEST.in
+README.md
+setup.py
+cfitsio3490/CMakeLists.txt
+cfitsio3490/FindPthreads.cmake
+cfitsio3490/License.txt
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+fitsio/header.py
+fitsio/test.py
+fitsio/util.py
+fitsio.egg-info/PKG-INFO
+fitsio.egg-info/SOURCES.txt
+fitsio.egg-info/dependency_links.txt
+fitsio.egg-info/requires.txt
+fitsio.egg-info/top_level.txt
+fitsio/hdu/__init__.py
+fitsio/hdu/base.py
+fitsio/hdu/image.py
+fitsio/hdu/table.py
+fitsio/test_images/test_gzip_compressed_image.fits.fz
+patches/README.md
+patches/build_cfitsio_patches.py
+patches/configure.in.patch
+patches/configure.patch
+patches/drvrnet.c.patch
+patches/fitscore.c.patch
+patches/fitsio.h.patch
+patches/putcols.c.patch
\ No newline at end of file
--- /dev/null
+# flake8: noqa
+"""
+A python library to read and write data to FITS files using cfitsio.
+See the docs at https://github.com/esheldon/fitsio for example
+usage.
+"""
+
+__version__ = '1.1.4'
+
+from . import fitslib
+
+from .fitslib import (
+ FITS,
+ read,
+ read_header,
+ read_scamp_head,
+ write,
+ READONLY,
+ READWRITE,
+
+ NOCOMPRESS,
+ RICE_1,
+ GZIP_1,
+ GZIP_2,
+ PLIO_1,
+ HCOMPRESS_1,
+
+ NO_DITHER,
+ SUBTRACTIVE_DITHER_1,
+ SUBTRACTIVE_DITHER_2,
+)
+
+from .header import FITSHDR, FITSRecord, FITSCard
+from .hdu import BINARY_TBL, ASCII_TBL, IMAGE_HDU
+
+from . import util
+from .util import cfitsio_version, FITSRuntimeWarning
+
+from . import test
--- /dev/null
+/*
+ * fitsio_pywrap.c
+ *
+ * This is a CPython wrapper for the cfitsio library.
+
+ Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include <string.h>
+#include <Python.h>
+#include "fitsio.h"
+#include "fitsio2.h"
+//#include "fitsio_pywrap_lists.h"
+#include <numpy/arrayobject.h>
+
+
+// this is not defined anywhere in cfitsio except in
+// the fits file structure
+#define CFITSIO_MAX_ARRAY_DIMS 99
+
+// not sure where this is defined in numpy...
+#define NUMPY_MAX_DIMS 32
+
+struct PyFITSObject {
+ PyObject_HEAD
+ fitsfile* fits;
+};
+
+#ifdef FITSIO_PYWRAP_ALWAYS_NONSTANDARD_STRINGS
+static int fits_use_standard_strings(void)
+{
+ return 0;
+}
+#endif
+
+
+// check unicode for python3, string for python2
+int is_python_string(const PyObject* obj)
+{
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_Check(obj) || PyBytes_Check(obj);
+#else
+ return PyUnicode_Check(obj) || PyString_Check(obj);
+#endif
+}
+
+
+/*
+ Ensure all elements of the null terminated string are ascii, replacing
+ non-ascii characters with a ?
+*/
+
+static void convert_to_ascii(char* str) {
+ size_t size=0, i=0;
+ int cval=0;
+
+ size = strlen(str);
+ for (i=0; i < size; i++) {
+ cval = (int)str[i];
+ if (cval < 0 || cval > 127) {
+ str[i] = '?';
+ }
+ }
+}
+
+/*
+ Replace bad keyword characters with valid keyword ascii characters,
+ namely A-Z,a-z,0-9,_,-
+
+ To make it clear what has happened, the first four characters will be
+ replaced with J U N K and later bad characters with underscore.
+
+ Does not check the keyword is otherwise valid
+*/
+static void convert_keyword_to_allowed_ascii(char* str) {
+ int isgood=0;
+ size_t size=0, i=0;
+ int cval=0;
+
+ size = strlen(str);
+ for (i=0; i < size; i++) {
+ cval = (int)str[i];
+
+ isgood =
+ (cval >= 'A' && cval <= 'Z')
+ ||
+ (cval >= 'a' && cval <= 'z')
+ ||
+ (cval >= '0' && cval <= '9')
+ ||
+ (cval == '-')
+ ||
+ (cval == '_');
+
+
+ if (!isgood) {
+ if (i==0) {
+ str[i] = 'J';
+ } else if (i==1) {
+ str[i] = 'U';
+ } else if (i==2) {
+ str[i] = 'N';
+ } else if (i==3) {
+ str[i] = 'K';
+ } else {
+ str[i] = '_';
+ }
+ }
+ }
+}
+
+
+/*
+
+ get a string version of the object. New memory
+ is allocated and the receiver must clean it up.
+
+*/
+
+// unicode is common to python 2 and 3
+static char* get_unicode_as_string(PyObject* obj)
+{
+ PyObject* tmp=NULL;
+ char* strdata=NULL;
+ tmp = PyObject_CallMethod(obj,"encode",NULL);
+
+ strdata = strdup( PyBytes_AsString(tmp) );
+ Py_XDECREF(tmp);
+
+ return strdata;
+}
+
+static char* get_object_as_string(PyObject* obj)
+{
+ PyObject* format=NULL;
+ PyObject* args=NULL;
+ char* strdata=NULL;
+ PyObject* tmpobj1=NULL;
+
+ if (PyUnicode_Check(obj)) {
+
+ strdata=get_unicode_as_string(obj);
+
+ } else {
+
+#if PY_MAJOR_VERSION >= 3
+
+ if (PyBytes_Check(obj)) {
+ strdata = strdup( PyBytes_AsString(obj) );
+ } else {
+ PyObject* tmpobj2=NULL;
+ format = Py_BuildValue("s","%s");
+ // this is not a string object
+ args=PyTuple_New(1);
+
+ PyTuple_SetItem(args,0,obj);
+ tmpobj2 = PyUnicode_Format(format, args);
+ tmpobj1 = PyObject_CallMethod(tmpobj2,"encode",NULL);
+
+ Py_XDECREF(args);
+ Py_XDECREF(tmpobj2);
+
+ strdata = strdup( PyBytes_AsString(tmpobj1) );
+ Py_XDECREF(tmpobj1);
+ Py_XDECREF(format);
+ }
+
+#else
+ // convert to a string as needed
+ if (PyString_Check(obj)) {
+ strdata = strdup( PyString_AsString(obj) );
+ } else {
+ format = Py_BuildValue("s","%s");
+ args=PyTuple_New(1);
+
+ PyTuple_SetItem(args,0,obj);
+ tmpobj1= PyString_Format(format, args);
+
+ strdata = strdup( PyString_AsString(tmpobj1) );
+ Py_XDECREF(args);
+ Py_XDECREF(tmpobj1);
+ Py_XDECREF(format);
+ }
+#endif
+ }
+
+ return strdata;
+}
+
+static void
+set_ioerr_string_from_status(int status) {
+ char status_str[FLEN_STATUS], errmsg[FLEN_ERRMSG];
+ char message[1024];
+
+ int nleft=1024;
+
+ if (status) {
+ fits_get_errstatus(status, status_str); /* get the error description */
+
+ sprintf(message, "FITSIO status = %d: %s\n", status, status_str);
+
+ nleft -= strlen(status_str)+1;
+
+ while ( nleft > 0 && fits_read_errmsg(errmsg) ) { /* get error stack messages */
+ strncat(message, errmsg, nleft-1);
+ nleft -= strlen(errmsg)+1;
+ if (nleft >= 2) {
+ strncat(message, "\n", nleft-1);
+ }
+ nleft-=2;
+ }
+ PyErr_SetString(PyExc_IOError, message);
+ }
+ return;
+}
+
+/*
+ string list helper functions
+*/
+
+struct stringlist {
+ size_t size;
+ char** data;
+};
+
+static struct stringlist* stringlist_new(void) {
+ struct stringlist* slist=NULL;
+
+ slist = malloc(sizeof(struct stringlist));
+ slist->size = 0;
+ slist->data=NULL;
+ return slist;
+}
+// push a copy of the string onto the string list
+static void stringlist_push(struct stringlist* slist, const char* str) {
+ size_t newsize=0;
+ size_t i=0;
+
+ newsize = slist->size+1;
+ slist->data = realloc(slist->data, sizeof(char*)*newsize);
+ slist->size += 1;
+
+ i = slist->size-1;
+
+ slist->data[i] = strdup(str);
+}
+
+static void stringlist_push_size(struct stringlist* slist, size_t slen) {
+ size_t newsize=0;
+ size_t i=0;
+
+ newsize = slist->size+1;
+ slist->data = realloc(slist->data, sizeof(char*)*newsize);
+ slist->size += 1;
+
+ i = slist->size-1;
+
+ slist->data[i] = calloc(slen+1,sizeof(char));
+ //slist->data[i] = malloc(sizeof(char)*(slen+1));
+ //memset(slist->data[i], 0, slen+1);
+}
+static struct stringlist* stringlist_delete(struct stringlist* slist) {
+ if (slist != NULL) {
+ size_t i=0;
+ if (slist->data != NULL) {
+ for (i=0; i < slist->size; i++) {
+ free(slist->data[i]);
+ }
+ }
+ free(slist->data);
+ free(slist);
+ }
+ return NULL;
+}
+
+
+/*
+static void stringlist_print(struct stringlist* slist) {
+ size_t i=0;
+ if (slist == NULL) {
+ return;
+ }
+ for (i=0; i<slist->size; i++) {
+ printf(" slist[%ld]: %s\n", i, slist->data[i]);
+ }
+}
+*/
+
+
+static int stringlist_addfrom_listobj(struct stringlist* slist,
+ PyObject* listObj,
+ const char* listname) {
+ size_t size=0, i=0;
+ char* tmpstr=NULL;
+
+ if (!PyList_Check(listObj)) {
+ PyErr_Format(PyExc_ValueError, "Expected a list for %s.", listname);
+ return 1;
+ }
+ size = PyList_Size(listObj);
+
+ for (i=0; i<size; i++) {
+ PyObject* tmp = PyList_GetItem(listObj, i);
+ if (!is_python_string(tmp)) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected only strings in %s list.", listname);
+ return 1;
+ }
+ tmpstr = get_object_as_string(tmp);
+ stringlist_push(slist, tmpstr);
+ free(tmpstr);
+ }
+ return 0;
+}
+
+static
+void add_double_to_dict(PyObject* dict, const char* key, double value) {
+ PyObject* tobj=NULL;
+ tobj=PyFloat_FromDouble(value);
+ PyDict_SetItemString(dict, key, tobj);
+ Py_XDECREF(tobj);
+}
+
+static
+void add_long_to_dict(PyObject* dict, const char* key, long value) {
+ PyObject* tobj=NULL;
+ tobj=PyLong_FromLong(value);
+ PyDict_SetItemString(dict, key, tobj);
+ Py_XDECREF(tobj);
+}
+
+static
+void add_long_long_to_dict(PyObject* dict, const char* key, long long value) {
+ PyObject* tobj=NULL;
+ tobj=PyLong_FromLongLong(value);
+ PyDict_SetItemString(dict, key, tobj);
+ Py_XDECREF(tobj);
+}
+
+static
+void add_string_to_dict(PyObject* dict, const char* key, const char* str) {
+ PyObject* tobj=NULL;
+ tobj=Py_BuildValue("s",str);
+ PyDict_SetItemString(dict, key, tobj);
+ Py_XDECREF(tobj);
+}
+
+static
+void add_none_to_dict(PyObject* dict, const char* key) {
+ PyDict_SetItemString(dict, key, Py_None);
+ Py_XINCREF(Py_None);
+}
+static
+void add_true_to_dict(PyObject* dict, const char* key) {
+ PyDict_SetItemString(dict, key, Py_True);
+ Py_XINCREF(Py_True);
+}
+void add_false_to_dict(PyObject* dict, const char* key) {
+ PyDict_SetItemString(dict, key, Py_False);
+ Py_XINCREF(Py_False);
+}
+
+
+/*
+static
+void append_long_to_list(PyObject* list, long value) {
+ PyObject* tobj=NULL;
+ tobj=PyLong_FromLong(value);
+ PyList_Append(list, tobj);
+ Py_XDECREF(tobj);
+}
+*/
+
+static
+void append_long_long_to_list(PyObject* list, long long value) {
+ PyObject* tobj=NULL;
+ tobj=PyLong_FromLongLong(value);
+ PyList_Append(list, tobj);
+ Py_XDECREF(tobj);
+}
+
+/*
+static
+void append_string_to_list(PyObject* list, const char* str) {
+ PyObject* tobj=NULL;
+ tobj=Py_BuildValue("s",str);
+ PyList_Append(list, tobj);
+ Py_XDECREF(tobj);
+}
+*/
+
+
+
+static int
+PyFITSObject_init(struct PyFITSObject* self, PyObject *args, PyObject *kwds)
+{
+ char* filename;
+ int mode;
+ int status=0;
+ int create=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"sii", &filename, &mode, &create)) {
+ return -1;
+ }
+
+ if (create) {
+ // create and open
+ if (fits_create_file(&self->fits, filename, &status)) {
+ set_ioerr_string_from_status(status);
+ return -1;
+ }
+ } else {
+ if (fits_open_file(&self->fits, filename, mode, &status)) {
+ set_ioerr_string_from_status(status);
+ return -1;
+ }
+ }
+
+ return 0;
+}
+
+
+static PyObject *
+PyFITSObject_repr(struct PyFITSObject* self) {
+
+ if (self->fits != NULL) {
+ int status=0;
+ char filename[FLEN_FILENAME];
+ char repr[2056];
+
+ if (fits_file_name(self->fits, filename, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ sprintf(repr, "fits file: %s", filename);
+ return Py_BuildValue("s",repr);
+ } else {
+ return Py_BuildValue("s","none");
+ }
+}
+
+static PyObject *
+PyFITSObject_filename(struct PyFITSObject* self) {
+
+ if (self->fits != NULL) {
+ int status=0;
+ char filename[FLEN_FILENAME];
+ PyObject* fnameObj=NULL;
+ if (fits_file_name(self->fits, filename, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ fnameObj = Py_BuildValue("s",filename);
+ return fnameObj;
+ } else {
+ PyErr_SetString(PyExc_ValueError, "file is not open, cannot determine name");
+ return NULL;
+ }
+}
+
+
+
+static PyObject *
+PyFITSObject_close(struct PyFITSObject* self)
+{
+ int status=0;
+ if (fits_close_file(self->fits, &status)) {
+ self->fits=NULL;
+ /*
+ set_ioerr_string_from_status(status);
+ return NULL;
+ */
+ }
+ self->fits=NULL;
+ Py_RETURN_NONE;
+}
+
+
+
+static void
+PyFITSObject_dealloc(struct PyFITSObject* self)
+{
+ int status=0;
+ fits_close_file(self->fits, &status);
+#if PY_MAJOR_VERSION >= 3
+ // introduced in python 2.6
+ Py_TYPE(self)->tp_free((PyObject*)self);
+#else
+ // old way, removed in python 3
+ self->ob_type->tp_free((PyObject*)self);
+#endif
+}
+
+
+// this will need to be updated for array string columns.
+// I'm using a tcolumn* here, could cause problems
+static long get_groupsize(tcolumn* colptr) {
+ long gsize=0;
+ if (colptr->tdatatype == TSTRING) {
+ //gsize = colptr->twidth;
+ gsize = colptr->trepeat;
+ } else {
+ gsize = colptr->twidth*colptr->trepeat;
+ }
+ return gsize;
+}
+static npy_int64* get_int64_from_array(PyObject* arr, npy_intp* ncols) {
+
+ npy_int64* colnums;
+ int npy_type=0, check=0;
+
+ if (!PyArray_Check(arr)) {
+ PyErr_SetString(PyExc_TypeError, "int64 array must be an array.");
+ return NULL;
+ }
+
+ npy_type = PyArray_TYPE(arr);
+
+ // on some platforms, creating an 'i8' array gives it a longlong
+ // dtype. Just make sure it is 8 bytes
+ check=
+ (npy_type == NPY_INT64)
+ |
+ (npy_type==NPY_LONGLONG && sizeof(npy_longlong)==sizeof(npy_int64));
+ if (!check) {
+ PyErr_Format(PyExc_TypeError,
+ "array must be an int64 array (%d), got %d.",
+ NPY_INT64,npy_type);
+ return NULL;
+ }
+ if (!PyArray_ISCONTIGUOUS(arr)) {
+ PyErr_SetString(PyExc_TypeError, "int64 array must be a contiguous.");
+ return NULL;
+ }
+
+ colnums = PyArray_DATA(arr);
+ *ncols = PyArray_SIZE(arr);
+
+ return colnums;
+}
+
+// move hdu by name and possibly version, return the hdu number
+static PyObject *
+PyFITSObject_movnam_hdu(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdutype=ANY_HDU; // means we don't care if its image or table
+ char* extname=NULL;
+ int extver=0; // zero means it is ignored
+ int hdunum=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"isi", &hdutype, &extname, &extver)) {
+ return NULL;
+ }
+
+ if (fits_movnam_hdu(self->fits, hdutype, extname, extver, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ fits_get_hdu_num(self->fits, &hdunum);
+ return PyLong_FromLong((long)hdunum);
+}
+
+
+
+static PyObject *
+PyFITSObject_movabs_hdu(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0, hdutype=0;
+ int status=0;
+ PyObject* hdutypeObj=NULL;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"i", &hdunum)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ hdutypeObj = PyLong_FromLong((long)hdutype);
+ return hdutypeObj;
+}
+
+// get info for the specified HDU
+static PyObject *
+PyFITSObject_get_hdu_info(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0, hdutype=0, ext=0, ignore_scaling=FALSE;
+ int status=0, tstatus=0, is_compressed=0;
+ PyObject* dict=NULL;
+
+ char extname[FLEN_VALUE];
+ char hduname[FLEN_VALUE];
+ int extver=0, hduver=0;
+
+ long long header_start;
+ long long data_start;
+ long long data_end;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"ii", &hdunum, &ignore_scaling)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (ignore_scaling == TRUE
+ && fits_set_bscale(self->fits, 1.0, 0.0, &status)) {
+ return NULL;
+ }
+
+ dict = PyDict_New();
+ ext=hdunum-1;
+
+ add_long_to_dict(dict, "hdunum", (long)hdunum);
+ add_long_to_dict(dict, "extnum", (long)ext);
+ add_long_to_dict(dict, "hdutype", (long)hdutype);
+
+
+ tstatus=0;
+ if (fits_read_key(self->fits, TSTRING, "EXTNAME", extname, NULL, &tstatus)==0) {
+ convert_keyword_to_allowed_ascii(extname);
+ add_string_to_dict(dict, "extname", extname);
+ } else {
+ add_string_to_dict(dict, "extname", "");
+ }
+
+ tstatus=0;
+ if (fits_read_key(self->fits, TSTRING, "HDUNAME", hduname, NULL, &tstatus)==0) {
+ convert_keyword_to_allowed_ascii(hduname);
+ add_string_to_dict(dict, "hduname", hduname);
+ } else {
+ add_string_to_dict(dict, "hduname", "");
+ }
+
+ tstatus=0;
+ if (fits_read_key(self->fits, TINT, "EXTVER", &extver, NULL, &tstatus)==0) {
+ add_long_to_dict(dict, "extver", (long)extver);
+ } else {
+ add_long_to_dict(dict, "extver", (long)0);
+ }
+
+ tstatus=0;
+ if (fits_read_key(self->fits, TINT, "HDUVER", &hduver, NULL, &tstatus)==0) {
+ add_long_to_dict(dict, "hduver", (long)hduver);
+ } else {
+ add_long_to_dict(dict, "hduver", (long)0);
+ }
+
+ tstatus=0;
+ is_compressed=fits_is_compressed_image(self->fits, &tstatus);
+ add_long_to_dict(dict, "is_compressed_image", (long)is_compressed);
+
+
+ // get byte offsets
+ if (0==fits_get_hduaddrll(self->fits, &header_start, &data_start, &data_end, &tstatus)) {
+ add_long_long_to_dict(dict, "header_start", (long)header_start);
+ add_long_long_to_dict(dict, "data_start", (long)data_start);
+ add_long_long_to_dict(dict, "data_end", (long)data_end);
+ } else {
+ add_long_long_to_dict(dict, "header_start", -1);
+ add_long_long_to_dict(dict, "data_start", -1);
+ add_long_long_to_dict(dict, "data_end", -1);
+ }
+
+
+ int ndims=0;
+ int maxdim=CFITSIO_MAX_ARRAY_DIMS;
+ LONGLONG dims[CFITSIO_MAX_ARRAY_DIMS];
+ if (hdutype == IMAGE_HDU) {
+ // move this into it's own func
+ int tstatus=0;
+ int bitpix=0;
+ int bitpix_equiv=0;
+ char comptype[20];
+ PyObject* dimsObj=PyList_New(0);
+ int i=0;
+
+ //if (fits_read_imghdrll(self->fits, maxdim, simple_p, &bitpix, &ndims,
+ // dims, pcount_p, gcount_p, extend_p, &status)) {
+ if (fits_get_img_paramll(self->fits, maxdim, &bitpix, &ndims, dims, &tstatus)) {
+ add_string_to_dict(dict,"error","could not determine image parameters");
+ } else {
+ add_long_to_dict(dict,"ndims",(long)ndims);
+ add_long_to_dict(dict,"img_type",(long)bitpix);
+
+ if (ignore_scaling == TRUE) {
+ // Get the raw type if scaling is being ignored.
+ fits_get_img_type(self->fits, &bitpix_equiv, &status);
+ } else {
+ fits_get_img_equivtype(self->fits, &bitpix_equiv, &status);
+ }
+
+ add_long_to_dict(dict,"img_equiv_type",(long)bitpix_equiv);
+
+ tstatus=0;
+ if (fits_read_key(self->fits, TSTRING, "ZCMPTYPE",
+ comptype, NULL, &tstatus)==0) {
+ convert_to_ascii(comptype);
+ add_string_to_dict(dict,"comptype",comptype);
+ } else {
+ add_none_to_dict(dict,"comptype");
+ }
+
+ for (i=0; i<ndims; i++) {
+ append_long_long_to_list(dimsObj, (long long)dims[i]);
+ }
+ PyDict_SetItemString(dict, "dims", dimsObj);
+ Py_XDECREF(dimsObj);
+
+ }
+
+ } else if (hdutype == BINARY_TBL) {
+ int tstatus=0;
+ LONGLONG nrows=0;
+ int ncols=0;
+ PyObject* colinfo = PyList_New(0);
+ int i=0,j=0;
+
+ fits_get_num_rowsll(self->fits, &nrows, &tstatus);
+ fits_get_num_cols(self->fits, &ncols, &tstatus);
+ add_long_long_to_dict(dict,"nrows",(long long)nrows);
+ add_long_to_dict(dict,"ncols",(long)ncols);
+
+ {
+ PyObject* d = NULL;
+ tcolumn* col=NULL;
+ struct stringlist* names=NULL;
+ struct stringlist* tforms=NULL;
+ names=stringlist_new();
+ tforms=stringlist_new();
+
+ for (i=0; i<ncols; i++) {
+ stringlist_push_size(names, 70);
+ stringlist_push_size(tforms, 70);
+ }
+ // just get the names: no other way to do it!
+ fits_read_btblhdrll(self->fits, ncols, NULL, NULL,
+ names->data, tforms->data,
+ NULL, NULL, NULL, &tstatus);
+
+ for (i=0; i<ncols; i++) {
+ d = PyDict_New();
+ int type=0;
+ LONGLONG repeat=0;
+ LONGLONG width=0;
+
+ convert_to_ascii(names->data[i]);
+ add_string_to_dict(d,"name",names->data[i]);
+ convert_to_ascii(tforms->data[i]);
+ add_string_to_dict(d,"tform",tforms->data[i]);
+
+ fits_get_coltypell(self->fits, i+1, &type, &repeat, &width, &tstatus);
+ add_long_to_dict(d,"type",(long)type);
+ add_long_long_to_dict(d,"repeat",(long long)repeat);
+ add_long_long_to_dict(d,"width",(long long)width);
+
+ fits_get_eqcoltypell(self->fits,i+1,&type,&repeat,&width, &tstatus);
+ add_long_to_dict(d,"eqtype",(long)type);
+
+ tstatus=0;
+ if (fits_read_tdimll(self->fits, i+1, maxdim, &ndims, dims,
+ &tstatus)) {
+ add_none_to_dict(d,"tdim");
+ } else {
+ PyObject* dimsObj=PyList_New(0);
+ for (j=0; j<ndims; j++) {
+ append_long_long_to_list(dimsObj, (long long)dims[j]);
+ }
+
+ PyDict_SetItemString(d, "tdim", dimsObj);
+ Py_XDECREF(dimsObj);
+ }
+
+ // using the struct, could cause problems
+ // actually, we can use ffgcprll to get this info, but will
+ // be redundant with some others above
+ col = &self->fits->Fptr->tableptr[i];
+ add_double_to_dict(d,"tscale",col->tscale);
+ add_double_to_dict(d,"tzero",col->tzero);
+
+ PyList_Append(colinfo, d);
+ Py_XDECREF(d);
+ }
+ names=stringlist_delete(names);
+ tforms=stringlist_delete(tforms);
+
+ PyDict_SetItemString(dict, "colinfo", colinfo);
+ Py_XDECREF(colinfo);
+ }
+ } else {
+ int tstatus=0;
+ LONGLONG nrows=0;
+ int ncols=0;
+ PyObject* colinfo = PyList_New(0);
+ int i=0,j=0;
+
+ fits_get_num_rowsll(self->fits, &nrows, &tstatus);
+ fits_get_num_cols(self->fits, &ncols, &tstatus);
+ add_long_long_to_dict(dict,"nrows",(long long)nrows);
+ add_long_to_dict(dict,"ncols",(long)ncols);
+
+ {
+ tcolumn* col=NULL;
+ struct stringlist* names=NULL;
+ struct stringlist* tforms=NULL;
+ names=stringlist_new();
+ tforms=stringlist_new();
+
+ for (i=0; i<ncols; i++) {
+ stringlist_push_size(names, 70);
+ stringlist_push_size(tforms, 70);
+ }
+ // just get the names: no other way to do it!
+
+ // rowlen nrows
+ fits_read_atblhdrll(self->fits, ncols, NULL, NULL,
+ // tfields tbcol units
+ NULL, names->data, NULL, tforms->data, NULL,
+ // extname
+ NULL, &tstatus);
+
+
+
+ for (i=0; i<ncols; i++) {
+ PyObject* d = PyDict_New();
+ int type=0;
+ LONGLONG repeat=0;
+ LONGLONG width=0;
+
+ convert_to_ascii(names->data[i]);
+ add_string_to_dict(d,"name",names->data[i]);
+ convert_to_ascii(tforms->data[i]);
+ add_string_to_dict(d,"tform",tforms->data[i]);
+
+ fits_get_coltypell(self->fits, i+1, &type, &repeat, &width, &tstatus);
+ add_long_to_dict(d,"type",(long)type);
+ add_long_long_to_dict(d,"repeat",(long long)repeat);
+ add_long_long_to_dict(d,"width",(long long)width);
+
+ fits_get_eqcoltypell(self->fits, i+1, &type, &repeat, &width, &tstatus);
+ add_long_to_dict(d,"eqtype",(long)type);
+
+ tstatus=0;
+ if (fits_read_tdimll(self->fits, i+1, maxdim, &ndims, dims,
+ &tstatus)) {
+ add_none_to_dict(dict,"tdim");
+ } else {
+ PyObject* dimsObj=PyList_New(0);
+ for (j=0; j<ndims; j++) {
+ append_long_long_to_list(dimsObj, (long long)dims[j]);
+ }
+
+ PyDict_SetItemString(d, "tdim", dimsObj);
+ Py_XDECREF(dimsObj);
+ }
+
+ // using the struct, could cause problems
+ // actually, we can use ffgcprll to get this info, but will
+ // be redundant with some others above
+ col = &self->fits->Fptr->tableptr[i];
+ add_double_to_dict(d,"tscale",col->tscale);
+ add_double_to_dict(d,"tzero",col->tzero);
+
+ PyList_Append(colinfo, d);
+ Py_XDECREF(d);
+ }
+ names=stringlist_delete(names);
+ tforms=stringlist_delete(tforms);
+
+ PyDict_SetItemString(dict, "colinfo", colinfo);
+ Py_XDECREF(colinfo);
+ }
+
+ }
+ return dict;
+}
+
+// get info for the specified HDU
+static PyObject *
+PyFITSObject_get_hdu_name_version(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0, hdutype=0;
+ int status=0;
+
+ char extname[FLEN_VALUE];
+ int extver=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"i", &hdunum)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ status=0;
+ if (fits_read_key(self->fits, TINT, "EXTVER", &extver, NULL, &status)!=0) {
+ extver=0;
+ }
+
+ status=0;
+ if (fits_read_key(self->fits, TSTRING, "EXTNAME", extname, NULL, &status)==0) {
+ return Py_BuildValue("si", extname, extver);
+ } else {
+ return Py_BuildValue("si", "", extver);
+ }
+}
+
+
+// this is the parameter that goes in the type for fits_write_col
+static int
+npy_to_fits_table_type(int npy_dtype, int write_bitcols) {
+
+ char mess[255];
+ switch (npy_dtype) {
+ case NPY_BOOL:
+ if (write_bitcols) {
+ return TBIT;
+ } else {
+ return TLOGICAL;
+ }
+ case NPY_UINT8:
+ return TBYTE;
+ case NPY_INT8:
+ return TSBYTE;
+ case NPY_UINT16:
+ return TUSHORT;
+ case NPY_INT16:
+ return TSHORT;
+ case NPY_UINT32:
+ if (sizeof(unsigned int) == sizeof(npy_uint32)) {
+ return TUINT;
+ } else if (sizeof(unsigned long) == sizeof(npy_uint32)) {
+ return TULONG;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 4 byte unsigned integer type");
+ return -9999;
+ }
+ case NPY_INT32:
+ if (sizeof(int) == sizeof(npy_int32)) {
+ return TINT;
+ } else if (sizeof(long) == sizeof(npy_int32)) {
+ return TLONG;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 4 byte integer type");
+ return -9999;
+ }
+
+ case NPY_INT64:
+ if (sizeof(long long) == sizeof(npy_int64)) {
+ return TLONGLONG;
+ } else if (sizeof(long) == sizeof(npy_int64)) {
+ return TLONG;
+ } else if (sizeof(int) == sizeof(npy_int64)) {
+ return TINT;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 8 byte integer type");
+ return -9999;
+ }
+
+
+ case NPY_FLOAT32:
+ return TFLOAT;
+ case NPY_FLOAT64:
+ return TDOUBLE;
+
+ case NPY_COMPLEX64:
+ return TCOMPLEX;
+ case NPY_COMPLEX128:
+ return TDBLCOMPLEX;
+
+ case NPY_STRING:
+ return TSTRING;
+
+ case NPY_UINT64:
+ PyErr_SetString(PyExc_TypeError, "Unsigned 8 byte integer images are not supported by the FITS standard");
+ return -9999;
+
+ default:
+ sprintf(mess,"Unsupported numpy table datatype %d", npy_dtype);
+ PyErr_SetString(PyExc_TypeError, mess);
+ return -9999;
+ }
+
+ return 0;
+}
+
+
+
+static int
+npy_to_fits_image_types(int npy_dtype, int *fits_img_type, int *fits_datatype) {
+
+ char mess[255];
+ switch (npy_dtype) {
+ case NPY_UINT8:
+ *fits_img_type = BYTE_IMG;
+ *fits_datatype = TBYTE;
+ break;
+ case NPY_INT8:
+ *fits_img_type = SBYTE_IMG;
+ *fits_datatype = TSBYTE;
+ break;
+ case NPY_UINT16:
+ *fits_img_type = USHORT_IMG;
+ *fits_datatype = TUSHORT;
+ break;
+ case NPY_INT16:
+ *fits_img_type = SHORT_IMG;
+ *fits_datatype = TSHORT;
+ break;
+
+ case NPY_UINT32:
+ //*fits_img_type = ULONG_IMG;
+ if (sizeof(unsigned short) == sizeof(npy_uint32)) {
+ *fits_img_type = USHORT_IMG;
+ *fits_datatype = TUSHORT;
+ } else if (sizeof(unsigned int) == sizeof(npy_uint32)) {
+ // there is no UINT_IMG, so use ULONG_IMG
+ *fits_img_type = ULONG_IMG;
+ *fits_datatype = TUINT;
+ } else if (sizeof(unsigned long) == sizeof(npy_uint32)) {
+ *fits_img_type = ULONG_IMG;
+ *fits_datatype = TULONG;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 4 byte unsigned integer type");
+ *fits_datatype = -9999;
+ return 1;
+ }
+ break;
+
+ case NPY_INT32:
+ //*fits_img_type = LONG_IMG;
+ if (sizeof(unsigned short) == sizeof(npy_uint32)) {
+ *fits_img_type = SHORT_IMG;
+ *fits_datatype = TINT;
+ } else if (sizeof(int) == sizeof(npy_int32)) {
+ // there is no UINT_IMG, so use ULONG_IMG
+ *fits_img_type = LONG_IMG;
+ *fits_datatype = TINT;
+ } else if (sizeof(long) == sizeof(npy_int32)) {
+ *fits_img_type = LONG_IMG;
+ *fits_datatype = TLONG;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 4 byte integer type");
+ *fits_datatype = -9999;
+ return 1;
+ }
+ break;
+
+ case NPY_INT64:
+ if (sizeof(LONGLONG) == sizeof(npy_int64)) {
+ *fits_img_type = LONGLONG_IMG;
+ *fits_datatype = TLONGLONG;
+ } else if (sizeof(long) == sizeof(npy_int64)) {
+ *fits_img_type = LONG_IMG;
+ *fits_datatype = TLONG;
+ } else if (sizeof(int) == sizeof(npy_int64)) {
+ // there is no UINT_IMG, so use ULONG_IMG
+ *fits_img_type = LONG_IMG;
+ *fits_datatype = TINT;
+ } else if (sizeof(long long) == sizeof(npy_int64)) {
+ // we don't expect to get here
+ *fits_img_type = LONGLONG_IMG;
+ *fits_datatype = TLONGLONG;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine 8 byte integer type");
+ *fits_datatype = -9999;
+ return 1;
+ }
+ break;
+
+
+ case NPY_FLOAT32:
+ *fits_img_type = FLOAT_IMG;
+ *fits_datatype = TFLOAT;
+ break;
+ case NPY_FLOAT64:
+ *fits_img_type = DOUBLE_IMG;
+ *fits_datatype = TDOUBLE;
+ break;
+
+ case NPY_UINT64:
+ PyErr_SetString(PyExc_TypeError, "Unsigned 8 byte integer images are not supported by the FITS standard");
+ *fits_datatype = -9999;
+ return 1;
+ break;
+
+ default:
+ sprintf(mess,"Unsupported numpy image datatype %d", npy_dtype);
+ PyErr_SetString(PyExc_TypeError, mess);
+ *fits_datatype = -9999;
+ return 1;
+ break;
+ }
+
+ return 0;
+}
+
+
+/*
+ * this is really only for reading variable length columns since we should be
+ * able to just read the bytes for normal columns
+ */
+static int fits_to_npy_table_type(int fits_dtype, int* isvariable) {
+
+ if (fits_dtype < 0) {
+ *isvariable=1;
+ } else {
+ *isvariable=0;
+ }
+
+ switch (abs(fits_dtype)) {
+ case TBIT:
+ return NPY_INT8;
+ case TLOGICAL: // literal T or F stored as char
+ return NPY_INT8;
+ case TBYTE:
+ return NPY_UINT8;
+ case TSBYTE:
+ return NPY_INT8;
+
+ case TUSHORT:
+ if (sizeof(unsigned short) == sizeof(npy_uint16)) {
+ return NPY_UINT16;
+ } else if (sizeof(unsigned short) == sizeof(npy_uint8)) {
+ return NPY_UINT8;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TUSHORT");
+ return -9999;
+ }
+ case TSHORT:
+ if (sizeof(short) == sizeof(npy_int16)) {
+ return NPY_INT16;
+ } else if (sizeof(short) == sizeof(npy_int8)) {
+ return NPY_INT8;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TSHORT");
+ return -9999;
+ }
+
+ case TUINT:
+ if (sizeof(unsigned int) == sizeof(npy_uint32)) {
+ return NPY_UINT32;
+ } else if (sizeof(unsigned int) == sizeof(npy_uint64)) {
+ return NPY_UINT64;
+ } else if (sizeof(unsigned int) == sizeof(npy_uint16)) {
+ return NPY_UINT16;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TUINT");
+ return -9999;
+ }
+ case TINT:
+ if (sizeof(int) == sizeof(npy_int32)) {
+ return NPY_INT32;
+ } else if (sizeof(int) == sizeof(npy_int64)) {
+ return NPY_INT64;
+ } else if (sizeof(int) == sizeof(npy_int16)) {
+ return NPY_INT16;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TINT");
+ return -9999;
+ }
+
+ case TULONG:
+ if (sizeof(unsigned long) == sizeof(npy_uint32)) {
+ return NPY_UINT32;
+ } else if (sizeof(unsigned long) == sizeof(npy_uint64)) {
+ return NPY_UINT64;
+ } else if (sizeof(unsigned long) == sizeof(npy_uint16)) {
+ return NPY_UINT16;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TULONG");
+ return -9999;
+ }
+ case TLONG:
+ if (sizeof(unsigned long) == sizeof(npy_int32)) {
+ return NPY_INT32;
+ } else if (sizeof(unsigned long) == sizeof(npy_int64)) {
+ return NPY_INT64;
+ } else if (sizeof(long) == sizeof(npy_int16)) {
+ return NPY_INT16;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TLONG");
+ return -9999;
+ }
+
+
+ case TLONGLONG:
+ if (sizeof(LONGLONG) == sizeof(npy_int64)) {
+ return NPY_INT64;
+ } else if (sizeof(LONGLONG) == sizeof(npy_int32)) {
+ return NPY_INT32;
+ } else if (sizeof(LONGLONG) == sizeof(npy_int16)) {
+ return NPY_INT16;
+ } else {
+ PyErr_SetString(PyExc_TypeError, "could not determine numpy type for fits TLONGLONG");
+ return -9999;
+ }
+
+
+
+ case TFLOAT:
+ return NPY_FLOAT32;
+ case TDOUBLE:
+ return NPY_FLOAT64;
+
+ case TCOMPLEX:
+ return NPY_COMPLEX64;
+ case TDBLCOMPLEX:
+ return NPY_COMPLEX128;
+
+
+ case TSTRING:
+ return NPY_STRING;
+
+ default:
+ PyErr_Format(PyExc_TypeError,"Unsupported FITS table datatype %d", fits_dtype);
+ return -9999;
+ }
+
+ return 0;
+}
+
+
+
+static int create_empty_hdu(struct PyFITSObject* self)
+{
+ int status=0;
+ int bitpix=SHORT_IMG;
+ int naxis=0;
+ long* naxes=NULL;
+ if (fits_create_img(self->fits, bitpix, naxis, naxes, &status)) {
+ set_ioerr_string_from_status(status);
+ return 1;
+ }
+
+ return 0;
+}
+
+
+// follows fits convention that return value is true
+// for failure
+//
+// exception strings are set internally
+//
+// length checking should happen in python
+//
+// note tile dims are written reverse order since
+// python orders C and fits orders Fortran
+static int set_compression(fitsfile *fits,
+ int comptype,
+ PyObject* tile_dims_obj,
+ int *status) {
+
+ npy_int64 *tile_dims_py=NULL;
+ long *tile_dims_fits=NULL;
+ npy_intp ndims=0, i=0;
+
+ // can be NOCOMPRESS (0)
+ if (fits_set_compression_type(fits, comptype, status)) {
+ set_ioerr_string_from_status(*status);
+ goto _set_compression_bail;
+ return 1;
+ }
+
+ if (tile_dims_obj != Py_None) {
+
+ tile_dims_py=get_int64_from_array(tile_dims_obj, &ndims);
+ if (tile_dims_py==NULL) {
+ *status=1;
+ } else {
+ tile_dims_fits = calloc(ndims,sizeof(long));
+ if (!tile_dims_fits) {
+ PyErr_Format(PyExc_MemoryError, "failed to allocate %ld longs",
+ ndims);
+ goto _set_compression_bail;
+ }
+
+ for (i=0; i<ndims; i++) {
+ tile_dims_fits[ndims-i-1] = tile_dims_py[i];
+ }
+
+ fits_set_tile_dim(fits, ndims, tile_dims_fits, status);
+
+ free(tile_dims_fits);tile_dims_fits=NULL;
+ }
+ }
+
+_set_compression_bail:
+ return *status;
+}
+
+static int pyarray_get_ndim(PyObject* obj) {
+ PyArrayObject* arr;
+ arr = (PyArrayObject*) obj;
+ return arr->nd;
+}
+
+/*
+ Create an image extension, possible writing data as well.
+
+ We allow creating from dimensions rather than from the input image shape,
+ writing into the HDU later
+
+ It is useful to create the extension first so we can write keywords into the
+ header before adding data. This avoids moving the data if the header grows
+ too large.
+
+ However, on distributed file systems it can be more efficient to write
+ the data at this time due to slowness with updating the file in place.
+
+ */
+
+static PyObject *
+PyFITSObject_create_image_hdu(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int ndims=0;
+ long *dims=NULL;
+ int image_datatype=0; // fits type for image, AKA bitpix
+ int datatype=0; // type for the data we entered
+
+ int comptype=0; // same as NOCOMPRESS in newer cfitsio
+ PyObject* tile_dims_obj=NULL;
+
+ PyObject* array, *dims_obj;
+ int npy_dtype=0, nkeys=0, write_data=0;
+ int i=0;
+ int status=0;
+
+ char* extname=NULL;
+ int extver=0;
+ float qlevel=0;
+ int qmethod=0;
+ float hcomp_scale=0;
+ int hcomp_smooth=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ static char *kwlist[] = {
+ "array","nkeys",
+ "dims",
+ "comptype",
+ "tile_dims",
+
+ "qlevel",
+ "qmethod",
+
+ "hcomp_scale",
+ "hcomp_smooth",
+
+ "extname",
+ "extver",
+ NULL,
+ };
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "Oi|OiOfifisi", kwlist,
+ &array, &nkeys,
+ &dims_obj,
+ &comptype,
+ &tile_dims_obj,
+
+ &qlevel,
+ &qmethod,
+
+ &hcomp_scale,
+ &hcomp_smooth,
+
+ &extname,
+ &extver)) {
+ goto create_image_hdu_cleanup;
+ }
+
+
+ if (array == Py_None) {
+ if (create_empty_hdu(self)) {
+ return NULL;
+ }
+ } else {
+ if (!PyArray_Check(array)) {
+ PyErr_SetString(PyExc_TypeError, "input must be an array.");
+ goto create_image_hdu_cleanup;
+ }
+
+ npy_dtype = PyArray_TYPE(array);
+ if (npy_to_fits_image_types(npy_dtype, &image_datatype, &datatype)) {
+ goto create_image_hdu_cleanup;
+ }
+
+ if (PyArray_Check(dims_obj)) {
+ // get dims from input, which must be of type 'i8'
+ // this means we are not writing the array that was input,
+ // it is only used to determine the data type
+ npy_int64 *tptr=NULL, tmp=0;
+ ndims = PyArray_SIZE(dims_obj);
+ dims = calloc(ndims,sizeof(long));
+ for (i=0; i<ndims; i++) {
+ tptr = (npy_int64 *) PyArray_GETPTR1(dims_obj, i);
+ tmp = *tptr;
+ dims[ndims-i-1] = (long) tmp;
+ }
+ write_data=0;
+ } else {
+ // we get the dimensions from the array, which means we are going
+ // to write it as well
+ ndims = pyarray_get_ndim(array);
+ dims = calloc(ndims,sizeof(long));
+ for (i=0; i<ndims; i++) {
+ dims[ndims-i-1] = PyArray_DIM(array, i);
+ }
+ write_data=1;
+ }
+
+ // 0 means NOCOMPRESS but that wasn't defined in the bundled version of cfitsio
+ // if (comptype >= 0) {
+ if (comptype > 0) {
+ // exception strings are set internally
+ if (set_compression(self->fits, comptype, tile_dims_obj, &status)) {
+ goto create_image_hdu_cleanup;
+ }
+
+ if (fits_set_quantize_level(self->fits, qlevel, &status)) {
+ goto create_image_hdu_cleanup;
+ }
+
+ if (fits_set_quantize_method(self->fits, qmethod, &status)) {
+ goto create_image_hdu_cleanup;
+ }
+
+ if (comptype == HCOMPRESS_1) {
+
+ if (fits_set_hcomp_scale(self->fits, hcomp_scale, &status)) {
+ goto create_image_hdu_cleanup;
+ }
+ if (fits_set_hcomp_smooth(self->fits, hcomp_smooth, &status)) {
+ goto create_image_hdu_cleanup;
+ }
+
+ }
+ }
+
+ if (fits_create_img(self->fits, image_datatype, ndims, dims, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+
+
+ }
+ if (extname != NULL) {
+ if (strlen(extname) > 0) {
+
+ // comments are NULL
+ if (fits_update_key_str(self->fits, "EXTNAME", extname, NULL, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+ if (extver > 0) {
+ if (fits_update_key_lng(self->fits, "EXTVER", (LONGLONG) extver, NULL, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+ }
+ }
+ }
+
+ if (nkeys > 0) {
+ if (fits_set_hdrsize(self->fits, nkeys, &status) ) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+ }
+
+ if (write_data) {
+ int firstpixel=1;
+ LONGLONG nelements = 0;
+ void* data=NULL;
+ nelements = PyArray_SIZE(array);
+ data = PyArray_DATA(array);
+ if (fits_write_img(self->fits, datatype, firstpixel, nelements, data, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_image_hdu_cleanup;
+ }
+
+
+create_image_hdu_cleanup:
+
+ if (status != 0) {
+ return NULL;
+ }
+
+ free(dims); dims=NULL;
+ Py_RETURN_NONE;
+}
+
+
+// reshape the image to specified dims
+// the input array must be of type int64
+static PyObject *
+PyFITSObject_reshape_image(struct PyFITSObject* self, PyObject* args) {
+
+ int status=0;
+ int hdunum=0, hdutype=0;
+ PyObject* dims_obj=NULL;
+ LONGLONG dims[CFITSIO_MAX_ARRAY_DIMS]={0};
+ LONGLONG dims_orig[CFITSIO_MAX_ARRAY_DIMS]={0};
+ int ndims=0, ndims_orig=0;
+ npy_int64 dim=0;
+ npy_intp i=0;
+ int bitpix=0, maxdim=CFITSIO_MAX_ARRAY_DIMS;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"iO", &hdunum, &dims_obj)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // existing image params, just to get bitpix
+ if (fits_get_img_paramll(self->fits, maxdim, &bitpix, &ndims_orig, dims_orig, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ ndims = PyArray_SIZE(dims_obj);
+ for (i=0; i<ndims; i++) {
+ dim= *(npy_int64 *) PyArray_GETPTR1(dims_obj, i);
+ dims[i] = (LONGLONG) dim;
+ }
+
+ if (fits_resize_imgll(self->fits, bitpix, ndims, dims, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+// write the image to an existing HDU created using create_image_hdu
+// dims are not checked
+static PyObject *
+PyFITSObject_write_image(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+ LONGLONG nelements=1;
+ PY_LONG_LONG firstpixel_py=0;
+ LONGLONG firstpixel=0;
+ int image_datatype=0; // fits type for image, AKA bitpix
+ int datatype=0; // type for the data we entered
+
+ PyObject* array;
+ void* data=NULL;
+ int npy_dtype=0;
+ int status=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"iOL", &hdunum, &array, &firstpixel_py)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (!PyArray_Check(array)) {
+ PyErr_SetString(PyExc_TypeError, "input must be an array.");
+ return NULL;
+ }
+
+ npy_dtype = PyArray_TYPE(array);
+ if (npy_to_fits_image_types(npy_dtype, &image_datatype, &datatype)) {
+ return NULL;
+ }
+
+
+ data = PyArray_DATA(array);
+ nelements = PyArray_SIZE(array);
+ firstpixel = (LONGLONG) firstpixel_py;
+ if (fits_write_img(self->fits, datatype, firstpixel, nelements, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this is a full file close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+/*
+ * Write tdims from the list. The list must be the expected length.
+ * Entries must be strings or None; if None the tdim is not written.
+ *
+ * The keys are written as TDIM{colnum}
+ */
+static int
+add_tdims_from_listobj(fitsfile* fits, PyObject* tdimObj, int ncols) {
+ int status=0, i=0;
+ size_t size=0;
+ char keyname[20];
+ int colnum=0;
+ PyObject* tmp=NULL;
+ char* tdim=NULL;
+
+ if (tdimObj == NULL || tdimObj == Py_None) {
+ // it is ok for it to be empty
+ return 0;
+ }
+
+ if (!PyList_Check(tdimObj)) {
+ PyErr_SetString(PyExc_ValueError, "Expected a list for tdims");
+ return 1;
+ }
+
+ size = PyList_Size(tdimObj);
+ if (size != (size_t)ncols) {
+ PyErr_Format(PyExc_ValueError, "Expected %d elements in tdims list, got %ld", ncols, size);
+ return 1;
+ }
+
+ for (i=0; i<ncols; i++) {
+ colnum=i+1;
+ tmp = PyList_GetItem(tdimObj, i);
+ if (tmp != Py_None) {
+ if (!is_python_string(tmp)) {
+ PyErr_SetString(PyExc_ValueError, "Expected only strings or None for tdim");
+ return 1;
+ }
+
+ sprintf(keyname, "TDIM%d", colnum);
+
+ tdim = get_object_as_string(tmp);
+ fits_write_key(fits, TSTRING, keyname, tdim, NULL, &status);
+ free(tdim);
+
+ if (status) {
+ set_ioerr_string_from_status(status);
+ return 1;
+ }
+ }
+ }
+
+
+ return 0;
+}
+
+
+// create a new table structure. No physical rows are added yet.
+static PyObject *
+PyFITSObject_create_table_hdu(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int table_type=0, nkeys=0;
+ int nfields=0;
+ LONGLONG nrows=0; // start empty
+
+ static char *kwlist[] = {
+ "table_type","nkeys", "ttyp","tform",
+ "tunit", "tdim", "extname", "extver", NULL};
+ // these are all strings
+ PyObject* ttypObj=NULL;
+ PyObject* tformObj=NULL;
+ PyObject* tunitObj=NULL; // optional
+ PyObject* tdimObj=NULL; // optional
+
+ // these must be freed
+ struct stringlist* ttyp=NULL;
+ struct stringlist* tform=NULL;
+ struct stringlist* tunit=NULL;
+ //struct stringlist* tdim=stringlist_new();
+ char* extname=NULL;
+ char* extname_use=NULL;
+ int extver=0;
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "iiOO|OOsi", kwlist,
+ &table_type, &nkeys, &ttypObj, &tformObj, &tunitObj, &tdimObj, &extname, &extver)) {
+ return NULL;
+ }
+
+ ttyp=stringlist_new();
+ tform=stringlist_new();
+ tunit=stringlist_new();
+ if (stringlist_addfrom_listobj(ttyp, ttypObj, "names")) {
+ status=99;
+ goto create_table_cleanup;
+ }
+
+ if (stringlist_addfrom_listobj(tform, tformObj, "formats")) {
+ status=99;
+ goto create_table_cleanup;
+ }
+
+ if (tunitObj != NULL && tunitObj != Py_None) {
+ if (stringlist_addfrom_listobj(tunit, tunitObj,"units")) {
+ status=99;
+ goto create_table_cleanup;
+ }
+ }
+
+ if (extname != NULL) {
+ if (strlen(extname) > 0) {
+ extname_use = extname;
+ }
+ }
+ nfields = ttyp->size;
+ if ( fits_create_tbl(self->fits, table_type, nrows, nfields,
+ ttyp->data, tform->data, tunit->data, extname_use, &status) ) {
+ set_ioerr_string_from_status(status);
+ goto create_table_cleanup;
+ }
+
+ if (add_tdims_from_listobj(self->fits, tdimObj, nfields)) {
+ status=99;
+ goto create_table_cleanup;
+ }
+
+ if (extname_use != NULL) {
+ if (extver > 0) {
+
+ if (fits_update_key_lng(self->fits, "EXTVER", (LONGLONG) extver, NULL, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_table_cleanup;
+ }
+ }
+ }
+
+ if (nkeys > 0) {
+ if (fits_set_hdrsize(self->fits, nkeys, &status) ) {
+ set_ioerr_string_from_status(status);
+ goto create_table_cleanup;
+ }
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ goto create_table_cleanup;
+ }
+
+create_table_cleanup:
+ ttyp = stringlist_delete(ttyp);
+ tform = stringlist_delete(tform);
+ tunit = stringlist_delete(tunit);
+ //tdim = stringlist_delete(tdim);
+
+
+ if (status != 0) {
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+
+// create a new table structure. No physical rows are added yet.
+static PyObject *
+PyFITSObject_insert_col(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+ int colnum=0;
+
+ int hdutype=0;
+
+ static char *kwlist[] = {"hdunum","colnum","ttyp","tform","tdim", NULL};
+ // these are all strings
+ char* ttype=NULL; // field name
+ char* tform=NULL; // format
+ PyObject* tdimObj=NULL; // optional, a list of len 1
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "iiss|O", kwlist,
+ &hdunum, &colnum, &ttype, &tform, &tdimObj)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_insert_col(self->fits, colnum, ttype, tform, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // OK if dims are not sent
+ if (tdimObj != NULL && tdimObj != Py_None) {
+ PyObject* tmp=NULL;
+ char* tdim=NULL;
+ char keyname[20];
+
+ sprintf(keyname, "TDIM%d", colnum);
+ tmp = PyList_GetItem(tdimObj, 0);
+
+ tdim = get_object_as_string(tmp);
+ fits_write_key(self->fits, TSTRING, keyname, tdim, NULL, &status);
+ free(tdim);
+
+ if (status) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+
+
+// No error checking performed here
+static
+int write_string_column(
+ fitsfile *fits, /* I - FITS file pointer */
+ int colnum, /* I - number of column to write (1 = 1st col) */
+ LONGLONG firstrow, /* I - first row to write (1 = 1st row) */
+ LONGLONG firstelem, /* I - first vector element to write (1 = 1st) */
+ LONGLONG nelem, /* I - number of strings to write */
+ char *data,
+ int *status) { /* IO - error status */
+
+ LONGLONG i=0;
+ LONGLONG twidth=0;
+ // need to create a char** representation of the data, just point back
+ // into the data array at string width offsets. the fits_write_col_str
+ // takes care of skipping between fields.
+ char* cdata=NULL;
+ char** strdata=NULL;
+
+ // using struct def here, could cause problems
+ twidth = fits->Fptr->tableptr[colnum-1].twidth;
+
+ strdata = malloc(nelem*sizeof(char*));
+ if (strdata == NULL) {
+ PyErr_SetString(PyExc_MemoryError, "could not allocate temporary string pointers");
+ *status = 99;
+ return 1;
+ }
+ cdata = (char* ) data;
+ for (i=0; i<nelem; i++) {
+ strdata[i] = &cdata[twidth*i];
+ }
+
+ if( fits_write_col_str(fits, colnum, firstrow, firstelem, nelem, strdata, status)) {
+ set_ioerr_string_from_status(*status);
+ free(strdata);
+ return 1;
+ }
+
+
+ free(strdata);
+
+ return 0;
+}
+
+
+// write a column, starting at firstrow. On the python side, the firstrow kwd
+// should default to 1.
+// You can append rows using firstrow = nrows+1
+/*
+static PyObject *
+PyFITSObject_write_column(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+ int colnum=0;
+ int write_bitcols=0;
+ PyObject* array=NULL;
+
+ void* data=NULL;
+ PY_LONG_LONG firstrow_py=0;
+ LONGLONG firstrow=1;
+ LONGLONG firstelem=1;
+ LONGLONG nelem=0;
+ int npy_dtype=0;
+ int fits_dtype=0;
+
+ static char *kwlist[] = {"hdunum","colnum","array","firstrow","write_bitcols", NULL};
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "iiOLi",
+ kwlist, &hdunum, &colnum, &array, &firstrow_py, &write_bitcols)) {
+ return NULL;
+ }
+ firstrow = (LONGLONG) firstrow_py;
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ if (!PyArray_Check(array)) {
+ PyErr_SetString(PyExc_ValueError,"only arrays can be written to columns");
+ return NULL;
+ }
+
+ npy_dtype = PyArray_TYPE(array);
+ fits_dtype = npy_to_fits_table_type(npy_dtype, write_bitcols);
+ if (fits_dtype == -9999) {
+ return NULL;
+ }
+ if (fits_dtype == TLOGICAL) {
+ int tstatus=0, ttype=0;
+ LONGLONG trepeat=0, twidth=0;
+ // if the column exists and is declared TBIT we will write
+ // that way instead
+ if (fits_get_coltypell(self->fits, colnum,
+ &ttype, &trepeat, &twidth, &tstatus)==0) {
+ // if we don't get here its because the column doesn't exist
+ // yet and that's ok
+ if (ttype==TBIT) {
+ fits_dtype=TBIT;
+ }
+ }
+ }
+
+
+
+ data = PyArray_DATA(array);
+ nelem = PyArray_SIZE(array);
+
+ if (fits_dtype == TSTRING) {
+
+ // this is my wrapper for strings
+ if (write_string_column(self->fits, colnum, firstrow, firstelem, nelem, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ } else if (fits_dtype == TBIT) {
+ if (fits_write_col_bit(self->fits, colnum, firstrow, firstelem, nelem, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ } else {
+ if( fits_write_col(self->fits, fits_dtype, colnum, firstrow, firstelem, nelem, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ }
+
+ // this is a full file close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ Py_RETURN_NONE;
+}
+*/
+
+static PyObject *
+PyFITSObject_write_columns(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+ int write_bitcols=0;
+ //void **data_ptrs=NULL;
+ PyObject* colnum_list=NULL;
+ PyObject* array_list=NULL;
+ PyObject *tmp_array=NULL, *tmp_obj=NULL;
+
+ Py_ssize_t ncols=0;
+
+ void* data=NULL;
+ PY_LONG_LONG firstrow_py=0;
+ LONGLONG firstrow=1, thisrow=0;
+ LONGLONG firstelem=1;
+ LONGLONG nelem=0;
+ LONGLONG *nperrow=NULL;
+ int npy_dtype=0;
+ int *fits_dtypes=NULL;
+ int *is_string=NULL, *colnums=NULL;
+ void **array_ptrs=NULL;
+
+ npy_intp ndim=0, *dims=NULL;
+ Py_ssize_t irow=0, icol=0, j=0;;
+
+ static char *kwlist[] = {"hdunum","colnums","arraylist","firstrow","write_bitcols", NULL};
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "iOOLi",
+ kwlist, &hdunum, &colnum_list, &array_list, &firstrow_py, &write_bitcols)) {
+ return NULL;
+ }
+ firstrow = (LONGLONG) firstrow_py;
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ if (!PyList_Check(colnum_list)) {
+ PyErr_SetString(PyExc_ValueError,"colnums must be a list");
+ return NULL;
+ }
+ if (!PyList_Check(array_list)) {
+ PyErr_SetString(PyExc_ValueError,"colnums must be a list");
+ return NULL;
+ }
+ ncols = PyList_Size(colnum_list);
+ if (ncols == 0) {
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+ if (ncols != PyList_Size(array_list)) {
+ PyErr_Format(PyExc_ValueError,"colnum and array lists not same size: %ld/%ld",
+ ncols, PyList_Size(array_list));
+ }
+
+ // from here on we'll have some temporary arrays we have to free
+ is_string = calloc(ncols, sizeof(int));
+ colnums = calloc(ncols, sizeof(int));
+ array_ptrs = calloc(ncols, sizeof(void*));
+ nperrow = calloc(ncols, sizeof(LONGLONG));
+ fits_dtypes = calloc(ncols, sizeof(int));
+
+ for (icol=0; icol<ncols; icol++) {
+
+ tmp_obj = PyList_GetItem(colnum_list,icol);
+#if PY_MAJOR_VERSION >= 3
+ colnums[icol] = 1+(int) PyLong_AsLong(tmp_obj);
+#else
+ colnums[icol] = 1+(int) PyInt_AsLong(tmp_obj);
+#endif
+
+ tmp_array = PyList_GetItem(array_list, icol);
+ npy_dtype = PyArray_TYPE(tmp_array);
+
+ fits_dtypes[icol] = npy_to_fits_table_type(npy_dtype, write_bitcols);
+ if (fits_dtypes[icol] == -9999) {
+ status=1;
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+ if (fits_dtypes[icol] == TLOGICAL) {
+ int tstatus=0, ttype=0;
+ LONGLONG trepeat=0, twidth=0;
+ // if the column exists and is declared TBIT we will write
+ // that way instead
+ if (fits_get_coltypell(self->fits, colnums[icol],
+ &ttype, &trepeat, &twidth, &tstatus)==0) {
+ // if we don't get here its because the column doesn't exist
+ // yet and that's ok
+ if (ttype==TBIT) {
+ fits_dtypes[icol]=TBIT;
+ }
+ }
+ }
+
+ if (fits_dtypes[icol]==TSTRING) {
+ is_string[icol] = 1;
+ }
+ ndim = PyArray_NDIM(tmp_array);
+ dims = PyArray_DIMS(tmp_array);
+ if (icol==0) {
+ nelem = dims[0];
+ } else {
+ if (dims[0] != nelem) {
+ PyErr_Format(PyExc_ValueError,
+ "not all entries have same row count, "
+ "%lld/%ld", nelem,dims[0]);
+ status=1;
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+ }
+
+ array_ptrs[icol] = tmp_array;
+
+ nperrow[icol] = 1;
+ for (j=1; j<ndim; j++) {
+ nperrow[icol] *= dims[j];
+ }
+ }
+
+ for (irow=0; irow<nelem; irow++) {
+ thisrow = firstrow + irow;
+ for (icol=0; icol<ncols; icol++) {
+ data=PyArray_GETPTR1(array_ptrs[icol], irow);
+ if (is_string[icol]) {
+ if (write_string_column(self->fits,
+ colnums[icol],
+ thisrow,
+ firstelem,
+ nperrow[icol],
+ (char*)data,
+ &status)) {
+ set_ioerr_string_from_status(status);
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+
+ } else if (fits_dtypes[icol] == TBIT) {
+ if (fits_write_col_bit(self->fits,
+ colnums[icol],
+ thisrow,
+ firstelem,
+ nperrow[icol],
+ data,
+ &status)) {
+ set_ioerr_string_from_status(status);
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+ } else {
+ if( fits_write_col(self->fits,
+ fits_dtypes[icol],
+ colnums[icol],
+ thisrow,
+ firstelem,
+ nperrow[icol],
+ data,
+ &status)) {
+ set_ioerr_string_from_status(status);
+ goto _fitsio_pywrap_write_columns_bail;
+ }
+ }
+ }
+ }
+ /*
+ nelem = PyArray_SIZE(array);
+
+ if (fits_dtype == TSTRING) {
+
+ // this is my wrapper for strings
+ if (write_string_column(self->fits, colnum, firstrow, firstelem, nelem, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ } else {
+ if( fits_write_col(self->fits, fits_dtype, colnum, firstrow, firstelem, nelem, data, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ }
+
+ // this is a full file close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ */
+
+_fitsio_pywrap_write_columns_bail:
+ free(is_string); is_string=NULL;
+ free(colnums); colnums=NULL;
+ free(array_ptrs); array_ptrs=NULL;
+ free(nperrow); nperrow=NULL;
+ free(fits_dtypes); fits_dtypes=NULL;
+ if (status != 0) {
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+
+
+
+
+
+// No error checking performed here
+static
+int write_var_string_column(
+ fitsfile *fits, /* I - FITS file pointer */
+ int colnum, /* I - number of column to write (1 = 1st col) */
+ LONGLONG firstrow, /* I - first row to write (1 = 1st row) */
+ PyObject* array,
+ int *status) { /* IO - error status */
+
+ LONGLONG firstelem=1; // ignored
+ LONGLONG nelem=1; // ignored
+ npy_intp nrows=0;
+ npy_intp i=0;
+ char* ptr=NULL;
+ int res=0;
+
+ PyObject* el=NULL;
+ char* strdata=NULL;
+ char* strarr[1];
+
+
+ nrows = PyArray_SIZE(array);
+ for (i=0; i<nrows; i++) {
+ ptr = PyArray_GetPtr((PyArrayObject*) array, &i);
+ el = PyArray_GETITEM(array, ptr);
+
+ strdata=get_object_as_string(el);
+
+ // just a container
+ strarr[0] = strdata;
+ res=fits_write_col_str(fits, colnum,
+ firstrow+i, firstelem, nelem,
+ strarr, status);
+
+ free(strdata);
+ if(res > 0) {
+ goto write_var_string_column_cleanup;
+ }
+ }
+
+write_var_string_column_cleanup:
+
+ if (*status > 0) {
+ return 1;
+ }
+
+ return 0;
+}
+
+/*
+ * No error checking performed here
+ */
+static
+int write_var_num_column(
+ fitsfile *fits, /* I - FITS file pointer */
+ int colnum, /* I - number of column to write (1 = 1st col) */
+ LONGLONG firstrow, /* I - first row to write (1 = 1st row) */
+ int fits_dtype,
+ PyObject* array,
+ int *status) { /* IO - error status */
+
+ LONGLONG firstelem=1;
+ npy_intp nelem=0;
+ npy_intp nrows=0;
+ npy_intp i=0;
+ PyObject* el=NULL;
+ PyObject* el_array=NULL;
+ void* data=NULL;
+ void* ptr=NULL;
+
+ int npy_dtype=0, isvariable=0;
+
+ int mindepth=1, maxdepth=0;
+ PyObject* context=NULL;
+ int requirements =
+ NPY_C_CONTIGUOUS
+ | NPY_ALIGNED
+ | NPY_NOTSWAPPED
+ | NPY_ELEMENTSTRIDES;
+
+ int res=0;
+
+ npy_dtype = fits_to_npy_table_type(fits_dtype, &isvariable);
+
+ nrows = PyArray_SIZE(array);
+ for (i=0; i<nrows; i++) {
+ ptr = PyArray_GetPtr((PyArrayObject*) array, &i);
+ el = PyArray_GETITEM(array, ptr);
+
+ // a copy is only made if needed
+ el_array = PyArray_CheckFromAny(el, PyArray_DescrFromType(npy_dtype),
+ mindepth, maxdepth,
+ requirements, context);
+ if (el_array == NULL) {
+ // error message will already be set
+ return 1;
+ }
+
+ nelem=PyArray_SIZE(el);
+ data=PyArray_DATA(el_array);
+ res=fits_write_col(fits, abs(fits_dtype), colnum,
+ firstrow+i, firstelem, (LONGLONG) nelem, data, status);
+ Py_XDECREF(el_array);
+
+ if(res > 0) {
+ set_ioerr_string_from_status(*status);
+ return 1;
+ }
+ }
+
+ return 0;
+}
+
+
+
+
+/*
+ * write a variable length column, starting at firstrow. On the python side,
+ * the firstrow kwd should default to 1. You can append rows using firstrow =
+ * nrows+1
+ *
+ * The input array should be of type NPY_OBJECT, and the elements
+ * should be either all strings or numpy arrays of the same type
+ */
+
+static PyObject *
+PyFITSObject_write_var_column(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+ int colnum=0;
+ PyObject* array=NULL;
+
+ PY_LONG_LONG firstrow_py=0;
+ LONGLONG firstrow=1;
+ int npy_dtype=0;
+ int fits_dtype=0;
+
+ static char *kwlist[] = {"hdunum","colnum","array","firstrow", NULL};
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "iiOL",
+ kwlist, &hdunum, &colnum, &array, &firstrow_py)) {
+ return NULL;
+ }
+ firstrow = (LONGLONG) firstrow_py;
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ if (!PyArray_Check(array)) {
+ PyErr_SetString(PyExc_ValueError,"only arrays can be written to columns");
+ return NULL;
+ }
+
+ npy_dtype = PyArray_TYPE(array);
+ if (npy_dtype != NPY_OBJECT) {
+ PyErr_SetString(PyExc_TypeError,"only object arrays can be written to variable length columns");
+ return NULL;
+ }
+
+ // determine the fits dtype for this column. We will use this to get data
+ // from the array for writing
+ if (fits_get_eqcoltypell(self->fits, colnum, &fits_dtype, NULL, NULL, &status) > 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_dtype == -TSTRING) {
+ if (write_var_string_column(self->fits, colnum, firstrow, array, &status)) {
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ }
+ return NULL;
+ }
+ } else {
+ if (write_var_num_column(self->fits, colnum, firstrow, fits_dtype, array, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ }
+
+ // this is a full file close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ Py_RETURN_NONE;
+}
+
+
+/*
+ case for writing an entire record
+*/
+static PyObject *
+PyFITSObject_write_record(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* cardin=NULL;
+ char card[FLEN_CARD];
+
+ if (!PyArg_ParseTuple(args, (char*)"is", &hdunum, &cardin)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ strncpy(card, cardin, FLEN_CARD);
+
+ if (fits_write_record(self->fits, card, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+// let python do the conversions
+static PyObject *
+PyFITSObject_write_string_key(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* keyname=NULL;
+ char* value=NULL;
+ char* comment=NULL;
+ char* comment_in=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"isss", &hdunum, &keyname, &value, &comment_in)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strlen(comment_in) > 0) {
+ comment=comment_in;
+ }
+
+ if (fits_write_key_longstr(self->fits, keyname, value, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static PyObject *
+PyFITSObject_write_double_key(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ int decimals=-15;
+
+ char* keyname=NULL;
+ double value=0;
+ char* comment=NULL;
+ char* comment_in=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"isds", &hdunum, &keyname, &value, &comment_in)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strlen(comment_in) > 0) {
+ comment=comment_in;
+ }
+
+ if (fits_update_key_dbl(self->fits, keyname, value, decimals, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ Py_RETURN_NONE;
+}
+
+static PyObject *
+PyFITSObject_write_long_long_key(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* keyname=NULL;
+ long long value=0;
+ char* comment=NULL;
+ char* comment_in=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"isLs", &hdunum, &keyname, &value, &comment_in)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strlen(comment_in) > 0) {
+ comment=comment_in;
+ }
+
+ if (fits_update_key_lng(self->fits, keyname, (LONGLONG) value, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static PyObject *
+PyFITSObject_write_logical_key(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* keyname=NULL;
+ int value=0;
+ char* comment=NULL;
+ char* comment_in=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"isis", &hdunum, &keyname, &value, &comment_in)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strlen(comment_in) > 0) {
+ comment=comment_in;
+ }
+
+ if (fits_update_key_log(self->fits, keyname, value, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+// let python do the conversions
+static PyObject *
+PyFITSObject_write_comment(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* comment=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"is", &hdunum, &comment)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_write_comment(self->fits, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+// let python do the conversions
+static PyObject *
+PyFITSObject_write_history(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* history=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"is", &hdunum, &history)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_write_history(self->fits, history, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+// ADW: Adapted from ffpcom and ffphis in putkey.c
+int fits_write_continue( fitsfile *fptr, /* I - FITS file pointer */
+ const char *cont, /* I - continue string */
+ int *status) /* IO - error status */
+/*
+ Write 1 or more CONTINUE keywords. If the history string is too
+ long to fit on a single keyword (72 chars) then it will automatically
+ be continued on multiple CONTINUE keywords.
+*/
+{
+ char card[FLEN_CARD];
+ int len, ii;
+
+ if (*status > 0) /* inherit input status value if > 0 */
+ return(*status);
+
+ len = strlen(cont);
+ ii = 0;
+
+ for (; len > 0; len -= 72)
+ {
+ strcpy(card, "CONTINUE");
+ strncat(card, &cont[ii], 72);
+ ffprec(fptr, card, status);
+ ii += 72;
+ }
+
+ return(*status);
+}
+
+// let python do the conversions
+static PyObject *
+PyFITSObject_write_continue(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* value=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"is", &hdunum, &value)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_write_continue(self->fits, value, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+static PyObject *
+PyFITSObject_write_undefined_key(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ char* keyname=NULL;
+ char* comment=NULL;
+ char* comment_in=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"iss", &hdunum, &keyname, &comment_in)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strlen(comment_in) > 0) {
+ comment=comment_in;
+ }
+
+ if (fits_update_key_null(self->fits, keyname, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does not close and reopen
+ if (fits_flush_buffer(self->fits, 0, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+
+/*
+ insert a set of rows
+*/
+
+static PyObject *
+PyFITSObject_insert_rows(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+
+ int hdutype=0;
+ PY_LONG_LONG firstrow_py=0, nrows_py=0;
+ LONGLONG firstrow=0, nrows=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"iLL",
+ &hdunum, &firstrow_py, &nrows_py)) {
+ return NULL;
+ }
+
+ firstrow = (LONGLONG) firstrow_py;
+ nrows = (LONGLONG) nrows_py;
+
+ if (nrows <= 0) {
+ // nothing to do, just return
+ Py_RETURN_NONE;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_insert_rows(self->fits, firstrow, nrows, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+/*
+
+ delete a range of rows
+
+ input stop is like a python slice, so exclusive, but 1-offset
+ rather than 0-offset
+*/
+
+static PyObject *
+PyFITSObject_delete_row_range(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+
+ int hdutype=0;
+ PY_LONG_LONG slice_start_py=0, slice_stop_py=0;
+ LONGLONG slice_start=0, slice_stop=0, nrows=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"iLL",
+ &hdunum, &slice_start_py, &slice_stop_py)) {
+ return NULL;
+ }
+
+ slice_start = (LONGLONG) slice_start_py;
+ slice_stop = (LONGLONG) slice_stop_py;
+ nrows = slice_stop - slice_start;
+
+ if (nrows <= 0) {
+ // nothing to do, just return
+ Py_RETURN_NONE;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_delete_rows(self->fits, slice_start, nrows, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+/*
+
+ delete a specific set of rows, 1-offset
+
+ no type checking is applied to the rows
+*/
+
+static PyObject *
+PyFITSObject_delete_rows(struct PyFITSObject* self, PyObject* args, PyObject* kwds) {
+ int status=0;
+ int hdunum=0;
+
+ int hdutype=0;
+ PyObject *rows_array=NULL;
+ LONGLONG *rows=NULL, nrows=0;
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_ValueError, "fits file is NULL");
+ return NULL;
+ }
+
+ if (!PyArg_ParseTuple(args, (char*)"iO",
+ &hdunum, &rows_array)) {
+ return NULL;
+ }
+
+ rows = (LONGLONG *) PyArray_DATA(rows_array);
+ nrows = PyArray_SIZE(rows_array);
+ if (nrows <= 0) {
+ Py_RETURN_NONE;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_delete_rowlistll(self->fits, rows, nrows, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this does a full close and reopen
+ if (fits_flush_file(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+
+
+/*
+ * read a single, entire column from an ascii table into the input array. This
+ * version uses the standard read column instead of our by-bytes version.
+ *
+ * A number of assumptions are made, such as that columns are scalar, which
+ * is true for ascii.
+ */
+
+static int read_ascii_column_all(fitsfile* fits, int colnum, PyObject* array, int* status) {
+
+ int npy_dtype=0;
+ int fits_dtype=0;
+
+ npy_intp nelem=0;
+ LONGLONG firstelem=1;
+ LONGLONG firstrow=1;
+ int* anynul=NULL;
+ void* nulval=0;
+ char* nulstr=" ";
+ void* data=NULL;
+ char* cdata=NULL;
+
+ npy_dtype = PyArray_TYPE(array);
+ fits_dtype = npy_to_fits_table_type(npy_dtype,0);
+
+ nelem = PyArray_SIZE(array);
+
+ if (fits_dtype == TSTRING) {
+ npy_intp i=0;
+ LONGLONG rownum=0;
+
+ for (i=0; i<nelem; i++) {
+ cdata = PyArray_GETPTR1(array, i);
+ rownum = (LONGLONG) (1+i);
+ if (fits_read_col_str(fits,colnum,rownum,firstelem,1,nulstr,&cdata,anynul,status) > 0) {
+ return 1;
+ }
+ }
+
+ /*
+
+ LONGLONG twidth=0;
+ char** strdata=NULL;
+
+ cdata = (char*) PyArray_DATA(array);
+
+ strdata=malloc(nelem*sizeof(char*));
+ if (NULL==strdata) {
+ PyErr_SetString(PyExc_MemoryError, "could not allocate temporary string pointers");
+ *status = 99;
+ return 1;
+
+ }
+
+
+ twidth=fits->Fptr->tableptr[colnum-1].twidth;
+ for (i=0; i<nelem; i++) {
+ //strdata[i] = &cdata[twidth*i];
+ // this 1-d assumption works because array fields are not allowedin ascii
+ strdata[i] = (char*) PyArray_GETPTR1(array, i);
+ }
+
+ if (fits_read_col_str(fits,colnum,firstrow,firstelem,nelem,nulstr,strdata,anynul,status) > 0) {
+ free(strdata);
+ return 1;
+ }
+
+ free(strdata);
+ */
+
+ } else {
+ data=PyArray_DATA(array);
+ if (fits_read_col(fits,fits_dtype,colnum,firstrow,firstelem,nelem,nulval,data,anynul,status) > 0) {
+ return 1;
+ }
+ }
+
+ return 0;
+
+}
+static int read_ascii_column_byrow(
+ fitsfile* fits, int colnum, PyObject* array, PyObject* rowsObj, int* status) {
+
+ int npy_dtype=0;
+ int fits_dtype=0;
+
+ npy_intp nelem=0;
+ LONGLONG firstelem=1;
+ LONGLONG rownum=0;
+ npy_intp nrows=-1;
+
+ int* anynul=NULL;
+ void* nulval=0;
+ char* nulstr=" ";
+ void* data=NULL;
+ char* cdata=NULL;
+
+ int dorows=0;
+
+ npy_intp i=0;
+
+ npy_dtype = PyArray_TYPE(array);
+ fits_dtype = npy_to_fits_table_type(npy_dtype,0);
+
+ nelem = PyArray_SIZE(array);
+
+
+ if (rowsObj != Py_None) {
+ dorows=1;
+ nrows = PyArray_SIZE(rowsObj);
+ if (nrows != nelem) {
+ PyErr_Format(PyExc_ValueError,
+ "input array[%ld] and rows[%ld] have different size", nelem,nrows);
+ return 1;
+ }
+ }
+
+ data = PyArray_GETPTR1(array, i);
+ for (i=0; i<nrows; i++) {
+ if (dorows) {
+ rownum = (LONGLONG) (1 + *(npy_int64*) PyArray_GETPTR1(rowsObj, i));
+ } else {
+ rownum = (LONGLONG) (1+i);
+ }
+ // assuming 1-D
+ data = PyArray_GETPTR1(array, i);
+ if (fits_dtype==TSTRING) {
+ cdata = (char* ) data;
+ if (fits_read_col_str(fits,colnum,rownum,firstelem,1,nulstr,&cdata,anynul,status) > 0) {
+ return 1;
+ }
+ } else {
+ if (fits_read_col(fits,fits_dtype,colnum,rownum,firstelem,1,nulval,data,anynul,status) > 0) {
+ return 1;
+ }
+ }
+ }
+
+ return 0;
+}
+
+
+static int read_ascii_column(fitsfile* fits, int colnum, PyObject* array, PyObject* rowsObj, int* status) {
+
+ int ret=0;
+ if (rowsObj != Py_None || !PyArray_ISCONTIGUOUS(array)) {
+ ret = read_ascii_column_byrow(fits, colnum, array, rowsObj, status);
+ } else {
+ ret = read_ascii_column_all(fits, colnum, array, status);
+ }
+
+ return ret;
+}
+
+
+
+
+
+// read a subset of rows for the input column
+// the row array is assumed to be unique and sorted.
+static int read_binary_column(
+ fitsfile* fits,
+ int colnum,
+ npy_intp nrows,
+ npy_int64* rows,
+ void* data,
+ npy_intp stride,
+ int* status) {
+
+ FITSfile* hdu=NULL;
+ tcolumn* colptr=NULL;
+ LONGLONG file_pos=0, irow=0;
+ npy_int64 row=0;
+
+ LONGLONG repeat=0;
+ LONGLONG width=0;
+
+ int rows_sent=0;
+
+ // use char for pointer arith. It's actually ok to use void as char but
+ // this is just in case.
+ char* ptr=NULL;
+
+ // using struct defs here, could cause problems
+ hdu = fits->Fptr;
+ colptr = hdu->tableptr + (colnum-1);
+
+ repeat = colptr->trepeat;
+ width = colptr->tdatatype == TSTRING ? 1 : colptr->twidth;
+
+ rows_sent = nrows == hdu->numrows ? 0 : 1;
+
+ ptr = (char*) data;
+ for (irow=0; irow<nrows; irow++) {
+ if (rows_sent) {
+ row = rows[irow];
+ } else {
+ row = irow;
+ }
+ file_pos = hdu->datastart + row*hdu->rowlength + colptr->tbcol;
+ ffmbyt(fits, file_pos, REPORT_EOF, status);
+ if (ffgbytoff(fits, width, repeat, 0, (void*)ptr, status)) {
+ return 1;
+ }
+ ptr += stride;
+ }
+
+ return 0;
+}
+
+
+
+
+/*
+ * read from a column into an input array
+ */
+static PyObject *
+PyFITSObject_read_column(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+ int colnum=0;
+
+ FITSfile* hdu=NULL;
+ int status=0;
+
+ PyObject* array=NULL;
+
+ PyObject* rowsObj;
+
+ if (!PyArg_ParseTuple(args, (char*)"iiOO", &hdunum, &colnum, &array, &rowsObj)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // using struct defs here, could cause problems
+ hdu = self->fits->Fptr;
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot yet read columns from an IMAGE_HDU");
+ return NULL;
+ }
+ if (colnum < 1 || colnum > hdu->tfield) {
+ PyErr_SetString(PyExc_RuntimeError, "requested column is out of bounds");
+ return NULL;
+ }
+
+
+ if (hdutype == ASCII_TBL) {
+ if (read_ascii_column(self->fits, colnum, array, rowsObj, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ } else {
+ void* data=PyArray_DATA(array);
+ npy_intp nrows=0;
+ npy_int64* rows=NULL;
+ npy_intp stride=PyArray_STRIDE(array,0);
+ if (rowsObj == Py_None) {
+ nrows = hdu->numrows;
+ } else {
+ rows = get_int64_from_array(rowsObj, &nrows);
+ }
+
+ if (read_binary_column(self->fits, colnum, nrows, rows, data, stride, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+
+/*
+ * Free all the elements in the python list as well as the list itself
+ */
+static void free_all_python_list(PyObject* list) {
+ if (PyList_Check(list)) {
+ Py_ssize_t i=0;
+ for (i=0; i<PyList_Size(list); i++) {
+ Py_XDECREF(PyList_GetItem(list,i));
+ }
+ }
+ Py_XDECREF(list);
+}
+
+static PyObject*
+read_var_string(fitsfile* fits, int colnum, LONGLONG row, LONGLONG nchar, int* status) {
+ LONGLONG firstelem=1;
+ char* str=NULL;
+ char* strarr[1];
+ PyObject* stringObj=NULL;
+ void* nulval=0;
+ int* anynul=NULL;
+
+ str=calloc(nchar+1,sizeof(char));
+ if (str == NULL) {
+ PyErr_Format(PyExc_MemoryError,
+ "Could not allocate string of size %lld", nchar);
+ return NULL;
+ }
+
+ strarr[0] = str;
+ if (fits_read_col(fits,TSTRING,colnum,row,firstelem,nchar,nulval,strarr,anynul,status) > 0) {
+ goto read_var_string_cleanup;
+ }
+#if PY_MAJOR_VERSION >= 3
+ // bytes
+ stringObj = Py_BuildValue("y",str);
+#else
+ stringObj = Py_BuildValue("s",str);
+#endif
+ if (NULL == stringObj) {
+ PyErr_Format(PyExc_MemoryError,
+ "Could not allocate py string of size %lld", nchar);
+ goto read_var_string_cleanup;
+ }
+
+read_var_string_cleanup:
+ free(str);
+
+ return stringObj;
+}
+static PyObject*
+read_var_nums(fitsfile* fits, int colnum, LONGLONG row, LONGLONG nelem,
+ int fits_dtype, int npy_dtype, int* status) {
+ LONGLONG firstelem=1;
+ PyObject* arrayObj=NULL;
+ void* nulval=0;
+ int* anynul=NULL;
+ npy_intp dims[1];
+ int fortran=0;
+ void* data=NULL;
+
+
+ dims[0] = nelem;
+ arrayObj=PyArray_ZEROS(1, dims, npy_dtype, fortran);
+ if (arrayObj==NULL) {
+ PyErr_Format(PyExc_MemoryError,
+ "Could not allocate array type %d size %lld",npy_dtype,nelem);
+ return NULL;
+ }
+ data = PyArray_DATA(arrayObj);
+ if (fits_read_col(fits,abs(fits_dtype),colnum,row,firstelem,nelem,nulval,data,anynul,status) > 0) {
+ Py_XDECREF(arrayObj);
+ return NULL;
+ }
+
+ return arrayObj;
+}
+/*
+ * read a variable length column as a list of arrays
+ * what about strings?
+ */
+static PyObject *
+PyFITSObject_read_var_column_as_list(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int colnum=0;
+ PyObject* rowsObj=NULL;
+
+ int hdutype=0;
+ int ncols=0;
+ const npy_int64* rows=NULL;
+ LONGLONG nrows=0;
+ int get_all_rows=0;
+
+ int status=0, tstatus=0;
+
+ int fits_dtype=0;
+ int npy_dtype=0;
+ int isvariable=0;
+ LONGLONG repeat=0;
+ LONGLONG width=0;
+ LONGLONG offset=0;
+ LONGLONG i=0;
+ LONGLONG row=0;
+
+ PyObject* listObj=NULL;
+ PyObject* tempObj=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"iiO", &hdunum, &colnum, &rowsObj)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot yet read columns from an IMAGE_HDU");
+ return NULL;
+ }
+ // using struct defs here, could cause problems
+ fits_get_num_cols(self->fits, &ncols, &status);
+ if (colnum < 1 || colnum > ncols) {
+ PyErr_SetString(PyExc_RuntimeError, "requested column is out of bounds");
+ return NULL;
+ }
+
+ if (fits_get_coltypell(self->fits, colnum, &fits_dtype, &repeat, &width, &status) > 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ npy_dtype = fits_to_npy_table_type(fits_dtype, &isvariable);
+ if (npy_dtype < 0) {
+ return NULL;
+ }
+ if (!isvariable) {
+ PyErr_Format(PyExc_TypeError,"Column %d not a variable length %d", colnum, fits_dtype);
+ return NULL;
+ }
+
+ if (rowsObj == Py_None) {
+ fits_get_num_rowsll(self->fits, &nrows, &tstatus);
+ get_all_rows=1;
+ } else {
+ npy_intp tnrows=0;
+ rows = (const npy_int64*) get_int64_from_array(rowsObj, &tnrows);
+ nrows=(LONGLONG) tnrows;
+ get_all_rows=0;
+ }
+
+ listObj = PyList_New(0);
+
+ for (i=0; i<nrows; i++) {
+ tempObj=NULL;
+
+ if (get_all_rows) {
+ row = i+1;
+ } else {
+ row = (LONGLONG) (rows[i]+1);
+ }
+
+ // repeat holds how many elements are in this row
+ if (fits_read_descriptll(self->fits, colnum, row, &repeat, &offset, &status) > 0) {
+ goto read_var_column_cleanup;
+ }
+
+ if (fits_dtype == -TSTRING) {
+ tempObj = read_var_string(self->fits,colnum,row,repeat,&status);
+ } else {
+ tempObj = read_var_nums(self->fits,colnum,row,repeat,
+ fits_dtype,npy_dtype,&status);
+ }
+ if (tempObj == NULL) {
+ tstatus=1;
+ goto read_var_column_cleanup;
+ }
+ PyList_Append(listObj, tempObj);
+ Py_XDECREF(tempObj);
+ }
+
+
+read_var_column_cleanup:
+
+ if (status != 0 || tstatus != 0) {
+ Py_XDECREF(tempObj);
+ free_all_python_list(listObj);
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ }
+ return NULL;
+ }
+
+ return listObj;
+}
+
+
+// read specified columns and rows
+static int read_binary_rec_columns(
+ fitsfile* fits,
+ npy_intp ncols, npy_int64* colnums,
+ npy_intp nrows, npy_int64* rows,
+ void* data, int* status) {
+ FITSfile* hdu=NULL;
+ tcolumn* colptr=NULL;
+ LONGLONG file_pos=0;
+ npy_intp col=0;
+ npy_int64 colnum=0;
+
+ int rows_sent=0;
+ npy_intp irow=0;
+ npy_int64 row=0;
+
+ // use char for pointer arith. It's actually ok to use void as char but
+ // this is just in case.
+ char* ptr;
+
+ LONGLONG gsize=0; // number of bytes in column
+ LONGLONG repeat=0;
+ LONGLONG width=0;
+
+ // using struct defs here, could cause problems
+ hdu = fits->Fptr;
+
+ rows_sent = nrows == hdu->numrows ? 0 : 1;
+
+ ptr = (char*) data;
+ for (irow=0; irow<nrows; irow++) {
+ if (rows_sent) {
+ row = rows[irow];
+ } else {
+ row = irow;
+ }
+ for (col=0; col < ncols; col++) {
+
+ colnum = colnums[col];
+ colptr = hdu->tableptr + (colnum-1);
+
+ repeat = colptr->trepeat;
+ width = colptr->tdatatype == TSTRING ? 1 : colptr->twidth;
+ gsize = repeat*width;
+
+ file_pos = hdu->datastart + row*hdu->rowlength + colptr->tbcol;
+
+ if (colptr->tdatatype == TBIT) {
+ if (fits_read_col_bit(fits, colnum, row+1, 1, repeat, (char*)ptr, status)) {
+ return 1;
+ }
+ } else {
+ // can just do one status check, since status are inherited.
+ ffmbyt(fits, file_pos, REPORT_EOF, status);
+ if (ffgbytoff(fits, width, repeat, 0, (void*)ptr, status)) {
+ return 1;
+ }
+ }
+ ptr += gsize;
+ }
+ }
+
+ return 0;
+}
+
+
+
+// python method for reading specified columns and rows
+static PyObject *
+PyFITSObject_read_columns_as_rec(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+ npy_intp ncols=0;
+ npy_int64* colnums=NULL;
+ FITSfile* hdu=NULL;
+
+ int status=0;
+
+ PyObject* columnsobj=NULL;
+ PyObject* array=NULL;
+ void* data=NULL;
+
+ PyObject* rowsobj=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"iOOO", &hdunum, &columnsobj, &array, &rowsobj)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ goto recread_columns_cleanup;
+ }
+
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot read IMAGE_HDU into a recarray");
+ return NULL;
+ }
+
+ colnums = get_int64_from_array(columnsobj, &ncols);
+ if (colnums == NULL) {
+ return NULL;
+ }
+
+ hdu = self->fits->Fptr;
+ data = PyArray_DATA(array);
+ npy_intp nrows;
+ npy_int64* rows=NULL;
+ if (rowsobj == Py_None) {
+ nrows = hdu->numrows;
+ } else {
+ rows = get_int64_from_array(rowsobj, &nrows);
+ }
+ if (read_binary_rec_columns(self->fits, ncols, colnums, nrows, rows, data, &status)) {
+ goto recread_columns_cleanup;
+ }
+
+recread_columns_cleanup:
+
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+/*
+ * read specified columns and rows
+ *
+ * Move by offset instead of just groupsize; this allows us to read into a
+ * recarray while skipping some fields, e.g. variable length array fields, to
+ * be read separately.
+ *
+ * If rows is NULL, then nrows are read consecutively.
+ */
+
+static int read_columns_as_rec_byoffset(
+ fitsfile* fits,
+ npy_intp ncols,
+ const npy_int64* colnums, // columns to read from file
+ const npy_int64* field_offsets, // offsets of corresponding fields within array
+ npy_intp nrows,
+ const npy_int64* rows,
+ char* data,
+ npy_intp recsize,
+ int* status) {
+
+ FITSfile* hdu=NULL;
+ tcolumn* colptr=NULL;
+ LONGLONG file_pos=0;
+ npy_intp col=0;
+ npy_int64 colnum=0;
+
+ char* ptr=NULL;
+
+ int get_all_rows=1;
+ npy_intp irow=0;
+ npy_int64 row=0;
+
+ long groupsize=0; // number of bytes in column
+ long ngroups=1; // number to read, one for row-by-row reading
+ long group_gap=0; // gap between groups, zero since we aren't using it
+
+ if (rows != NULL) {
+ get_all_rows=0;
+ }
+
+ // using struct defs here, could cause problems
+ hdu = fits->Fptr;
+ for (irow=0; irow<nrows; irow++) {
+ if (get_all_rows) {
+ row=irow;
+ } else {
+ row = rows[irow];
+ }
+ for (col=0; col < ncols; col++) {
+
+ // point to this field in the array, allows for skipping
+ ptr = data + irow*recsize + field_offsets[col];
+
+ colnum = colnums[col];
+ colptr = hdu->tableptr + (colnum-1);
+
+ groupsize = get_groupsize(colptr);
+
+ file_pos = hdu->datastart + row*hdu->rowlength + colptr->tbcol;
+
+ // can just do one status check, since status are inherited.
+ ffmbyt(fits, file_pos, REPORT_EOF, status);
+ if (ffgbytoff(fits, groupsize, ngroups, group_gap, (void*) ptr, status)) {
+ return 1;
+ }
+ }
+ }
+
+ return 0;
+}
+
+
+
+
+
+
+
+/* python method for reading specified columns and rows, moving by offset in
+ * the array to allow some fields not read.
+ *
+ * columnsObj is the columns in the fits file to read.
+ * offsetsObj is the offsets of the corresponding fields into the array.
+ */
+static PyObject *
+PyFITSObject_read_columns_as_rec_byoffset(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ npy_intp ncols=0;
+ npy_intp noffsets=0;
+ npy_intp nrows=0;
+ const npy_int64* colnums=NULL;
+ const npy_int64* offsets=NULL;
+ const npy_int64* rows=NULL;
+
+ PyObject* columnsObj=NULL;
+ PyObject* offsetsObj=NULL;
+ PyObject* rowsObj=NULL;
+
+ PyObject* array=NULL;
+ void* data=NULL;
+ npy_intp recsize=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"iOOOO", &hdunum, &columnsObj, &offsetsObj, &array, &rowsObj)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ goto recread_columns_byoffset_cleanup;
+ }
+
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot read IMAGE_HDU into a recarray");
+ return NULL;
+ }
+
+ colnums = (const npy_int64*) get_int64_from_array(columnsObj, &ncols);
+ if (colnums == NULL) {
+ return NULL;
+ }
+ offsets = (const npy_int64*) get_int64_from_array(offsetsObj, &noffsets);
+ if (offsets == NULL) {
+ return NULL;
+ }
+ if (noffsets != ncols) {
+ PyErr_Format(PyExc_ValueError,
+ "%ld columns requested but got %ld offsets",
+ ncols, noffsets);
+ return NULL;
+ }
+
+ if (rowsObj != Py_None) {
+ rows = (const npy_int64*) get_int64_from_array(rowsObj, &nrows);
+ } else {
+ nrows = PyArray_SIZE(array);
+ }
+
+ data = PyArray_DATA(array);
+ recsize = PyArray_ITEMSIZE(array);
+ if (read_columns_as_rec_byoffset(
+ self->fits,
+ ncols, colnums, offsets,
+ nrows,
+ rows,
+ (char*) data,
+ recsize,
+ &status) > 0) {
+ goto recread_columns_byoffset_cleanup;
+ }
+
+recread_columns_byoffset_cleanup:
+
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+// read specified rows, all columns
+static int read_rec_bytes_byrow(
+ fitsfile* fits,
+ npy_intp nrows, npy_int64* rows,
+ void* data, int* status) {
+
+ FITSfile* hdu=NULL;
+
+ npy_intp irow=0;
+ LONGLONG firstrow=1;
+ LONGLONG firstchar=1;
+
+ // use char for pointer arith. It's actually ok to use void as char but
+ // this is just in case.
+ unsigned char* ptr;
+
+ // using struct defs here, could cause problems
+ hdu = fits->Fptr;
+ ptr = (unsigned char*) data;
+
+ for (irow=0; irow<nrows; irow++) {
+ // Input is zero-offset
+ firstrow = 1 + (LONGLONG) rows[irow];
+
+ if (fits_read_tblbytes(fits, firstrow, firstchar, hdu->rowlength, ptr, status)) {
+ return 1;
+ }
+
+ ptr += hdu->rowlength;
+ }
+
+ return 0;
+}
+// read specified rows, all columns
+/*
+static int read_rec_bytes_byrowold(
+ fitsfile* fits,
+ npy_intp nrows, npy_int64* rows,
+ void* data, int* status) {
+ FITSfile* hdu=NULL;
+ LONGLONG file_pos=0;
+
+ npy_intp irow=0;
+ npy_int64 row=0;
+
+ // use char for pointer arith. It's actually ok to use void as char but
+ // this is just in case.
+ char* ptr;
+
+ long ngroups=1; // number to read, one for row-by-row reading
+ long offset=0; // gap between groups, not stride. zero since we aren't using it
+
+ // using struct defs here, could cause problems
+ hdu = fits->Fptr;
+ ptr = (char*) data;
+
+ for (irow=0; irow<nrows; irow++) {
+ row = rows[irow];
+ file_pos = hdu->datastart + row*hdu->rowlength;
+
+ // can just do one status check, since status are inherited.
+ ffmbyt(fits, file_pos, REPORT_EOF, status);
+ if (ffgbytoff(fits, hdu->rowlength, ngroups, offset, (void*) ptr, status)) {
+ return 1;
+ }
+ ptr += hdu->rowlength;
+ }
+
+ return 0;
+}
+*/
+
+
+// python method to read all columns but subset of rows
+static PyObject *
+PyFITSObject_read_rows_as_rec(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+
+ int status=0;
+ PyObject* array=NULL;
+ void* data=NULL;
+
+ PyObject* rowsObj=NULL;
+ npy_intp nrows=0;
+ npy_int64* rows=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"iOO", &hdunum, &array, &rowsObj)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ goto recread_byrow_cleanup;
+ }
+
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot read IMAGE_HDU into a recarray");
+ return NULL;
+ }
+
+ data = PyArray_DATA(array);
+
+ rows = get_int64_from_array(rowsObj, &nrows);
+ if (rows == NULL) {
+ return NULL;
+ }
+
+ if (read_rec_bytes_byrow(self->fits, nrows, rows, data, &status)) {
+ goto recread_byrow_cleanup;
+ }
+
+recread_byrow_cleanup:
+
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+
+
+ /* Read the range of rows, 1-offset. It is assumed the data match the table
+ * perfectly.
+ */
+
+static int read_rec_range(fitsfile* fits, LONGLONG firstrow, LONGLONG nrows, void* data, int* status) {
+ // can also use this for reading row ranges
+ LONGLONG firstchar=1;
+ LONGLONG nchars=0;
+
+ nchars = (fits->Fptr)->rowlength*nrows;
+
+ if (fits_read_tblbytes(fits, firstrow, firstchar, nchars, (unsigned char*) data, status)) {
+ return 1;
+ }
+
+ return 0;
+}
+
+
+
+
+/* here rows are 1-offset, unlike when reading a specific subset of rows */
+static PyObject *
+PyFITSObject_read_as_rec(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+
+ int status=0;
+ PyObject* array=NULL;
+ void* data=NULL;
+
+ PY_LONG_LONG firstrow=0;
+ PY_LONG_LONG lastrow=0;
+ PY_LONG_LONG nrows=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"iLLO", &hdunum, &firstrow, &lastrow, &array)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ goto recread_asrec_cleanup;
+ }
+
+ if (hdutype == IMAGE_HDU) {
+ PyErr_SetString(PyExc_RuntimeError, "Cannot read IMAGE_HDU into a recarray");
+ return NULL;
+ }
+
+ data = PyArray_DATA(array);
+
+ nrows=lastrow-firstrow+1;
+ if (read_rec_range(self->fits, (LONGLONG)firstrow, (LONGLONG)nrows, data, &status)) {
+ goto recread_asrec_cleanup;
+ }
+
+recread_asrec_cleanup:
+
+ if (status != 0) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ Py_RETURN_NONE;
+}
+
+
+// read an n-dimensional "image" into the input array. Only minimal checking
+// of the input array is done.
+// Note numpy allows a maximum of 32 dimensions
+static PyObject *
+PyFITSObject_read_image(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+ int status=0;
+ PyObject* array=NULL;
+ void* data=NULL;
+ int npy_dtype=0;
+ int dummy=0, fits_read_dtype=0;
+
+ int maxdim=NUMPY_MAX_DIMS; // numpy maximum
+ int datatype=0; // type info for axis
+ int naxis=0; // number of axes
+ int i=0;
+ LONGLONG naxes[NUMPY_MAX_DIMS];; // size of each axis
+ LONGLONG firstpixels[NUMPY_MAX_DIMS];
+ LONGLONG size=0;
+ npy_intp arrsize=0;
+
+ int anynul=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"iO", &hdunum, &array)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ return NULL;
+ }
+
+ if (fits_get_img_paramll(self->fits, maxdim, &datatype, &naxis,
+ naxes, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // make sure dims match
+ size=0;
+ size = naxes[0];
+ for (i=1; i< naxis; i++) {
+ size *= naxes[i];
+ }
+ arrsize = PyArray_SIZE(array);
+ data = PyArray_DATA(array);
+
+ if (size != arrsize) {
+ PyErr_Format(PyExc_RuntimeError,
+ "Input array size is %ld but on disk array size is %lld",
+ arrsize, size);
+ return NULL;
+ }
+
+ npy_dtype = PyArray_TYPE(array);
+ npy_to_fits_image_types(npy_dtype, &dummy, &fits_read_dtype);
+
+ for (i=0; i<naxis; i++) {
+ firstpixels[i] = 1;
+ }
+ if (fits_read_pixll(self->fits, fits_read_dtype, firstpixels, size,
+ 0, data, &anynul, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+
+ Py_RETURN_NONE;
+}
+
+static PyObject *
+PyFITSObject_read_raw(struct PyFITSObject* self, PyObject* args) {
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ //fitsfile* fits = self->fits;
+ FITSfile* FITS = self->fits->Fptr;
+ int status = 0;
+ char* filedata;
+ LONGLONG sz;
+ LONGLONG io_pos;
+ PyObject *stringobj;
+
+ // Flush (close & reopen HDU) to make everything consistent
+ ffflus(self->fits, &status);
+ if (status) {
+ PyErr_Format(PyExc_RuntimeError,
+ "Failed to flush FITS file data to disk; CFITSIO code %i",
+ status);
+ return NULL;
+ }
+ // Allocate buffer for string
+ sz = FITS->filesize;
+ // Create python string object of requested size, unitialized
+ stringobj = PyBytes_FromStringAndSize(NULL, sz);
+ if (!stringobj) {
+ PyErr_Format(PyExc_RuntimeError,
+ "Failed to allocate python string object to hold FITS file data: %i bytes",
+ (int)sz);
+ return NULL;
+ }
+ // Grab pointer to the memory buffer of the python string object
+ filedata = PyBytes_AsString(stringobj);
+ if (!filedata) {
+ Py_DECREF(stringobj);
+ return NULL;
+ }
+ // Remember old file position
+ io_pos = FITS->io_pos;
+ // Seek to beginning of file
+ if (ffseek(FITS, 0)) {
+ Py_DECREF(stringobj);
+ PyErr_Format(PyExc_RuntimeError,
+ "Failed to seek to beginning of FITS file");
+ return NULL;
+ }
+ // Read into filedata
+ if (ffread(FITS, sz, filedata, &status)) {
+ Py_DECREF(stringobj);
+ PyErr_Format(PyExc_RuntimeError,
+ "Failed to read file data into memory: CFITSIO code %i",
+ status);
+ return NULL;
+ }
+ // Seek back to where we were
+ if (ffseek(FITS, io_pos)) {
+ Py_DECREF(stringobj);
+ PyErr_Format(PyExc_RuntimeError,
+ "Failed to seek back to original FITS file position");
+ return NULL;
+ }
+ return stringobj;
+}
+
+static int get_long_slices(PyObject* fpix_arr,
+ PyObject* lpix_arr,
+ PyObject* step_arr,
+ long** fpix,
+ long** lpix,
+ long** step) {
+
+ int i=0;
+ npy_int64* ptr=NULL;
+ npy_intp fsize=0, lsize=0, ssize=0;
+
+ fsize=PyArray_SIZE(fpix_arr);
+ lsize=PyArray_SIZE(lpix_arr);
+ ssize=PyArray_SIZE(step_arr);
+
+ if (lsize != fsize || ssize != fsize) {
+ PyErr_SetString(PyExc_RuntimeError,
+ "start/end/step must be same len");
+ return 1;
+ }
+
+ *fpix=calloc(fsize, sizeof(long));
+ *lpix=calloc(fsize, sizeof(long));
+ *step=calloc(fsize, sizeof(long));
+
+ for (i=0;i<fsize;i++) {
+ ptr=PyArray_GETPTR1(fpix_arr, i);
+ (*fpix)[i] = *ptr;
+ ptr=PyArray_GETPTR1(lpix_arr, i);
+ (*lpix)[i] = *ptr;
+ ptr=PyArray_GETPTR1(step_arr, i);
+ (*step)[i] = *ptr;
+ }
+ return 0;
+}
+
+// read an n-dimensional "image" into the input array. Only minimal checking
+// of the input array is done.
+static PyObject *
+PyFITSObject_read_image_slice(struct PyFITSObject* self, PyObject* args) {
+ int hdunum=0;
+ int hdutype=0;
+ int status=0;
+ PyObject* fpix_arr=NULL;
+ PyObject* lpix_arr=NULL;
+ PyObject* step_arr=NULL;
+ int ignore_scaling=FALSE;
+ PyObject* array=NULL;
+ long* fpix=NULL;
+ long* lpix=NULL;
+ long* step=NULL;
+ void* data=NULL;
+ int npy_dtype=0;
+ int dummy=0, fits_read_dtype=0;
+
+ int anynul=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"iOOOiO",
+ &hdunum, &fpix_arr, &lpix_arr, &step_arr, &ignore_scaling,
+ &array)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ return NULL;
+ }
+
+ if (ignore_scaling == TRUE
+ && fits_set_bscale(self->fits, 1.0, 0.0, &status)) {
+ return NULL;
+ }
+
+ if (get_long_slices(fpix_arr,lpix_arr,step_arr,
+ &fpix,&lpix,&step)) {
+ return NULL;
+ }
+ data = PyArray_DATA(array);
+
+ npy_dtype = PyArray_TYPE(array);
+ npy_to_fits_image_types(npy_dtype, &dummy, &fits_read_dtype);
+
+ if (fits_read_subset(self->fits, fits_read_dtype, fpix, lpix, step,
+ 0, data, &anynul, &status)) {
+ set_ioerr_string_from_status(status);
+ goto read_image_slice_cleanup;
+ }
+
+read_image_slice_cleanup:
+ free(fpix);
+ free(lpix);
+ free(step);
+
+ if (status != 0) {
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+
+static int hierarch_is_string(const char* card)
+{
+ int i=0, is_string_value=1;
+
+ for (i=0; i<78; i++) {
+ if (card[i] == '=') {
+ // we found the equals, now if it is a string we
+ // now exactly where the quote must be
+ if (card[i+2] == '\'') {
+ is_string_value = 1;
+ } else {
+ is_string_value = 0;
+ }
+ }
+ }
+ return is_string_value;
+}
+
+// read the entire header as list of dicts with name,value,comment and full
+// card
+static PyObject *
+PyFITSObject_read_header(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+ int lcont=0, lcomm=0, ls=0;
+ int tocomp=0;
+ int is_comment_or_history=0, is_blank_key=0;
+ char *longstr=NULL;
+
+ char keyname[FLEN_KEYWORD];
+ char value[FLEN_VALUE];
+ char comment[FLEN_COMMENT];
+ char scomment[FLEN_COMMENT];
+ char card[FLEN_CARD];
+ long is_string_value=0;
+
+ LONGLONG lval=0;
+ double dval=0;
+
+ int nkeys=0, morekeys=0, i=0;
+ int has_equals=0, has_quote=0;
+
+ PyObject* list=NULL;
+ PyObject* dict=NULL; // to hold the dict for each record
+
+ lcont=strlen("CONTINUE");
+ lcomm=strlen("COMMENT");
+
+ if (!PyArg_ParseTuple(args, (char*)"i", &hdunum)) {
+ return NULL;
+ }
+
+ if (self->fits == NULL) {
+ PyErr_SetString(PyExc_RuntimeError, "FITS file is NULL");
+ return NULL;
+ }
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_get_hdrspace(self->fits, &nkeys, &morekeys, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ list=PyList_New(0);
+ for (i=0; i<nkeys; i++) {
+
+ // the full card
+ if (fits_read_record(self->fits, i+1, card, &status)) {
+ Py_XDECREF(list);
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ // this just returns the character string stored in the header; we
+ // can eval in python
+ if (fits_read_keyn(self->fits, i+1, keyname, value, scomment, &status)) {
+ Py_XDECREF(list);
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ ls = strlen(keyname);
+ tocomp = (ls < lcont) ? ls : lcont;
+
+ is_blank_key = 0;
+ if (ls == 0) {
+ is_blank_key = 1;
+ } else {
+
+ // skip CONTINUE, we already read the data
+ if (strncmp(keyname,"CONTINUE",tocomp)==0) {
+ continue;
+ }
+
+ if (strncmp(keyname, "COMMENT", tocomp) ==0
+ || strncmp(keyname, "HISTORY", tocomp )==0) {
+ is_comment_or_history = 1;
+
+ } else {
+ is_comment_or_history = 0;
+
+ if (fits_read_key_longstr(self->fits, keyname, &longstr, comment, &status)) {
+ Py_XDECREF(list);
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (strncmp(card,"HIERARCH",8)==0) {
+ if (hierarch_is_string(card)) {
+ is_string_value=1;
+ } else {
+ is_string_value=0;
+ }
+ } else {
+ has_equals = (card[8] == '=') ? 1 : 0;
+ has_quote = (card[10] == '\'') ? 1 : 0;
+ if (has_equals && has_quote) {
+ is_string_value=1;
+ } else {
+ is_string_value=0;
+ }
+ }
+ }
+ }
+
+ dict = PyDict_New();
+
+ add_string_to_dict(dict, "card_string", card);
+
+ if (is_blank_key) {
+ add_none_to_dict(dict, "name");
+ add_string_to_dict(dict, "value", "");
+ convert_to_ascii(scomment);
+ add_string_to_dict(dict, "comment", scomment);
+
+ } else if (is_comment_or_history) {
+ // comment or history
+ convert_to_ascii(scomment);
+ add_string_to_dict(dict, "name", keyname);
+ add_string_to_dict(dict, "value", scomment);
+ add_string_to_dict(dict, "comment", scomment);
+
+ } else {
+ convert_keyword_to_allowed_ascii(keyname);
+ add_string_to_dict(dict,"name",keyname);
+ convert_to_ascii(comment);
+ add_string_to_dict(dict,"comment",comment);
+
+ // if not a comment but empty value, put in None
+ tocomp = (ls < lcomm) ? ls : lcomm;
+ // if (!is_string_value && 0==strlen(longstr) && !is_comment) {
+ if (!is_string_value && 0==strlen(longstr)) {
+
+ add_none_to_dict(dict, "value");
+
+ } else {
+
+ if (is_string_value) {
+ convert_to_ascii(longstr);
+ add_string_to_dict(dict,"value",longstr);
+ } else if ( longstr[0]=='T' ) {
+ add_true_to_dict(dict, "value");
+ } else if (longstr[0]=='F') {
+ add_false_to_dict(dict, "value");
+ } else if (
+ (strchr(longstr,'.') != NULL)
+ || (strchr(longstr,'E') != NULL)
+ || (strchr(longstr,'e') != NULL) ) {
+ // we found a floating point value
+ fits_read_key(self->fits, TDOUBLE, keyname, &dval, comment, &status);
+ add_double_to_dict(dict,"value",dval);
+ } else {
+
+ // we might have found an integer
+ if (fits_read_key(self->fits,
+ TLONGLONG,
+ keyname,
+ &lval,
+ comment,
+ &status)) {
+
+ // something non standard, just store it as a string
+ convert_to_ascii(longstr);
+ add_string_to_dict(dict,"value",longstr);
+ status=0;
+
+ } else {
+ add_long_long_to_dict(dict,"value",(long long)lval);
+ }
+ }
+
+ }
+ }
+
+ free(longstr); longstr=NULL;
+
+ PyList_Append(list, dict);
+ Py_XDECREF(dict);
+
+ }
+
+ return list;
+}
+
+static PyObject *
+PyFITSObject_write_checksum(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ unsigned long datasum=0;
+ unsigned long hdusum=0;
+
+ PyObject* dict=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"i", &hdunum)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_write_chksum(self->fits, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+ if (fits_get_chksum(self->fits, &datasum, &hdusum, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ dict=PyDict_New();
+ add_long_long_to_dict(dict,"datasum",(long long)datasum);
+ add_long_long_to_dict(dict,"hdusum",(long long)hdusum);
+
+ return dict;
+}
+static PyObject *
+PyFITSObject_verify_checksum(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+
+ int dataok=0, hduok=0;
+
+ PyObject* dict=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"i", &hdunum)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_verify_chksum(self->fits, &dataok, &hduok, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ dict=PyDict_New();
+ add_long_to_dict(dict,"dataok",(long)dataok);
+ add_long_to_dict(dict,"hduok",(long)hduok);
+
+ return dict;
+}
+
+
+
+static PyObject *
+PyFITSObject_where(struct PyFITSObject* self, PyObject* args) {
+ int status=0;
+ int hdunum=0;
+ int hdutype=0;
+ char* expression=NULL;
+
+ LONGLONG nrows=0;
+
+ long firstrow=1;
+ long ngood=0;
+ char* row_status=NULL;
+
+
+ // Indices of rows for which expression is true
+ PyObject* indicesObj=NULL;
+ int ndim=1;
+ npy_intp dims[1];
+ npy_intp* data=NULL;
+ long i=0;
+
+
+ if (!PyArg_ParseTuple(args, (char*)"is", &hdunum, &expression)) {
+ return NULL;
+ }
+
+ if (fits_movabs_hdu(self->fits, hdunum, &hdutype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ if (fits_get_num_rowsll(self->fits, &nrows, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ row_status = malloc(nrows*sizeof(char));
+ if (row_status==NULL) {
+ PyErr_SetString(PyExc_MemoryError, "Could not allocate row_status array");
+ return NULL;
+ }
+
+ if (fits_find_rows(self->fits, expression, firstrow, (long) nrows, &ngood, row_status, &status)) {
+ set_ioerr_string_from_status(status);
+ goto where_function_cleanup;
+ }
+
+ dims[0] = ngood;
+ indicesObj = PyArray_EMPTY(ndim, dims, NPY_INTP, 0);
+ if (indicesObj == NULL) {
+ PyErr_SetString(PyExc_MemoryError, "Could not allocate index array");
+ goto where_function_cleanup;
+ }
+
+ if (ngood > 0) {
+ data = PyArray_DATA(indicesObj);
+
+ for (i=0; i<nrows; i++) {
+ if (row_status[i]) {
+ *data = (npy_intp) i;
+ data++;
+ }
+ }
+ }
+where_function_cleanup:
+ free(row_status);
+ return indicesObj;
+}
+
+// generic functions, not tied to an object
+
+static PyObject *
+PyFITS_cfitsio_version(void) {
+ float version=0;
+ fits_get_version(&version);
+ return PyFloat_FromDouble((double)version);
+}
+
+static PyObject *
+PyFITS_cfitsio_use_standard_strings(void) {
+ if ( fits_use_standard_strings() ) {
+ Py_RETURN_TRUE;
+ } else {
+ Py_RETURN_FALSE;
+ }
+}
+
+
+/*
+
+'C', 'L', 'I', 'F' 'X'
+character string, logical, integer, floating point, complex
+
+*/
+
+static PyObject *
+PyFITS_get_keytype(PyObject* self, PyObject* args) {
+
+ int status=0;
+ char* card=NULL;
+ char dtype[2]={0};
+
+ if (!PyArg_ParseTuple(args, (char*)"s", &card)) {
+ return NULL;
+ }
+
+
+ if (fits_get_keytype(card, dtype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ } else {
+ return Py_BuildValue("s", dtype);
+ }
+}
+static PyObject *
+PyFITS_get_key_meta(PyObject* self, PyObject* args) {
+
+ int status=0;
+ char* card=NULL;
+ char dtype[2]={0};
+ int keyclass=0;
+
+ if (!PyArg_ParseTuple(args, (char*)"s", &card)) {
+ return NULL;
+ }
+
+
+ keyclass=fits_get_keyclass(card);
+
+ if (fits_get_keytype(card, dtype, &status)) {
+ set_ioerr_string_from_status(status);
+ return NULL;
+ }
+
+ return Py_BuildValue("is", keyclass, dtype);
+
+}
+
+/*
+
+ note the special first four comment fields will not be called comment but
+ structural! That will cause an exception to be raised, so the card should
+ be checked before calling this function
+
+*/
+
+static PyObject *
+PyFITS_parse_card(PyObject* self, PyObject* args) {
+
+ int status=0;
+ char name[FLEN_VALUE]={0};
+ char value[FLEN_VALUE]={0};
+ char comment[FLEN_COMMENT]={0};
+ int keylen=0;
+ int keyclass=0;
+ int is_undefined=0;
+
+ char* card=NULL;
+ char dtype[2]={0};
+ PyObject* output=NULL;
+
+ if (!PyArg_ParseTuple(args, (char*)"s", &card)) {
+ goto bail;
+ }
+
+ keyclass=fits_get_keyclass(card);
+
+ // only proceed if not comment or history, but note the special first four
+ // comment fields will not be called comment but structural! That will
+ // cause an exception to be raised, so the card should be checked before
+ // calling this function
+
+ if (keyclass != TYP_COMM_KEY && keyclass != TYP_CONT_KEY) {
+
+ if (fits_get_keyname(card, name, &keylen, &status)) {
+ set_ioerr_string_from_status(status);
+ goto bail;
+ }
+ if (fits_parse_value(card, value, comment, &status)) {
+ set_ioerr_string_from_status(status);
+ goto bail;
+ }
+ if (fits_get_keytype(value, dtype, &status)) {
+
+ if (status == VALUE_UNDEFINED) {
+ is_undefined=1;
+ status=0;
+ } else {
+ set_ioerr_string_from_status(status);
+ goto bail;
+ }
+ }
+ }
+
+bail:
+ if (status != 0) {
+ return NULL;
+ }
+
+ if (is_undefined) {
+ output=Py_BuildValue("isss", keyclass, name, dtype, comment);
+ } else {
+ output=Py_BuildValue("issss", keyclass, name, value, dtype, comment);
+ }
+ return output;
+}
+
+
+
+static PyMethodDef PyFITSObject_methods[] = {
+ {"filename", (PyCFunction)PyFITSObject_filename, METH_VARARGS, "filename\n\nReturn the name of the file."},
+
+ {"where", (PyCFunction)PyFITSObject_where, METH_VARARGS, "where\n\nReturn an index array where the input expression evaluates to true."},
+
+ {"movabs_hdu", (PyCFunction)PyFITSObject_movabs_hdu, METH_VARARGS, "movabs_hdu\n\nMove to the specified HDU."},
+ {"movnam_hdu", (PyCFunction)PyFITSObject_movnam_hdu, METH_VARARGS, "movnam_hdu\n\nMove to the specified HDU by name and return the hdu number."},
+
+ {"get_hdu_name_version", (PyCFunction)PyFITSObject_get_hdu_name_version, METH_VARARGS, "get_hdu_name_version\n\nReturn a tuple (extname,extvers)."},
+ {"get_hdu_info", (PyCFunction)PyFITSObject_get_hdu_info, METH_VARARGS, "get_hdu_info\n\nReturn a dict with info about the specified HDU."},
+ {"read_raw", (PyCFunction)PyFITSObject_read_raw, METH_NOARGS, "read_raw\n\nRead the entire raw contents of the FITS file, returning a python string."},
+ {"read_image", (PyCFunction)PyFITSObject_read_image, METH_VARARGS, "read_image\n\nRead the entire n-dimensional image array. No checking of array is done."},
+ {"read_image_slice", (PyCFunction)PyFITSObject_read_image_slice, METH_VARARGS, "read_image_slice\n\nRead an image slice."},
+ {"read_column", (PyCFunction)PyFITSObject_read_column, METH_VARARGS, "read_column\n\nRead the column into the input array. No checking of array is done."},
+ {"read_var_column_as_list", (PyCFunction)PyFITSObject_read_var_column_as_list, METH_VARARGS, "read_var_column_as_list\n\nRead the variable length column as a list of arrays."},
+ {"read_columns_as_rec", (PyCFunction)PyFITSObject_read_columns_as_rec, METH_VARARGS, "read_columns_as_rec\n\nRead the specified columns into the input rec array. No checking of array is done."},
+ {"read_columns_as_rec_byoffset", (PyCFunction)PyFITSObject_read_columns_as_rec_byoffset, METH_VARARGS, "read_columns_as_rec_byoffset\n\nRead the specified columns into the input rec array at the specified offsets. No checking of array is done."},
+ {"read_rows_as_rec", (PyCFunction)PyFITSObject_read_rows_as_rec, METH_VARARGS, "read_rows_as_rec\n\nRead the subset of rows into the input rec array. No checking of array is done."},
+ {"read_as_rec", (PyCFunction)PyFITSObject_read_as_rec, METH_VARARGS, "read_as_rec\n\nRead a set of rows into the input rec array. No significant checking of array is done."},
+ {"read_header", (PyCFunction)PyFITSObject_read_header, METH_VARARGS | METH_VARARGS, "read_header\n\nRead the entire header as a list of dictionaries."},
+
+ {"create_image_hdu", (PyCFunction)PyFITSObject_create_image_hdu, METH_VARARGS | METH_KEYWORDS, "create_image_hdu\n\nWrite the input image to a new extension."},
+ {"create_table_hdu", (PyCFunction)PyFITSObject_create_table_hdu, METH_VARARGS | METH_KEYWORDS, "create_table_hdu\n\nCreate a new table with the input parameters."},
+ {"insert_col", (PyCFunction)PyFITSObject_insert_col, METH_VARARGS | METH_KEYWORDS, "insert_col\n\nInsert a new column."},
+
+ {"write_checksum", (PyCFunction)PyFITSObject_write_checksum, METH_VARARGS, "write_checksum\n\nCompute and write the checksums into the header."},
+ {"verify_checksum", (PyCFunction)PyFITSObject_verify_checksum, METH_VARARGS, "verify_checksum\n\nReturn a dict with dataok and hduok."},
+
+ {"reshape_image", (PyCFunction)PyFITSObject_reshape_image, METH_VARARGS, "reshape_image\n\nReshape the image."},
+ {"write_image", (PyCFunction)PyFITSObject_write_image, METH_VARARGS, "write_image\n\nWrite the input image to a new extension."},
+ //{"write_column", (PyCFunction)PyFITSObject_write_column, METH_VARARGS | METH_KEYWORDS, "write_column\n\nWrite a column into the specified hdu."},
+ {"write_columns", (PyCFunction)PyFITSObject_write_columns, METH_VARARGS | METH_KEYWORDS, "write_columns\n\nWrite columns into the specified hdu."},
+ {"write_var_column", (PyCFunction)PyFITSObject_write_var_column, METH_VARARGS | METH_KEYWORDS, "write_var_column\n\nWrite a variable length column into the specified hdu from an object array."},
+ {"write_record", (PyCFunction)PyFITSObject_write_record, METH_VARARGS, "write_record\n\nWrite a header card."},
+ {"write_string_key", (PyCFunction)PyFITSObject_write_string_key, METH_VARARGS, "write_string_key\n\nWrite a string key into the specified HDU."},
+ {"write_double_key", (PyCFunction)PyFITSObject_write_double_key, METH_VARARGS, "write_double_key\n\nWrite a double key into the specified HDU."},
+
+ {"write_long_long_key", (PyCFunction)PyFITSObject_write_long_long_key, METH_VARARGS, "write_long_long_key\n\nWrite a long long key into the specified HDU."},
+ {"write_logical_key", (PyCFunction)PyFITSObject_write_logical_key, METH_VARARGS, "write_logical_key\n\nWrite a logical key into the specified HDU."},
+
+ {"write_comment", (PyCFunction)PyFITSObject_write_comment, METH_VARARGS, "write_comment\n\nWrite a comment into the header of the specified HDU."},
+ {"write_history", (PyCFunction)PyFITSObject_write_history, METH_VARARGS, "write_history\n\nWrite history into the header of the specified HDU."},
+ {"write_continue", (PyCFunction)PyFITSObject_write_continue, METH_VARARGS, "write_continue\n\nWrite contineu into the header of the specified HDU."},
+
+ {"write_undefined_key", (PyCFunction)PyFITSObject_write_undefined_key, METH_VARARGS, "write_undefined_key\n\nWrite a key without a value field into the header of the specified HDU."},
+
+ {"insert_rows", (PyCFunction)PyFITSObject_insert_rows, METH_VARARGS, "Insert blank rows"},
+
+ {"delete_row_range", (PyCFunction)PyFITSObject_delete_row_range, METH_VARARGS, "Delete a range of rows"},
+ {"delete_rows", (PyCFunction)PyFITSObject_delete_rows, METH_VARARGS, "Delete a set of rows"},
+
+ {"close", (PyCFunction)PyFITSObject_close, METH_VARARGS, "close\n\nClose the fits file."},
+ {NULL} /* Sentinel */
+};
+
+static PyTypeObject PyFITSType = {
+#if PY_MAJOR_VERSION >= 3
+ PyVarObject_HEAD_INIT(NULL, 0)
+#else
+ PyObject_HEAD_INIT(NULL)
+ 0, /*ob_size*/
+#endif
+ "_fitsio.FITS", /*tp_name*/
+ sizeof(struct PyFITSObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)PyFITSObject_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ //0, /*tp_repr*/
+ (reprfunc)PyFITSObject_repr, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "FITSIO Class", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ PyFITSObject_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ //0, /* tp_init */
+ (initproc)PyFITSObject_init, /* tp_init */
+ 0, /* tp_alloc */
+ //PyFITSObject_new, /* tp_new */
+ PyType_GenericNew, /* tp_new */
+};
+
+
+static PyMethodDef fitstype_methods[] = {
+ {"cfitsio_version", (PyCFunction)PyFITS_cfitsio_version, METH_NOARGS, "cfitsio_version\n\nReturn the cfitsio version."},
+ {"cfitsio_use_standard_strings", (PyCFunction)PyFITS_cfitsio_use_standard_strings, METH_NOARGS, "cfitsio_use_standard_strings\n\nReturn True if using string code that matches the FITS standard."},
+ {"parse_card", (PyCFunction)PyFITS_parse_card, METH_VARARGS, "parse_card\n\nparse the card to get the key name, value (as a string), data type and comment."},
+ {"get_keytype", (PyCFunction)PyFITS_get_keytype, METH_VARARGS, "get_keytype\n\nparse the card to get the key type."},
+ {"get_key_meta", (PyCFunction)PyFITS_get_key_meta, METH_VARARGS, "get_key_meta\n\nparse the card to get key metadata (keyclass,dtype)."},
+ {NULL} /* Sentinel */
+};
+
+#if PY_MAJOR_VERSION >= 3
+ static struct PyModuleDef moduledef = {
+ PyModuleDef_HEAD_INIT,
+ "_fitsio_wrap", /* m_name */
+ "Defines the FITS class and some methods", /* m_doc */
+ -1, /* m_size */
+ fitstype_methods, /* m_methods */
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
+ NULL, /* m_free */
+ };
+#endif
+
+
+#ifndef PyMODINIT_FUNC /* declarations for DLL import/export */
+#define PyMODINIT_FUNC void
+#endif
+PyMODINIT_FUNC
+#if PY_MAJOR_VERSION >= 3
+PyInit__fitsio_wrap(void)
+#else
+init_fitsio_wrap(void)
+#endif
+{
+ PyObject* m;
+
+ PyFITSType.tp_new = PyType_GenericNew;
+
+#if PY_MAJOR_VERSION >= 3
+ if (PyType_Ready(&PyFITSType) < 0) {
+ return NULL;
+ }
+ m = PyModule_Create(&moduledef);
+ if (m==NULL) {
+ return NULL;
+ }
+
+#else
+ if (PyType_Ready(&PyFITSType) < 0) {
+ return;
+ }
+ m = Py_InitModule3("_fitsio_wrap", fitstype_methods, "Define FITS type and methods.");
+ if (m==NULL) {
+ return;
+ }
+#endif
+
+ Py_INCREF(&PyFITSType);
+ PyModule_AddObject(m, "FITS", (PyObject *)&PyFITSType);
+
+ import_array();
+#if PY_MAJOR_VERSION >= 3
+ return m;
+#endif
+}
--- /dev/null
+"""
+fitslib, part of the fitsio package.
+
+See the main docs at https://github.com/esheldon/fitsio
+
+ Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+"""
+from __future__ import with_statement, print_function
+import os
+import numpy
+
+from . import _fitsio_wrap
+from .util import IS_PY3, mks, array_to_native, isstring
+from .header import FITSHDR
+from .hdu import (
+ ANY_HDU, IMAGE_HDU, BINARY_TBL, ASCII_TBL,
+ ImageHDU, AsciiTableHDU, TableHDU,
+ _table_npy2fits_form, _npy2fits, _hdu_type_map)
+
+# for python3 compat
+if IS_PY3:
+ xrange = range
+
+
+READONLY = 0
+READWRITE = 1
+
+NOCOMPRESS = 0
+RICE_1 = 11
+GZIP_1 = 21
+GZIP_2 = 22
+PLIO_1 = 31
+HCOMPRESS_1 = 41
+
+NO_DITHER = -1
+SUBTRACTIVE_DITHER_1 = 1
+SUBTRACTIVE_DITHER_2 = 2
+
+# defaults follow fpack
+DEFAULT_QLEVEL = 4.0
+DEFAULT_QMETHOD = 'SUBTRACTIVE_DITHER_1'
+DEFAULT_HCOMP_SCALE = 0.0
+
+
+def read(filename, ext=None, extver=None, columns=None, rows=None,
+ header=False, case_sensitive=False, upper=False, lower=False,
+ vstorage='fixed', verbose=False, trim_strings=False, **keys):
+ """
+ Convenience function to read data from the specified FITS HDU
+
+ By default, all data are read. For tables, send columns= and rows= to
+ select subsets of the data. Table data are read into a recarray; use a
+ FITS object and read_column() to get a single column as an ordinary array.
+ For images, create a FITS object and use slice notation to read subsets.
+
+ Under the hood, a FITS object is constructed and data are read using
+ an associated FITSHDU object.
+
+ parameters
+ ----------
+ filename: string
+ A filename.
+ ext: number or string, optional
+ The extension. Either the numerical extension from zero
+ or a string extension name. If not sent, data is read from
+ the first HDU that has data.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname). These
+ extensions can optionally specify an EXTVER version number in the
+ header. Send extver= to select a particular version. If extver is not
+ sent, the first one will be selected. If ext is an integer, the extver
+ is ignored.
+ columns: list or array, optional
+ An optional set of columns to read from table HDUs. Default is to
+ read all. Can be string or number.
+ rows: optional
+ An optional list of rows to read from table HDUS. Default is to
+ read all.
+ header: bool, optional
+ If True, read the FITS header and return a tuple (data,header)
+ Default is False.
+ case_sensitive: bool, optional
+ Match column names and extension names with case-sensitivity. Default
+ is False.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Default is
+ False.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Default is
+ False.
+ vstorage: string, optional
+ Set the default method to store variable length columns. Can be
+ 'fixed' or 'object'. See docs on fitsio.FITS for details. Default is
+ 'fixed'.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ verbose: bool, optional
+ If True, print more info when doing various FITS operations.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ kwargs = {
+ 'lower': lower,
+ 'upper': upper,
+ 'vstorage': vstorage,
+ 'case_sensitive': case_sensitive,
+ 'verbose': verbose,
+ 'trim_strings': trim_strings
+ }
+
+ read_kwargs = {}
+ if columns is not None:
+ read_kwargs['columns'] = columns
+ if rows is not None:
+ read_kwargs['rows'] = rows
+
+ with FITS(filename, **kwargs) as fits:
+
+ if ext is None:
+ for i in xrange(len(fits)):
+ if fits[i].has_data():
+ ext = i
+ break
+ if ext is None:
+ raise IOError("No extensions have data")
+
+ item = _make_item(ext, extver=extver)
+
+ data = fits[item].read(**read_kwargs)
+ if header:
+ h = fits[item].read_header()
+ return data, h
+ else:
+ return data
+
+
+def read_header(filename, ext=0, extver=None, case_sensitive=False, **keys):
+ """
+ Convenience function to read the header from the specified FITS HDU
+
+ The FITSHDR allows access to the values and comments by name and
+ number.
+
+ parameters
+ ----------
+ filename: string
+ A filename.
+ ext: number or string, optional
+ The extension. Either the numerical extension from zero
+ or a string extension name. Default read primary header.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname). These
+ extensions can optionally specify an EXTVER version number in the
+ header. Send extver= to select a particular version. If extver is not
+ sent, the first one will be selected. If ext is an integer, the extver
+ is ignored.
+ case_sensitive: bool, optional
+ Match extension names with case-sensitivity. Default is False.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ filename = extract_filename(filename)
+
+ dont_create = 0
+ try:
+ hdunum = ext+1
+ except TypeError:
+ hdunum = None
+
+ _fits = _fitsio_wrap.FITS(filename, READONLY, dont_create)
+
+ if hdunum is None:
+ extname = mks(ext)
+ if extver is None:
+ extver_num = 0
+ else:
+ extver_num = extver
+
+ if not case_sensitive:
+ # the builtin movnam_hdu is not case sensitive
+ hdunum = _fits.movnam_hdu(ANY_HDU, extname, extver_num)
+ else:
+ # for case sensitivity we'll need to run through
+ # all the hdus
+ found = False
+ current_ext = 0
+ while True:
+ hdunum = current_ext+1
+ try:
+ hdu_type = _fits.movabs_hdu(hdunum) # noqa - not used
+ name, vers = _fits.get_hdu_name_version(hdunum)
+ if name == extname:
+ if extver is None:
+ # take the first match
+ found = True
+ break
+ else:
+ if extver_num == vers:
+ found = True
+ break
+ except OSError:
+ break
+
+ current_ext += 1
+
+ if not found:
+ raise IOError(
+ 'hdu not found: %s (extver %s)' % (extname, extver))
+
+ return FITSHDR(_fits.read_header(hdunum))
+
+
+def read_scamp_head(fname, header=None):
+ """
+ read a SCAMP .head file as a fits header FITSHDR object
+
+ parameters
+ ----------
+ fname: string
+ The path to the SCAMP .head file
+
+ header: FITSHDR, optional
+ Optionally combine the header with the input one. The input can
+ be any object convertable to a FITSHDR object
+
+ returns
+ -------
+ header: FITSHDR
+ A fits header object of type FITSHDR
+ """
+
+ with open(fname) as fobj:
+ lines = fobj.readlines()
+
+ lines = [l.strip() for l in lines if l[0:3] != 'END']
+
+ # if header is None an empty FITSHDR is created
+ hdr = FITSHDR(header)
+
+ for l in lines:
+ hdr.add_record(l)
+
+ return hdr
+
+
+def _make_item(ext, extver=None):
+ if extver is not None:
+ # e
+ item = (ext, extver)
+ else:
+ item = ext
+
+ return item
+
+
+def write(filename, data, extname=None, extver=None, header=None,
+ clobber=False, ignore_empty=False, units=None, table_type='binary',
+ names=None, write_bitcols=False, compress=None, tile_dims=None,
+ qlevel=DEFAULT_QLEVEL,
+ qmethod=DEFAULT_QMETHOD,
+ hcomp_scale=DEFAULT_HCOMP_SCALE,
+ hcomp_smooth=False,
+ **keys):
+ """
+ Convenience function to create a new HDU and write the data.
+
+ Under the hood, a FITS object is constructed. If you want to append rows
+ to an existing HDU, or modify data in an HDU, please construct a FITS
+ object.
+
+ parameters
+ ----------
+ filename: string
+ A filename.
+ data: numpy.ndarray or recarray
+ Either a normal n-dimensional array or a recarray. Images are written
+ to a new IMAGE_HDU and recarrays are written to BINARY_TBl or
+ ASCII_TBL hdus.
+ extname: string, optional
+ An optional name for the new header unit.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ header: FITSHDR, list, dict, optional
+ A set of header keys to write. The keys are written before the data
+ is written to the table, preventing a resizing of the table area.
+
+ Can be one of these:
+ - FITSHDR object
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
+ clobber: bool, optional
+ If True, overwrite any existing file. Default is to append
+ a new extension on existing files.
+ ignore_empty: bool, optional
+ Default False. Unless set to True, only allow
+ empty HDUs in the zero extension.
+
+ table-only keywords
+ -------------------
+ units: list
+ A list of strings representing units for each column.
+ table_type: string, optional
+ Either 'binary' or 'ascii', default 'binary'
+ Matching is case-insensitive
+ write_bitcols: bool, optional
+ Write boolean arrays in the FITS bitcols format, default False
+ names: list, optional
+ If data is a list of arrays, you must send `names` as a list
+ of names or column numbers.
+
+ image-only keywords
+ -------------------
+ compress: string, optional
+ A string representing the compression algorithm for images,
+ default None.
+ Can be one of
+ 'RICE'
+ 'GZIP'
+ 'GZIP_2'
+ 'PLIO' (no unsigned or negative integers)
+ 'HCOMPRESS'
+ (case-insensitive) See the cfitsio manual for details.
+ tile_dims: tuple of ints, optional
+ The size of the tiles used to compress images.
+ qlevel: float, optional
+ Quantization level for floating point data. Lower generally result in
+ more compression, we recommend one reads the FITS standard or cfitsio
+ manual to fully understand the effects of quantization. None or 0
+ means no quantization, and for gzip also implies lossless. Default is
+ 4.0 which follows the fpack defaults
+ qmethod: string or int
+ The quantization method as string or integer.
+ 'NO_DITHER' or fitsio.NO_DITHER (-1)
+ No dithering is performed
+ 'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
+ Standard dithering
+ 'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
+ Preserves zeros
+
+ Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
+
+ hcomp_scale: float
+ Scale value for HCOMPRESS, 0.0 means lossless compression. Default is 0.0
+ following the fpack defaults.
+ hcomp_smooth: bool
+ If True, apply smoothing when decompressing. Default False
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ kwargs = {
+ 'clobber': clobber,
+ 'ignore_empty': ignore_empty
+ }
+ with FITS(filename, 'rw', **kwargs) as fits:
+ fits.write(
+ data,
+ table_type=table_type,
+ units=units,
+ extname=extname,
+ extver=extver,
+ header=header,
+ names=names,
+ write_bitcols=write_bitcols,
+
+ compress=compress,
+ tile_dims=tile_dims,
+ qlevel=qlevel,
+ qmethod=qmethod,
+ hcomp_scale=hcomp_scale,
+ hcomp_smooth=hcomp_smooth,
+ )
+
+
+class FITS(object):
+ """
+ A class to read and write FITS images and tables.
+
+ This class uses the cfitsio library for almost all relevant work.
+
+ parameters
+ ----------
+ filename: string
+ The filename to open.
+ mode: int/string, optional
+ The mode, either a string or integer.
+ For reading only
+ 'r' or 0
+ For reading and writing
+ 'rw' or 1
+ You can also use fitsio.READONLY and fitsio.READWRITE.
+
+ Default is 'r'
+ clobber: bool, optional
+ If the mode is READWRITE, and clobber=True, then remove any existing
+ file before opening.
+ case_sensitive: bool, optional
+ Match column names and extension names with case-sensitivity. Default
+ is False.
+ lower: bool, optional
+ If True, force all columns names to lower case in output
+ upper: bool, optional
+ If True, force all columns names to upper case in output
+ vstorage: string, optional
+ A string describing how, by default, to store variable length columns
+ in the output array. This can be over-ridden when reading by using the
+ using vstorage keyword to the individual read methods. The options are
+
+ 'fixed': Use a fixed length field in the array, with
+ dimensions equal to the max possible size for column.
+ Arrays are padded with zeros.
+ 'object': Use an object for the field in the array.
+ Each element will then be an array of the right type,
+ but only using the memory needed to hold that element.
+
+ Default is 'fixed'. The rationale is that this is the option
+ of 'least surprise'
+ iter_row_buffer: integer
+ Number of rows to buffer when iterating over table HDUs.
+ Default is 1.
+ ignore_empty: bool, optional
+ Default False. Unless set to True, only allow
+ empty HDUs in the zero extension.
+ verbose: bool, optional
+ If True, print more info when doing various FITS operations.
+
+ See the docs at https://github.com/esheldon/fitsio
+ """
+ def __init__(self, filename, mode='r', lower=False, upper=False,
+ trim_strings=False, vstorage='fixed', case_sensitive=False,
+ iter_row_buffer=1, write_bitcols=False, ignore_empty=False,
+ verbose=False, clobber=False, **keys):
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ self.lower = lower
+ self.upper = upper
+ self.trim_strings = trim_strings
+ self.vstorage = vstorage
+ self.case_sensitive = case_sensitive
+ self.iter_row_buffer = iter_row_buffer
+ self.write_bitcols = write_bitcols
+ filename = extract_filename(filename)
+ self._filename = filename
+
+ # self.mode=keys.get('mode','r')
+ self.mode = mode
+ self.ignore_empty = ignore_empty
+
+ self.verbose = verbose
+
+ if self.mode not in _int_modemap:
+ raise IOError("mode should be one of 'r', 'rw', "
+ "READONLY,READWRITE")
+
+ self.charmode = _char_modemap[self.mode]
+ self.intmode = _int_modemap[self.mode]
+
+ # Will not test existence when reading, let cfitsio
+ # do the test and report an error. This allows opening
+ # urls etc.
+ create = 0
+ if self.mode in [READWRITE, 'rw']:
+ if clobber:
+ create = 1
+ if filename[0] != '!':
+ filename = '!' + filename
+ else:
+ if os.path.exists(filename):
+ create = 0
+ else:
+ create = 1
+
+ self._did_create = (create == 1)
+ self._FITS = _fitsio_wrap.FITS(filename, self.intmode, create)
+
+ def close(self):
+ """
+ Close the fits file and set relevant metadata to None
+ """
+ if hasattr(self, '_FITS'):
+ if self._FITS is not None:
+ self._FITS.close()
+ self._FITS = None
+ self._filename = None
+ self.mode = None
+ self.charmode = None
+ self.intmode = None
+ self.hdu_list = None
+ self.hdu_map = None
+
+ def movabs_ext(self, ext):
+ """
+ Move to the indicated zero-offset extension.
+
+ In general, it is not necessary to use this method explicitly.
+ """
+ return self._FITS.movabs_hdu(ext+1)
+
+ def movabs_hdu(self, hdunum):
+ """
+ Move to the indicated one-offset hdu number.
+
+ In general, it is not necessary to use this method explicitly.
+ """
+ return self._FITS.movabs_hdu(hdunum)
+
+ def movnam_ext(self, extname, hdutype=ANY_HDU, extver=0):
+ """
+ Move to the indicated extension by name
+
+ In general, it is not necessary to use this method explicitly.
+
+ returns the zero-offset extension number
+ """
+ extname = mks(extname)
+ hdu = self._FITS.movnam_hdu(hdutype, extname, extver)
+ return hdu-1
+
+ def movnam_hdu(self, extname, hdutype=ANY_HDU, extver=0):
+ """
+ Move to the indicated HDU by name
+
+ In general, it is not necessary to use this method explicitly.
+
+ returns the one-offset extension number
+ """
+ extname = mks(extname)
+ hdu = self._FITS.movnam_hdu(hdutype, extname, extver)
+ return hdu
+
+ def reopen(self):
+ """
+ close and reopen the fits file with the same mode
+ """
+ self._FITS.close()
+ del self._FITS
+ self._FITS = _fitsio_wrap.FITS(self._filename, self.intmode, 0)
+ self.update_hdu_list()
+
+ def write(self, data, units=None, extname=None, extver=None,
+ compress=None,
+ tile_dims=None,
+ qlevel=DEFAULT_QLEVEL,
+ qmethod=DEFAULT_QMETHOD,
+ hcomp_scale=DEFAULT_HCOMP_SCALE,
+ hcomp_smooth=False,
+ header=None, names=None,
+ table_type='binary', write_bitcols=False, **keys):
+ """
+ Write the data to a new HDU.
+
+ This method is a wrapper. If this is an IMAGE_HDU, write_image is
+ called, otherwise write_table is called.
+
+ parameters
+ ----------
+ data: ndarray
+ An n-dimensional image or an array with fields.
+ extname: string, optional
+ An optional extension name.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ header: FITSHDR, list, dict, optional
+ A set of header keys to write. Can be one of these:
+ - FITSHDR object
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
+
+ image-only keywords
+ -------------------
+ compress: string, optional
+ A string representing the compression algorithm for images,
+ default None.
+ Can be one of
+ 'RICE'
+ 'GZIP'
+ 'GZIP_2'
+ 'PLIO' (no unsigned or negative integers)
+ 'HCOMPRESS'
+ (case-insensitive) See the cfitsio manual for details.
+ tile_dims: tuple of ints, optional
+ The size of the tiles used to compress images.
+ qlevel: float, optional
+ Quantization level for floating point data. Lower generally result in
+ more compression, we recommend one reads the FITS standard or cfitsio
+ manual to fully understand the effects of quantization. None or 0
+ means no quantization, and for gzip also implies lossless. Default is
+ 4.0 which follows the fpack defaults
+ qmethod: string or int
+ The quantization method as string or integer.
+ 'NO_DITHER' or fitsio.NO_DITHER (-1)
+ No dithering is performed
+ 'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
+ Standard dithering
+ 'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
+ Preserves zeros
+
+ Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
+
+ hcomp_scale: float
+ Scale value for HCOMPRESS, 0.0 means lossless compression. Default is 0.0
+ following the fpack defaults.
+ hcomp_smooth: bool
+ If True, apply smoothing when decompressing. Default False
+
+ table-only keywords
+ -------------------
+ units: list/dec, optional:
+ A list of strings with units for each column.
+ table_type: string, optional
+ Either 'binary' or 'ascii', default 'binary'
+ Matching is case-insensitive
+ write_bitcols: bool, optional
+ Write boolean arrays in the FITS bitcols format, default False
+ names: list, optional
+ If data is a list of arrays, you must send `names` as a list
+ of names or column numbers.
+
+ restrictions
+ ------------
+ The File must be opened READWRITE
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ isimage = False
+ if data is None:
+ isimage = True
+ elif isinstance(data, numpy.ndarray):
+ if data.dtype.fields == None: # noqa - probably should be is None
+ isimage = True
+
+ if isimage:
+ self.write_image(data, extname=extname, extver=extver,
+ compress=compress,
+ tile_dims=tile_dims,
+ qlevel=qlevel,
+ qmethod=qmethod,
+ hcomp_scale=hcomp_scale,
+ hcomp_smooth=hcomp_smooth,
+ header=header)
+ else:
+ self.write_table(data, units=units,
+ extname=extname, extver=extver, header=header,
+ names=names,
+ table_type=table_type,
+ write_bitcols=write_bitcols)
+
+ def write_image(self, img, extname=None, extver=None,
+ compress=None, tile_dims=None,
+ qlevel=DEFAULT_QLEVEL,
+ qmethod=DEFAULT_QMETHOD,
+ hcomp_scale=DEFAULT_HCOMP_SCALE,
+ hcomp_smooth=False,
+ header=None):
+ """
+ Create a new image extension and write the data.
+
+ parameters
+ ----------
+ img: ndarray
+ An n-dimensional image.
+ extname: string, optional
+ An optional extension name.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ compress: string, optional
+ A string representing the compression algorithm for images,
+ default None.
+ Can be one of
+ 'RICE'
+ 'GZIP'
+ 'GZIP_2'
+ 'PLIO' (no unsigned or negative integers)
+ 'HCOMPRESS'
+ (case-insensitive) See the cfitsio manual for details.
+ tile_dims: tuple of ints, optional
+ The size of the tiles used to compress images.
+ qlevel: float, optional
+ Quantization level for floating point data. Lower generally result in
+ more compression, we recommend one reads the FITS standard or cfitsio
+ manual to fully understand the effects of quantization. None or 0
+ means no quantization, and for gzip also implies lossless. Default is
+ 4.0 which follows the fpack defaults
+ qmethod: string or int
+ The quantization method as string or integer.
+ 'NO_DITHER' or fitsio.NO_DITHER (-1)
+ No dithering is performed
+ 'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
+ Standard dithering
+ 'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
+ Preserves zeros
+
+ Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
+
+ hcomp_scale: float
+ Scale value for HCOMPRESS, 0.0 means lossless compression. Default is 0.0
+ following the fpack defaults.
+ hcomp_smooth: bool
+ If True, apply smoothing when decompressing. Default False
+
+ header: FITSHDR, list, dict, optional
+ A set of header keys to write. Can be one of these:
+ - FITSHDR object
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
+
+
+ restrictions
+ ------------
+ The File must be opened READWRITE
+ """
+
+ self.create_image_hdu(
+ img,
+ header=header,
+ extname=extname,
+ extver=extver,
+ compress=compress,
+ tile_dims=tile_dims,
+ qlevel=qlevel,
+ qmethod=qmethod,
+ hcomp_scale=hcomp_scale,
+ hcomp_smooth=hcomp_smooth,
+ )
+
+ if header is not None:
+ self[-1].write_keys(header)
+ self[-1]._update_info()
+
+ # if img is not None:
+ # self[-1].write(img)
+
+ def create_image_hdu(self,
+ img=None,
+ dims=None,
+ dtype=None,
+ extname=None,
+ extver=None,
+ compress=None,
+ tile_dims=None,
+ qlevel=DEFAULT_QLEVEL,
+ qmethod=DEFAULT_QMETHOD,
+ hcomp_scale=DEFAULT_HCOMP_SCALE,
+ hcomp_smooth=False,
+ header=None):
+ """
+ Create a new, empty image HDU and reload the hdu list. Either
+ create from an input image or from input dims and dtype
+
+ fits.create_image_hdu(image, ...)
+ fits.create_image_hdu(dims=dims, dtype=dtype)
+
+ If an image is sent, the data are also written.
+
+ You can write data into the new extension using
+ fits[extension].write(image)
+
+ Alternatively you can skip calling this function and instead just use
+
+ fits.write(image)
+ or
+ fits.write_image(image)
+
+ which will create the new image extension for you with the appropriate
+ structure, and write the data.
+
+ parameters
+ ----------
+ img: ndarray, optional
+ An image with which to determine the properties of the HDU. The
+ data will be written.
+ dims: sequence, optional
+ A sequence describing the dimensions of the image to be created
+ on disk. You must also send a dtype=
+ dtype: numpy data type
+ When sending dims= also send the data type. Can be of the
+ various numpy data type declaration styles, e.g. 'f8',
+ numpy.float64.
+ extname: string, optional
+ An optional extension name.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ compress: string, optional
+ A string representing the compression algorithm for images,
+ default None.
+ Can be one of
+ 'RICE'
+ 'GZIP'
+ 'GZIP_2'
+ 'PLIO' (no unsigned or negative integers)
+ 'HCOMPRESS'
+ (case-insensitive) See the cfitsio manual for details.
+ tile_dims: tuple of ints, optional
+ The size of the tiles used to compress images.
+ qlevel: float, optional
+ Quantization level for floating point data. Lower generally result in
+ more compression, we recommend one reads the FITS standard or cfitsio
+ manual to fully understand the effects of quantization. None or 0
+ means no quantization, and for gzip also implies lossless. Default is
+ 4.0 which follows the fpack defaults.
+ qmethod: string or int
+ The quantization method as string or integer.
+ 'NO_DITHER' or fitsio.NO_DITHER (-1)
+ No dithering is performed
+ 'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
+ Standard dithering
+ 'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
+ Preserves zeros
+
+ Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
+
+ hcomp_scale: float
+ Scale value for HCOMPRESS, 0.0 means lossless compression. Default is 0.0
+ following the fpack defaults.
+ hcomp_smooth: bool
+ If True, apply smoothing when decompressing. Default False
+
+ header: FITSHDR, list, dict, optional
+ This is only used to determine how many slots to reserve for
+ header keywords
+
+ restrictions
+ ------------
+ The File must be opened READWRITE
+ """
+
+ if (img is not None) or (img is None and dims is None):
+ from_image = True
+ elif dims is not None:
+ from_image = False
+
+ if from_image:
+ img2send = img
+ if img is not None:
+ dims = img.shape
+ dtstr = img.dtype.descr[0][1][1:]
+ if img.size == 0:
+ raise ValueError("data must have at least 1 row")
+
+ # data must be c-contiguous and native byte order
+ if not img.flags['C_CONTIGUOUS']:
+ # this always makes a copy
+ img2send = numpy.ascontiguousarray(img)
+ array_to_native(img2send, inplace=True)
+ else:
+ img2send = array_to_native(img, inplace=False)
+
+ if IS_PY3 and img2send.dtype.char == 'U':
+ # for python3, we convert unicode to ascii
+ # this will error if the character is not in ascii
+ img2send = img2send.astype('S', copy=False)
+
+ else:
+ self._ensure_empty_image_ok()
+ compress = None
+ tile_dims = None
+
+ # we get dims from the input image
+ dims2send = None
+ else:
+ # img was None and dims was sent
+ if dtype is None:
+ raise ValueError("send dtype= with dims=")
+
+ # this must work!
+ dtype = numpy.dtype(dtype)
+ dtstr = dtype.descr[0][1][1:]
+ # use the example image to build the type in C
+ img2send = numpy.zeros(1, dtype=dtype)
+
+ # sending an array simplifies access
+ dims2send = numpy.array(dims, dtype='i8', ndmin=1)
+
+ if img2send is not None:
+ if img2send.dtype.fields is not None:
+ raise ValueError(
+ "got record data type, expected regular ndarray")
+
+ if extname is None:
+ # will be ignored
+ extname = ""
+ else:
+ if not isstring(extname):
+ raise ValueError("extension name must be a string")
+ extname = mks(extname)
+
+ if extname is not None and extver is not None:
+ extver = check_extver(extver)
+
+ if extver is None:
+ # will be ignored
+ extver = 0
+
+ comptype = get_compress_type(compress)
+ qmethod = get_qmethod(qmethod)
+
+ tile_dims = get_tile_dims(tile_dims, dims)
+ if qlevel is None:
+ # 0.0 is the sentinel value for "no quantization" in cfitsio
+ qlevel = 0.0
+ else:
+ qlevel = float(qlevel)
+
+ if img2send is not None:
+ check_comptype_img(comptype, dtstr)
+
+ if header is not None:
+ nkeys = len(header)
+ else:
+ nkeys = 0
+
+ if hcomp_smooth:
+ hcomp_smooth = 1
+ else:
+ hcomp_smooth = 0
+
+ self._FITS.create_image_hdu(
+ img2send,
+ nkeys,
+ dims=dims2send,
+ comptype=comptype,
+ tile_dims=tile_dims,
+
+ qlevel=qlevel,
+ qmethod=qmethod,
+
+ hcomp_scale=hcomp_scale,
+ hcomp_smooth=hcomp_smooth,
+
+ extname=extname,
+ extver=extver,
+ )
+
+ # don't rebuild the whole list unless this is the first hdu
+ # to be created
+ self.update_hdu_list(rebuild=False)
+
+ def _ensure_empty_image_ok(self):
+ """
+ If ignore_empty was not set to True, we only allow empty HDU for first
+ HDU and if there is no data there already
+ """
+ if self.ignore_empty:
+ return
+
+ if len(self) > 1:
+ raise RuntimeError(
+ "Cannot write None image at extension %d" % len(self))
+ if 'ndims' in self[0]._info:
+ raise RuntimeError("Can only write None images to extension zero, "
+ "which already exists")
+
+ def write_table(self, data, table_type='binary',
+ names=None, formats=None, units=None,
+ extname=None, extver=None, header=None,
+ write_bitcols=False):
+ """
+ Create a new table extension and write the data.
+
+ The table definition is taken from the fields in the input array. If
+ you want to append new rows to the table, access the HDU directly and
+ use the write() function, e.g.
+
+ fits[extension].append(data)
+
+ parameters
+ ----------
+ data: recarray
+ A numpy array with fields. The table definition will be
+ determined from this array.
+ table_type: string, optional
+ Either 'binary' or 'ascii', default 'binary'
+ Matching is case-insensitive
+ extname: string, optional
+ An optional string for the extension name.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ units: list/dec, optional:
+ A list of strings with units for each column.
+ header: FITSHDR, list, dict, optional
+ A set of header keys to write. The keys are written before the data
+ is written to the table, preventing a resizing of the table area.
+
+ Can be one of these:
+ - FITSHDR object
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
+ write_bitcols: boolean, optional
+ Write boolean arrays in the FITS bitcols format, default False
+
+ restrictions
+ ------------
+ The File must be opened READWRITE
+ """
+
+ """
+ if data.dtype.fields == None:
+ raise ValueError("data must have fields")
+ if data.size == 0:
+ raise ValueError("data must have at least 1 row")
+ """
+
+ self.create_table_hdu(data=data,
+ header=header,
+ names=names,
+ units=units,
+ extname=extname,
+ extver=extver,
+ table_type=table_type,
+ write_bitcols=write_bitcols)
+
+ if header is not None:
+ self[-1].write_keys(header)
+ self[-1]._update_info()
+
+ self[-1].write(data, names=names)
+
+ def read_raw(self):
+ """
+ Reads the raw FITS file contents, returning a Python string.
+ """
+ return self._FITS.read_raw()
+
+ def create_table_hdu(self, data=None, dtype=None,
+ header=None,
+ names=None, formats=None,
+ units=None, dims=None, extname=None, extver=None,
+ table_type='binary', write_bitcols=False):
+ """
+ Create a new, empty table extension and reload the hdu list.
+
+ There are three ways to do it:
+ 1) send a numpy dtype, from which the formats in the fits file will
+ be determined.
+ 2) Send an array in data= keyword. this is required if you have
+ object fields for writing to variable length columns.
+ 3) send the names,formats and dims yourself
+
+ You can then write data into the new extension using
+ fits[extension].write(array)
+ If you want to write to a single column
+ fits[extension].write_column(array)
+ But be careful as the other columns will be left zeroed.
+
+ Often you will instead just use write_table to do this all
+ atomically.
+
+ fits.write_table(recarray)
+
+ write_table will create the new table extension for you with the
+ appropriate fields.
+
+ parameters
+ ----------
+ dtype: numpy dtype or descriptor, optional
+ If you have an array with fields, you can just send arr.dtype. You
+ can also use a list of tuples, e.g. [('x','f8'),('index','i4')] or
+ a dictionary representation.
+ data: a numpy array with fields, optional
+ or a dictionary
+
+ An array or dict from which to determine the table definition. You
+ must use this instead of sending a descriptor if you have object
+ array fields, as this is the only way to determine the type and max
+ size.
+
+ names: list of strings, optional
+ The list of field names
+ formats: list of strings, optional
+ The TFORM format strings for each field.
+ dims: list of strings, optional
+ An optional list of dimension strings for each field. Should
+ match the repeat count for the formats fields. Be careful of
+ the order since FITS is more like fortran. See the descr2tabledef
+ function.
+
+ table_type: string, optional
+ Either 'binary' or 'ascii', default 'binary'
+ Matching is case-insensitive
+ units: list of strings, optional
+ An optional list of unit strings for each field.
+ extname: string, optional
+ An optional extension name.
+ extver: integer, optional
+ FITS allows multiple extensions to have the same name (extname).
+ These extensions can optionally specify an EXTVER version number in
+ the header. Send extver= to set a particular version, which will
+ be represented in the header with keyname EXTVER. The extver must
+ be an integer > 0. If extver is not sent, the first one will be
+ selected. If ext is an integer, the extver is ignored.
+ write_bitcols: bool, optional
+ Write boolean arrays in the FITS bitcols format, default False
+
+ header: FITSHDR, list, dict, optional
+ This is only used to determine how many slots to reserve for
+ header keywords
+
+
+ restrictions
+ ------------
+ The File must be opened READWRITE
+ """
+
+ # record this for the TableHDU object
+ write_bitcols = self.write_bitcols or write_bitcols
+
+ # can leave as turn
+ table_type_int = _extract_table_type(table_type)
+
+ if data is not None:
+ if isinstance(data, numpy.ndarray):
+ names, formats, dims = array2tabledef(
+ data, table_type=table_type, write_bitcols=write_bitcols)
+ elif isinstance(data, (list, dict)):
+ names, formats, dims = collection2tabledef(
+ data, names=names, table_type=table_type,
+ write_bitcols=write_bitcols)
+ else:
+ raise ValueError(
+ "data must be an ndarray with fields or a dict")
+ elif dtype is not None:
+ dtype = numpy.dtype(dtype)
+ names, formats, dims = descr2tabledef(
+ dtype.
+ descr,
+ write_bitcols=write_bitcols,
+ table_type=table_type,
+ )
+ else:
+ if names is None or formats is None:
+ raise ValueError(
+ "send either dtype=, data=, or names= and formats=")
+
+ if not isinstance(names, list) or not isinstance(formats, list):
+ raise ValueError("names and formats should be lists")
+ if len(names) != len(formats):
+ raise ValueError("names and formats must be same length")
+
+ if dims is not None:
+ if not isinstance(dims, list):
+ raise ValueError("dims should be a list")
+ if len(dims) != len(names):
+ raise ValueError("names and dims must be same length")
+
+ if units is not None:
+ if not isinstance(units, list):
+ raise ValueError("units should be a list")
+ if len(units) != len(names):
+ raise ValueError("names and units must be same length")
+
+ if extname is None:
+ # will be ignored
+ extname = ""
+ else:
+ if not isstring(extname):
+ raise ValueError("extension name must be a string")
+ extname = mks(extname)
+
+ if extname is not None and extver is not None:
+ extver = check_extver(extver)
+ if extver is None:
+ # will be ignored
+ extver = 0
+ if extname is None:
+ # will be ignored
+ extname = ""
+
+ if header is not None:
+ nkeys = len(header)
+ else:
+ nkeys = 0
+
+ # note we can create extname in the c code for tables, but not images
+ self._FITS.create_table_hdu(table_type_int, nkeys,
+ names, formats, tunit=units, tdim=dims,
+ extname=extname, extver=extver)
+
+ # don't rebuild the whole list unless this is the first hdu
+ # to be created
+ self.update_hdu_list(rebuild=False)
+
+ def update_hdu_list(self, rebuild=True):
+ """
+ Force an update of the entire HDU list
+
+ Normally you don't need to call this method directly
+
+ if rebuild is false or the hdu_list is not yet set, the list is
+ rebuilt from scratch
+ """
+ if not hasattr(self, 'hdu_list'):
+ rebuild = True
+
+ if rebuild:
+ self.hdu_list = []
+ self.hdu_map = {}
+
+ # we don't know how many hdus there are, so iterate
+ # until we can't open any more
+ ext_start = 0
+ else:
+ # start from last
+ ext_start = len(self)
+
+ ext = ext_start
+ while True:
+ try:
+ self._append_hdu_info(ext)
+ except IOError:
+ break
+ except RuntimeError:
+ break
+
+ ext = ext + 1
+
+ def _append_hdu_info(self, ext):
+ """
+ internal routine
+
+ append info for indiciated extension
+ """
+
+ # raised IOError if not found
+ hdu_type = self._FITS.movabs_hdu(ext+1)
+
+ if hdu_type == IMAGE_HDU:
+ hdu = ImageHDU(self._FITS, ext)
+ elif hdu_type == BINARY_TBL:
+ hdu = TableHDU(
+ self._FITS, ext,
+ lower=self.lower, upper=self.upper,
+ trim_strings=self.trim_strings,
+ vstorage=self.vstorage, case_sensitive=self.case_sensitive,
+ iter_row_buffer=self.iter_row_buffer,
+ write_bitcols=self.write_bitcols)
+ elif hdu_type == ASCII_TBL:
+ hdu = AsciiTableHDU(
+ self._FITS, ext,
+ lower=self.lower, upper=self.upper,
+ trim_strings=self.trim_strings,
+ vstorage=self.vstorage, case_sensitive=self.case_sensitive,
+ iter_row_buffer=self.iter_row_buffer,
+ write_bitcols=self.write_bitcols)
+ else:
+ mess = ("extension %s is of unknown type %s "
+ "this is probably a bug")
+ mess = mess % (ext, hdu_type)
+ raise IOError(mess)
+
+ self.hdu_list.append(hdu)
+ self.hdu_map[ext] = hdu
+
+ extname = hdu.get_extname()
+ if not self.case_sensitive:
+ extname = extname.lower()
+ if extname != '':
+ # this will guarantee we default to *first* version,
+ # if version is not requested, using __getitem__
+ if extname not in self.hdu_map:
+ self.hdu_map[extname] = hdu
+
+ ver = hdu.get_extver()
+ if ver > 0:
+ key = '%s-%s' % (extname, ver)
+ self.hdu_map[key] = hdu
+
+ def __iter__(self):
+ """
+ begin iteration over HDUs
+ """
+ if not hasattr(self, 'hdu_list'):
+ self.update_hdu_list()
+ self._iter_index = 0
+ return self
+
+ def next(self):
+ """
+ Move to the next iteration
+ """
+ if self._iter_index == len(self.hdu_list):
+ raise StopIteration
+ hdu = self.hdu_list[self._iter_index]
+ self._iter_index += 1
+ return hdu
+
+ __next__ = next
+
+ def __len__(self):
+ """
+ get the number of extensions
+ """
+ if not hasattr(self, 'hdu_list'):
+ self.update_hdu_list()
+ return len(self.hdu_list)
+
+ def _extract_item(self, item):
+ """
+ utility function to extract an "item", meaning
+ a extension number,name plus version.
+ """
+ ver = 0
+ if isinstance(item, tuple):
+ ver_sent = True
+ nitem = len(item)
+ if nitem == 1:
+ ext = item[0]
+ elif nitem == 2:
+ ext, ver = item
+ else:
+ ver_sent = False
+ ext = item
+ return ext, ver, ver_sent
+
+ def __getitem__(self, item):
+ """
+ Get an hdu by number, name, and possibly version
+ """
+ if not hasattr(self, 'hdu_list'):
+ if self._did_create:
+ # we created the file and haven't written anything yet
+ raise ValueError("Requested hdu '%s' not present" % item)
+
+ self.update_hdu_list()
+
+ if len(self) == 0:
+ raise ValueError("Requested hdu '%s' not present" % item)
+
+ ext, ver, ver_sent = self._extract_item(item)
+
+ try:
+ # if it is an int
+ hdu = self.hdu_list[ext]
+ except Exception:
+ # might be a string
+ ext = mks(ext)
+ if not self.case_sensitive:
+ mess = '(case insensitive)'
+ ext = ext.lower()
+ else:
+ mess = '(case sensitive)'
+
+ if ver > 0:
+ key = '%s-%s' % (ext, ver)
+ if key not in self.hdu_map:
+ raise IOError("extension not found: %s, "
+ "version %s %s" % (ext, ver, mess))
+ hdu = self.hdu_map[key]
+ else:
+ if ext not in self.hdu_map:
+ raise IOError("extension not found: %s %s" % (ext, mess))
+ hdu = self.hdu_map[ext]
+
+ return hdu
+
+ def __contains__(self, item):
+ """
+ tell whether specified extension exists, possibly
+ with version sent as well
+ """
+ try:
+ hdu = self[item] # noqa
+ return True
+ except Exception:
+ return False
+
+ def __repr__(self):
+ """
+ Text representation of some fits file metadata
+ """
+ spacing = ' '*2
+ rep = ['']
+ rep.append("%sfile: %s" % (spacing, self._filename))
+ rep.append("%smode: %s" % (spacing, _modeprint_map[self.intmode]))
+
+ rep.append('%sextnum %-15s %s' % (spacing, "hdutype", "hduname[v]"))
+
+ if not hasattr(self, 'hdu_list'):
+ if not self._did_create:
+ # we expect some stuff
+ self.update_hdu_list()
+
+ for i, hdu in enumerate(self.hdu_list):
+ t = hdu._info['hdutype']
+ name = hdu.get_extname()
+ if name != '':
+ ver = hdu.get_extver()
+ if ver != 0:
+ name = '%s[%s]' % (name, ver)
+
+ rep.append(
+ "%s%-6d %-15s %s" % (spacing, i, _hdu_type_map[t], name))
+
+ rep = '\n'.join(rep)
+ return rep
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exception_type, exception_value, traceback):
+ self.close()
+
+
+def check_extver(extver):
+ if extver is None:
+ return 0
+ extver = int(extver)
+ if extver <= 0:
+ raise ValueError("extver must be > 0")
+ return extver
+
+
+def extract_filename(filename):
+ filename = mks(filename)
+ filename = filename.strip()
+ if filename[0] == "!":
+ filename = filename[1:]
+ filename = os.path.expandvars(filename)
+ filename = os.path.expanduser(filename)
+ return filename
+
+
+def array2tabledef(data, table_type='binary', write_bitcols=False):
+ """
+ Similar to descr2tabledef but if there are object columns a type
+ and max length will be extracted and used for the tabledef
+ """
+ is_ascii = (table_type == 'ascii')
+
+ if data.dtype.fields is None:
+ raise ValueError("data must have fields")
+ names = []
+ names_nocase = {}
+ formats = []
+ dims = []
+
+ descr = data.dtype.descr
+ for d in descr:
+ # these have the form '<f4' or '|S25', etc. Extract the pure type
+ npy_dtype = d[1][1:]
+ if is_ascii:
+ if npy_dtype in ['u1', 'i1']:
+ raise ValueError(
+ "1-byte integers are not supported for "
+ "ascii tables: '%s'" % npy_dtype)
+ if npy_dtype in ['u2']:
+ raise ValueError(
+ "unsigned 2-byte integers are not supported for "
+ "ascii tables: '%s'" % npy_dtype)
+
+ if npy_dtype[0] == 'O':
+ # this will be a variable length column 1Pt(len) where t is the
+ # type and len is max length. Each element must be convertible to
+ # the same type as the first
+ name = d[0]
+ form, dim = npy_obj2fits(data, name)
+ elif npy_dtype[0] == "V":
+ continue
+ else:
+ name, form, dim = _npy2fits(
+ d, table_type=table_type, write_bitcols=write_bitcols)
+
+ if name == '':
+ raise ValueError("field name is an empty string")
+
+ """
+ if is_ascii:
+ if dim is not None:
+ raise ValueError("array columns are not supported for "
+ "ascii tables")
+ """
+ name_nocase = name.upper()
+ if name_nocase in names_nocase:
+ raise ValueError(
+ "duplicate column name found: '%s'. Note "
+ "FITS column names are not case sensitive" % name_nocase)
+
+ names.append(name)
+ names_nocase[name_nocase] = name_nocase
+
+ formats.append(form)
+ dims.append(dim)
+
+ return names, formats, dims
+
+
+def collection2tabledef(
+ data, names=None, table_type='binary', write_bitcols=False):
+ if isinstance(data, dict):
+ if names is None:
+ names = list(data.keys())
+ isdict = True
+ elif isinstance(data, list):
+ if names is None:
+ raise ValueError("For list of array, send names=")
+ isdict = False
+ else:
+ raise ValueError("expected a dict")
+
+ is_ascii = (table_type == 'ascii')
+ formats = []
+ dims = []
+
+ for i, name in enumerate(names):
+
+ if isdict:
+ this_data = data[name]
+ else:
+ this_data = data[i]
+
+ dt = this_data.dtype.descr[0]
+ dname = dt[1][1:]
+
+ if is_ascii:
+ if dname in ['u1', 'i1']:
+ raise ValueError(
+ "1-byte integers are not supported for "
+ "ascii tables: '%s'" % dname)
+ if dname in ['u2']:
+ raise ValueError(
+ "unsigned 2-byte integers are not supported for "
+ "ascii tables: '%s'" % dname)
+
+ if dname[0] == 'O':
+ # this will be a variable length column 1Pt(len) where t is the
+ # type and len is max length. Each element must be convertible to
+ # the same type as the first
+ form, dim = npy_obj2fits(this_data)
+ else:
+ send_dt = dt
+ if len(this_data.shape) > 1:
+ send_dt = list(dt) + [this_data.shape[1:]]
+ _, form, dim = _npy2fits(
+ send_dt, table_type=table_type, write_bitcols=write_bitcols)
+
+ formats.append(form)
+ dims.append(dim)
+
+ return names, formats, dims
+
+
+def descr2tabledef(descr, table_type='binary', write_bitcols=False):
+ """
+ Create a FITS table def from the input numpy descriptor.
+
+ parameters
+ ----------
+ descr: list
+ A numpy recarray type descriptor array.dtype.descr
+
+ returns
+ -------
+ names, formats, dims: tuple of lists
+ These are the ttyp, tform and tdim header entries
+ for each field. dim entries may be None
+ """
+ names = []
+ formats = []
+ dims = []
+
+ for d in descr:
+
+ """
+ npy_dtype = d[1][1:]
+ if is_ascii and npy_dtype in ['u1','i1']:
+ raise ValueError("1-byte integers are not supported for "
+ "ascii tables")
+ """
+
+ if d[1][1] == 'O':
+ raise ValueError(
+ 'cannot automatically declare a var column without '
+ 'some data to determine max len')
+
+ name, form, dim = _npy2fits(
+ d, table_type=table_type, write_bitcols=write_bitcols)
+
+ if name == '':
+ raise ValueError("field name is an empty string")
+
+ """
+ if is_ascii:
+ if dim is not None:
+ raise ValueError("array columns are not supported "
+ "for ascii tables")
+ """
+
+ names.append(name)
+ formats.append(form)
+ dims.append(dim)
+
+ return names, formats, dims
+
+
+def npy_obj2fits(data, name=None):
+ # this will be a variable length column 1Pt(len) where t is the
+ # type and len is max length. Each element must be convertible to
+ # the same type as the first
+
+ if name is None:
+ d = data.dtype.descr
+ first = data[0]
+ else:
+ d = data[name].dtype.descr # noqa - not used
+ first = data[name][0]
+
+ # note numpy._string is an instance of str in python2, bytes
+ # in python3
+ if isinstance(first, str) or (IS_PY3 and isinstance(first, bytes)):
+ if IS_PY3:
+ if isinstance(first, str):
+ fits_dtype = _table_npy2fits_form['U']
+ else:
+ fits_dtype = _table_npy2fits_form['S']
+ else:
+ fits_dtype = _table_npy2fits_form['S']
+ else:
+ arr0 = numpy.array(first, copy=False)
+ dtype0 = arr0.dtype
+ npy_dtype = dtype0.descr[0][1][1:]
+ if npy_dtype[0] == 'S' or npy_dtype[0] == 'U':
+ raise ValueError("Field '%s' is an arrays of strings, this is "
+ "not allowed in variable length columns" % name)
+ if npy_dtype not in _table_npy2fits_form:
+ raise ValueError(
+ "Field '%s' has unsupported type '%s'" % (name, npy_dtype))
+ fits_dtype = _table_npy2fits_form[npy_dtype]
+
+ # Q uses 64-bit addressing, should try at some point but the cfitsio manual
+ # says it is experimental
+ # form = '1Q%s' % fits_dtype
+ form = '1P%s' % fits_dtype
+ dim = None
+
+ return form, dim
+
+
+def get_tile_dims(tile_dims, imshape):
+ """
+ Just make sure the tile dims has the appropriate number of dimensions
+ """
+
+ if tile_dims is None:
+ td = None
+ else:
+ td = numpy.array(tile_dims, dtype='i8')
+ nd = len(imshape)
+ if td.size != nd:
+ msg = "expected tile_dims to have %d dims, got %d" % (td.size, nd)
+ raise ValueError(msg)
+
+ return td
+
+
+def get_compress_type(compress):
+ if compress is not None:
+ compress = str(compress).upper()
+ if compress not in _compress_map:
+ raise ValueError(
+ "compress must be one of %s" % list(_compress_map.keys()))
+ return _compress_map[compress]
+
+
+def get_qmethod(qmethod):
+ if qmethod not in _qmethod_map:
+ if isinstance(qmethod, str):
+ qmethod = qmethod.upper()
+ elif isinstance(qmethod, bytes):
+ # in py27, bytes are str, so we can safely assume
+ # py3 here
+ qmethod = str(qmethod, 'ascii').upper()
+
+ if qmethod not in _qmethod_map:
+ raise ValueError(
+ "qmethod must be one of %s" % list(_qmethod_map.keys()))
+
+ return _qmethod_map[qmethod]
+
+
+def check_comptype_img(comptype, dtype_str):
+
+ if comptype == NOCOMPRESS:
+ return
+
+ # if dtype_str == 'i8':
+ # no i8 allowed for tile-compressed images
+ # raise ValueError("8-byte integers not supported when "
+ # "using tile compression")
+
+ if comptype == PLIO_1:
+ # no unsigned u4/u8 for plio
+ if dtype_str == 'u4' or dtype_str == 'u8':
+ raise ValueError("Unsigned 4/8-byte integers currently not "
+ "allowed when writing using PLIO "
+ "tile compression")
+
+
+def _extract_table_type(type):
+ """
+ Get the numerical table type
+ """
+ if isinstance(type, str):
+ type = type.lower()
+ if type[0:7] == 'binary':
+ table_type = BINARY_TBL
+ elif type[0:6] == 'ascii':
+ table_type = ASCII_TBL
+ else:
+ raise ValueError(
+ "table type string should begin with 'binary' or 'ascii' "
+ "(case insensitive)")
+ else:
+ type = int(type)
+ if type not in [BINARY_TBL, ASCII_TBL]:
+ raise ValueError(
+ "table type num should be BINARY_TBL (%d) or "
+ "ASCII_TBL (%d)" % (BINARY_TBL, ASCII_TBL))
+ table_type = type
+
+ return table_type
+
+
+_compress_map = {
+ None: NOCOMPRESS,
+ 'RICE': RICE_1,
+ 'RICE_1': RICE_1,
+ 'GZIP': GZIP_1,
+ 'GZIP_1': GZIP_1,
+ 'GZIP_2': GZIP_2,
+ 'PLIO': PLIO_1,
+ 'PLIO_1': PLIO_1,
+ 'HCOMPRESS': HCOMPRESS_1,
+ 'HCOMPRESS_1': HCOMPRESS_1,
+ NOCOMPRESS: None,
+ RICE_1: 'RICE_1',
+ GZIP_1: 'GZIP_1',
+ GZIP_2: 'GZIP_2',
+ PLIO_1: 'PLIO_1',
+ HCOMPRESS_1: 'HCOMPRESS_1',
+}
+
+_qmethod_map = {
+ None: NO_DITHER,
+ 'NO_DITHER': NO_DITHER,
+ 'SUBTRACTIVE_DITHER_1': SUBTRACTIVE_DITHER_1,
+ 'SUBTRACTIVE_DITHER_2': SUBTRACTIVE_DITHER_2,
+ NO_DITHER: NO_DITHER,
+ SUBTRACTIVE_DITHER_1: SUBTRACTIVE_DITHER_1,
+ SUBTRACTIVE_DITHER_2: SUBTRACTIVE_DITHER_2,
+}
+
+_modeprint_map = {
+ 'r': 'READONLY', 'rw': 'READWRITE', 0: 'READONLY', 1: 'READWRITE'}
+_char_modemap = {
+ 'r': 'r', 'rw': 'rw',
+ READONLY: 'r', READWRITE: 'rw'}
+_int_modemap = {
+ 'r': READONLY, 'rw': READWRITE, READONLY: READONLY, READWRITE: READWRITE}
--- /dev/null
+from .base import ( # noqa
+ ANY_HDU, BINARY_TBL, ASCII_TBL, IMAGE_HDU, _hdu_type_map)
+from .image import ImageHDU # noqa
+from .table import ( # noqa
+ TableHDU,
+ AsciiTableHDU,
+ _table_npy2fits_form,
+ _npy2fits,
+)
--- /dev/null
+import copy
+import warnings
+
+from ..util import _stypes, _itypes, _ftypes, FITSRuntimeWarning
+from ..header import FITSHDR
+
+ANY_HDU = -1
+IMAGE_HDU = 0
+ASCII_TBL = 1
+BINARY_TBL = 2
+
+_hdu_type_map = {
+ IMAGE_HDU: 'IMAGE_HDU',
+ ASCII_TBL: 'ASCII_TBL',
+ BINARY_TBL: 'BINARY_TBL',
+ 'IMAGE_HDU': IMAGE_HDU,
+ 'ASCII_TBL': ASCII_TBL,
+ 'BINARY_TBL': BINARY_TBL}
+
+
+class HDUBase(object):
+ """
+ A representation of a FITS HDU
+
+ parameters
+ ----------
+ fits: FITS object
+ An instance of a _fistio_wrap.FITS object. This is the low-level
+ python object, not the FITS object defined above.
+ ext: integer
+ The extension number.
+ """
+ def __init__(self, fits, ext, **keys):
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ self._FITS = fits
+ self._ext = ext
+ self._ignore_scaling = False
+
+ self._update_info()
+ self._filename = self._FITS.filename()
+
+ @property
+ def ignore_scaling(self):
+ """
+ :return: Flag to indicate whether scaling (BZERO/BSCALE) values should
+ be ignored.
+ """
+ return self._ignore_scaling
+
+ @ignore_scaling.setter
+ def ignore_scaling(self, ignore_scaling_flag):
+ """
+ Set the flag to ignore scaling.
+ """
+ old_val = self._ignore_scaling
+ self._ignore_scaling = ignore_scaling_flag
+
+ # Only endure the overhead of updating the info if the new value is
+ # actually different.
+ if old_val != self._ignore_scaling:
+ self._update_info()
+
+ def get_extnum(self):
+ """
+ Get the extension number
+ """
+ return self._ext
+
+ def get_extname(self):
+ """
+ Get the name for this extension, can be an empty string
+ """
+ name = self._info['extname']
+ if name.strip() == '':
+ name = self._info['hduname']
+ return name.strip()
+
+ def get_extver(self):
+ """
+ Get the version for this extension.
+
+ Used when a name is given to multiple extensions
+ """
+ ver = self._info['extver']
+ if ver == 0:
+ ver = self._info['hduver']
+ return ver
+
+ def get_exttype(self, num=False):
+ """
+ Get the extension type
+
+ By default the result is a string that mirrors
+ the enumerated type names in cfitsio
+ 'IMAGE_HDU', 'ASCII_TBL', 'BINARY_TBL'
+ which have numeric values
+ 0 1 2
+ send num=True to get the numbers. The values
+ fitsio.IMAGE_HDU .ASCII_TBL, and .BINARY_TBL
+ are available for comparison
+
+ parameters
+ ----------
+ num: bool, optional
+ Return the numeric values.
+ """
+ if num:
+ return self._info['hdutype']
+ else:
+ name = _hdu_type_map[self._info['hdutype']]
+ return name
+
+ def get_offsets(self):
+ """
+ returns
+ -------
+ a dictionary with these entries
+
+ header_start:
+ byte offset from beginning of the file to the start
+ of the header
+ data_start:
+ byte offset from beginning of the file to the start
+ of the data section
+ data_end:
+ byte offset from beginning of the file to the end
+ of the data section
+
+ Note these are also in the information dictionary, which
+ you can access with get_info()
+ """
+ return dict(
+ header_start=self._info['header_start'],
+ data_start=self._info['data_start'],
+ data_end=self._info['data_end'],
+ )
+
+ def get_info(self):
+ """
+ Get a copy of the internal dictionary holding extension information
+ """
+ return copy.deepcopy(self._info)
+
+ def get_filename(self):
+ """
+ Get a copy of the filename for this fits file
+ """
+ return copy.copy(self._filename)
+
+ def write_checksum(self):
+ """
+ Write the checksum into the header for this HDU.
+
+ Computes the checksum for the HDU, both the data portion alone (DATASUM
+ keyword) and the checksum complement for the entire HDU (CHECKSUM).
+
+ returns
+ -------
+ A dict with keys 'datasum' and 'hdusum'
+ """
+ return self._FITS.write_checksum(self._ext+1)
+
+ def verify_checksum(self):
+ """
+ Verify the checksum in the header for this HDU.
+ """
+ res = self._FITS.verify_checksum(self._ext+1)
+ if res['dataok'] != 1:
+ raise ValueError("data checksum failed")
+ if res['hduok'] != 1:
+ raise ValueError("hdu checksum failed")
+
+ def write_comment(self, comment):
+ """
+ Write a comment into the header
+ """
+ self._FITS.write_comment(self._ext+1, str(comment))
+
+ def write_history(self, history):
+ """
+ Write history text into the header
+ """
+ self._FITS.write_history(self._ext+1, str(history))
+
+ def _write_continue(self, value):
+ """
+ Write history text into the header
+ """
+ self._FITS.write_continue(self._ext+1, str(value))
+
+ def write_key(self, name, value, comment=""):
+ """
+ Write the input value to the header
+
+ parameters
+ ----------
+ name: string
+ Name of keyword to write/update
+ value: scalar
+ Value to write, can be string float or integer type,
+ including numpy scalar types.
+ comment: string, optional
+ An optional comment to write for this key
+
+ Notes
+ -----
+ Write COMMENT and HISTORY using the write_comment and write_history
+ methods
+ """
+
+ if name is None:
+
+ # we write a blank keyword and the rest is a comment
+ # string
+
+ if not isinstance(comment, _stypes):
+ raise ValueError('when writing blank key the value '
+ 'must be a string')
+
+ # this might be longer than 80 but that's ok, the routine
+ # will take care of it
+ # card = ' ' + str(comment)
+ card = ' ' + str(comment)
+ self._FITS.write_record(
+ self._ext+1,
+ card,
+ )
+
+ elif value is None:
+ self._FITS.write_undefined_key(self._ext+1,
+ str(name),
+ str(comment))
+
+ elif isinstance(value, bool):
+ if value:
+ v = 1
+ else:
+ v = 0
+ self._FITS.write_logical_key(self._ext+1,
+ str(name),
+ v,
+ str(comment))
+ elif isinstance(value, _stypes):
+ self._FITS.write_string_key(self._ext+1,
+ str(name),
+ str(value),
+ str(comment))
+ elif isinstance(value, _ftypes):
+ self._FITS.write_double_key(self._ext+1,
+ str(name),
+ float(value),
+ str(comment))
+ elif isinstance(value, _itypes):
+ self._FITS.write_long_long_key(self._ext+1,
+ str(name),
+ int(value),
+ str(comment))
+ elif isinstance(value, (tuple, list)):
+ vl = [str(el) for el in value]
+ sval = ','.join(vl)
+ self._FITS.write_string_key(self._ext+1,
+ str(name),
+ sval,
+ str(comment))
+ else:
+ sval = str(value)
+ mess = (
+ "warning, keyword '%s' has non-standard "
+ "value type %s, "
+ "Converting to string: '%s'")
+ warnings.warn(mess % (name, type(value), sval), FITSRuntimeWarning)
+ self._FITS.write_string_key(self._ext+1,
+ str(name),
+ sval,
+ str(comment))
+
+ def write_keys(self, records_in, clean=True):
+ """
+ Write the keywords to the header.
+
+ parameters
+ ----------
+ records: FITSHDR or list or dict
+ Can be one of these:
+ - FITSHDR object
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ clean: boolean
+ If True, trim out the standard fits header keywords that are
+ created on HDU creation, such as EXTEND, SIMPLE, STTYPE, TFORM,
+ TDIM, XTENSION, BITPIX, NAXIS, etc.
+
+ Notes
+ -----
+ Input keys named COMMENT and HISTORY are written using the
+ write_comment and write_history methods.
+ """
+
+ if isinstance(records_in, FITSHDR):
+ hdr = records_in
+ else:
+ hdr = FITSHDR(records_in)
+
+ if clean:
+ is_table = hasattr(self, '_table_type_str')
+ # is_table = isinstance(self, TableHDU)
+ hdr.clean(is_table=is_table)
+
+ for r in hdr.records():
+ name = r['name']
+ if name is not None:
+ name = name.upper()
+
+ value = r['value']
+
+ if name == 'COMMENT':
+ self.write_comment(value)
+ elif name == 'HISTORY':
+ self.write_history(value)
+ elif name == 'CONTINUE':
+ self._write_continue(value)
+ else:
+ comment = r.get('comment', '')
+ self.write_key(name, value, comment=comment)
+
+ def read_header(self):
+ """
+ Read the header as a FITSHDR
+
+ The FITSHDR allows access to the values and comments by name and
+ number.
+ """
+ # note converting strings
+ return FITSHDR(self.read_header_list())
+
+ def read_header_list(self):
+ """
+ Read the header as a list of dictionaries.
+
+ You will usually use read_header instead, which just sends the output
+ of this functioin to the constructor of a FITSHDR, which allows access
+ to the values and comments by name and number.
+
+ Each dictionary is
+ 'name': the keyword name
+ 'value': the value field as a string
+ 'comment': the comment field as a string.
+ """
+ return self._FITS.read_header(self._ext+1)
+
+ def _update_info(self):
+ """
+ Update metadata for this HDU
+ """
+ try:
+ self._FITS.movabs_hdu(self._ext+1)
+ except IOError:
+ raise RuntimeError("no such hdu")
+
+ self._info = self._FITS.get_hdu_info(self._ext+1, self._ignore_scaling)
+
+ def _get_repr_list(self):
+ """
+ Get some representation data common to all HDU types
+ """
+ spacing = ' '*2
+ text = ['']
+ text.append("%sfile: %s" % (spacing, self._filename))
+ text.append("%sextension: %d" % (spacing, self._info['hdunum']-1))
+ text.append(
+ "%stype: %s" % (spacing, _hdu_type_map[self._info['hdutype']]))
+
+ extname = self.get_extname()
+ if extname != "":
+ text.append("%sextname: %s" % (spacing, extname))
+ extver = self.get_extver()
+ if extver != 0:
+ text.append("%sextver: %s" % (spacing, extver))
+
+ return text, spacing
--- /dev/null
+"""
+image HDU classes for fitslib, part of the fitsio package.
+
+See the main docs at https://github.com/esheldon/fitsio
+
+ Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+"""
+from __future__ import with_statement, print_function
+from functools import reduce
+
+import numpy
+
+from math import floor
+from .base import HDUBase, IMAGE_HDU
+from ..util import IS_PY3, array_to_native
+
+# for python3 compat
+if IS_PY3:
+ xrange = range
+
+
+class ImageHDU(HDUBase):
+ def _update_info(self):
+ """
+ Call parent method and make sure this is in fact a
+ image HDU. Set dims in C order
+ """
+ super(ImageHDU, self)._update_info()
+
+ if self._info['hdutype'] != IMAGE_HDU:
+ mess = "Extension %s is not a Image HDU" % self.ext
+ raise ValueError(mess)
+
+ # convert to c order
+ if 'dims' in self._info:
+ self._info['dims'] = list(reversed(self._info['dims']))
+
+ def has_data(self):
+ """
+ Determine if this HDU has any data
+
+ For images, check that the dimensions are not zero.
+
+ For tables, check that the row count is not zero
+ """
+ ndims = self._info.get('ndims', 0)
+ if ndims == 0:
+ return False
+ else:
+ return True
+
+ def is_compressed(self):
+ """
+ returns true of this extension is compressed
+ """
+ return self._info['is_compressed_image'] == 1
+
+ def get_comptype(self):
+ """
+ Get the compression type.
+
+ None if the image is not compressed.
+ """
+ return self._info['comptype']
+
+ def get_dims(self):
+ """
+ get the shape of the image. Returns () for empty
+ """
+ if self._info['ndims'] != 0:
+ dims = self._info['dims']
+ else:
+ dims = ()
+
+ return dims
+
+ def reshape(self, dims):
+ """
+ reshape an existing image to the requested dimensions
+
+ parameters
+ ----------
+ dims: sequence
+ Any sequence convertible to i8
+ """
+
+ adims = numpy.array(dims, ndmin=1, dtype='i8')
+ self._FITS.reshape_image(self._ext+1, adims)
+
+ def write(self, img, start=0, **keys):
+ """
+ Write the image into this HDU
+
+ If data already exist in this HDU, they will be overwritten. If the
+ image to write is larger than the image on disk, or if the start
+ position is such that the write would extend beyond the existing
+ dimensions, the on-disk image is expanded.
+
+ parameters
+ ----------
+ img: ndarray
+ A simple numpy ndarray
+ start: integer or sequence
+ Where to start writing data. Can be an integer offset
+ into the entire array, or a sequence determining where
+ in N-dimensional space to start.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ dims = self.get_dims()
+
+ if img.dtype.fields is not None:
+ raise ValueError("got recarray, expected regular ndarray")
+ if img.size == 0:
+ raise ValueError("data must have at least 1 row")
+
+ # data must be c-contiguous and native byte order
+ if not img.flags['C_CONTIGUOUS']:
+ # this always makes a copy
+ img_send = numpy.ascontiguousarray(img)
+ array_to_native(img_send, inplace=True)
+ else:
+ img_send = array_to_native(img, inplace=False)
+
+ if IS_PY3 and img_send.dtype.char == 'U':
+ # for python3, we convert unicode to ascii
+ # this will error if the character is not in ascii
+ img_send = img_send.astype('S', copy=False)
+
+ if not numpy.isscalar(start):
+ # convert to scalar offset
+ # note we use the on-disk data type to get itemsize
+
+ offset = _convert_full_start_to_offset(dims, start)
+ else:
+ offset = start
+
+ # see if we need to resize the image
+ if self.has_data():
+ self._expand_if_needed(dims, img.shape, start, offset)
+
+ self._FITS.write_image(self._ext+1, img_send, offset+1)
+ self._update_info()
+
+ def read(self, **keys):
+ """
+ Read the image.
+
+ If the HDU is an IMAGE_HDU, read the corresponding image. Compression
+ and scaling are dealt with properly.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if not self.has_data():
+ return None
+
+ dtype, shape = self._get_dtype_and_shape()
+ array = numpy.zeros(shape, dtype=dtype)
+ self._FITS.read_image(self._ext+1, array)
+ return array
+
+ def _get_dtype_and_shape(self):
+ """
+ Get the numpy dtype and shape for image
+ """
+ npy_dtype = self._get_image_numpy_dtype()
+
+ if self._info['ndims'] != 0:
+ shape = self._info['dims']
+ else:
+ raise IOError("no image present in HDU")
+
+ return npy_dtype, shape
+
+ def _get_image_numpy_dtype(self):
+ """
+ Get the numpy dtype for the image
+ """
+ try:
+ ftype = self._info['img_equiv_type']
+ npy_type = _image_bitpix2npy[ftype]
+ except KeyError:
+ raise KeyError("unsupported fits data type: %d" % ftype)
+
+ return npy_type
+
+ def __getitem__(self, arg):
+ """
+ Get data from an image using python [] slice notation.
+
+ e.g., [2:25, 4:45].
+ """
+ return self._read_image_slice(arg)
+
+ def _read_image_slice(self, arg):
+ """
+ workhorse to read a slice
+ """
+ if 'ndims' not in self._info:
+ raise ValueError("Attempt to slice empty extension")
+
+ if isinstance(arg, slice):
+ # one-dimensional, e.g. 2:20
+ return self._read_image_slice((arg,))
+
+ if not isinstance(arg, tuple):
+ raise ValueError("arguments must be slices, one for each "
+ "dimension, e.g. [2:5] or [2:5,8:25] etc.")
+
+ # should be a tuple of slices, one for each dimension
+ # e.g. [2:3, 8:100]
+ nd = len(arg)
+ if nd != self._info['ndims']:
+ raise ValueError("Got slice dimensions %d, "
+ "expected %d" % (nd, self._info['ndims']))
+
+ targ = arg
+ arg = []
+ for a in targ:
+ if isinstance(a, slice):
+ arg.append(a)
+ elif isinstance(a, int):
+ arg.append(slice(a, a+1, 1))
+ else:
+ raise ValueError("arguments must be slices, e.g. 2:12")
+
+ dims = self._info['dims']
+ arrdims = []
+ first = []
+ last = []
+ steps = []
+ npy_dtype = self._get_image_numpy_dtype()
+
+ # check the args and reverse dimensions since
+ # fits is backwards from numpy
+ dim = 0
+ for slc in arg:
+ start = slc.start
+ stop = slc.stop
+ step = slc.step
+
+ if start is None:
+ start = 0
+ if stop is None:
+ stop = dims[dim]
+ if step is None:
+ # Ensure sane defaults.
+ if start <= stop:
+ step = 1
+ else:
+ step = -1
+
+ # Sanity checks for proper syntax.
+ if (step > 0 and stop < start) or (step < 0 and start < stop):
+ return numpy.empty(0, dtype=npy_dtype)
+ if start < 0:
+ start = dims[dim] + start
+ if start < 0:
+ raise IndexError("Index out of bounds")
+
+ if stop < 0:
+ stop = dims[dim] + start + 1
+
+ # move to 1-offset
+ start = start + 1
+
+ if stop > dims[dim]:
+ stop = dims[dim]
+ if stop < start:
+ # A little black magic here. The stop is offset by 2 to
+ # accommodate the 1-offset of CFITSIO, and to move past the end
+ # pixel to get the complete set after it is flipped along the
+ # axis. Maybe there is a clearer way to accomplish what this
+ # offset is glossing over.
+ # @at88mph 2019.10.10
+ stop = stop + 2
+
+ first.append(start)
+ last.append(stop)
+
+ # Negative step values are not used in CFITSIO as the dimension is
+ # already properly calcualted.
+ # @at88mph 2019.10.21
+ steps.append(abs(step))
+ arrdims.append(int(floor((stop - start) / step)) + 1)
+
+ dim += 1
+
+ first.reverse()
+ last.reverse()
+ steps.reverse()
+ first = numpy.array(first, dtype='i8')
+ last = numpy.array(last, dtype='i8')
+ steps = numpy.array(steps, dtype='i8')
+
+ array = numpy.zeros(arrdims, dtype=npy_dtype)
+ self._FITS.read_image_slice(self._ext+1, first, last, steps,
+ self._ignore_scaling, array)
+ return array
+
+ def _expand_if_needed(self, dims, write_dims, start, offset):
+ """
+ expand the on-disk image if the indended write will extend
+ beyond the existing dimensions
+ """
+ from operator import mul
+
+ if numpy.isscalar(start):
+ start_is_scalar = True
+ else:
+ start_is_scalar = False
+
+ existing_size = reduce(mul, dims, 1)
+ required_size = offset + reduce(mul, write_dims, 1)
+
+ if required_size > existing_size:
+ # we need to expand the image
+ ndim = len(dims)
+ idim = len(write_dims)
+
+ if start_is_scalar:
+ if start == 0:
+ start = [0]*ndim
+ else:
+ raise ValueError(
+ "When expanding "
+ "an existing image while writing, the start keyword "
+ "must have the same number of dimensions "
+ "as the image or be exactly 0, got %s " % start)
+
+ if idim != ndim:
+ raise ValueError(
+ "When expanding "
+ "an existing image while writing, the input image "
+ "must have the same number of dimensions "
+ "as the original. "
+ "Got %d instead of %d" % (idim, ndim))
+ new_dims = []
+ for i in xrange(ndim):
+ required_dim = start[i] + write_dims[i]
+
+ if required_dim < dims[i]:
+ # careful not to shrink the image!
+ dimsize = dims[i]
+ else:
+ dimsize = required_dim
+
+ new_dims.append(dimsize)
+
+ self.reshape(new_dims)
+
+ def __repr__(self):
+ """
+ Representation for ImageHDU
+ """
+ text, spacing = self._get_repr_list()
+ text.append("%simage info:" % spacing)
+ cspacing = ' '*4
+
+ # need this check for when we haven't written data yet
+ if 'ndims' in self._info:
+ if self._info['comptype'] is not None:
+ text.append(
+ "%scompression: %s" % (cspacing, self._info['comptype']))
+
+ if self._info['ndims'] != 0:
+ dimstr = [str(d) for d in self._info['dims']]
+ dimstr = ",".join(dimstr)
+ else:
+ dimstr = ''
+
+ dt = _image_bitpix2npy[self._info['img_equiv_type']]
+ text.append("%sdata type: %s" % (cspacing, dt))
+ text.append("%sdims: [%s]" % (cspacing, dimstr))
+
+ text = '\n'.join(text)
+ return text
+
+
+def _convert_full_start_to_offset(dims, start):
+ # convert to scalar offset
+ # note we use the on-disk data type to get itemsize
+ ndim = len(dims)
+
+ # convert sequence to pixel start
+ if len(start) != ndim:
+ m = "start has len %d, which does not match requested dims %d"
+ raise ValueError(m % (len(start), ndim))
+
+ # this is really strides / itemsize
+ strides = [1]
+ for i in xrange(1, ndim):
+ strides.append(strides[i-1] * dims[ndim-i])
+
+ strides.reverse()
+ s = start
+ start_index = sum([s[i]*strides[i] for i in xrange(ndim)])
+
+ return start_index
+
+
+# remember, you should be using the equivalent image type for this
+_image_bitpix2npy = {
+ 8: 'u1',
+ 10: 'i1',
+ 16: 'i2',
+ 20: 'u2',
+ 32: 'i4',
+ 40: 'u4',
+ 64: 'i8',
+ -32: 'f4',
+ -64: 'f8'}
--- /dev/null
+"""
+image HDU classes for fitslib, part of the fitsio package.
+
+See the main docs at https://github.com/esheldon/fitsio
+
+ Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+"""
+from __future__ import with_statement, print_function
+import copy
+import warnings
+from functools import reduce
+
+import numpy
+
+from ..util import (
+ IS_PY3,
+ isstring,
+ isinteger,
+ is_object,
+ fields_are_object,
+ array_to_native,
+ array_to_native_c,
+ FITSRuntimeWarning,
+ mks
+)
+from .base import HDUBase, ASCII_TBL, IMAGE_HDU, _hdu_type_map
+
+# for python3 compat
+if IS_PY3:
+ xrange = range
+
+
+class TableHDU(HDUBase):
+ """
+ A table HDU
+
+ parameters
+ ----------
+ fits: FITS object
+ An instance of a _fistio_wrap.FITS object. This is the low-level
+ python object, not the FITS object defined above.
+ ext: integer
+ The extension number.
+ lower: bool, optional
+ If True, force all columns names to lower case in output
+ upper: bool, optional
+ If True, force all columns names to upper case in output
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Default is False.
+ vstorage: string, optional
+ Set the default method to store variable length columns. Can be
+ 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ case_sensitive: bool, optional
+ Match column names and extension names with case-sensitivity. Default
+ is False.
+ iter_row_buffer: integer
+ Number of rows to buffer when iterating over table HDUs.
+ Default is 1.
+ write_bitcols: bool, optional
+ If True, write logicals a a bit column. Default is False.
+ """
+ def __init__(self, fits, ext,
+ lower=False, upper=False, trim_strings=False,
+ vstorage='fixed', case_sensitive=False, iter_row_buffer=1,
+ write_bitcols=False, **keys):
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ # NOTE: The defaults of False above cannot be changed since they
+ # are or'ed with the method defaults below.
+ super(TableHDU, self).__init__(fits, ext)
+
+ self.lower = lower
+ self.upper = upper
+ self.trim_strings = trim_strings
+
+ self._vstorage = vstorage
+ self.case_sensitive = case_sensitive
+ self._iter_row_buffer = iter_row_buffer
+ self.write_bitcols = write_bitcols
+
+ if self._info['hdutype'] == ASCII_TBL:
+ self._table_type_str = 'ascii'
+ else:
+ self._table_type_str = 'binary'
+
+ def get_nrows(self):
+ """
+ Get number of rows in the table.
+ """
+ nrows = self._info.get('nrows', None)
+ if nrows is None:
+ raise ValueError("nrows not in info table; this is a bug")
+ return nrows
+
+ def get_colnames(self):
+ """
+ Get a copy of the column names for a table HDU
+ """
+ return copy.copy(self._colnames)
+
+ def get_colname(self, colnum):
+ """
+ Get the name associated with the given column number
+
+ parameters
+ ----------
+ colnum: integer
+ The number for the column, zero offset
+ """
+ if colnum < 0 or colnum > (len(self._colnames)-1):
+ raise ValueError(
+ "colnum out of range [0,%s-1]" % (0, len(self._colnames)))
+ return self._colnames[colnum]
+
+ def get_vstorage(self):
+ """
+ Get a string representing the storage method for variable length
+ columns
+ """
+ return copy.copy(self._vstorage)
+
+ def has_data(self):
+ """
+ Determine if this HDU has any data
+
+ Check that the row count is not zero
+ """
+ if self._info['nrows'] > 0:
+ return True
+ else:
+ return False
+
+ def where(self, expression):
+ """
+ Return the indices where the expression evaluates to true.
+
+ parameters
+ ----------
+ expression: string
+ A fits row selection expression. E.g.
+ "x > 3 && y < 5"
+ """
+ return self._FITS.where(self._ext+1, expression)
+
+ def write(self, data, firstrow=0, columns=None, names=None, slow=False,
+ **keys):
+ """
+ Write data into this HDU
+
+ parameters
+ ----------
+ data: ndarray or list of ndarray
+ A numerical python array. Should be an ordinary array for image
+ HDUs, should have fields for tables. To write an ordinary array to
+ a column in a table HDU, use write_column. If data already exists
+ in this HDU, it will be overwritten. See the append(() method to
+ append new rows to a table HDU.
+ firstrow: integer, optional
+ At which row you should begin writing to tables. Be sure you know
+ what you are doing! For appending see the append() method.
+ Default 0.
+ columns: list, optional
+ If data is a list of arrays, you must send columns as a list
+ of names or column numbers. You can also use the `names` keyword
+ argument.
+ names: list, optional
+ If data is a list of arrays, you must send columns as a list
+ of names or column numbers. You can also use the `columns` keyword
+ argument.
+ slow: bool, optional
+ If True, use a slower method to write one column at a time. Useful
+ for debugging.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ isrec = False
+ if isinstance(data, (list, dict)):
+ if isinstance(data, list):
+ data_list = data
+ if columns is not None:
+ columns_all = columns
+ elif names is not None:
+ columns_all = names
+ else:
+ raise ValueError(
+ "you must send `columns` or `names` "
+ "with a list of arrays")
+ else:
+ columns_all = list(data.keys())
+ data_list = [data[n] for n in columns_all]
+
+ colnums_all = [self._extract_colnum(c) for c in columns_all]
+ names = [self.get_colname(c) for c in colnums_all]
+
+ isobj = numpy.zeros(len(data_list), dtype=bool)
+ for i in xrange(len(data_list)):
+ isobj[i] = is_object(data_list[i])
+
+ else:
+ if data.dtype.fields is None:
+ raise ValueError("You are writing to a table, so I expected "
+ "an array with fields as input. If you want "
+ "to write a simple array, you should use "
+ "write_column to write to a single column, "
+ "or instead write to an image hdu")
+
+ if data.shape == ():
+ raise ValueError("cannot write data with shape ()")
+
+ isrec = True
+ names = data.dtype.names
+ # only write object types (variable-length columns) after
+ # writing the main table
+ isobj = fields_are_object(data)
+
+ data_list = []
+ colnums_all = []
+ for i, name in enumerate(names):
+ colnum = self._extract_colnum(name)
+ data_list.append(data[name])
+ colnums_all.append(colnum)
+
+ if slow:
+ for i, name in enumerate(names):
+ if not isobj[i]:
+ self.write_column(name, data_list[i], firstrow=firstrow)
+ else:
+
+ nonobj_colnums = []
+ nonobj_arrays = []
+ for i in xrange(len(data_list)):
+ if not isobj[i]:
+ nonobj_colnums.append(colnums_all[i])
+ if isrec:
+ # this still leaves possibility of f-order sub-arrays..
+ colref = array_to_native(data_list[i], inplace=False)
+ else:
+ colref = array_to_native_c(data_list[i], inplace=False)
+
+ if IS_PY3 and colref.dtype.char == 'U':
+ # for python3, we convert unicode to ascii
+ # this will error if the character is not in ascii
+ colref = colref.astype('S', copy=False)
+
+ nonobj_arrays.append(colref)
+
+ for tcolnum, tdata in zip(nonobj_colnums, nonobj_arrays):
+ self._verify_column_data(tcolnum, tdata)
+
+ if len(nonobj_arrays) > 0:
+ self._FITS.write_columns(
+ self._ext+1, nonobj_colnums, nonobj_arrays,
+ firstrow=firstrow+1, write_bitcols=self.write_bitcols)
+
+ # writing the object arrays always occurs the same way
+ # need to make sure this works for array fields
+ for i, name in enumerate(names):
+ if isobj[i]:
+ self.write_var_column(name, data_list[i], firstrow=firstrow)
+
+ self._update_info()
+
+ def write_column(self, column, data, firstrow=0, **keys):
+ """
+ Write data to a column in this HDU
+
+ This HDU must be a table HDU.
+
+ parameters
+ ----------
+ column: scalar string/integer
+ The column in which to write. Can be the name or number (0 offset)
+ data: ndarray
+ Numerical python array to write. This should match the
+ shape of the column. You are probably better using
+ fits.write_table() to be sure.
+ firstrow: integer, optional
+ At which row you should begin writing. Be sure you know what you
+ are doing! For appending see the append() method. Default 0.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ colnum = self._extract_colnum(column)
+
+ # need it to be contiguous and native byte order. For now, make a
+ # copy. but we may be able to avoid this with some care.
+
+ if not data.flags['C_CONTIGUOUS']:
+ # this always makes a copy
+ data_send = numpy.ascontiguousarray(data)
+ # this is a copy, we can make sure it is native
+ # and modify in place if needed
+ array_to_native(data_send, inplace=True)
+ else:
+ # we can avoid the copy with a try-finally block and
+ # some logic
+ data_send = array_to_native(data, inplace=False)
+
+ if IS_PY3 and data_send.dtype.char == 'U':
+ # for python3, we convert unicode to ascii
+ # this will error if the character is not in ascii
+ data_send = data_send.astype('S', copy=False)
+
+ self._verify_column_data(colnum, data_send)
+
+ self._FITS.write_columns(
+ self._ext+1,
+ [colnum],
+ [data_send],
+ firstrow=firstrow+1,
+ write_bitcols=self.write_bitcols,
+ )
+
+ del data_send
+ self._update_info()
+
+ def _verify_column_data(self, colnum, data):
+ """
+ verify the input data is of the correct type and shape
+ """
+ this_dt = data.dtype.descr[0]
+
+ if len(data.shape) > 2:
+ this_shape = data.shape[1:]
+ elif len(data.shape) == 2 and data.shape[1] > 1:
+ this_shape = data.shape[1:]
+ else:
+ this_shape = ()
+
+ this_npy_type = this_dt[1][1:]
+
+ npy_type, isvar, istbit = self._get_tbl_numpy_dtype(colnum)
+ info = self._info['colinfo'][colnum]
+
+ if npy_type[0] in ['>', '<', '|']:
+ npy_type = npy_type[1:]
+
+ col_name = info['name']
+ col_tdim = info['tdim']
+ col_shape = _tdim2shape(
+ col_tdim, col_name, is_string=(npy_type[0] == 'S'))
+
+ if col_shape is None:
+ if this_shape == ():
+ this_shape = None
+
+ if col_shape is not None and not isinstance(col_shape, tuple):
+ col_shape = (col_shape,)
+
+ """
+ print('column name:',col_name)
+ print(data.shape)
+ print('col tdim', info['tdim'])
+ print('column dtype:',npy_type)
+ print('input dtype:',this_npy_type)
+ print('column shape:',col_shape)
+ print('input shape:',this_shape)
+ print()
+ """
+
+ # this mismatch is OK
+ if npy_type == 'i1' and this_npy_type == 'b1':
+ this_npy_type = 'i1'
+
+ if isinstance(self, AsciiTableHDU):
+ # we don't enforce types exact for ascii
+ if npy_type == 'i8' and this_npy_type in ['i2', 'i4']:
+ this_npy_type = 'i8'
+ elif npy_type == 'f8' and this_npy_type == 'f4':
+ this_npy_type = 'f8'
+
+ if this_npy_type != npy_type:
+ raise ValueError(
+ "bad input data for column '%s': "
+ "expected '%s', got '%s'" % (
+ col_name, npy_type, this_npy_type))
+
+ if this_shape != col_shape:
+ raise ValueError(
+ "bad input shape for column '%s': "
+ "expected '%s', got '%s'" % (col_name, col_shape, this_shape))
+
+ def write_var_column(self, column, data, firstrow=0, **keys):
+ """
+ Write data to a variable-length column in this HDU
+
+ This HDU must be a table HDU.
+
+ parameters
+ ----------
+ column: scalar string/integer
+ The column in which to write. Can be the name or number (0 offset)
+ column: ndarray
+ Numerical python array to write. This must be an object array.
+ firstrow: integer, optional
+ At which row you should begin writing. Be sure you know what you
+ are doing! For appending see the append() method. Default 0.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if not is_object(data):
+ raise ValueError("Only object fields can be written to "
+ "variable-length arrays")
+ colnum = self._extract_colnum(column)
+
+ self._FITS.write_var_column(self._ext+1, colnum+1, data,
+ firstrow=firstrow+1)
+ self._update_info()
+
+ def insert_column(self, name, data, colnum=None, write_bitcols=None,
+ **keys):
+ """
+ Insert a new column.
+
+ parameters
+ ----------
+ name: string
+ The column name
+ data:
+ The data to write into the new column.
+ colnum: int, optional
+ The column number for the new column, zero-offset. Default
+ is to add the new column after the existing ones.
+ write_bitcols: bool, optional
+ If set, write logical as bit cols. This can over-ride the
+ internal class setting. Default of None respects the inner
+ class setting.
+
+ Notes
+ -----
+ This method is used un-modified by ascii tables as well.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if write_bitcols is None:
+ write_bitcols = self.write_bitcols
+
+ if name in self._colnames:
+ raise ValueError("column '%s' already exists" % name)
+
+ if IS_PY3 and data.dtype.char == 'U':
+ # fast dtype conversion using an empty array
+ # we could hack at the actual text description, but using
+ # the numpy API is probably safer
+ # this also avoids doing a dtype conversion on every array
+ # element which could b expensive
+ descr = numpy.empty(1).astype(data.dtype).astype('S').dtype.descr
+ else:
+ descr = data.dtype.descr
+
+ if len(descr) > 1:
+ raise ValueError("you can only insert a single column, "
+ "requested: %s" % descr)
+
+ this_descr = descr[0]
+ this_descr = [name, this_descr[1]]
+ if len(data.shape) > 1:
+ this_descr += [data.shape[1:]]
+ this_descr = tuple(this_descr)
+
+ name, fmt, dims = _npy2fits(
+ this_descr,
+ table_type=self._table_type_str,
+ write_bitcols=write_bitcols,
+ )
+ if dims is not None:
+ dims = [dims]
+
+ if colnum is None:
+ new_colnum = len(self._info['colinfo']) + 1
+ else:
+ new_colnum = colnum+1
+
+ self._FITS.insert_col(self._ext+1, new_colnum, name, fmt, tdim=dims)
+
+ self._update_info()
+
+ self.write_column(name, data)
+
+ def append(self, data, columns=None, names=None, **keys):
+ """
+ Append new rows to a table HDU
+
+ parameters
+ ----------
+ data: ndarray or list of arrays
+ A numerical python array with fields (recarray) or a list of
+ arrays. Should have the same fields as the existing table. If only
+ a subset of the table columns are present, the other columns are
+ filled with zeros.
+ columns: list, optional
+ If data is a list of arrays, you must send columns as a list
+ of names or column numbers. You can also use the `names` keyword
+ argument.
+ names: list, optional
+ If data is a list of arrays, you must send columns as a list
+ of names or column numbers. You can also use the `columns` keyword
+ argument.
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ firstrow = self._info['nrows']
+ self.write(data, firstrow=firstrow, columns=None, names=None)
+
+ def delete_rows(self, rows):
+ """
+ Delete rows from the table
+
+ parameters
+ ----------
+ rows: sequence or slice
+ The exact rows to delete as a sequence, or a slice.
+
+ examples
+ --------
+ # delete a range of rows
+ with fitsio.FITS(fname,'rw') as fits:
+ fits['mytable'].delete_rows(slice(3,20))
+
+ # delete specific rows
+ with fitsio.FITS(fname,'rw') as fits:
+ rows2delete = [3,88,76]
+ fits['mytable'].delete_rows(rows2delete)
+ """
+
+ if rows is None:
+ return
+
+ # extract and convert to 1-offset for C routine
+ if isinstance(rows, slice):
+ rows = self._process_slice(rows)
+ if rows.step is not None and rows.step != 1:
+ rows = numpy.arange(
+ rows.start+1,
+ rows.stop+1,
+ rows.step,
+ )
+ else:
+ # rows must be 1-offset
+ rows = slice(rows.start+1, rows.stop+1)
+ else:
+ rows = self._extract_rows(rows)
+ # rows must be 1-offset
+ rows += 1
+
+ if isinstance(rows, slice):
+ self._FITS.delete_row_range(self._ext+1, rows.start, rows.stop)
+ else:
+ if rows.size == 0:
+ return
+
+ self._FITS.delete_rows(self._ext+1, rows)
+
+ self._update_info()
+
+ def resize(self, nrows, front=False):
+ """
+ Resize the table to the given size, removing or adding rows as
+ necessary. Note if expanding the table at the end, it is more
+ efficient to use the append function than resizing and then
+ writing.
+
+ New added rows are zerod, except for 'i1', 'u2' and 'u4' data types
+ which get -128,32768,2147483648 respectively
+
+ parameters
+ ----------
+ nrows: int
+ new size of table
+ front: bool, optional
+ If True, add or remove rows from the front. Default
+ is False
+ """
+
+ nrows_current = self.get_nrows()
+ if nrows == nrows_current:
+ return
+
+ if nrows < nrows_current:
+ rowdiff = nrows_current - nrows
+ if front:
+ # delete from the front
+ start = 0
+ stop = rowdiff
+ else:
+ # delete from the back
+ start = nrows
+ stop = nrows_current
+
+ self.delete_rows(slice(start, stop))
+ else:
+ rowdiff = nrows - nrows_current
+ if front:
+ # in this case zero is what we want, since the code inserts
+ firstrow = 0
+ else:
+ firstrow = nrows_current
+ self._FITS.insert_rows(self._ext+1, firstrow, rowdiff)
+
+ self._update_info()
+
+ def read(self, columns=None, rows=None, vstorage=None,
+ upper=False, lower=False, trim_strings=False, **keys):
+ """
+ Read data from this HDU
+
+ By default, all data are read. You can set the `columns` and/or
+ `rows` keywords to read subsets of the data.
+
+ Table data is read into a numpy recarray. To get a single column as
+ a numpy.ndarray, use the `read_column` method.
+
+ Slice notation is also supported for `TableHDU` types.
+
+ >>> fits = fitsio.FITS(filename)
+ >>> fits[ext][:]
+ >>> fits[ext][2:5]
+ >>> fits[ext][200:235:2]
+ >>> fits[ext][rows]
+ >>> fits[ext][cols][rows]
+
+ parameters
+ ----------
+ columns: optional
+ An optional set of columns to read from table HDUs. Default is to
+ read all. Can be string or number. If a sequence, a recarray
+ is always returned. If a scalar, an ordinary array is returned.
+ rows: optional
+ An optional list of rows to read from table HDUS. Default is to
+ read all.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if columns is not None:
+ data = self.read_columns(
+ columns, rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+ elif rows is not None:
+ # combinations of row and column subsets are covered by
+ # read_columns so we pass colnums=None here to get all columns
+ data = self.read_rows(
+ rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+ else:
+ data = self._read_all(
+ vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ return data
+
+ def _read_all(self, vstorage=None,
+ upper=False, lower=False, trim_strings=False, colnums=None,
+ **keys):
+ """
+ Read all data in the HDU.
+
+ parameters
+ ----------
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ colnums: integer array, optional
+ The column numbers, 0 offset
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ dtype, offsets, isvar = self.get_rec_dtype(
+ colnums=colnums, vstorage=vstorage)
+
+ w, = numpy.where(isvar == True) # noqa
+ has_tbit = self._check_tbit()
+
+ if w.size > 0:
+ if vstorage is None:
+ _vstorage = self._vstorage
+ else:
+ _vstorage = vstorage
+ colnums = self._extract_colnums()
+ rows = None
+ array = self._read_rec_with_var(colnums, rows, dtype,
+ offsets, isvar, _vstorage)
+ elif has_tbit:
+ # drop down to read_columns since we can't stuff into a
+ # contiguous array
+ colnums = self._extract_colnums()
+ array = self.read_columns(
+ colnums,
+ rows=None, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+ else:
+ firstrow = 1 # noqa - not used?
+ nrows = self._info['nrows']
+ array = numpy.zeros(nrows, dtype=dtype)
+
+ self._FITS.read_as_rec(self._ext+1, 1, nrows, array)
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(array)
+
+ for colnum, name in enumerate(array.dtype.names):
+ self._rescale_and_convert_field_inplace(
+ array,
+ name,
+ self._info['colinfo'][colnum]['tscale'],
+ self._info['colinfo'][colnum]['tzero'])
+
+ if self.lower or lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper or upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array, trim_strings=trim_strings)
+ return array
+
+ def read_column(self, col, rows=None, vstorage=None,
+ upper=False, lower=False, trim_strings=False, **keys):
+ """
+ Read the specified column
+
+ Alternatively, you can use slice notation
+
+ >>> fits=fitsio.FITS(filename)
+ >>> fits[ext][colname][:]
+ >>> fits[ext][colname][2:5]
+ >>> fits[ext][colname][200:235:2]
+ >>> fits[ext][colname][rows]
+
+ Note, if reading multiple columns, it is more efficient to use
+ read(columns=) or slice notation with a list of column names.
+
+ parameters
+ ----------
+ col: string/int, required
+ The column name or number.
+ rows: optional
+ An optional set of row numbers to read.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ res = self.read_columns(
+ [col], rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+ colname = res.dtype.names[0]
+ data = res[colname]
+
+ self._maybe_trim_strings(data, trim_strings=trim_strings)
+ return data
+
+ def read_rows(self, rows, vstorage=None,
+ upper=False, lower=False, trim_strings=False, **keys):
+ """
+ Read the specified rows.
+
+ parameters
+ ----------
+ rows: list,array
+ A list or array of row indices.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if rows is None:
+ # we actually want all rows!
+ return self._read_all()
+
+ if self._info['hdutype'] == ASCII_TBL:
+ return self.read(
+ rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ rows = self._extract_rows(rows)
+ dtype, offsets, isvar = self.get_rec_dtype(vstorage=vstorage)
+
+ w, = numpy.where(isvar == True) # noqa
+ if w.size > 0:
+ if vstorage is None:
+ _vstorage = self._vstorage
+ else:
+ _vstorage = vstorage
+ colnums = self._extract_colnums()
+ return self._read_rec_with_var(
+ colnums, rows, dtype, offsets, isvar, _vstorage)
+ else:
+ array = numpy.zeros(rows.size, dtype=dtype)
+ self._FITS.read_rows_as_rec(self._ext+1, array, rows)
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(array)
+
+ for colnum, name in enumerate(array.dtype.names):
+ self._rescale_and_convert_field_inplace(
+ array,
+ name,
+ self._info['colinfo'][colnum]['tscale'],
+ self._info['colinfo'][colnum]['tzero'])
+
+ if self.lower or lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper or upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array, trim_strings=trim_strings)
+
+ return array
+
+ def read_columns(self, columns, rows=None, vstorage=None,
+ upper=False, lower=False, trim_strings=False, **keys):
+ """
+ read a subset of columns from this binary table HDU
+
+ By default, all rows are read. Send rows= to select subsets of the
+ data. Table data are read into a recarray for multiple columns,
+ plain array for a single column.
+
+ parameters
+ ----------
+ columns: list/array
+ An optional set of columns to read from table HDUs. Can be string
+ or number. If a sequence, a recarray is always returned. If a
+ scalar, an ordinary array is returned.
+ rows: list/array, optional
+ An optional list of rows to read from table HDUS. Default is to
+ read all.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if self._info['hdutype'] == ASCII_TBL:
+ return self.read(
+ columns=columns, rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ # if columns is None, returns all. Guaranteed to be unique and sorted
+ colnums = self._extract_colnums(columns)
+ if isinstance(colnums, int):
+ # scalar sent, don't read as a recarray
+ return self.read_column(
+ columns,
+ rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ # if rows is None still returns None, and is correctly interpreted
+ # by the reader to mean all
+ rows = self._extract_rows(rows)
+
+ # this is the full dtype for all columns
+ dtype, offsets, isvar = self.get_rec_dtype(
+ colnums=colnums, vstorage=vstorage)
+
+ w, = numpy.where(isvar == True) # noqa
+ if w.size > 0:
+ if vstorage is None:
+ _vstorage = self._vstorage
+ else:
+ _vstorage = vstorage
+ array = self._read_rec_with_var(
+ colnums, rows, dtype, offsets, isvar, _vstorage)
+ else:
+
+ if rows is None:
+ nrows = self._info['nrows']
+ else:
+ nrows = rows.size
+ array = numpy.zeros(nrows, dtype=dtype)
+
+ colnumsp = colnums[:].copy()
+ colnumsp[:] += 1
+ self._FITS.read_columns_as_rec(self._ext+1, colnumsp, array, rows)
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(array)
+
+ for i in xrange(colnums.size):
+ colnum = int(colnums[i])
+ name = array.dtype.names[i]
+ self._rescale_and_convert_field_inplace(
+ array,
+ name,
+ self._info['colinfo'][colnum]['tscale'],
+ self._info['colinfo'][colnum]['tzero'])
+
+ if (self._check_tbit(colnums=colnums)):
+ array = self._fix_tbit_dtype(array, colnums)
+
+ if self.lower or lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper or upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array, trim_strings=trim_strings)
+
+ return array
+
+ def read_slice(self, firstrow, lastrow, step=1,
+ vstorage=None, lower=False, upper=False,
+ trim_strings=False, **keys):
+ """
+ Read the specified row slice from a table.
+
+ Read all rows between firstrow and lastrow (non-inclusive, as per
+ python slice notation). Note you must use slice notation for
+ images, e.g. f[ext][20:30, 40:50]
+
+ parameters
+ ----------
+ firstrow: integer
+ The first row to read
+ lastrow: integer
+ The last row to read, non-inclusive. This follows the python list
+ slice convention that one does not include the last element.
+ step: integer, optional
+ Step between rows, default 1. e.g., if step is 2, skip every other
+ row.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if self._info['hdutype'] == ASCII_TBL:
+ rows = numpy.arange(firstrow, lastrow, step, dtype='i8')
+ return self.read_ascii(
+ rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ if self._info['hdutype'] == IMAGE_HDU:
+ raise ValueError("slices currently only supported for tables")
+
+ maxrow = self._info['nrows']
+ if firstrow < 0 or lastrow > maxrow:
+ raise ValueError(
+ "slice must specify a sub-range of [%d,%d]" % (0, maxrow))
+
+ dtype, offsets, isvar = self.get_rec_dtype(vstorage=vstorage)
+
+ w, = numpy.where(isvar == True) # noqa
+ if w.size > 0:
+ if vstorage is None:
+ _vstorage = self._vstorage
+ else:
+ _vstorage = vstorage
+ rows = numpy.arange(firstrow, lastrow, step, dtype='i8')
+ colnums = self._extract_colnums()
+ array = self._read_rec_with_var(
+ colnums, rows, dtype, offsets, isvar, _vstorage)
+ else:
+ if step != 1:
+ rows = numpy.arange(firstrow, lastrow, step, dtype='i8')
+ array = self.read(rows=rows)
+ else:
+ # no +1 because lastrow is non-inclusive
+ nrows = lastrow - firstrow
+ array = numpy.zeros(nrows, dtype=dtype)
+
+ # only first needs to be +1. This is becuase the c code is
+ # inclusive
+ self._FITS.read_as_rec(self._ext+1, firstrow+1, lastrow, array)
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(
+ array)
+
+ for colnum, name in enumerate(array.dtype.names):
+ self._rescale_and_convert_field_inplace(
+ array,
+ name,
+ self._info['colinfo'][colnum]['tscale'],
+ self._info['colinfo'][colnum]['tzero'])
+
+ if self.lower or lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper or upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array, trim_strings=trim_strings)
+
+ return array
+
+ def get_rec_dtype(self, colnums=None, vstorage=None, **keys):
+ """
+ Get the dtype for the specified columns
+
+ parameters
+ ----------
+ colnums: integer array, optional
+ The column numbers, 0 offset
+ vstorage: string, optional
+ See docs in read_columns
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if vstorage is None:
+ _vstorage = self._vstorage
+ else:
+ _vstorage = vstorage
+
+ if colnums is None:
+ colnums = self._extract_colnums()
+
+ descr = []
+ isvararray = numpy.zeros(len(colnums), dtype=bool)
+ for i, colnum in enumerate(colnums):
+ dt, isvar = self.get_rec_column_descr(colnum, _vstorage)
+ descr.append(dt)
+ isvararray[i] = isvar
+ dtype = numpy.dtype(descr)
+
+ offsets = numpy.zeros(len(colnums), dtype='i8')
+ for i, n in enumerate(dtype.names):
+ offsets[i] = dtype.fields[n][1]
+ return dtype, offsets, isvararray
+
+ def _check_tbit(self, colnums=None, **keys):
+ """
+ Check if one of the columns is a TBIT column
+
+ parameters
+ ----------
+ colnums: integer array, optional
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if colnums is None:
+ colnums = self._extract_colnums()
+
+ has_tbit = False
+ for i, colnum in enumerate(colnums):
+ npy_type, isvar, istbit = self._get_tbl_numpy_dtype(colnum)
+ if (istbit):
+ has_tbit = True
+ break
+
+ return has_tbit
+
+ def _fix_tbit_dtype(self, array, colnums):
+ """
+ If necessary, patch up the TBIT to convert to bool array
+
+ parameters
+ ----------
+ array: record array
+ colnums: column numbers for lookup
+ """
+ descr = array.dtype.descr
+ for i, colnum in enumerate(colnums):
+ npy_type, isvar, istbit = self._get_tbl_numpy_dtype(colnum)
+ if (istbit):
+ coldescr = list(descr[i])
+ coldescr[1] = '?'
+ descr[i] = tuple(coldescr)
+
+ return array.view(descr)
+
+ def _get_simple_dtype_and_shape(self, colnum, rows=None):
+ """
+ When reading a single column, we want the basic data
+ type and the shape of the array.
+
+ for scalar columns, shape is just nrows, otherwise
+ it is (nrows, dim1, dim2)
+
+ Note if rows= is sent and only a single row is requested,
+ the shape will be (dim2,dim2)
+ """
+
+ # basic datatype
+ npy_type, isvar, istbit = self._get_tbl_numpy_dtype(colnum)
+ info = self._info['colinfo'][colnum]
+ name = info['name']
+
+ if rows is None:
+ nrows = self._info['nrows']
+ else:
+ nrows = rows.size
+
+ shape = None
+ tdim = info['tdim']
+
+ shape = _tdim2shape(tdim, name, is_string=(npy_type[0] == 'S'))
+ if shape is not None:
+ if nrows > 1:
+ if not isinstance(shape, tuple):
+ # vector
+ shape = (nrows, shape)
+ else:
+ # multi-dimensional
+ shape = tuple([nrows] + list(shape))
+ else:
+ # scalar
+ shape = nrows
+ return npy_type, shape
+
+ def get_rec_column_descr(self, colnum, vstorage):
+ """
+ Get a descriptor entry for the specified column.
+
+ parameters
+ ----------
+ colnum: integer
+ The column number, 0 offset
+ vstorage: string
+ See docs in read_columns
+ """
+ npy_type, isvar, istbit = self._get_tbl_numpy_dtype(colnum)
+ name = self._info['colinfo'][colnum]['name']
+
+ if isvar:
+ if vstorage == 'object':
+ descr = (name, 'O')
+ else:
+ tform = self._info['colinfo'][colnum]['tform']
+ max_size = _extract_vararray_max(tform)
+
+ if max_size <= 0:
+ name = self._info['colinfo'][colnum]['name']
+ mess = 'Will read as an object field'
+ if max_size < 0:
+ mess = "Column '%s': No maximum size: '%s'. %s"
+ mess = mess % (name, tform, mess)
+ warnings.warn(mess, FITSRuntimeWarning)
+ else:
+ mess = "Column '%s': Max size is zero: '%s'. %s"
+ mess = mess % (name, tform, mess)
+ warnings.warn(mess, FITSRuntimeWarning)
+
+ # we are forced to read this as an object array
+ return self.get_rec_column_descr(colnum, 'object')
+
+ if npy_type[0] == 'S':
+ # variable length string columns cannot
+ # themselves be arrays I don't think
+ npy_type = 'S%d' % max_size
+ descr = (name, npy_type)
+ elif npy_type[0] == 'U':
+ # variable length string columns cannot
+ # themselves be arrays I don't think
+ npy_type = 'U%d' % max_size
+ descr = (name, npy_type)
+ else:
+ descr = (name, npy_type, max_size)
+ else:
+ tdim = self._info['colinfo'][colnum]['tdim']
+ shape = _tdim2shape(
+ tdim, name,
+ is_string=(npy_type[0] == 'S' or npy_type[0] == 'U'))
+ if shape is not None:
+ descr = (name, npy_type, shape)
+ else:
+ descr = (name, npy_type)
+ return descr, isvar
+
+ def _read_rec_with_var(
+ self, colnums, rows, dtype, offsets, isvar, vstorage):
+ """
+ Read columns from a table into a rec array, including variable length
+ columns. This is special because, for efficiency, it involves reading
+ from the main table as normal but skipping the columns in the array
+ that are variable. Then reading the variable length columns, with
+ accounting for strides appropriately.
+
+ row and column numbers should be checked before calling this function
+ """
+
+ colnumsp = colnums+1
+ if rows is None:
+ nrows = self._info['nrows']
+ else:
+ nrows = rows.size
+ array = numpy.zeros(nrows, dtype=dtype)
+
+ # read from the main table first
+ wnotvar, = numpy.where(isvar == False) # noqa
+ if wnotvar.size > 0:
+ # this will be contiguous (not true for slices)
+ thesecol = colnumsp[wnotvar]
+ theseoff = offsets[wnotvar]
+ self._FITS.read_columns_as_rec_byoffset(self._ext+1,
+ thesecol,
+ theseoff,
+ array,
+ rows)
+ for i in xrange(thesecol.size):
+
+ name = array.dtype.names[wnotvar[i]]
+ colnum = thesecol[i]-1
+ self._rescale_and_convert_field_inplace(
+ array,
+ name,
+ self._info['colinfo'][colnum]['tscale'],
+ self._info['colinfo'][colnum]['tzero'])
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(array)
+
+ # now read the variable length arrays we may be able to speed this up
+ # by storing directly instead of reading first into a list
+ wvar, = numpy.where(isvar == True) # noqa
+ if wvar.size > 0:
+ # this will be contiguous (not true for slices)
+ thesecol = colnumsp[wvar]
+ for i in xrange(thesecol.size):
+ colnump = thesecol[i]
+ name = array.dtype.names[wvar[i]]
+ dlist = self._FITS.read_var_column_as_list(
+ self._ext+1, colnump, rows)
+
+ if (isinstance(dlist[0], str) or
+ (IS_PY3 and isinstance(dlist[0], bytes))):
+ is_string = True
+ else:
+ is_string = False
+
+ if array[name].dtype.descr[0][1][1] == 'O':
+ # storing in object array
+ # get references to each, no copy made
+ for irow, item in enumerate(dlist):
+ if IS_PY3 and isinstance(item, bytes):
+ item = item.decode('ascii')
+ array[name][irow] = item
+ else:
+ for irow, item in enumerate(dlist):
+ if IS_PY3 and isinstance(item, bytes):
+ item = item.decode('ascii')
+
+ if is_string:
+ array[name][irow] = item
+ else:
+ ncopy = len(item)
+
+ if IS_PY3:
+ ts = array[name].dtype.descr[0][1][1]
+ if ts != 'S' and ts != 'U':
+ array[name][irow][0:ncopy] = item[:]
+ else:
+ array[name][irow] = item
+ else:
+ array[name][irow][0:ncopy] = item[:]
+
+ return array
+
+ def _extract_rows(self, rows):
+ """
+ Extract an array of rows from an input scalar or sequence
+ """
+ if rows is not None:
+ rows = numpy.array(rows, ndmin=1, copy=False, dtype='i8')
+ # returns unique, sorted
+ rows = numpy.unique(rows)
+
+ maxrow = self._info['nrows']-1
+ if len(rows) > 0 and (rows[0] < 0 or rows[-1] > maxrow):
+ raise ValueError("rows must be in [%d,%d]" % (0, maxrow))
+ return rows
+
+ def _process_slice(self, arg):
+ """
+ process the input slice for use calling the C code
+ """
+ start = arg.start
+ stop = arg.stop
+ step = arg.step
+
+ nrows = self._info['nrows']
+ if step is None:
+ step = 1
+ if start is None:
+ start = 0
+ if stop is None:
+ stop = nrows
+
+ if start < 0:
+ start = nrows + start
+ if start < 0:
+ raise IndexError("Index out of bounds")
+
+ if stop < 0:
+ stop = nrows + start + 1
+
+ if stop < start:
+ # will return an empty struct
+ stop = start
+
+ if stop > nrows:
+ stop = nrows
+ return slice(start, stop, step)
+
+ def _slice2rows(self, start, stop, step=None):
+ """
+ Convert a slice to an explicit array of rows
+ """
+ nrows = self._info['nrows']
+ if start is None:
+ start = 0
+ if stop is None:
+ stop = nrows
+ if step is None:
+ step = 1
+
+ tstart = self._fix_range(start)
+ tstop = self._fix_range(stop)
+ if tstart == 0 and tstop == nrows and step is None:
+ # this is faster: if all fields are also requested, then a
+ # single fread will be done
+ return None
+ if stop < start:
+ raise ValueError("start is greater than stop in slice")
+ return numpy.arange(tstart, tstop, step, dtype='i8')
+
+ def _fix_range(self, num, isslice=True):
+ """
+ Ensure the input is within range.
+
+ If el=True, then don't treat as a slice element
+ """
+
+ nrows = self._info['nrows']
+ if isslice:
+ # include the end
+ if num < 0:
+ num = nrows + (1+num)
+ elif num > nrows:
+ num = nrows
+ else:
+ # single element
+ if num < 0:
+ num = nrows + num
+ elif num > (nrows-1):
+ num = nrows-1
+
+ return num
+
+ def _rescale_and_convert_field_inplace(self, array, name, scale, zero):
+ """
+ Apply fits scalings. Also, convert bool to proper
+ numpy boolean values
+ """
+ self._rescale_array(array[name], scale, zero)
+ if array[name].dtype == bool:
+ array[name] = self._convert_bool_array(array[name])
+ return array
+
+ def _rescale_and_convert(self, array, scale, zero, name=None):
+ """
+ Apply fits scalings. Also, convert bool to proper
+ numpy boolean values
+ """
+ self._rescale_array(array, scale, zero)
+ if array.dtype == bool:
+ array = self._convert_bool_array(array)
+
+ return array
+
+ def _rescale_array(self, array, scale, zero):
+ """
+ Scale the input array
+ """
+ if scale != 1.0:
+ sval = numpy.array(scale, dtype=array.dtype)
+ array *= sval
+ if zero != 0.0:
+ zval = numpy.array(zero, dtype=array.dtype)
+ array += zval
+
+ def _maybe_trim_strings(self, array, trim_strings=False, **keys):
+ """
+ if requested, trim trailing white space from
+ all string fields in the input array
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if self.trim_strings or trim_strings:
+ _trim_strings(array)
+
+ def _maybe_decode_fits_ascii_strings_to_unicode_py3(self, array):
+ if IS_PY3:
+ do_conversion = False
+ new_dt = []
+ for _dt in array.dtype.descr:
+ if 'S' in _dt[1]:
+ do_conversion = True
+ if len(_dt) == 3:
+ new_dt.append((
+ _dt[0],
+ _dt[1].replace('S', 'U').replace('|', ''),
+ _dt[2]))
+ else:
+ new_dt.append((
+ _dt[0],
+ _dt[1].replace('S', 'U').replace('|', '')))
+ else:
+ new_dt.append(_dt)
+ if do_conversion:
+ array = array.astype(new_dt, copy=False)
+ return array
+
+ def _convert_bool_array(self, array):
+ """
+ cfitsio reads as characters 'T' and 'F' -- convert to real boolean
+ If input is a fits bool, convert to numpy boolean
+ """
+
+ output = (array.view(numpy.int8) == ord('T')).astype(bool)
+ return output
+
+ def _get_tbl_numpy_dtype(self, colnum, include_endianness=True):
+ """
+ Get numpy type for the input column
+ """
+ table_type = self._info['hdutype']
+ table_type_string = _hdu_type_map[table_type]
+ try:
+ ftype = self._info['colinfo'][colnum]['eqtype']
+ if table_type == ASCII_TBL:
+ npy_type = _table_fits2npy_ascii[abs(ftype)]
+ else:
+ npy_type = _table_fits2npy[abs(ftype)]
+ except KeyError:
+ raise KeyError("unsupported %s fits data "
+ "type: %d" % (table_type_string, ftype))
+
+ istbit = False
+ if (ftype == 1):
+ istbit = True
+
+ isvar = False
+ if ftype < 0:
+ isvar = True
+ if include_endianness:
+ # if binary we will read the big endian bytes directly,
+ # if ascii we read into native byte order
+ if table_type == ASCII_TBL:
+ addstr = ''
+ else:
+ addstr = '>'
+ if npy_type not in ['u1', 'i1', 'S', 'U']:
+ npy_type = addstr+npy_type
+
+ if npy_type == 'S':
+ width = self._info['colinfo'][colnum]['width']
+ npy_type = 'S%d' % width
+ elif npy_type == 'U':
+ width = self._info['colinfo'][colnum]['width']
+ npy_type = 'U%d' % width
+
+ return npy_type, isvar, istbit
+
+ def _process_args_as_rows_or_columns(self, arg, unpack=False):
+ """
+ We must be able to interpret the args as as either a column name or
+ row number, or sequences thereof. Numpy arrays and slices are also
+ fine.
+
+ Examples:
+ 'field'
+ 35
+ [35,55,86]
+ ['f1',f2',...]
+ Can also be tuples or arrays.
+ """
+
+ flags = set()
+ #
+ if isinstance(arg, (tuple, list, numpy.ndarray)):
+ # a sequence was entered
+ if isstring(arg[0]):
+ result = arg
+ else:
+ result = arg
+ flags.add('isrows')
+ elif isstring(arg):
+ # a single string was entered
+ result = arg
+ elif isinstance(arg, slice):
+ if unpack:
+ flags.add('isrows')
+ result = self._slice2rows(arg.start, arg.stop, arg.step)
+ else:
+ flags.add('isrows')
+ flags.add('isslice')
+ result = self._process_slice(arg)
+ else:
+ # a single object was entered.
+ # Probably should apply some more checking on this
+ result = arg
+ flags.add('isrows')
+ if numpy.ndim(arg) == 0:
+ flags.add('isscalar')
+
+ return result, flags
+
+ def _read_var_column(self, colnum, rows, vstorage):
+ """
+
+ first read as a list of arrays, then copy into either a fixed length
+ array or an array of objects, depending on vstorage.
+
+ """
+
+ if IS_PY3:
+ stype = bytes
+ else:
+ stype = str
+
+ dlist = self._FITS.read_var_column_as_list(self._ext+1, colnum+1, rows)
+
+ if vstorage == 'fixed':
+ tform = self._info['colinfo'][colnum]['tform']
+ max_size = _extract_vararray_max(tform)
+
+ if max_size <= 0:
+ name = self._info['colinfo'][colnum]['name']
+ mess = 'Will read as an object field'
+ if max_size < 0:
+ mess = "Column '%s': No maximum size: '%s'. %s"
+ mess = mess % (name, tform, mess)
+ warnings.warn(mess, FITSRuntimeWarning)
+ else:
+ mess = "Column '%s': Max size is zero: '%s'. %s"
+ mess = mess % (name, tform, mess)
+ warnings.warn(mess, FITSRuntimeWarning)
+
+ # we are forced to read this as an object array
+ return self._read_var_column(colnum, rows, 'object')
+
+ if isinstance(dlist[0], stype):
+ descr = 'S%d' % max_size
+ array = numpy.fromiter(dlist, descr)
+ if IS_PY3:
+ array = array.astype('U', copy=False)
+ else:
+ descr = dlist[0].dtype.str
+ array = numpy.zeros((len(dlist), max_size), dtype=descr)
+
+ for irow, item in enumerate(dlist):
+ ncopy = len(item)
+ array[irow, 0:ncopy] = item[:]
+ else:
+ array = numpy.zeros(len(dlist), dtype='O')
+ for irow, item in enumerate(dlist):
+ if IS_PY3 and isinstance(item, bytes):
+ item = item.decode('ascii')
+ array[irow] = item
+
+ return array
+
+ def _extract_colnums(self, columns=None):
+ """
+ Extract an array of columns from the input
+ """
+ if columns is None:
+ return numpy.arange(self._ncol, dtype='i8')
+
+ if not isinstance(columns, (tuple, list, numpy.ndarray)):
+ # is a scalar
+ return self._extract_colnum(columns)
+
+ colnums = numpy.zeros(len(columns), dtype='i8')
+ for i in xrange(colnums.size):
+ colnums[i] = self._extract_colnum(columns[i])
+
+ # returns unique sorted
+ colnums = numpy.unique(colnums)
+ return colnums
+
+ def _extract_colnum(self, col):
+ """
+ Get the column number for the input column
+ """
+ if isinteger(col):
+ colnum = col
+
+ if (colnum < 0) or (colnum > (self._ncol-1)):
+ raise ValueError(
+ "column number should be in [0,%d]" % (0, self._ncol-1))
+ else:
+ colstr = mks(col)
+ try:
+ if self.case_sensitive:
+ mess = "column name '%s' not found (case sensitive)" % col
+ colnum = self._colnames.index(colstr)
+ else:
+ mess \
+ = "column name '%s' not found (case insensitive)" % col
+ colnum = self._colnames_lower.index(colstr.lower())
+ except ValueError:
+ raise ValueError(mess)
+ return int(colnum)
+
+ def _update_info(self):
+ """
+ Call parent method and make sure this is in fact a
+ table HDU. Set some convenience data.
+ """
+ super(TableHDU, self)._update_info()
+ if self._info['hdutype'] == IMAGE_HDU:
+ mess = "Extension %s is not a Table HDU" % self.ext
+ raise ValueError(mess)
+ if 'colinfo' in self._info:
+ self._colnames = [i['name'] for i in self._info['colinfo']]
+ self._colnames_lower = [
+ i['name'].lower() for i in self._info['colinfo']]
+ self._ncol = len(self._colnames)
+
+ def __getitem__(self, arg):
+ """
+ Get data from a table using python [] notation.
+
+ You can use [] to extract column and row subsets, or read everything.
+ The notation is essentially the same as numpy [] notation, except that
+ a sequence of column names may also be given. Examples reading from
+ "filename", extension "ext"
+
+ fits=fitsio.FITS(filename)
+ fits[ext][:]
+ fits[ext][2] # returns a scalar
+ fits[ext][2:5]
+ fits[ext][200:235:2]
+ fits[ext][rows]
+ fits[ext][cols][rows]
+
+ Note data are only read once the rows are specified.
+
+ Note you can only read variable length arrays the default way,
+ using this function, so set it as you want on construction.
+
+ This function is used for ascii tables as well
+ """
+
+ res, flags = \
+ self._process_args_as_rows_or_columns(arg)
+
+ if 'isrows' in flags:
+ # rows were entered: read all columns
+ if 'isslice' in flags:
+ array = self.read_slice(res.start, res.stop, res.step)
+ else:
+ # will also get here if slice is entered but this
+ # is an ascii table
+ array = self.read(rows=res)
+ else:
+ return TableColumnSubset(self, res)
+
+ if self.lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array)
+
+ if 'isscalar' in flags:
+ assert array.shape[0] == 1
+ array = array[0]
+ return array
+
+ def __iter__(self):
+ """
+ Get an iterator for a table
+
+ e.g.
+ f=fitsio.FITS(fname)
+ hdu1 = f[1]
+ for row in hdu1:
+ ...
+ """
+
+ # always start with first row
+ self._iter_row = 0
+
+ # for iterating we must assume the number of rows will not change
+ self._iter_nrows = self.get_nrows()
+
+ self._buffer_iter_rows(0)
+ return self
+
+ def next(self):
+ """
+ get the next row when iterating
+
+ e.g.
+ f=fitsio.FITS(fname)
+ hdu1 = f[1]
+ for row in hdu1:
+ ...
+
+ By default read one row at a time. Send iter_row_buffer to get a more
+ efficient buffering.
+ """
+ return self._get_next_buffered_row()
+
+ __next__ = next
+
+ def _get_next_buffered_row(self):
+ """
+ Get the next row for iteration.
+ """
+ if self._iter_row == self._iter_nrows:
+ raise StopIteration
+
+ if self._row_buffer_index >= self._iter_row_buffer:
+ self._buffer_iter_rows(self._iter_row)
+
+ data = self._row_buffer[self._row_buffer_index]
+ self._iter_row += 1
+ self._row_buffer_index += 1
+ return data
+
+ def _buffer_iter_rows(self, start):
+ """
+ Read in the buffer for iteration
+ """
+ self._row_buffer = self[start:start+self._iter_row_buffer]
+
+ # start back at the front of the buffer
+ self._row_buffer_index = 0
+
+ def __repr__(self):
+ """
+ textual representation for some metadata
+ """
+ text, spacing = self._get_repr_list()
+
+ text.append('%srows: %d' % (spacing, self._info['nrows']))
+ text.append('%scolumn info:' % spacing)
+
+ cspacing = ' '*4
+ nspace = 4
+ nname = 15
+ ntype = 6
+ format = cspacing + "%-" + str(nname) + "s %" + str(ntype) + "s %s"
+ pformat = (
+ cspacing + "%-" +
+ str(nname) + "s\n %" +
+ str(nspace+nname+ntype) + "s %s")
+
+ for colnum, c in enumerate(self._info['colinfo']):
+ if len(c['name']) > nname:
+ f = pformat
+ else:
+ f = format
+
+ dt, isvar, istbit = self._get_tbl_numpy_dtype(
+ colnum, include_endianness=False)
+ if isvar:
+ tform = self._info['colinfo'][colnum]['tform']
+ if dt[0] == 'S':
+ dt = 'S0'
+ dimstr = 'vstring[%d]' % _extract_vararray_max(tform)
+ else:
+ dimstr = 'varray[%s]' % _extract_vararray_max(tform)
+ else:
+ if dt[0] == 'S':
+ is_string = True
+ else:
+ is_string = False
+ dimstr = _get_col_dimstr(c['tdim'], is_string=is_string)
+
+ s = f % (c['name'], dt, dimstr)
+ text.append(s)
+
+ text = '\n'.join(text)
+ return text
+
+
+class AsciiTableHDU(TableHDU):
+ def read(self, rows=None, columns=None, vstorage=None,
+ upper=False, lower=False, trim_strings=False, **keys):
+ """
+ read a data from an ascii table HDU
+
+ By default, all rows are read. Send rows= to select subsets of the
+ data. Table data are read into a recarray for multiple columns,
+ plain array for a single column.
+
+ parameters
+ ----------
+ columns: list/array
+ An optional set of columns to read from table HDUs. Can be string
+ or number. If a sequence, a recarray is always returned. If a
+ scalar, an ordinary array is returned.
+ rows: list/array, optional
+ An optional list of rows to read from table HDUS. Default is to
+ read all.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ # if columns is None, returns all. Guaranteed to be unique and sorted
+ colnums = self._extract_colnums(columns)
+ if isinstance(colnums, int):
+ # scalar sent, don't read as a recarray
+ return self.read_column(
+ columns, rows=rows, vstorage=vstorage,
+ upper=upper, lower=lower, trim_strings=trim_strings)
+
+ rows = self._extract_rows(rows)
+ if rows is None:
+ nrows = self._info['nrows']
+ else:
+ nrows = rows.size
+
+ # if rows is None still returns None, and is correctly interpreted
+ # by the reader to mean all
+ rows = self._extract_rows(rows)
+
+ # this is the full dtype for all columns
+ dtype, offsets, isvar = self.get_rec_dtype(
+ colnums=colnums, vstorage=vstorage)
+ array = numpy.zeros(nrows, dtype=dtype)
+
+ # note reading into existing data
+ wnotvar, = numpy.where(isvar == False) # noqa
+ if wnotvar.size > 0:
+ for i in wnotvar:
+ colnum = colnums[i]
+ name = array.dtype.names[i]
+ a = array[name].copy()
+ self._FITS.read_column(self._ext+1, colnum+1, a, rows)
+ array[name] = a
+ del a
+
+ array = self._maybe_decode_fits_ascii_strings_to_unicode_py3(array)
+
+ wvar, = numpy.where(isvar == True) # noqa
+ if wvar.size > 0:
+ for i in wvar:
+ colnum = colnums[i]
+ name = array.dtype.names[i]
+ dlist = self._FITS.read_var_column_as_list(
+ self._ext+1, colnum+1, rows)
+ if (isinstance(dlist[0], str) or
+ (IS_PY3 and isinstance(dlist[0], bytes))):
+ is_string = True
+ else:
+ is_string = False
+
+ if array[name].dtype.descr[0][1][1] == 'O':
+ # storing in object array
+ # get references to each, no copy made
+ for irow, item in enumerate(dlist):
+ if IS_PY3 and isinstance(item, bytes):
+ item = item.decode('ascii')
+ array[name][irow] = item
+ else:
+ for irow, item in enumerate(dlist):
+ if IS_PY3 and isinstance(item, bytes):
+ item = item.decode('ascii')
+ if is_string:
+ array[name][irow] = item
+ else:
+ ncopy = len(item)
+ array[name][irow][0:ncopy] = item[:]
+
+ if self.lower or lower:
+ _names_to_lower_if_recarray(array)
+ elif self.upper or upper:
+ _names_to_upper_if_recarray(array)
+
+ self._maybe_trim_strings(array, trim_strings=trim_strings)
+
+ return array
+
+ read_ascii = read
+
+
+class TableColumnSubset(object):
+ """
+
+ A class representing a subset of the the columns on disk. When called
+ with .read() or [ rows ] the data are read from disk.
+
+ Useful because subsets can be passed around to functions, or chained
+ with a row selection.
+
+ This class is returned when using [ ] notation to specify fields in a
+ TableHDU class
+
+ fits = fitsio.FITS(fname)
+ colsub = fits[ext][field_list]
+
+ returns a TableColumnSubset object. To read rows:
+
+ data = fits[ext][field_list][row_list]
+
+ colsub = fits[ext][field_list]
+ data = colsub[row_list]
+ data = colsub.read(rows=row_list)
+
+ to read all, use .read() with no args or [:]
+ """
+
+ def __init__(self, fitshdu, columns):
+ """
+ Input is the FITS instance and a list of column names.
+ """
+
+ self.columns = columns
+ if isstring(columns) or isinteger(columns):
+ # this is to check if it exists
+ self.colnums = [fitshdu._extract_colnum(columns)]
+
+ self.is_scalar = True
+ self.columns_list = [columns]
+ else:
+ # this is to check if it exists
+ self.colnums = fitshdu._extract_colnums(columns)
+
+ self.is_scalar = False
+ self.columns_list = columns
+
+ self.fitshdu = fitshdu
+
+ def read(self, columns=None, rows=None, vstorage=None, lower=False,
+ upper=False, trim_strings=False, **keys):
+ """
+ Read the data from disk and return as a numpy array
+
+ parameters
+ ----------
+ columns: list/array, optional
+ An optional set of columns to read from table HDUs. Can be string
+ or number. If a sequence, a recarray is always returned. If a
+ scalar, an ordinary array is returned.
+ rows: optional
+ An optional list of rows to read from table HDUS. Default is to
+ read all.
+ vstorage: string, optional
+ Over-ride the default method to store variable length columns. Can
+ be 'fixed' or 'object'. See docs on fitsio.FITS for details.
+ lower: bool, optional
+ If True, force all columns names to lower case in output. Will over
+ ride the lower= keyword from construction.
+ upper: bool, optional
+ If True, force all columns names to upper case in output. Will over
+ ride the lower= keyword from construction.
+ trim_strings: bool, optional
+ If True, trim trailing spaces from strings. Will over-ride the
+ trim_strings= keyword from constructor.
+ """
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if self.is_scalar:
+ data = self.fitshdu.read_column(
+ self.columns,
+ rows=rows, vstorage=vstorage, lower=lower, upper=upper,
+ trim_strings=trim_strings)
+ else:
+ if columns is None:
+ c = self.columns
+ else:
+ c = columns
+ data = self.fitshdu.read(
+ columns=c,
+ rows=rows, vstorage=vstorage, lower=lower, upper=upper,
+ trim_strings=trim_strings)
+
+ return data
+
+ def __getitem__(self, arg):
+ """
+ If columns are sent, then the columns will just get reset and
+ we'll return a new object
+
+ If rows are sent, they are read and the result returned.
+ """
+
+ # we have to unpack the rows if we are reading a subset
+ # of the columns because our slice operator only works
+ # on whole rows. We could allow rows= keyword to
+ # be a slice...
+
+ res, flags = \
+ self.fitshdu._process_args_as_rows_or_columns(arg, unpack=True)
+ if 'isrows' in flags:
+ # rows was entered: read all current column subset
+ array = self.read(rows=res)
+ if 'isscalar' in flags:
+ assert array.shape[0] == 1
+ array = array[0]
+ return array
+ else:
+ # columns was entered. Return a subset objects
+ return TableColumnSubset(self.fitshdu, columns=res)
+
+ def __repr__(self):
+ """
+ Representation for TableColumnSubset
+ """
+ spacing = ' '*2
+ cspacing = ' '*4
+
+ hdu = self.fitshdu
+ info = self.fitshdu._info
+ colinfo = info['colinfo']
+
+ text = []
+ text.append("%sfile: %s" % (spacing, hdu._filename))
+ text.append("%sextension: %d" % (spacing, info['hdunum']-1))
+ text.append("%stype: %s" % (spacing, _hdu_type_map[info['hdutype']]))
+ text.append('%srows: %d' % (spacing, info['nrows']))
+ text.append("%scolumn subset:" % spacing)
+
+ cspacing = ' '*4
+ nspace = 4
+ nname = 15
+ ntype = 6
+ format = cspacing + "%-" + str(nname) + "s %" + str(ntype) + "s %s"
+ pformat = (
+ cspacing + "%-" + str(nname) + "s\n %" +
+ str(nspace+nname+ntype) + "s %s")
+
+ for colnum in self.colnums:
+ cinfo = colinfo[colnum]
+
+ if len(cinfo['name']) > nname:
+ f = pformat
+ else:
+ f = format
+
+ dt, isvar, istbit = hdu._get_tbl_numpy_dtype(
+ colnum, include_endianness=False)
+ if isvar:
+ tform = cinfo['tform']
+ if dt[0] == 'S':
+ dt = 'S0'
+ dimstr = 'vstring[%d]' % _extract_vararray_max(tform)
+ else:
+ dimstr = 'varray[%s]' % _extract_vararray_max(tform)
+ else:
+ dimstr = _get_col_dimstr(cinfo['tdim'])
+
+ s = f % (cinfo['name'], dt, dimstr)
+ text.append(s)
+
+ s = "\n".join(text)
+ return s
+
+
+def _tdim2shape(tdim, name, is_string=False):
+ shape = None
+ if tdim is None:
+ raise ValueError("field '%s' has malformed TDIM" % name)
+
+ if len(tdim) > 1 or tdim[0] > 1:
+ if is_string:
+ shape = list(reversed(tdim[1:]))
+ else:
+ shape = list(reversed(tdim))
+
+ if len(shape) == 1:
+ shape = shape[0]
+ else:
+ shape = tuple(shape)
+
+ return shape
+
+
+def _names_to_lower_if_recarray(data):
+ if data.dtype.names is not None:
+ data.dtype.names = [n.lower() for n in data.dtype.names]
+
+
+def _names_to_upper_if_recarray(data):
+ if data.dtype.names is not None:
+ data.dtype.names = [n.upper() for n in data.dtype.names]
+
+
+def _trim_strings(data):
+ names = data.dtype.names
+ if names is not None:
+ # run through each field separately
+ for n in names:
+ if data[n].dtype.descr[0][1][1] in ['S', 'U']:
+ data[n] = numpy.char.rstrip(data[n])
+ else:
+ if data.dtype.descr[0][1][1] in ['S', 'U']:
+ data[:] = numpy.char.rstrip(data[:])
+
+
+def _extract_vararray_max(tform):
+ """
+ Extract number from PX(number)
+ """
+ first = tform.find('(')
+ last = tform.rfind(')')
+
+ if first == -1 or last == -1:
+ # no max length specified
+ return -1
+
+ maxnum = int(tform[first+1:last])
+ return maxnum
+
+
+def _get_col_dimstr(tdim, is_string=False):
+ """
+ not for variable length
+ """
+ dimstr = ''
+ if tdim is None:
+ dimstr = 'array[bad TDIM]'
+ else:
+ if is_string:
+ if len(tdim) > 1:
+ dimstr = [str(d) for d in tdim[1:]]
+ else:
+ if len(tdim) > 1 or tdim[0] > 1:
+ dimstr = [str(d) for d in tdim]
+ if dimstr != '':
+ dimstr = ','.join(dimstr)
+ dimstr = 'array[%s]' % dimstr
+
+ return dimstr
+
+
+# no support yet for complex
+# all strings are read as bytes for python3 and then decoded to unicode
+_table_fits2npy = {1: 'i1',
+ 11: 'u1',
+ 12: 'i1',
+ # logical. Note pyfits uses this for i1,
+ # cfitsio casts to char*
+ 14: 'b1',
+ 16: 'S',
+ 20: 'u2',
+ 21: 'i2',
+ 30: 'u4', # 30=TUINT
+ 31: 'i4', # 31=TINT
+ 40: 'u4', # 40=TULONG
+ 41: 'i4', # 41=TLONG
+ 42: 'f4',
+ 81: 'i8',
+ 82: 'f8',
+ 83: 'c8', # TCOMPLEX
+ 163: 'c16'} # TDBLCOMPLEX
+
+# cfitsio returns only types f8, i4 and strings for column types. in order to
+# avoid data loss, we always use i8 for integer types
+# all strings are read as bytes for python3 and then decoded to unicode
+_table_fits2npy_ascii = {16: 'S',
+ 31: 'i8', # listed as TINT, reading as i8
+ 41: 'i8', # listed as TLONG, reading as i8
+ 81: 'i8',
+ 21: 'i4', # listed as TSHORT, reading as i4
+ 42: 'f8', # listed as TFLOAT, reading as f8
+ 82: 'f8'}
+
+# for TFORM
+_table_npy2fits_form = {'b1': 'L',
+ 'u1': 'B',
+ 'i1': 'S', # gets converted to unsigned
+ 'S': 'A',
+ 'U': 'A',
+ 'u2': 'U', # gets converted to signed
+ 'i2': 'I',
+ 'u4': 'V', # gets converted to signed
+ 'i4': 'J',
+ 'i8': 'K',
+ 'f4': 'E',
+ 'f8': 'D',
+ 'c8': 'C',
+ 'c16': 'M'}
+
+# from mrdfits; note G gets turned into E
+# types= ['A', 'I', 'L', 'B', 'F', 'D', 'C', 'M', 'K']
+# formats=['A1', 'I6', 'I10', 'I4', 'G15.9','G23.17', 'G15.9', 'G23.17',
+# 'I20']
+
+_table_npy2fits_form_ascii = {'S': 'A1', # Need to add max here
+ 'U': 'A1', # Need to add max here
+ 'i2': 'I7', # I
+ 'i4': 'I12', # ??
+ # 'i8':'I21', # K # i8 aren't supported
+ # 'f4':'E15.7', # F
+ # F We must write as f8 since we can only
+ # read as f8
+ 'f4': 'E26.17',
+ # D 25.16 looks right, but this is recommended
+ 'f8': 'E26.17'}
+
+
+def _npy2fits(d, table_type='binary', write_bitcols=False):
+ """
+ d is the full element from the descr
+ """
+ npy_dtype = d[1][1:]
+ if npy_dtype[0] == 'S' or npy_dtype[0] == 'U':
+ name, form, dim = _npy_string2fits(d, table_type=table_type)
+ else:
+ name, form, dim = _npy_num2fits(
+ d, table_type=table_type, write_bitcols=write_bitcols)
+
+ return name, form, dim
+
+
+def _npy_num2fits(d, table_type='binary', write_bitcols=False):
+ """
+ d is the full element from the descr
+
+ For vector,array columns the form is the total counts
+ followed by the code.
+
+ For array columns with dimension greater than 1, the dim is set to
+ (dim1, dim2, ...)
+ So it is treated like an extra dimension
+
+ """
+
+ dim = None
+
+ name = d[0]
+
+ npy_dtype = d[1][1:]
+ if npy_dtype[0] == 'S' or npy_dtype[0] == 'U':
+ raise ValueError("got S or U type: use _npy_string2fits")
+
+ if npy_dtype not in _table_npy2fits_form:
+ raise ValueError("unsupported type '%s'" % npy_dtype)
+
+ if table_type == 'binary':
+ form = _table_npy2fits_form[npy_dtype]
+ else:
+ form = _table_npy2fits_form_ascii[npy_dtype]
+
+ # now the dimensions
+ if len(d) > 2:
+ if table_type == 'ascii':
+ raise ValueError(
+ "Ascii table columns must be scalar, got %s" % str(d))
+
+ if write_bitcols and npy_dtype == 'b1':
+ # multi-dimensional boolean
+ form = 'X'
+
+ # Note, depending on numpy version, even 1-d can be a tuple
+ if isinstance(d[2], tuple):
+ count = reduce(lambda x, y: x*y, d[2])
+ form = '%d%s' % (count, form)
+
+ if len(d[2]) > 1:
+ # this is multi-dimensional array column. the form
+ # should be total elements followed by A
+ dim = list(reversed(d[2]))
+ dim = [str(e) for e in dim]
+ dim = '(' + ','.join(dim)+')'
+ else:
+ # this is a vector (1d array) column
+ count = d[2]
+ form = '%d%s' % (count, form)
+
+ return name, form, dim
+
+
+def _npy_string2fits(d, table_type='binary'):
+ """
+ d is the full element from the descr
+
+ form for strings is the total number of bytes followed by A. Thus
+ for vector or array columns it is the size of the string times the
+ total number of elements in the array.
+
+ Then the dim is set to
+ (sizeofeachstring, dim1, dim2, ...)
+ So it is treated like an extra dimension
+
+ """
+
+ dim = None
+
+ name = d[0]
+
+ npy_dtype = d[1][1:]
+ if npy_dtype[0] != 'S' and npy_dtype[0] != 'U':
+ raise ValueError("expected S or U type, got %s" % npy_dtype[0])
+
+ # get the size of each string
+ string_size_str = npy_dtype[1:]
+ string_size = int(string_size_str)
+
+ if string_size <= 0:
+ raise ValueError('string sizes must be > 0, '
+ 'got %s for field %s' % (npy_dtype, name))
+
+ # now the dimensions
+ if len(d) == 2:
+ if table_type == 'ascii':
+ form = 'A'+string_size_str
+ else:
+ form = string_size_str+'A'
+ else:
+ if table_type == 'ascii':
+ raise ValueError(
+ "Ascii table columns must be scalar, got %s" % str(d))
+ if isinstance(d[2], tuple):
+ # this is an array column. the form
+ # should be total elements followed by A
+ # count = 1
+ # count = [count*el for el in d[2]]
+ count = reduce(lambda x, y: x*y, d[2])
+ count = string_size*count
+ form = '%dA' % count
+
+ # will have to do tests to see if this is the right order
+ dim = list(reversed(d[2]))
+ # dim = d[2]
+ dim = [string_size_str] + [str(e) for e in dim]
+ dim = '(' + ','.join(dim)+')'
+ else:
+ # this is a vector (1d array) column
+ count = string_size*d[2]
+ form = '%dA' % count
+
+ # will have to do tests to see if this is the right order
+ dim = [string_size_str, str(d[2])]
+ dim = '(' + ','.join(dim)+')'
+
+ return name, form, dim
--- /dev/null
+"""
+header classes for fitslib, part of the fitsio package.
+
+See the main docs at https://github.com/esheldon/fitsio
+
+ Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+"""
+from __future__ import with_statement, print_function
+import warnings
+
+from . import _fitsio_wrap
+from .util import isstring, FITSRuntimeWarning, IS_PY3
+
+# for python3 compat
+if IS_PY3:
+ xrange = range
+
+TYP_STRUC_KEY = 10
+TYP_CMPRS_KEY = 20
+TYP_SCAL_KEY = 30
+TYP_NULL_KEY = 40
+TYP_DIM_KEY = 50
+TYP_RANG_KEY = 60
+TYP_UNIT_KEY = 70
+TYP_DISP_KEY = 80
+TYP_HDUID_KEY = 90
+TYP_CKSUM_KEY = 100
+TYP_WCS_KEY = 110
+TYP_REFSYS_KEY = 120
+TYP_COMM_KEY = 130
+TYP_CONT_KEY = 140
+TYP_USER_KEY = 150
+
+
+class FITSHDR(object):
+ """
+ A class representing a FITS header.
+
+ parameters
+ ----------
+ record_list: optional
+ A list of dicts, or dict, or another FITSHDR
+ - list of dictionaries containing 'name','value' and optionally
+ a 'comment' field; the order is preserved.
+ - a dictionary of keyword-value pairs; no comments are written
+ in this case, and the order is arbitrary.
+ - another FITSHDR object; the order is preserved.
+
+ examples:
+
+ hdr=FITSHDR()
+
+ # set a simple value
+ hdr['blah'] = 35
+
+ # set from a dict to include a comment.
+ rec={'name':'fromdict', 'value':3, 'comment':'my comment'}
+ hdr.add_record(rec)
+
+ # can do the same with a full FITSRecord
+ rec=FITSRecord( {'name':'temp', 'value':35, 'comment':'temp in C'} )
+ hdr.add_record(rec)
+
+ # in the above, the record is replaced if one with the same name
+ # exists, except for COMMENT and HISTORY, which can exist as
+ # duplicates
+
+ # print the header
+ print(hdr)
+
+ # print a single record
+ print(hdr['fromdict'])
+
+
+ # can also set from a card
+ hdr.add_record('test = 77')
+ # using a FITSRecord object (internally uses FITSCard)
+ card=FITSRecord('test = 77')
+ hdr.add_record(card)
+
+ # can also construct with a record list
+ recs=[{'name':'test', 'value':35, 'comment':'a comment'},
+ {'name':'blah', 'value':'some string'}]
+ hdr=FITSHDR(recs)
+
+ # if you have no comments, you can construct with a simple dict
+ recs={'day':'saturday',
+ 'telescope':'blanco'}
+ hdr=FITSHDR(recs)
+
+ """
+ def __init__(self, record_list=None):
+
+ self._record_list = []
+ self._record_map = {}
+ self._index_map = {}
+
+ if isinstance(record_list, FITSHDR):
+ for r in record_list.records():
+ self.add_record(r)
+ elif isinstance(record_list, dict):
+ for k in record_list:
+ r = {'name': k, 'value': record_list[k]}
+ self.add_record(r)
+ elif isinstance(record_list, list):
+ for r in record_list:
+ self.add_record(r)
+ elif record_list is not None:
+ raise ValueError("expected a dict or list of dicts or FITSHDR")
+
+ def add_record(self, record_in):
+ """
+ Add a new record. Strip quotes from around strings.
+
+ This will over-write if the key already exists, except
+ for COMMENT and HISTORY fields
+
+ parameters
+ -----------
+ record:
+ The record, either a dict or a header card string
+ or a FITSRecord or FITSCard
+ """
+ if (isinstance(record_in, dict) and
+ 'name' in record_in and 'value' in record_in):
+ record = {}
+ record.update(record_in)
+ else:
+ record = FITSRecord(record_in)
+
+ # only append when this name already exists if it is
+ # a comment or history field, otherwise simply over-write
+ key = record['name']
+ if key is not None:
+ key = key.upper()
+
+ key_exists = key in self._record_map
+
+ if not key_exists or key in ('COMMENT', 'HISTORY', 'CONTINUE', None):
+ # append new record
+ self._record_list.append(record)
+ index = len(self._record_list)-1
+ self._index_map[key] = index
+ else:
+ # over-write existing
+ index = self._index_map[key]
+ self._record_list[index] = record
+
+ self._record_map[key] = record
+
+ def _add_to_map(self, record):
+ key = record['name'].upper()
+ self._record_map[key] = record
+
+ def get_comment(self, item):
+ """
+ Get the comment for the requested entry
+ """
+ key = item.upper()
+ if key not in self._record_map:
+ raise KeyError("unknown record: %s" % key)
+
+ if 'comment' not in self._record_map[key]:
+ return None
+ else:
+ return self._record_map[key]['comment']
+
+ def records(self):
+ """
+ Return the list of full records as a list of dictionaries.
+ """
+ return self._record_list
+
+ def keys(self):
+ """
+ Return a copy of the current key list.
+ """
+ return [e['name'] for e in self._record_list]
+
+ def delete(self, name):
+ """
+ Delete the specified entry if it exists.
+ """
+ if isinstance(name, (list, tuple)):
+ for xx in name:
+ self.delete(xx)
+ else:
+ if name in self._record_map:
+ del self._record_map[name]
+ self._record_list = [
+ r for r in self._record_list if r['name'] != name]
+
+ def clean(self, is_table=False):
+ """
+ Remove reserved keywords from the header.
+
+ These are keywords that the fits writer must write in order
+ to maintain consistency between header and data.
+
+ keywords
+ --------
+ is_table: bool, optional
+ Set True if this is a table, so extra keywords will be cleaned
+ """
+
+ rmnames = [
+ 'SIMPLE', 'EXTEND', 'XTENSION', 'BITPIX', 'PCOUNT', 'GCOUNT',
+ 'THEAP',
+ 'EXTNAME',
+ # 'BLANK',
+ 'ZQUANTIZ', 'ZDITHER0', 'ZIMAGE', 'ZCMPTYPE',
+ 'ZSIMPLE', 'ZTENSION', 'ZPCOUNT', 'ZGCOUNT',
+ 'ZBITPIX', 'ZEXTEND',
+ # 'FZTILELN','FZALGOR',
+ 'CHECKSUM', 'DATASUM']
+
+ if is_table:
+ # these are not allowed in tables
+ rmnames += [
+ 'BUNIT', 'BSCALE', 'BZERO',
+ ]
+
+ self.delete(rmnames)
+
+ r = self._record_map.get('NAXIS', None)
+ if r is not None:
+ naxis = int(r['value'])
+ self.delete('NAXIS')
+
+ rmnames = ['NAXIS%d' % i for i in xrange(1, naxis+1)]
+ self.delete(rmnames)
+
+ r = self._record_map.get('ZNAXIS', None)
+ self.delete('ZNAXIS')
+ if r is not None:
+
+ znaxis = int(r['value'])
+
+ rmnames = ['ZNAXIS%d' % i for i in xrange(1, znaxis+1)]
+ self.delete(rmnames)
+ rmnames = ['ZTILE%d' % i for i in xrange(1, znaxis+1)]
+ self.delete(rmnames)
+ rmnames = ['ZNAME%d' % i for i in xrange(1, znaxis+1)]
+ self.delete(rmnames)
+ rmnames = ['ZVAL%d' % i for i in xrange(1, znaxis+1)]
+ self.delete(rmnames)
+
+ r = self._record_map.get('TFIELDS', None)
+ if r is not None:
+ tfields = int(r['value'])
+ self.delete('TFIELDS')
+
+ if tfields > 0:
+
+ nbase = [
+ 'TFORM', 'TTYPE', 'TDIM', 'TUNIT', 'TSCAL', 'TZERO',
+ 'TNULL', 'TDISP', 'TDMIN', 'TDMAX', 'TDESC', 'TROTA',
+ 'TRPIX', 'TRVAL', 'TDELT', 'TCUNI',
+ # 'FZALG'
+ ]
+ for i in xrange(1, tfields+1):
+ names = ['%s%d' % (n, i) for n in nbase]
+ self.delete(names)
+
+ def get(self, item, default_value=None):
+ """
+ Get the requested header entry by keyword name
+ """
+
+ found, name = self._contains_and_name(item)
+ if found:
+ return self._record_map[name]['value']
+ else:
+ return default_value
+
+ def __len__(self):
+ return len(self._record_list)
+
+ def __contains__(self, item):
+ found, _ = self._contains_and_name(item)
+ return found
+
+ def _contains_and_name(self, item):
+
+ if isinstance(item, FITSRecord):
+ name = item['name']
+ elif isinstance(item, dict):
+ name = item.get('name', None)
+ if name is None:
+ raise ValueError("dict record must have 'name' field")
+ else:
+ name = item
+
+ found = False
+ if name is None:
+ if None in self._record_map:
+ found = True
+ else:
+ name = name.upper()
+ if name in self._record_map:
+ found = True
+ elif name[0:8] == 'HIERARCH':
+ if len(name) > 9:
+ name = name[9:]
+ if name in self._record_map:
+ found = True
+
+ return found, name
+
+ def __setitem__(self, item, value):
+ if isinstance(value, (dict, FITSRecord)):
+ if item.upper() != value['name'].upper():
+ raise ValueError("when setting using a FITSRecord, the "
+ "name field must match")
+ rec = value
+ else:
+ rec = {'name': item, 'value': value}
+
+ try:
+ # the entry may already exist; if so, preserve the comment
+ comment = self.get_comment(item)
+ rec['comment'] = comment
+ except KeyError:
+ pass
+
+ self.add_record(rec)
+
+ def __getitem__(self, item):
+ if item not in self:
+ raise KeyError("unknown record: %s" % item)
+
+ return self.get(item)
+
+ def __iter__(self):
+ self._current = 0
+ return self
+
+ def next(self):
+ """
+ for iteration over the header entries
+ """
+ if self._current < len(self._record_list):
+ rec = self._record_list[self._current]
+ key = rec['name']
+ self._current += 1
+ return key
+ else:
+ raise StopIteration
+ __next__ = next
+
+ def _record2card(self, record):
+ """
+ when we add new records they don't have a card,
+ this sort of fakes it up similar to what cfitsio
+ does, just for display purposes. e.g.
+
+ DBL = 23.299843
+ LNG = 3423432
+ KEYSNC = 'hello '
+ KEYSC = 'hello ' / a comment for string
+ KEYDC = 3.14159265358979 / a comment for pi
+ KEYLC = 323423432 / a comment for long
+
+ basically,
+ - 8 chars, left aligned, for the keyword name
+ - a space
+ - 20 chars for value, left aligned for strings, right aligned for
+ numbers
+ - if there is a comment, one space followed by / then another space
+ then the comment out to 80 chars
+
+ """
+ name = record['name']
+ value = record['value']
+ comment = record.get('comment', '')
+
+ v_isstring = isstring(value)
+
+ if name is None:
+ card = ' %s' % comment
+ elif name == 'COMMENT':
+ card = 'COMMENT %s' % comment
+ elif name == 'CONTINUE':
+ card = 'CONTINUE %s' % value
+ elif name == 'HISTORY':
+ card = 'HISTORY %s' % value
+ else:
+ if len(name) > 8:
+ card = 'HIERARCH %s= ' % name
+ else:
+ card = '%-8s= ' % name[0:8]
+
+ # these may be string representations of data, or actual strings
+ if v_isstring:
+ value = str(value)
+ if len(value) > 0:
+ if value[0] != "'":
+ # this is a string representing a string header field
+ # make it look like it will look in the header
+ value = "'" + value + "'"
+ vstr = '%-20s' % value
+ else:
+ vstr = "%20s" % value
+ else:
+ vstr = "''"
+ else:
+ if value is True:
+ value = 'T'
+ elif value is False:
+ value = 'F'
+
+ vstr = '%20s' % value
+
+ card += vstr
+
+ if 'comment' in record:
+ card += ' / %s' % record['comment']
+
+ if v_isstring and len(card) > 80:
+ card = card[0:79] + "'"
+ else:
+ card = card[0:80]
+
+ return card
+
+ def __repr__(self):
+ rep = ['']
+ for r in self._record_list:
+ card = self._record2card(r)
+ # if 'card_string' not in r:
+ # card = self._record2card(r)
+ # else:
+ # card = r['card_string']
+
+ rep.append(card)
+ return '\n'.join(rep)
+
+
+class FITSRecord(dict):
+ """
+ Class to represent a FITS header record
+
+ parameters
+ ----------
+ record: string or dict
+ If a string, it should represent a FITS header card
+
+ If a dict it should have 'name' and 'value' fields.
+ Can have a 'comment' field.
+
+ examples
+ --------
+
+ # from a dict. Can include a comment
+ rec=FITSRecord( {'name':'temp', 'value':35, 'comment':'temperature in C'} )
+
+ # from a card
+ card=FITSRecord('test = 77 / My comment')
+
+ """
+ def __init__(self, record):
+ self.set_record(record)
+
+ def set_record(self, record, **keys):
+ """
+ check the record is valid and set keys in the dict
+
+ parameters
+ ----------
+ record: string
+ Dict representing a record or a string representing a FITS header
+ card
+ """
+
+ if keys:
+ import warnings
+ warnings.warn(
+ "The keyword arguments '%s' are being ignored! This warning "
+ "will be an error in a future version of `fitsio`!" % keys,
+ DeprecationWarning, stacklevel=2)
+
+ if isstring(record):
+ card = FITSCard(record)
+ self.update(card)
+
+ self.verify()
+
+ else:
+
+ if isinstance(record, FITSRecord):
+ self.update(record)
+ elif isinstance(record, dict):
+ if 'name' in record and 'value' in record:
+ self.update(record)
+
+ elif 'card_string' in record:
+ self.set_record(record['card_string'])
+
+ else:
+ raise ValueError('record must have name,value fields '
+ 'or a card_string field')
+ else:
+ raise ValueError("record must be a string card or "
+ "dictionary or FITSRecord")
+
+ def verify(self):
+ """
+ make sure name,value exist
+ """
+ if 'name' not in self:
+ raise ValueError("each record must have a 'name' field")
+ if 'value' not in self:
+ raise ValueError("each record must have a 'value' field")
+
+
+_BLANK = ' '
+
+
+class FITSCard(FITSRecord):
+ """
+ class to represent ordinary FITS cards.
+
+ CONTINUE not supported
+
+ examples
+ --------
+
+ # from a card
+ card=FITSRecord('test = 77 / My comment')
+ """
+ def __init__(self, card_string):
+ self.set_card(card_string)
+
+ def set_card(self, card_string):
+ self['card_string'] = card_string
+
+ self._check_hierarch()
+
+ if self._is_hierarch:
+ self._set_as_key()
+ else:
+ self._check_equals()
+
+ self._check_type()
+ self._check_len()
+
+ front = card_string[0:7]
+ if (not self.has_equals() or
+ front in ['COMMENT', 'HISTORY', 'CONTINU', _BLANK]):
+
+ if front == 'HISTORY':
+ self._set_as_history()
+ elif front == 'CONTINU':
+ self._set_as_continue()
+ elif front == _BLANK:
+ self._set_as_blank()
+ else:
+ # note anything without an = and not history and not blank
+ # key comment is treated as COMMENT; this is built into
+ # cfitsio as well
+ self._set_as_comment()
+
+ if self.has_equals():
+ mess = (
+ "warning: It is not FITS-compliant for a %s header "
+ "card to include an = sign. There may be slight "
+ "inconsistencies if you write this back out to a "
+ "file.")
+ mess = mess % (card_string[:8])
+ warnings.warn(mess, FITSRuntimeWarning)
+ else:
+ self._set_as_key()
+
+ def has_equals(self):
+ """
+ True if = is in position 8
+ """
+ return self._has_equals
+
+ def _check_hierarch(self):
+ card_string = self['card_string']
+ if card_string[0:8].upper() == 'HIERARCH':
+ self._is_hierarch = True
+ else:
+ self._is_hierarch = False
+
+ def _check_equals(self):
+ """
+ check for = in position 8, set attribute _has_equals
+ """
+ card_string = self['card_string']
+ if len(card_string) < 9:
+ self._has_equals = False
+ elif card_string[8] == '=':
+ self._has_equals = True
+ else:
+ self._has_equals = False
+
+ def _set_as_key(self):
+ card_string = self['card_string']
+ res = _fitsio_wrap.parse_card(card_string)
+ if len(res) == 5:
+ keyclass, name, value, dtype, comment = res
+ else:
+ keyclass, name, dtype, comment = res
+ value = None
+
+ if keyclass == TYP_CONT_KEY:
+ raise ValueError("bad card '%s'. CONTINUE not "
+ "supported" % card_string)
+
+ self['class'] = keyclass
+ self['name'] = name
+ self['value_orig'] = value
+ self['value'] = self._convert_value(value)
+ self['dtype'] = dtype
+ self['comment'] = comment
+
+ def _set_as_blank(self):
+ self['class'] = TYP_USER_KEY
+ self['name'] = None
+ self['value'] = None
+ self['comment'] = self['card_string'][8:]
+
+ def _set_as_comment(self):
+ comment = self._extract_comm_or_hist_value()
+
+ self['class'] = TYP_COMM_KEY
+ self['name'] = 'COMMENT'
+ self['value'] = comment
+
+ def _set_as_history(self):
+ history = self._extract_comm_or_hist_value()
+
+ self['class'] = TYP_COMM_KEY
+ self['name'] = 'HISTORY'
+ self['value'] = history
+
+ def _set_as_continue(self):
+ value = self._extract_comm_or_hist_value()
+
+ self['class'] = TYP_CONT_KEY
+ self['name'] = 'CONTINUE'
+ self['value'] = value
+
+ def _convert_value(self, value_orig):
+ """
+ things like 6 and 1.25 are converted with ast.literal_value
+
+ Things like 'hello' are stripped of quotes
+ """
+ import ast
+ if value_orig is None:
+ return value_orig
+
+ if value_orig.startswith("'") and value_orig.endswith("'"):
+ value = value_orig[1:-1]
+ else:
+
+ try:
+ avalue = ast.parse(value_orig).body[0].value
+ if isinstance(avalue, ast.BinOp):
+ # this is probably a string that happens to look like
+ # a binary operation, e.g. '25-3'
+ value = value_orig
+ else:
+ value = ast.literal_eval(value_orig)
+ except Exception:
+ value = self._convert_string(value_orig)
+
+ if isinstance(value, int) and '_' in value_orig:
+ value = value_orig
+
+ return value
+
+ def _convert_string(self, s):
+ if s == 'T':
+ return True
+ elif s == 'F':
+ return False
+ else:
+ return s
+
+ def _extract_comm_or_hist_value(self):
+ card_string = self['card_string']
+ if self._has_equals:
+ if len(card_string) >= 9:
+ value = card_string[9:]
+ else:
+ value = ''
+ else:
+ if len(card_string) >= 8:
+ # value=card_string[7:]
+ value = card_string[8:]
+ else:
+ value = ''
+ return value
+
+ def _check_type(self):
+ card_string = self['card_string']
+ if not isstring(card_string):
+ raise TypeError(
+ "card must be a string, got type %s" % type(card_string))
+
+ def _check_len(self):
+ ln = len(self['card_string'])
+ if ln > 80:
+ mess = "len(card) is %d. cards must have length < 80"
+ raise ValueError(mess)
--- /dev/null
+from __future__ import with_statement, print_function
+import sys, os
+import tempfile
+import warnings
+import numpy
+from numpy import arange, array
+from pkg_resources import resource_filename
+import fitsio
+
+from ._fitsio_wrap import cfitsio_use_standard_strings
+
+import unittest
+
+try:
+ xrange=xrange
+except:
+ xrange=range
+
+lorem_ipsum = (
+ 'Lorem ipsum dolor sit amet, consectetur adipiscing '
+ 'elit, sed do eiusmod tempor incididunt ut labore '
+ 'et dolore magna aliqua'
+)
+def test():
+ suite_warnings = unittest.TestLoader().loadTestsFromTestCase(TestWarnings)
+ res1=unittest.TextTestRunner(verbosity=2).run(suite_warnings).wasSuccessful()
+
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestReadWrite)
+ res2=unittest.TextTestRunner(verbosity=2).run(suite).wasSuccessful()
+
+ if not res1 or not res2:
+ sys.exit(1)
+
+class TestWarnings(unittest.TestCase):
+ """
+ tests of warnings
+
+ TODO: write test cases for bad column size
+ """
+ def setUp(self):
+ pass
+
+ def testNonStandardKeyValue(self):
+ fname=tempfile.mktemp(prefix='fitsio-TestWarning-',suffix='.fits')
+
+ im=numpy.zeros( (3,3) )
+ with warnings.catch_warnings(record=True) as w:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write(im)
+ # now write a key with a non-standard value
+ value={'test':3}
+ fits[-1].write_key("odd",value)
+
+ # DeprecationWarnings have crept into the Warning list. This will filter the list to be just
+ # FITSRuntimeWarning instances.
+ # @at88mph 2019.10.09
+ filtered_warnings = list(filter(lambda x: 'FITSRuntimeWarning' in '{}'.format(x.category), w))
+
+ assert len(filtered_warnings) == 1, 'Wrong length of output (Expected {} but got {}.)'.format(1, len(filtered_warnings))
+ assert issubclass(filtered_warnings[-1].category, fitsio.FITSRuntimeWarning)
+
+class TestReadWrite(unittest.TestCase):
+
+ def setUp(self):
+
+ nvec = 2
+ ashape=(21,21)
+ Sdtype = 'S6'
+ Udtype = 'U6'
+
+ # all currently available types, scalar, 1-d and 2-d array columns
+ dtype=[
+ ('u1scalar','u1'),
+ ('i1scalar','i1'),
+ ('b1scalar','?'),
+ ('u2scalar','u2'),
+ ('i2scalar','i2'),
+ ('u4scalar','u4'),
+ ('i4scalar','<i4'), # mix the byte orders a bit, test swapping
+ ('i8scalar','i8'),
+ ('f4scalar','f4'),
+ ('f8scalar','>f8'),
+ ('c8scalar','c8'), # complex, two 32-bit
+ ('c16scalar','c16'), # complex, two 32-bit
+
+ ('u1vec','u1',nvec),
+ ('i1vec','i1',nvec),
+ ('b1vec','?',nvec),
+ ('u2vec','u2',nvec),
+ ('i2vec','i2',nvec),
+ ('u4vec','u4',nvec),
+ ('i4vec','i4',nvec),
+ ('i8vec','i8',nvec),
+ ('f4vec','f4',nvec),
+ ('f8vec','f8',nvec),
+ ('c8vec','c8',nvec),
+ ('c16vec','c16',nvec),
+
+ ('u1arr','u1',ashape),
+ ('i1arr','i1',ashape),
+ ('b1arr','?',ashape),
+ ('u2arr','u2',ashape),
+ ('i2arr','i2',ashape),
+ ('u4arr','u4',ashape),
+ ('i4arr','i4',ashape),
+ ('i8arr','i8',ashape),
+ ('f4arr','f4',ashape),
+ ('f8arr','f8',ashape),
+ ('c8arr','c8',ashape),
+ ('c16arr','c16',ashape),
+
+ # special case of (1,)
+ ('f8arr_dim1','f8',(1,)),
+
+
+ ('Sscalar',Sdtype),
+ ('Svec', Sdtype, nvec),
+ ('Sarr', Sdtype, ashape),
+ ]
+
+ if cfitsio_use_standard_strings():
+ dtype += [
+ ('Sscalar_nopad',Sdtype),
+ ('Svec_nopad', Sdtype, nvec),
+ ('Sarr_nopad', Sdtype, ashape),
+ ]
+
+ if sys.version_info > (3,0,0):
+ dtype += [
+ ('Uscalar',Udtype),
+ ('Uvec', Udtype, nvec),
+ ('Uarr', Udtype, ashape),
+ ]
+
+ if cfitsio_use_standard_strings():
+ dtype += [
+ ('Uscalar_nopad',Udtype),
+ ('Uvec_nopad', Udtype, nvec),
+ ('Uarr_nopad', Udtype, ashape),
+ ]
+
+
+ dtype2=[('index','i4'),
+ ('x','f8'),
+ ('y','f8')]
+
+ nrows=4
+ data=numpy.zeros(nrows, dtype=dtype)
+
+ dtypes=['u1','i1','u2','i2','u4','i4','i8','f4','f8','c8','c16']
+ for t in dtypes:
+ if t in ['c8','c16']:
+ data[t+'scalar'] = [complex(i+1,(i+1)*2) for i in xrange(nrows)]
+ vname=t+'vec'
+ for row in xrange(nrows):
+ for i in xrange(nvec):
+ index=(row+1)*(i+1)
+ data[vname][row,i] = complex(index,index*2)
+ aname=t+'arr'
+ for row in xrange(nrows):
+ for i in xrange(ashape[0]):
+ for j in xrange(ashape[1]):
+ index=(row+1)*(i+1)*(j+1)
+ data[aname][row,i,j] = complex(index,index*2)
+
+ else:
+ data[t+'scalar'] = 1 + numpy.arange(nrows, dtype=t)
+ data[t+'vec'] = 1 + numpy.arange(nrows*nvec,dtype=t).reshape(nrows,nvec)
+ arr = 1 + numpy.arange(nrows*ashape[0]*ashape[1],dtype=t)
+ data[t+'arr'] = arr.reshape(nrows,ashape[0],ashape[1])
+
+ for t in ['b1']:
+ data[t+'scalar'] = (numpy.arange(nrows) % 2 == 0).astype('?')
+ data[t+'vec'] = (numpy.arange(nrows*nvec) % 2 == 0).astype('?').reshape(nrows,nvec)
+ arr = (numpy.arange(nrows*ashape[0]*ashape[1]) % 2 == 0).astype('?')
+ data[t+'arr'] = arr.reshape(nrows,ashape[0],ashape[1])
+
+
+ # strings get padded when written to the fits file. And the way I do
+ # the read, I read all bytes (ala mrdfits) so the spaces are preserved.
+ #
+ # so we need to pad out the strings with blanks so we can compare
+
+ data['Sscalar'] = ['%-6s' % s for s in ['hello','world','good','bye']]
+ data['Svec'][:,0] = '%-6s' % 'hello'
+ data['Svec'][:,1] = '%-6s' % 'world'
+
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%-6s' % el for el in s]
+ data['Sarr'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+ if cfitsio_use_standard_strings():
+ data['Sscalar_nopad'] = ['hello','world','good','bye']
+ data['Svec_nopad'][:,0] = 'hello'
+ data['Svec_nopad'][:,1] = 'world'
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%s' % el for el in s]
+ data['Sarr_nopad'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+ if sys.version_info >= (3, 0, 0):
+ data['Uscalar'] = ['%-6s' % s for s in ['hello','world','good','bye']]
+ data['Uvec'][:,0] = '%-6s' % 'hello'
+ data['Uvec'][:,1] = '%-6s' % 'world'
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%-6s' % el for el in s]
+ data['Uarr'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+
+ if cfitsio_use_standard_strings():
+ data['Uscalar_nopad'] = ['hello','world','good','bye']
+ data['Uvec_nopad'][:,0] = 'hello'
+ data['Uvec_nopad'][:,1] = 'world'
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%s' % el for el in s]
+ data['Uarr_nopad'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+ self.data = data
+
+ # use a dict list so we can have comments
+ # for long key we used the largest possible
+ self.keys = [{'name':'test1','value':35},
+ {'name':'empty','value':''},
+ {'name':'long_keyword_name','value':'stuff'},
+ {'name':'test2','value':'stuff','comment':'this is a string keyword'},
+ {'name':'dbl', 'value':23.299843,'comment':"this is a double keyword"},
+ {'name':'edbl', 'value':1.384123233e+43,'comment':"double keyword with exponent"},
+ {'name':'lng','value':2**63-1,'comment':'this is a long keyword'},
+ {'name':'lngstr','value':lorem_ipsum,'comment':'long string'}]
+
+ # a second extension using the convenience function
+ nrows2=10
+ data2 = numpy.zeros(nrows2, dtype=dtype2)
+ data2['index'] = numpy.arange(nrows2,dtype='i4')
+ data2['x'] = numpy.arange(nrows2,dtype='f8')
+ data2['y'] = numpy.arange(nrows2,dtype='f8')
+ self.data2 = data2
+
+ #
+ # ascii table
+ #
+
+ nvec = 2
+ ashape = (2,3)
+ Sdtype = 'S6'
+ Udtype = 'U6'
+
+ # we support writing i2, i4, i8, f4 f8, but when reading cfitsio always
+ # reports their types as i4 and f8, so can't really use i8 and we are
+ # forced to read all floats as f8 precision
+
+ adtype=[('i2scalar','i2'),
+ ('i4scalar','i4'),
+ #('i8scalar','i8'),
+ ('f4scalar','f4'),
+ ('f8scalar','f8'),
+ ('Sscalar',Sdtype)]
+ if sys.version_info >= (3, 0, 0):
+ adtype += [('Uscalar', Udtype)]
+
+ nrows=4
+ try:
+ tdt = numpy.dtype(adtype, align=True)
+ except TypeError: # older numpy may not understand `align` argument
+ tdt = numpy.dtype(adtype)
+ adata=numpy.zeros(nrows, dtype=tdt)
+
+ adata['i2scalar'][:] = -32222 + numpy.arange(nrows,dtype='i2')
+ adata['i4scalar'][:] = -1353423423 + numpy.arange(nrows,dtype='i4')
+ #adata['i8scalar'][:] = -9223372036854775807 + numpy.arange(nrows,dtype='i8')
+ adata['f4scalar'][:] = -2.55555555555555555555555e35 + numpy.arange(nrows,dtype='f4')*1.e35
+ adata['f8scalar'][:] = -2.55555555555555555555555e110 + numpy.arange(nrows,dtype='f8')*1.e110
+ adata['Sscalar'] = ['hello','world','good','bye']
+
+ if sys.version_info >= (3, 0, 0):
+ adata['Uscalar'] = ['hello','world','good','bye']
+
+ self.ascii_data = adata
+
+
+
+ #
+ # for variable length columns
+ #
+
+ # all currently available types, scalar, 1-d and 2-d array columns
+ dtype=[
+ ('u1scalar','u1'),
+ ('u1obj','O'),
+ ('i1scalar','i1'),
+ ('i1obj','O'),
+ ('u2scalar','u2'),
+ ('u2obj','O'),
+ ('i2scalar','i2'),
+ ('i2obj','O'),
+ ('u4scalar','u4'),
+ ('u4obj','O'),
+ ('i4scalar','<i4'), # mix the byte orders a bit, test swapping
+ ('i4obj','O'),
+ ('i8scalar','i8'),
+ ('i8obj','O'),
+ ('f4scalar','f4'),
+ ('f4obj','O'),
+ ('f8scalar','>f8'),
+ ('f8obj','O'),
+
+ ('u1vec','u1',nvec),
+ ('i1vec','i1',nvec),
+ ('u2vec','u2',nvec),
+ ('i2vec','i2',nvec),
+ ('u4vec','u4',nvec),
+ ('i4vec','i4',nvec),
+ ('i8vec','i8',nvec),
+ ('f4vec','f4',nvec),
+ ('f8vec','f8',nvec),
+
+ ('u1arr','u1',ashape),
+ ('i1arr','i1',ashape),
+ ('u2arr','u2',ashape),
+ ('i2arr','i2',ashape),
+ ('u4arr','u4',ashape),
+ ('i4arr','i4',ashape),
+ ('i8arr','i8',ashape),
+ ('f4arr','f4',ashape),
+ ('f8arr','f8',ashape),
+
+ # special case of (1,)
+ ('f8arr_dim1','f8',(1,)),
+
+ ('Sscalar',Sdtype),
+ ('Sobj','O'),
+ ('Svec', Sdtype, nvec),
+ ('Sarr', Sdtype, ashape),
+ ]
+
+ if sys.version_info > (3,0,0):
+ dtype += [
+ ('Uscalar',Udtype),
+ ('Uvec', Udtype, nvec),
+ ('Uarr', Udtype, ashape)]
+
+ dtype2=[('index','i4'),
+ ('x','f8'),
+ ('y','f8')]
+
+ nrows=4
+ data=numpy.zeros(nrows, dtype=dtype)
+
+ for t in ['u1','i1','u2','i2','u4','i4','i8','f4','f8']:
+ data[t+'scalar'] = 1 + numpy.arange(nrows, dtype=t)
+ data[t+'vec'] = 1 + numpy.arange(nrows*nvec,dtype=t).reshape(nrows,nvec)
+ arr = 1 + numpy.arange(nrows*ashape[0]*ashape[1],dtype=t)
+ data[t+'arr'] = arr.reshape(nrows,ashape[0],ashape[1])
+
+ for i in xrange(nrows):
+ data[t+'obj'][i] = data[t+'vec'][i]
+
+
+ # strings get padded when written to the fits file. And the way I do
+ # the read, I real all bytes (ala mrdfits) so the spaces are preserved.
+ #
+ # so for comparisons, we need to pad out the strings with blanks so we
+ # can compare
+
+ data['Sscalar'] = ['%-6s' % s for s in ['hello','world','good','bye']]
+ data['Svec'][:,0] = '%-6s' % 'hello'
+ data['Svec'][:,1] = '%-6s' % 'world'
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%-6s' % el for el in s]
+ data['Sarr'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+ if sys.version_info >= (3, 0, 0):
+ data['Uscalar'] = ['%-6s' % s for s in ['hello','world','good','bye']]
+ data['Uvec'][:,0] = '%-6s' % 'hello'
+ data['Uvec'][:,1] = '%-6s' % 'world'
+
+ s = 1 + numpy.arange(nrows*ashape[0]*ashape[1])
+ s = ['%-6s' % el for el in s]
+ data['Uarr'] = numpy.array(s).reshape(nrows,ashape[0],ashape[1])
+
+ for i in xrange(nrows):
+ data['Sobj'][i] = data['Sscalar'][i].rstrip()
+
+ self.vardata = data
+
+ #
+ # for bitcol columns
+ #
+ nvec = 2
+ ashape=(21,21)
+
+ dtype=[('b1vec','?',nvec),
+
+ ('b1arr','?',ashape)]
+
+ nrows=4
+ data=numpy.zeros(nrows, dtype=dtype)
+
+ for t in ['b1']:
+ data[t+'vec'] = (numpy.arange(nrows*nvec) % 2 == 0).astype('?').reshape(nrows,nvec)
+ arr = (numpy.arange(nrows*ashape[0]*ashape[1]) % 2 == 0).astype('?')
+ data[t+'arr'] = arr.reshape(nrows,ashape[0],ashape[1])
+
+ self.bdata = data
+
+
+ def testHeaderWriteRead(self):
+ """
+ Test a basic header write and read
+
+ Note the other read/write tests also are checking header writing with
+ a list of dicts
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderWrite-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data=numpy.zeros(10)
+ header={
+ 'x':35,
+ 'y':88.215,
+ 'eval':1.384123233e+43,
+ 'empty':'',
+ 'funky':'35-8', # test old bug when strings look
+ #like expressions
+ 'name':'J. Smith',
+ 'what': '89113e6', # test bug where converted to float
+ 'und':None,
+ 'binop':'25-3', # test string with binary operation in it
+ 'unders':'1_000_000', # test string with underscore
+ 'longs':lorem_ipsum,
+ }
+ fits.write_image(data, header=header)
+
+ rh = fits[0].read_header()
+ self.check_header(header, rh)
+
+ with fitsio.FITS(fname) as fits:
+ rh = fits[0].read_header()
+ self.check_header(header, rh)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testReadHeaderCase(self):
+ """
+ Test read_header with and without case sensitivity
+
+ The reason we need a special test for this is because
+ the read_header code is optimized for speed and has
+ a different code path
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderCase-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data=numpy.zeros(10)
+ fits.write_image(data, header=self.keys, extname='First')
+ fits.write_image(data, header=self.keys, extname='second')
+
+ cases = [
+ ('First',True),
+ ('FIRST',False),
+ ('second',True),
+ ('seConD',False),
+ ]
+ for ext,ci in cases:
+ h = fitsio.read_header(fname,ext=ext,case_sensitive=ci)
+ self.compare_headerlist_header(self.keys, h)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testHeaderCommentPreserved(self):
+ """
+ Test that the comment is preserved after resetting the value
+ """
+
+ l1 = 'KEY1 = 77 / My comment1'
+ l2 = 'KEY2 = 88 / My comment2'
+ hdr=fitsio.FITSHDR()
+ hdr.add_record(l1)
+ hdr.add_record(l2)
+
+ hdr['key1'] = 99
+ self.assertEqual(hdr.get_comment('key1'), 'My comment1',
+ 'comment not preserved')
+
+ def testBlankKeyComments(self):
+ """
+ test a few different comments
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderComments-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ records = [
+ # empty should return empty
+ {'name':None, 'value':'', 'comment':''},
+ # this will also return empty
+ {'name':None, 'value':'', 'comment':' '},
+ # this will return exactly
+ {'name':None, 'value':'', 'comment':' h'},
+ # this will return exactly
+ {'name':None, 'value':'', 'comment':'--- test comment ---'},
+ ]
+ header = fitsio.FITSHDR(records)
+
+ fits.write(None, header=header)
+
+ rh = fits[0].read_header()
+
+ rrecords = rh.records()
+
+ for i, ri in ((0, 6), (1,7), (2, 8)):
+ rec = records[i]
+ rrec = rrecords[ri]
+
+ self.assertEqual(
+ rec['name'],
+ None,
+ 'checking name is None',
+ )
+ comment = rec['comment']
+ rcomment = rrec['comment']
+ if '' == comment.strip():
+ comment = ''
+
+ self.assertEqual(
+ comment,
+ rcomment,
+ "check empty key comment",
+ )
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testBlankKeyCommentsFromCards(self):
+ """
+ test a few different comments
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderComments-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ records = [
+ ' ',
+ ' --- testing comment --- ',
+ ' --- testing comment --- ',
+ "COMMENT testing ",
+ ]
+ header = fitsio.FITSHDR(records)
+
+ fits.write(None, header=header)
+
+ rh = fits[0].read_header()
+
+ rrecords = rh.records()
+ from pprint import pprint
+ # print()
+ # pprint(rrecords)
+
+ self.assertEqual(
+ rrecords[6]['name'],
+ None,
+ 'checking name is None',
+ )
+ self.assertEqual(
+ rrecords[6]['comment'],
+ '',
+ "check empty key comment",
+ )
+ self.assertEqual(
+ rrecords[7]['name'],
+ None,
+ 'checking name is None',
+ )
+ self.assertEqual(
+ rrecords[7]['comment'],
+ ' --- testing comment ---',
+ "check empty key comment",
+ )
+ self.assertEqual(
+ rrecords[8]['name'],
+ None,
+ 'checking name is None',
+ )
+ self.assertEqual(
+ rrecords[8]['comment'],
+ '--- testing comment ---',
+ "check empty key comment",
+ )
+
+
+ self.assertEqual(
+ rrecords[9]['name'],
+ 'COMMENT',
+ 'checking name is COMMENT',
+ )
+ self.assertEqual(
+ rrecords[9]['comment'],
+ 'testing',
+ "check comment",
+ )
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testHeaderFromCards(self):
+ """
+ test generating a header from cards, writing it out and getting
+ back what we put in
+ """
+ hdr_from_cards=fitsio.FITSHDR([
+ "IVAL = 35 / integer value ",
+ "SHORTS = 'hello world' ",
+ "UND = ",
+ "LONGS = 'Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiu&'",
+ "CONTINUE 'smod tempor incididunt ut labore et dolore magna aliqua' ",
+ "DBL = 1.25 ",
+ ])
+ header = [
+ {'name':'ival','value':35,'comment':'integer value'},
+ {'name':'shorts','value':'hello world'},
+ {'name':'und','value':None},
+ {'name':'longs','value':lorem_ipsum},
+ {'name':'dbl','value':1.25},
+ ]
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderFromCars-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data=numpy.zeros(10)
+ fits.write_image(data, header=hdr_from_cards)
+
+ rh = fits[0].read_header()
+ self.compare_headerlist_header(header, rh)
+
+ with fitsio.FITS(fname) as fits:
+ rh = fits[0].read_header()
+ self.compare_headerlist_header(header, rh)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testHeaderJunk(self):
+ """
+ test lenient treatment of garbage written by IDL mwrfits
+ """
+
+ data="""SIMPLE = T /Primary Header created by MWRFITS v1.11 BITPIX = 16 / NAXIS = 0 / EXTEND = T /Extensions may be present BLAT = 1 /integer FOO = 1.00000 /float (or double?) BAR = NAN /float NaN BIZ = NaN /double NaN BAT = INF /1.0 / 0.0 BOO = -INF /-1.0 / 0.0 QUAT = ' ' /blank string QUIP = '1.0 ' /number in quotes QUIZ = ' 1.0 ' /number in quotes with a leading space QUIL = 'NaN ' /NaN in quotes QUID = 'Inf ' /Inf in quotes END """ # noqa
+
+ fname=tempfile.mktemp(prefix='fitsio-HeaderJunk-',suffix='.fits')
+ try:
+ with open(fname,'w') as fobj:
+ fobj.write(data)
+
+ h = fitsio.read_header(fname)
+ self.assertEqual(h['bar'],'NAN', "NAN garbage")
+ self.assertEqual(h['biz'],'NaN', "NaN garbage")
+ self.assertEqual(h['bat'],'INF', "INF garbage")
+ self.assertEqual(h['boo'],'-INF', "-INF garbage")
+ self.assertEqual(h['quat'], '', 'blank')
+ self.assertEqual(h['quip'], '1.0', '1.0 in quotes')
+ self.assertEqual(h['quiz'], ' 1.0', '1.0 in quotes')
+ self.assertEqual(h['quil'], 'NaN', 'NaN in quotes')
+ self.assertEqual(h['quid'], 'Inf', 'Inf in quotes')
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testHeaderTemplate(self):
+ """
+ test adding bunch of cards from a split template
+ """
+
+ header_template = """SIMPLE = T /
+BITPIX = 8 / bits per data value
+NAXIS = 0 / number of axes
+EXTEND = T / Extensions are permitted
+ORIGIN = 'LSST DM Header Service'/ FITS file originator
+
+ ---- Date, night and basic image information ----
+DATE = / Creation Date and Time of File
+DATE-OBS= / Date of the observation (image acquisition)
+DATE-BEG= / Time at the start of integration
+DATE-END= / end date of the observation
+MJD = / Modified Julian Date that the file was written
+MJD-OBS = / Modified Julian Date of observation
+MJD-BEG = / Modified Julian Date derived from DATE-BEG
+MJD-END = / Modified Julian Date derived from DATE-END
+OBSID = / ImageName from Camera StartIntergration
+GROUPID = / imageSequenceName from StartIntergration
+OBSTYPE = / BIAS, DARK, FLAT, OBJECT
+BUNIT = 'adu ' / Brightness units for pixel array
+
+ ---- Telescope info, location, observer ----
+TELESCOP= 'LSST AuxTelescope' / Telescope name
+INSTRUME= 'LATISS' / Instrument used to obtain these data
+OBSERVER= 'LSST' / Observer name(s)
+OBS-LONG= -70.749417 / [deg] Observatory east longitude
+OBS-LAT = -30.244639 / [deg] Observatory latitude
+OBS-ELEV= 2663.0 / [m] Observatory elevation
+OBSGEO-X= 1818938.94 / [m] X-axis Geocentric coordinate
+OBSGEO-Y= -5208470.95 / [m] Y-axis Geocentric coordinate
+OBSGEO-Z= -3195172.08 / [m] Z-axis Geocentric coordinate
+
+ ---- Pointing info, etc. ----
+
+DECTEL = / Telescope DEC of observation
+ROTPATEL= / Telescope Rotation
+ROTCOORD= 'sky' / Telescope Rotation Coordinates
+RA = / RA of Target
+DEC = / DEC of Target
+ROTPA = / Rotation angle relative to the sky (deg)
+HASTART = / [HH:MM:SS] Telescope hour angle at start
+ELSTART = / [deg] Telescope zenith distance at start
+AZSTART = / [deg] Telescope azimuth angle at start
+AMSTART = / Airmass at start
+HAEND = / [HH:MM:SS] Telescope hour angle at end
+ELEND = / [deg] Telescope zenith distance at end
+AZEND = / [deg] Telescope azimuth angle at end
+AMEND = / Airmass at end
+
+ ---- Image-identifying used to build OBS-ID ----
+TELCODE = 'AT' / The code for the telecope
+CONTRLLR= / The controller (e.g. O for OCS, C for CCS)
+DAYOBS = / The observation day as defined by image name
+SEQNUM = / The sequence number from the image name
+GROUPID = /
+
+ ---- Information from Camera
+CCD_MANU= 'ITL' / CCD Manufacturer
+CCD_TYPE= '3800C' / CCD Model Number
+CCD_SERN= '20304' / Manufacturers? CCD Serial Number
+LSST_NUM= 'ITL-3800C-098' / LSST Assigned CCD Number
+SEQCKSUM= / Checksum of Sequencer
+SEQNAME = / SequenceName from Camera StartIntergration
+REBNAME = / Name of the REB
+CONTNUM = / CCD Controller (WREB) Serial Number
+IMAGETAG= / DAQ Image id
+TEMP_SET= / Temperature set point (deg C)
+CCDTEMP = / Measured temperature (deg C)
+
+ ---- Geometry from Camera ----
+DETSIZE = / Size of sensor
+OVERH = / Over-scan pixels
+OVERV = / Vert-overscan pix
+PREH = / Pre-scan pixels
+
+ ---- Filter/grating information ----
+FILTER = / Name of the filter
+FILTPOS = / Filter position
+GRATING = / Name of the second disperser
+GRATPOS = / disperser position
+LINSPOS = / Linear Stage
+
+ ---- Exposure-related information ----
+EXPTIME = / Exposure time in seconds
+SHUTTIME= / Shutter exposure time in seconds
+DARKTIME= / Dark time in seconds
+
+ ---- Header information ----
+FILENAME= / Original file name
+HEADVER = / Version of header
+
+ ---- Checksums ----
+CHECKSUM= / checksum for the current HDU
+DATASUM = / checksum of the data records\n"""
+
+ lines = header_template.splitlines()
+ hdr = fitsio.FITSHDR()
+ for l in lines:
+ hdr.add_record(l)
+
+ def testCorruptContinue(self):
+ """
+ test with corrupt continue, just make sure it doesn't crash
+ """
+ with warnings.catch_warnings(record=True) as w:
+ fname=tempfile.mktemp(prefix='fitsio-TestCorruptContinue-',suffix='.fits')
+
+ hdr_from_cards=fitsio.FITSHDR([
+ "IVAL = 35 / integer value ",
+ "SHORTS = 'hello world' ",
+ "CONTINUE= ' ' / '&' / Current observing orogram ",
+ "UND = ",
+ "DBL = 1.25 ",
+ ])
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write(None, header=hdr_from_cards)
+
+ rhdr = fitsio.read_header(fname)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ with warnings.catch_warnings(record=True) as w:
+ fname=tempfile.mktemp(prefix='fitsio-TestCorruptContinue-',suffix='.fits')
+
+ hdr_from_cards=fitsio.FITSHDR([
+ "IVAL = 35 / integer value ",
+ "SHORTS = 'hello world' ",
+ "PROGRAM = 'Setting the Scale: Determining the Absolute Mass Normalization and &'",
+ "CONTINUE 'Scaling Relations for Clusters at z~0.1&' ",
+ "CONTINUE '&' / Current observing orogram ",
+ "UND = ",
+ "DBL = 1.25 ",
+ ])
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write(None, header=hdr_from_cards)
+
+ rhdr = fitsio.read_header(fname)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testImageWriteRead(self):
+ """
+ Test a basic image write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits')
+ dtypes=['u1','i1','u2','i2','<u4','i4','i8','>f4','f8']
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note mixing up byte orders a bit
+ for dtype in dtypes:
+ data = numpy.arange(5*20,dtype=dtype).reshape(5,20)
+ header={'DTYPE':dtype,'NBYTES':data.dtype.itemsize}
+ fits.write_image(data, header=header)
+ rdata = fits[-1].read()
+
+ self.compare_array(data, rdata, "images")
+
+ rh = fits[-1].read_header()
+ self.check_header(header, rh)
+
+ with fitsio.FITS(fname) as fits:
+ for i in xrange(len(dtypes)):
+ self.assertEqual(fits[i].is_compressed(), False, "not compressed")
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testImageWriteEmpty(self):
+ """
+ Test a basic image write, with no data and just a header, then reading
+ back in to check the values
+ """
+ fname=tempfile.mktemp(prefix='fitsio-ImageWriteEmpty-',suffix='.fits')
+ try:
+ data=None
+ header={'EXPTIME':120, 'OBSERVER':'Beatrice Tinsley','INSTRUME':'DECam','FILTER':'r'}
+ with fitsio.FITS(fname,'rw',clobber=True, ignore_empty=True) as fits:
+ for extname in ['CCD1','CCD2','CCD3','CCD4','CCD5','CCD6','CCD7','CCD8']:
+ fits.write_image(data, header=header)
+ rdata = fits[-1].read()
+ rh = fits[-1].read_header()
+ self.check_header(header, rh)
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testImageWriteReadFromDims(self):
+ """
+ Test creating an image from dims and writing in place
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-ImageWriteFromDims-',suffix='.fits')
+ dtypes=['u1','i1','u2','i2','<u4','i4','i8','>f4','f8']
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note mixing up byte orders a bit
+ for dtype in dtypes:
+ data = numpy.arange(5*20,dtype=dtype).reshape(5,20)
+
+ fits.create_image_hdu(dims=data.shape,
+ dtype=data.dtype)
+
+ fits[-1].write(data)
+ rdata = fits[-1].read()
+
+ self.compare_array(data, rdata, "images")
+
+ with fitsio.FITS(fname) as fits:
+ for i in xrange(len(dtypes)):
+ self.assertEqual(fits[i].is_compressed(), False, "not compressed")
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testImageWriteReadFromDimsChunks(self):
+ """
+ Test creating an image and reading/writing chunks
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-ImageWriteFromDims-',suffix='.fits')
+ dtypes=['u1','i1','u2','i2','<u4','i4','i8','>f4','f8']
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note mixing up byte orders a bit
+ for dtype in dtypes:
+ data = numpy.arange(5*3,dtype=dtype).reshape(5,3)
+
+ fits.create_image_hdu(dims=data.shape,
+ dtype=data.dtype)
+
+ chunk1 = data[0:2, :]
+ chunk2 = data[2: , :]
+
+ #
+ # first using scalar pixel offset
+ #
+
+ fits[-1].write(chunk1)
+
+ start=chunk1.size
+ fits[-1].write(chunk2, start=start)
+
+ rdata = fits[-1].read()
+
+ self.compare_array(data, rdata, "images")
+
+
+ #
+ # now using sequence, easier to calculate
+ #
+
+ fits.create_image_hdu(dims=data.shape,
+ dtype=data.dtype)
+
+ # first using pixel offset
+ fits[-1].write(chunk1)
+
+ start=[2,0]
+ fits[-1].write(chunk2, start=start)
+
+ rdata2 = fits[-1].read()
+
+ self.compare_array(data, rdata2, "images")
+
+
+ with fitsio.FITS(fname) as fits:
+ for i in xrange(len(dtypes)):
+ self.assertEqual(fits[i].is_compressed(), False, "not compressed")
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testImageSlice(self):
+ """
+ test reading an image slice
+ """
+ fname=tempfile.mktemp(prefix='fitsio-ImageSlice-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note mixing up byte orders a bit
+ for dtype in ['u1','i1','u2','i2','<u4','i4','i8','>f4','f8']:
+ data = numpy.arange(16*20,dtype=dtype).reshape(16,20)
+ header={'DTYPE':dtype,'NBYTES':data.dtype.itemsize}
+ fits.write_image(data, header=header)
+ rdata = fits[-1][4:12, 9:17]
+
+ self.compare_array(data[4:12,9:17], rdata, "images")
+
+ rh = fits[-1].read_header()
+ self.check_header(header, rh)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testReadFlipAxisSlice(self):
+ """
+ Test reading a slice when the slice's start is less than the slice's stop.
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-ReadFlipAxisSlice-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname, 'rw', clobber=True) as fits:
+ dtype = numpy.int16
+ data = numpy.arange(100 * 200, dtype=dtype).reshape(100, 200)
+ fits.write_image(data)
+ hdu = fits[-1]
+ rdata = hdu[:,130:70]
+
+ # Expanded by two to emulate adding one to the start value, and adding one to the calculated dimension.
+ expected_data = data[:,130:70:-1]
+
+ numpy.testing.assert_array_equal(expected_data, rdata,
+ "Data are not the same (Expected shape: {}, actual shape: {}.".format(
+ expected_data.shape, rdata.shape))
+
+ rdata = hdu[:,130:70:-6]
+
+ # Expanded by two to emulate adding one to the start value, and adding one to the calculated dimension.
+ expected_data = data[:,130:70:-6]
+
+ numpy.testing.assert_array_equal(expected_data, rdata,
+ "Data are not the same (Expected shape: {}, actual shape: {}.".format(
+ expected_data.shape, rdata.shape))
+
+
+ rdata = hdu[:,90:60:4] # Positive step integer with start > stop will return an empty array
+ expected_data = numpy.empty(0, dtype=dtype)
+ numpy.testing.assert_array_equal(expected_data, rdata,
+ "Data are not the same (Expected shape: {}, actual shape: {}.".format(
+ expected_data.shape, rdata.shape))
+
+ rdata = hdu[:,60:90:-4] # Negative step integer with start < stop will return an empty array.
+ expected_data = numpy.empty(0, dtype=dtype)
+ numpy.testing.assert_array_equal(expected_data, rdata,
+ "Data are not the same (Expected shape: {}, actual shape: {}.".format(
+ expected_data.shape, rdata.shape))
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testImageSliceStriding(self):
+ """
+ test reading an image slice
+ """
+ fname=tempfile.mktemp(prefix='fitsio-ImageSliceStriding-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note mixing up byte orders a bit
+ for dtype in ['u1','i1','u2','i2','<u4','i4','i8','>f4','f8']:
+ data = numpy.arange(16*20,dtype=dtype).reshape(16,20)
+ header={'DTYPE':dtype,'NBYTES':data.dtype.itemsize}
+ fits.write_image(data, header=header)
+
+ rdata = fits[-1][4:16:4, 2:20:2]
+ expected_data = data[4:16:4, 2:20:2]
+ self.assertEqual(rdata.shape, expected_data.shape, "Shapes differ with dtype %s" % dtype)
+ self.compare_array(expected_data, rdata, "images with dtype %s" % dtype)
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testRiceTileCompressedWriteRead(self):
+ """
+ Test writing and reading a rice compressed image
+ """
+ nrows=30
+ ncols=100
+ tile_dims=[5,10]
+ compress='rice'
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ dtypes = ['u1','i1','u2','i2','u4','i4','f4','f8']
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note i8 not supported for compressed!
+
+ for dtype in dtypes:
+ if dtype[0] == 'f':
+ data = numpy.random.normal(size=nrows*ncols).reshape(nrows,ncols).astype(dtype)
+ else:
+ data = numpy.arange(nrows*ncols,dtype=dtype).reshape(nrows,ncols)
+
+ fits.write_image(data, compress=compress, qlevel=16)
+ rdata = fits[-1].read()
+
+ if dtype[0] == 'f':
+ self.compare_array_abstol(
+ data,
+ rdata,
+ 0.2,
+ "%s compressed images ('%s')" % (compress,dtype),
+ )
+ else:
+ # for integers we have chosen a wide range of values, so
+ # there will be no quantization and we expect no information
+ # loss
+ self.compare_array(data, rdata,
+ "%s compressed images ('%s')" % (compress,dtype))
+
+ with fitsio.FITS(fname) as fits:
+ for ii in xrange(len(dtypes)):
+ i=ii+1
+ self.assertEqual(fits[i].is_compressed(), True, "is compressed")
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testPLIOTileCompressedWriteRead(self):
+ """
+ Test writing and reading gzip compressed image
+ """
+
+ compress='plio'
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ dtypes = ['i1','i2','i4','f4','f8']
+
+ for dtype in dtypes:
+
+ if dtype[0] == 'f':
+ data = numpy.random.normal(size=5*20).reshape(5,20).astype(dtype).clip(min=0)
+ else:
+ data = numpy.arange(5*20, dtype=dtype).reshape(5,20)
+
+ fits.write_image(data, compress=compress, qlevel=16)
+ rdata = fits[-1].read()
+
+ if dtype[0] == 'f':
+ self.compare_array_abstol(
+ data,
+ rdata,
+ 0.2,
+ "%s compressed images ('%s')" % (compress,dtype),
+ )
+ else:
+ # for integers we have chosen a wide range of values, so
+ # there will be no quantization and we expect no information
+ # loss
+ self.compare_array(data, rdata, "%s compressed images ('%s')" % (compress,dtype))
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testGZIPTileCompressedWriteRead(self):
+ """
+ Test writing and reading gzip compressed image
+ """
+
+ for compress in ['gzip', 'gzip_2']:
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ dtypes = ['u1','i1','u2','i2','u4','i4','f4','f8']
+
+ for dtype in dtypes:
+
+ if dtype[0] == 'f':
+ data = numpy.random.normal(size=5*20).reshape(5,20).astype(dtype)
+ else:
+ data = numpy.arange(5*20, dtype=dtype).reshape(5,20)
+
+ fits.write_image(data, compress=compress, qlevel=16)
+ rdata = fits[-1].read()
+
+ if dtype[0] == 'f':
+ self.compare_array_abstol(
+ data,
+ rdata,
+ 0.2,
+ "%s compressed images ('%s')" % (compress,dtype),
+ )
+ else:
+ # for integers we have chosen a wide range of values, so
+ # there will be no quantization and we expect no information
+ # loss
+ self.compare_array(data, rdata, "%s compressed images ('%s')" % (compress,dtype))
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testGZIPTileCompressedWriteReadLossless(self):
+ """
+ Test writing and reading gzip compressed image
+ """
+
+ for compress in ['gzip', 'gzip_2']:
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ # note i8 not supported for compressed!
+ dtypes = ['u1','i1','u2','i2','u4','i4','f4','f8']
+
+ for dtype in dtypes:
+ data = numpy.random.normal(size=50*20).reshape(50, 20)
+ fits.write_image(data, compress=compress, qlevel=None)
+ rdata = fits[-1].read()
+
+ self.compare_array(data, rdata, "%s compressed images ('%s')" % (compress,dtype))
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testGZIPTileCompressedReadLosslessAstropy(self):
+ """
+ Test reading an image gzip compressed by astropy (fixed by cfitsio 3.49)
+ """
+ gzip_file = resource_filename(__name__, 'test_images/test_gzip_compressed_image.fits.fz')
+ data = fitsio.read(gzip_file)
+ self.compare_array(data, data*0.0, "astropy lossless compressed image")
+
+ def testHCompressTileCompressedWriteRead(self):
+ """
+ Test writing and reading gzip compressed image
+ """
+
+ compress='hcompress'
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ dtypes = ['u1','i1','u2','i2','u4','i4','f4','f8']
+
+ for dtype in dtypes:
+
+ if dtype[0] == 'f':
+ data = numpy.random.normal(size=5*20).reshape(5,20).astype(dtype)
+ else:
+ data = numpy.arange(5*20, dtype=dtype).reshape(5,20)
+
+ # smoke test on these keywords
+ fits.write_image(data, compress=compress, qlevel=16,
+ hcomp_scale=1, hcomp_smooth=True)
+
+ fits.write_image(data, compress=compress, qlevel=16)
+ rdata = fits[-1].read()
+
+ if dtype[0] == 'f':
+ self.compare_array_abstol(
+ data,
+ rdata,
+ 0.2,
+ "%s compressed images ('%s')" % (compress,dtype),
+ )
+ else:
+ # for integers we have chosen a wide range of values, so
+ # there will be no quantization and we expect no information
+ # loss
+ self.compare_array(data, rdata, "%s compressed images ('%s')" % (compress,dtype))
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testCompressPreserveZeros(self):
+ """
+ Test writing and reading gzip compressed image
+ """
+
+ zinds = [
+ (1, 3),
+ (2, 9),
+ ]
+ for compress in ['gzip', 'gzip_2', 'rice', 'hcompress']:
+ fname=tempfile.mktemp(prefix='fitsio-ImageWrite-',suffix='.fits.fz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ dtypes = ['f4','f8']
+
+ for dtype in dtypes:
+
+ data = numpy.random.normal(size=5*20).reshape(5,20).astype(dtype)
+ for zind in zinds:
+ data[zind[0], zind[1]] = 0.0
+
+ fits.write_image(
+ data,
+ compress=compress,
+ qlevel=16,
+ qmethod='SUBTRACTIVE_DITHER_2',
+ )
+ rdata = fits[-1].read()
+
+ for zind in zinds:
+ assert rdata[zind[0], zind[1]] == 0.0
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testReadIgnoreScaling(self):
+ """
+ Test the flag to ignore scaling when reading an HDU.
+ """
+ fname = tempfile.mktemp(prefix='fitsio-ReadIgnoreScaling-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ dtype = 'i2'
+ data = numpy.arange(10 * 20, dtype=dtype).reshape(10, 20)
+ header={
+ 'DTYPE': dtype,
+ 'BITPIX': 16,
+ 'NBYTES': data.dtype.itemsize,
+ 'BZERO': 9.33,
+ 'BSCALE': 3.281
+ }
+
+ fits.write_image(data, header=header)
+ hdu = fits[-1]
+
+ rdata = hdu.read()
+ self.assertEqual(rdata.dtype, numpy.float32, 'Wrong dtype.')
+
+ hdu.ignore_scaling = True
+ rdata = hdu[:,:]
+ self.assertEqual(rdata.dtype, dtype, 'Wrong dtype when ignoring.')
+ numpy.testing.assert_array_equal(data, rdata, err_msg='Wrong unscaled data.')
+
+ rh = fits[-1].read_header()
+ self.check_header(header, rh)
+
+ hdu.ignore_scaling = False
+ rdata = hdu[:,:]
+ self.assertEqual(rdata.dtype, numpy.float32, 'Wrong dtype when not ignoring.')
+ numpy.testing.assert_array_equal(data.astype(numpy.float32), rdata, err_msg='Wrong scaled data returned.')
+ finally:
+ # Clean up, if necessary. Using the "with" keyword above _should_
+ # take care of this auatomatically.
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testWriteKeyDict(self):
+ """
+ test that write_key works using a standard key dict
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-WriteKeyDict-',suffix='.fits')
+ nrows=3
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ im=numpy.zeros( (10,10), dtype='i2' )
+ fits.write(im)
+
+ keydict = {
+ 'name':'test',
+ 'value':35,
+ 'comment':'keydict test',
+ }
+ fits[-1].write_key(**keydict)
+
+ h = fits[-1].read_header()
+
+ self.assertEqual(h['test'],keydict['value'])
+ self.assertEqual(h.get_comment('test'),keydict['comment'])
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+
+ def testMoveByName(self):
+ """
+ test moving hdus by name
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-MoveByName-',suffix='.fits')
+ nrows=3
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ data1=numpy.zeros(nrows,dtype=[('ra','f8'),('dec','f8')])
+ data1['ra'] = numpy.random.random(nrows)
+ data1['dec'] = numpy.random.random(nrows)
+ fits.write_table(data1, extname='mytable')
+
+ fits[-1].write_key("EXTVER", 1)
+
+ data2=numpy.zeros(nrows,dtype=[('ra','f8'),('dec','f8')])
+ data2['ra'] = numpy.random.random(nrows)
+ data2['dec'] = numpy.random.random(nrows)
+
+ fits.write_table(data2, extname='mytable')
+ fits[-1].write_key("EXTVER", 2)
+
+ hdunum1=fits.movnam_hdu('mytable',extver=1)
+ self.assertEqual(hdunum1,2)
+ hdunum2=fits.movnam_hdu('mytable',extver=2)
+ self.assertEqual(hdunum2,3)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testExtVer(self):
+ """
+ Test using extname and extver, all combinations I can think of
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-ExtVer-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ img1=numpy.arange(2*3,dtype='i4').reshape(2,3) + 5
+ img2=numpy.arange(2*3,dtype='i4').reshape(2,3) + 6
+ img3=numpy.arange(2*3,dtype='i4').reshape(2,3) + 7
+
+ nrows=3
+ data1=numpy.zeros(nrows,dtype=[('num','i4'),('ra','f8'),('dec','f8')])
+ data1['num'] = 1
+ data1['ra'] = numpy.random.random(nrows)
+ data1['dec'] = numpy.random.random(nrows)
+
+ data2=numpy.zeros(nrows,dtype=[('num','i4'),('ra','f8'),('dec','f8')])
+ data2['num'] = 2
+ data2['ra'] = numpy.random.random(nrows)
+ data2['dec'] = numpy.random.random(nrows)
+
+ data3=numpy.zeros(nrows,dtype=[('num','i4'),('ra','f8'),('dec','f8')])
+ data3['num'] = 3
+ data3['ra'] = numpy.random.random(nrows)
+ data3['dec'] = numpy.random.random(nrows)
+
+
+ hdr1={'k1':'key1'}
+ hdr2={'k2':'key2'}
+
+ fits.write_image(img1, extname='myimage', header=hdr1, extver=1)
+ fits.write_table(data1)
+ fits.write_table(data2,extname='mytable', extver=1)
+ fits.write_image(img2, extname='myimage', header=hdr2, extver=2)
+ fits.write_table(data3, extname='mytable',extver=2)
+ fits.write_image(img3)
+
+ d1 = fits[1].read()
+ d2 = fits['mytable'].read()
+ d2b = fits['mytable',1].read()
+ d3 = fits['mytable',2].read()
+
+
+ for f in data1.dtype.names:
+ self.compare_rec(data1, d1, "data1")
+ self.compare_rec(data2, d2, "data2")
+ self.compare_rec(data2, d2b, "data2b")
+ self.compare_rec(data3, d3, "data3")
+
+ dimg1 = fits[0].read()
+ dimg1b = fits['myimage',1].read()
+ dimg2 = fits['myimage',2].read()
+ dimg3 = fits[5].read()
+
+ self.compare_array(img1, dimg1,"img1")
+ self.compare_array(img1, dimg1b,"img1b")
+ self.compare_array(img2, dimg2,"img2")
+ self.compare_array(img3, dimg3,"img3")
+
+ rhdr1 = fitsio.read_header(fname, ext='myimage', extver=1)
+ rhdr2 = fitsio.read_header(fname, ext='myimage', extver=2)
+ self.assertTrue('k1' in rhdr1,'testing k1 in header version 1')
+ self.assertTrue('k2' in rhdr2,'testing k2 in header version 2')
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testVariableLengthColumns(self):
+ """
+ Write and read variable length columns
+ """
+
+ for vstorage in ['fixed','object']:
+ fname=tempfile.mktemp(prefix='fitsio-VarCol-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True,vstorage=vstorage) as fits:
+ fits.write(self.vardata)
+
+
+ # reading multiple columns
+ d = fits[1].read()
+ self.compare_rec_with_var(self.vardata,d,"read all test '%s'" % vstorage)
+
+ cols=['u2scalar','Sobj']
+ d = fits[1].read(columns=cols)
+ self.compare_rec_with_var(self.vardata,d,"read all test subcols '%s'" % vstorage)
+
+ # one at a time
+ for f in self.vardata.dtype.names:
+ d = fits[1].read_column(f)
+ if fitsio.util.is_object(self.vardata[f]):
+ self.compare_object_array(self.vardata[f], d,
+ "read all field '%s'" % f)
+
+ # same as above with slices
+ # reading multiple columns
+ d = fits[1][:]
+ self.compare_rec_with_var(self.vardata,d,"read all test '%s'" % vstorage)
+
+ d = fits[1][cols][:]
+ self.compare_rec_with_var(self.vardata,d,"read all test subcols '%s'" % vstorage)
+
+ # one at a time
+ for f in self.vardata.dtype.names:
+ d = fits[1][f][:]
+ if fitsio.util.is_object(self.vardata[f]):
+ self.compare_object_array(self.vardata[f], d,
+ "read all field '%s'" % f)
+
+
+
+ #
+ # now same with sub rows
+ #
+
+ # reading multiple columns
+ rows = numpy.array([0,2])
+ d = fits[1].read(rows=rows)
+ self.compare_rec_with_var(self.vardata,d,"read subrows test '%s'" % vstorage,
+ rows=rows)
+
+ d = fits[1].read(columns=cols, rows=rows)
+ self.compare_rec_with_var(self.vardata,d,"read subrows test subcols '%s'" % vstorage,
+ rows=rows)
+
+ # one at a time
+ for f in self.vardata.dtype.names:
+ d = fits[1].read_column(f,rows=rows)
+ if fitsio.util.is_object(self.vardata[f]):
+ self.compare_object_array(self.vardata[f], d,
+ "read subrows field '%s'" % f,
+ rows=rows)
+
+ # same as above with slices
+ # reading multiple columns
+ d = fits[1][rows]
+ self.compare_rec_with_var(self.vardata,d,"read subrows slice test '%s'" % vstorage,
+ rows=rows)
+ d = fits[1][2:4]
+ self.compare_rec_with_var(self.vardata,d,"read slice test '%s'" % vstorage,
+ rows=numpy.array([2,3]))
+
+ d = fits[1][cols][rows]
+ self.compare_rec_with_var(self.vardata,d,"read subcols subrows slice test '%s'" % vstorage,
+ rows=rows)
+ d = fits[1][cols][2:4]
+ self.compare_rec_with_var(self.vardata,d,"read subcols slice test '%s'" % vstorage,
+ rows=numpy.array([2,3]))
+
+ # one at a time
+ for f in self.vardata.dtype.names:
+ d = fits[1][f][rows]
+ if fitsio.util.is_object(self.vardata[f]):
+ self.compare_object_array(self.vardata[f], d,
+ "read subrows field '%s'" % f,
+ rows=rows)
+ d = fits[1][f][2:4]
+ if fitsio.util.is_object(self.vardata[f]):
+ self.compare_object_array(self.vardata[f], d,
+ "read slice field '%s'" % f,
+ rows=numpy.array([2,3]))
+
+
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testTableWriteRead(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWrite-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"testing write does not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fits[1].read()
+ self.compare_rec(self.data, d, "table read/write")
+
+ h = fits[1].read_header()
+ self.compare_headerlist_header(self.keys, h)
+
+ # see if our convenience functions are working
+ fitsio.write(fname, self.data2,
+ extname="newext",
+ header={'ra':335.2,'dec':-25.2})
+ d = fitsio.read(fname, ext='newext')
+ self.compare_rec(self.data2, d, "table data2")
+ # now test read_column
+ with fitsio.FITS(fname) as fits:
+
+ for f in self.data.dtype.names:
+ d = fits[1].read_column(f)
+ self.compare_array(self.data[f], d, "table 1 single field read '%s'" % f)
+
+ for f in self.data2.dtype.names:
+ d = fits['newext'].read_column(f)
+ self.compare_array(self.data2[f], d, "table 2 single field read '%s'" % f)
+
+ # now list of columns
+ for cols in [['u2scalar','f4vec','Sarr'],
+ ['f8scalar','u2arr','Sscalar']]:
+ d = fits[1].read(columns=cols)
+ for f in d.dtype.names:
+ self.compare_array(self.data[f][:], d[f], "test column list %s" % f)
+
+
+ rows = [1,3]
+ d = fits[1].read(columns=cols, rows=rows)
+ for f in d.dtype.names:
+ self.compare_array(self.data[f][rows], d[f], "test column list %s row subset" % f)
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableColumnIndexScalar(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWrite-',suffix='.fits')
+
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data = numpy.empty(1, dtype=[('Z', 'f8')])
+ data['Z'][:] = 1.0
+ fits.write_table(data)
+ fits.write_table(data)
+ try:
+ with fitsio.FITS(fname,'r',clobber=True) as fits:
+ assert fits[1]['Z'][0].ndim == 0
+ assert fits[1][0].ndim == 0
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableReadEmptyRows(self):
+ """
+ test reading empty list of rows from an table.
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWrite-',suffix='.fits')
+
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data = numpy.empty(1, dtype=[('Z', 'f8')])
+ data['Z'][:] = 1.0
+ fits.write_table(data)
+ fits.write_table(data)
+ try:
+ with fitsio.FITS(fname,'r',clobber=True) as fits:
+ assert len(fits[1].read(rows=[])) == 0
+ assert len(fits[1].read(rows=range(0, 0))) == 0
+ assert len(fits[1].read(rows=numpy.arange(0, 0))) == 0
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableFormatColumnSubset(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWrite-',suffix='.fits')
+
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data = numpy.empty(1, dtype=[('Z', 'f8'), ('Z_PERSON', 'f8')])
+ data['Z'][:] = 1.0
+ data['Z_PERSON'][:] = 1.0
+ fits.write_table(data)
+ fits.write_table(data)
+ fits.write_table(data)
+ try:
+ with fitsio.FITS(fname,'r',clobber=True) as fits:
+ # assert we do not have an extra row of 'Z'
+ sz = str(fits[2]['Z_PERSON']).split('\n')
+ s = str(fits[2][('Z_PERSON', 'Z')]).split('\n')
+ assert len(sz) == len(s) - 1
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableWriteDictOfArraysScratch(self):
+ """
+ This version creating the table from a dict of arrays, creating
+ table first
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableDict-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ d={}
+ for n in self.data.dtype.names:
+ d[n] = self.data[n]
+
+ fits.write(d)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname)
+ self.compare_rec(self.data, d, "list of dicts, scratch")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableWriteDictOfArrays(self):
+ """
+ This version creating the table from a dict of arrays
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableDict-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ fits.create_table_hdu(self.data, extname='mytable')
+
+ d={}
+ for n in self.data.dtype.names:
+ d[n] = self.data[n]
+
+ fits[-1].write(d)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname)
+ self.compare_rec(self.data, d, "list of dicts")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+
+ def testTableWriteDictOfArraysVar(self):
+ """
+ This version creating the table from a dict of arrays, variable
+ lenght columns
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableDictVar-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ d={}
+ for n in self.vardata.dtype.names:
+ d[n] = self.vardata[n]
+
+ fits.write(d)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname)
+ self.compare_rec_with_var(self.vardata,d,"dict of arrays, var")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+
+ def testTableWriteListOfArraysScratch(self):
+ """
+ This version creating the table from the names and list, creating
+ table first
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableListScratch-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ names = [n for n in self.data.dtype.names]
+ dlist = [self.data[n] for n in self.data.dtype.names]
+ fits.write(dlist, names=names)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname)
+ self.compare_rec(self.data, d, "list of arrays, scratch")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+
+
+ def testTableWriteListOfArrays(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWriteList-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ fits.create_table_hdu(self.data, extname='mytable')
+
+ columns = [n for n in self.data.dtype.names]
+ dlist = [self.data[n] for n in self.data.dtype.names]
+ fits[-1].write(dlist, columns=columns)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname, ext='mytable')
+ self.compare_rec(self.data, d, "list of arrays")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableWriteListOfArraysVar(self):
+ """
+ This version creating the table from the names and list, variable
+ lenght cols
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableListScratch-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ names = [n for n in self.vardata.dtype.names]
+ dlist = [self.vardata[n] for n in self.vardata.dtype.names]
+ fits.write(dlist, names=names)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"write should not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d = fitsio.read(fname)
+ self.compare_rec_with_var(self.vardata,d,"list of arrays, var")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableWriteBadString(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWriteBadString-',suffix='.fits')
+
+ try:
+ for d in ['S0','U0']:
+ dt=[('s',d)]
+
+ # old numpy didn't allow this dtype, so will throw
+ # a TypeError for empty dtype
+ try:
+ data = numpy.zeros(1, dtype=dt)
+ supported = True
+ except TypeError:
+ supported = False
+
+ if supported:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ fits.write(data)
+ got_error=False
+ except ValueError:
+ got_error=True
+
+ self.assertTrue(got_error == True,
+ "expected an error for zero sized string")
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testTableIter(self):
+ """
+ Test iterating over rows of a table
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableIter-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ try:
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"testing write does not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ # one row at a time
+ with fitsio.FITS(fname) as fits:
+ hdu = fits["mytable"]
+ i=0
+ for row_data in hdu:
+ self.compare_rec(self.data[i], row_data, "table data")
+ i+=1
+
+ finally:
+ if os.path.exists(fname):
+ #pass
+ os.remove(fname)
+
+ def testAsciiTableWriteRead(self):
+ """
+ Test write and read for an ascii table
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-AsciiTableWrite-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write_table(self.ascii_data, table_type='ascii', header=self.keys, extname='mytable')
+
+ # cfitsio always reports type as i4 and f8, period, even if if
+ # written with higher precision. Need to fix that somehow
+ for f in self.ascii_data.dtype.names:
+ d = fits[1].read_column(f)
+ if d.dtype == numpy.float64:
+ # note we should be able to do 1.11e-16 in principle, but in practice
+ # we get more like 2.15e-16
+ self.compare_array_tol(self.ascii_data[f], d, 2.15e-16, "table field read '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f], d, "table field read '%s'" % f)
+
+ rows = [1,3]
+ for f in self.ascii_data.dtype.names:
+ d = fits[1].read_column(f,rows=rows)
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f][rows], d, 2.15e-16,
+ "table field read subrows '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f][rows], d,
+ "table field read subrows '%s'" % f)
+
+ beg=1
+ end=3
+ for f in self.ascii_data.dtype.names:
+ d = fits[1][f][beg:end]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f][beg:end], d, 2.15e-16,
+ "table field read slice '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f][beg:end], d,
+ "table field read slice '%s'" % f)
+
+ cols = ['i2scalar','f4scalar']
+ for f in self.ascii_data.dtype.names:
+ data = fits[1].read(columns=cols)
+ for f in data.dtype.names:
+ d=data[f]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f], d, 2.15e-16, "table subcol, '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f], d, "table subcol, '%s'" % f)
+
+ data = fits[1][cols][:]
+ for f in data.dtype.names:
+ d=data[f]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f], d, 2.15e-16, "table subcol, '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f], d, "table subcol, '%s'" % f)
+
+ rows=[1,3]
+ for f in self.ascii_data.dtype.names:
+ data = fits[1].read(columns=cols,rows=rows)
+ for f in data.dtype.names:
+ d=data[f]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f][rows], d, 2.15e-16,
+ "table subcol, '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f][rows], d,
+ "table subcol, '%s'" % f)
+
+ data = fits[1][cols][rows]
+ for f in data.dtype.names:
+ d=data[f]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f][rows], d, 2.15e-16,
+ "table subcol/row, '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f][rows], d,
+ "table subcol/row, '%s'" % f)
+
+ for f in self.ascii_data.dtype.names:
+
+ data = fits[1][cols][beg:end]
+ for f in data.dtype.names:
+ d=data[f]
+ if d.dtype == numpy.float64:
+ self.compare_array_tol(self.ascii_data[f][beg:end], d, 2.15e-16,
+ "table subcol/slice, '%s'" % f)
+ else:
+ self.compare_array(self.ascii_data[f][beg:end], d,
+ "table subcol/slice, '%s'" % f)
+
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testTableInsertColumn(self):
+ """
+ Insert a new column
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableInsertColumn-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+
+ d = fits[1].read()
+
+ for n in d.dtype.names:
+ newname = n+'_insert'
+
+ fits[1].insert_column(newname, d[n])
+
+ newdata = fits[1][newname][:]
+
+ self.compare_array(d[n], newdata, "table single field insert and read '%s'" % n)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableDeleteRowRange(self):
+ """
+ Test deleting a range of rows using the delete_rows method
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableDeleteRowRange-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+
+ rowslice = slice(1,3)
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].delete_rows(rowslice)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = self.data[ [0,3] ]
+ self.compare_rec(compare_data, d, "delete row range")
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableDeleteRows(self):
+ """
+ Test deleting specific set of rows using the delete_rows method
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableDeleteRows-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+
+ rows2delete = [1,3]
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].delete_rows(rows2delete)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = self.data[ [0,2] ]
+ self.compare_rec(compare_data, d, "delete rows")
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableResize(self):
+ """
+ Use the resize method to change the size of a table
+
+ default values get filled in and these are tested
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableResize-',suffix='.fits')
+ try:
+
+ #
+ # shrink from back
+ #
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+
+ nrows = 2
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].resize(nrows)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = self.data[0:nrows]
+ self.compare_rec(compare_data, d, "shrink from back")
+
+
+ #
+ # shrink from front
+ #
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].resize(nrows, front=True)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = self.data[nrows-self.data.size:]
+ self.compare_rec(compare_data, d, "shrink from front")
+
+
+ # These don't get zerod
+
+ nrows = 10
+ add_data = numpy.zeros(nrows-self.data.size,dtype=self.data.dtype)
+ add_data['i1scalar'] = -128
+ add_data['i1vec'] = -128
+ add_data['i1arr'] = -128
+ add_data['u2scalar'] = 32768
+ add_data['u2vec'] = 32768
+ add_data['u2arr'] = 32768
+ add_data['u4scalar'] = 2147483648
+ add_data['u4vec'] = 2147483648
+ add_data['u4arr'] = 2147483648
+
+
+ #
+ # expand at the back
+ #
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].resize(nrows)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = numpy.hstack( (self.data, add_data) )
+ self.compare_rec(compare_data, d, "expand at the back")
+
+ #
+ # expand at the front
+ #
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write_table(self.data)
+ with fitsio.FITS(fname,'rw') as fits:
+ fits[1].resize(nrows, front=True)
+
+ with fitsio.FITS(fname) as fits:
+ d = fits[1].read()
+
+ compare_data = numpy.hstack( (add_data, self.data) )
+ # These don't get zerod
+ self.compare_rec(compare_data, d, "expand at the front")
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+
+ def testSlice(self):
+ """
+ Test reading by slice
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableAppend-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ # initial write
+ fits.write_table(self.data)
+
+ # test reading single columns
+ for f in self.data.dtype.names:
+ d = fits[1][f][:]
+ self.compare_array(self.data[f], d, "test read all rows %s column subset" % f)
+
+ # test reading row subsets
+ rows = [1,3]
+ for f in self.data.dtype.names:
+ d = fits[1][f][rows]
+ self.compare_array(self.data[f][rows], d, "test %s row subset" % f)
+ for f in self.data.dtype.names:
+ d = fits[1][f][1:3]
+ self.compare_array(self.data[f][1:3], d, "test %s row slice" % f)
+ for f in self.data.dtype.names:
+ d = fits[1][f][1:4:2]
+ self.compare_array(self.data[f][1:4:2], d, "test %s row slice with step" % f)
+ for f in self.data.dtype.names:
+ d = fits[1][f][::2]
+ self.compare_array(self.data[f][::2], d, "test %s row slice with only setp" % f)
+
+ # now list of columns
+ cols=['u2scalar','f4vec','Sarr']
+ d = fits[1][cols][:]
+ for f in d.dtype.names:
+ self.compare_array(self.data[f][:], d[f], "test column list %s" % f)
+
+
+ cols=['u2scalar','f4vec','Sarr']
+ d = fits[1][cols][rows]
+ for f in d.dtype.names:
+ self.compare_array(self.data[f][rows], d[f], "test column list %s row subset" % f)
+
+ cols=['u2scalar','f4vec','Sarr']
+ d = fits[1][cols][1:3]
+ for f in d.dtype.names:
+ self.compare_array(self.data[f][1:3], d[f], "test column list %s row slice" % f)
+
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+
+
+ def testTableAppend(self):
+ """
+ Test creating a table and appending new rows.
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableAppend-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ # initial write
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+ # now append
+ data2 = self.data.copy()
+ data2['f4scalar'] = 3
+ fits[1].append(data2)
+
+ d = fits[1].read()
+ self.assertEqual(d.size, self.data.size*2)
+
+ self.compare_rec(self.data, d[0:self.data.size], "Comparing initial write")
+ self.compare_rec(data2, d[self.data.size:], "Comparing appended data")
+
+ h = fits[1].read_header()
+ self.compare_headerlist_header(self.keys, h)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableSubsets(self):
+ """
+ testing reading subsets
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWrite-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+
+
+ rows = [1,3]
+ d = fits[1].read(rows=rows)
+ self.compare_rec_subrows(self.data, d, rows, "table subset")
+ columns = ['i1scalar','f4arr']
+ d = fits[1].read(columns=columns, rows=rows)
+
+ for f in columns:
+ d = fits[1].read_column(f,rows=rows)
+ self.compare_array(self.data[f][rows], d, "row subset, multi-column '%s'" % f)
+ for f in self.data.dtype.names:
+ d = fits[1].read_column(f,rows=rows)
+ self.compare_array(self.data[f][rows], d, "row subset, column '%s'" % f)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+
+ def testGZWriteRead(self):
+ """
+ Test a basic table write, data and a header, then reading back in to
+ check the values
+
+ this code all works, but the file is zere size when done!
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-GZTableWrite-',suffix='.fits.gz')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+
+ d = fits[1].read()
+ self.compare_rec(self.data, d, "gzip write/read")
+
+ h = fits[1].read_header()
+ for entry in self.keys:
+ name=entry['name'].upper()
+ value=entry['value']
+ hvalue = h[name]
+ if isinstance(hvalue,str):
+ hvalue = hvalue.strip()
+ self.assertEqual(value,hvalue,"testing header key '%s'" % name)
+
+ if 'comment' in entry:
+ self.assertEqual(entry['comment'].strip(),
+ h.get_comment(name).strip(),
+ "testing comment for header key '%s'" % name)
+ stat=os.stat(fname)
+ self.assertNotEqual(stat.st_size, 0, "Making sure the data was flushed to disk")
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testBz2Read(self):
+ '''
+ Write a normal .fits file, run bzip2 on it, then read the bz2
+ file and verify that it's the same as what we put in; we don't
+ [currently support or] test *writing* bzip2.
+ '''
+
+ if 'SKIP_BZIP_TEST' in os.environ:
+ if sys.version_info >= (2,7,0):
+ self.skipTest("skipping bzip tests")
+ else:
+ # skipTest only works for python 2.7+
+ # just return
+ return
+
+ fname=tempfile.mktemp(prefix='fitsio-BZ2TableWrite-',suffix='.fits')
+ bzfname = fname + '.bz2'
+
+ try:
+ fits = fitsio.FITS(fname,'rw',clobber=True)
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+ fits.close()
+
+ os.system('bzip2 %s' % fname)
+ f2 = fitsio.FITS(bzfname)
+ d = f2[1].read()
+ self.compare_rec(self.data, d, "bzip2 read")
+
+ h = f2[1].read_header()
+ for entry in self.keys:
+ name=entry['name'].upper()
+ value=entry['value']
+ hvalue = h[name]
+ if isinstance(hvalue,str):
+ hvalue = hvalue.strip()
+ self.assertEqual(value,hvalue,"testing header key '%s'" % name)
+ if 'comment' in entry:
+ self.assertEqual(entry['comment'].strip(),
+ h.get_comment(name).strip(),
+ "testing comment for header key '%s'" % name)
+ except:
+ import traceback
+ traceback.print_exc()
+ self.assertTrue(False, 'Exception in testing bzip2 reading')
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+ if os.path.exists(bzfname):
+ os.remove(bzfname)
+ pass
+
+ def testChecksum(self):
+ """
+ test that checksumming works
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-Checksum-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ fits.write_table(self.data, header=self.keys, extname='mytable')
+ fits[1].write_checksum()
+ fits[1].verify_checksum()
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTrimStrings(self):
+ """
+ test mode where we strim strings on read
+ """
+ fname=tempfile.mktemp(prefix='fitsio-Trim-',suffix='.fits')
+ dt=[('fval','f8'),('name','S15'),('vec','f4',2)]
+ n=3
+ data=numpy.zeros(n, dtype=dt)
+ data['fval'] = numpy.random.random(n)
+ data['vec'] = numpy.random.random(n*2).reshape(n,2)
+
+ data['name'] = ['mike','really_long_name_to_fill','jan']
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write(data)
+
+ for onconstruct in [True,False]:
+ if onconstruct:
+ ctrim=True
+ otrim=False
+ else:
+ ctrim=False
+ otrim=True
+
+ with fitsio.FITS(fname,'rw', trim_strings=ctrim) as fits:
+
+ if ctrim:
+ dread=fits[1][:]
+ self.compare_rec(
+ data,
+ dread,
+ "trimmed strings constructor",
+ )
+
+ dname=fits[1]['name'][:]
+ self.compare_array(
+ data['name'],
+ dname,
+ "trimmed strings col read, constructor",
+ )
+ dread=fits[1][ ['name'] ][:]
+ self.compare_array(
+ data['name'],
+ dread['name'],
+ "trimmed strings col read, constructor",
+ )
+
+
+
+ dread=fits[1].read(trim_strings=otrim)
+ self.compare_rec(
+ data,
+ dread,
+ "trimmed strings keyword",
+ )
+ dname=fits[1].read(columns='name', trim_strings=otrim)
+ self.compare_array(
+ data['name'],
+ dname,
+ "trimmed strings col keyword",
+ )
+ dread=fits[1].read(columns=['name'], trim_strings=otrim)
+ self.compare_array(
+ data['name'],
+ dread['name'],
+ "trimmed strings col keyword",
+ )
+
+
+
+ # convenience function
+ dread=fitsio.read(fname, trim_strings=True)
+ self.compare_rec(
+ data,
+ dread,
+ "trimmed strings convenience function",
+ )
+ dname=fitsio.read(fname, columns='name', trim_strings=True)
+ self.compare_array(
+ data['name'],
+ dname,
+ "trimmed strings col convenience function",
+ )
+ dread=fitsio.read(fname, columns=['name'], trim_strings=True)
+ self.compare_array(
+ data['name'],
+ dread['name'],
+ "trimmed strings col convenience function",
+ )
+
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def testLowerUpper(self):
+ """
+ test forcing names to upper and lower
+ """
+ fname=tempfile.mktemp(prefix='fitsio-LowerUpper-',suffix='.fits')
+ dt=[('MyName','f8'),('StuffThings','i4'),('Blah','f4')]
+ data=numpy.zeros(3, dtype=dt)
+ data['MyName'] = numpy.random.random(data.size)
+ data['StuffThings'] = numpy.random.random(data.size)
+ data['Blah'] = numpy.random.random(data.size)
+
+ lnames = [n.lower() for n in data.dtype.names]
+ unames = [n.upper() for n in data.dtype.names]
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write(data)
+
+ for i in [1,2]:
+ if i == 1:
+ lower=True
+ upper=False
+ else:
+ lower=False
+ upper=True
+
+ with fitsio.FITS(fname,'rw', lower=lower, upper=upper) as fits:
+ for rows in [None, [1,2]]:
+
+ d=fits[1].read(rows=rows)
+ self.compare_names(d.dtype.names,data.dtype.names,
+ lower=lower,upper=upper)
+
+
+ d=fits[1].read(rows=rows, columns=['MyName','stuffthings'])
+ self.compare_names(d.dtype.names,data.dtype.names[0:2],
+ lower=lower,upper=upper)
+
+ d = fits[1][1:2]
+ self.compare_names(d.dtype.names,data.dtype.names,
+ lower=lower,upper=upper)
+
+ if rows is not None:
+ d = fits[1][rows]
+ else:
+ d = fits[1][:]
+ self.compare_names(d.dtype.names,data.dtype.names,
+ lower=lower,upper=upper)
+
+ if rows is not None:
+ d = fits[1][['myname','stuffthings']][rows]
+ else:
+ d = fits[1][['myname','stuffthings']][:]
+ self.compare_names(d.dtype.names,data.dtype.names[0:2],
+ lower=lower,upper=upper)
+
+ # using overrides
+ with fitsio.FITS(fname,'rw') as fits:
+ for rows in [None, [1,2]]:
+
+ d=fits[1].read(rows=rows, lower=lower, upper=upper)
+ self.compare_names(d.dtype.names,data.dtype.names,
+ lower=lower,upper=upper)
+
+
+ d=fits[1].read(rows=rows, columns=['MyName','stuffthings'],
+ lower=lower,upper=upper)
+ self.compare_names(d.dtype.names,data.dtype.names[0:2],
+ lower=lower,upper=upper)
+
+
+
+ for rows in [None, [1,2]]:
+ d=fitsio.read(fname, rows=rows, lower=lower, upper=upper)
+ self.compare_names(d.dtype.names,data.dtype.names,
+ lower=lower,upper=upper)
+
+ d=fitsio.read(fname, rows=rows, columns=['MyName','stuffthings'],
+ lower=lower, upper=upper)
+ self.compare_names(d.dtype.names,data.dtype.names[0:2],
+ lower=lower,upper=upper)
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testReadRaw(self):
+ """
+ testing reading the file as raw bytes
+ """
+ fname=tempfile.mktemp(prefix='fitsio-readraw-',suffix='.fits')
+
+ dt=[('MyName','f8'),('StuffThings','i4'),('Blah','f4')]
+ data=numpy.zeros(3, dtype=dt)
+ data['MyName'] = numpy.random.random(data.size)
+ data['StuffThings'] = numpy.random.random(data.size)
+ data['Blah'] = numpy.random.random(data.size)
+
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ fits.write(data)
+ raw1 = fits.read_raw()
+
+ with fitsio.FITS('mem://', 'rw') as fits:
+ fits.write(data)
+ raw2 = fits.read_raw()
+
+ f = open(fname, 'rb')
+ raw3 = f.read()
+ f.close()
+
+ self.assertEqual(raw1, raw2)
+ self.assertEqual(raw1, raw3)
+ except:
+ import traceback
+ traceback.print_exc()
+ self.assertTrue(False, 'Exception in testing read_raw')
+
+ def testTableBitcolReadWrite(self):
+ """
+ Test basic write/read with bitcols
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableWriteBitcol-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ try:
+ fits.write_table(self.bdata, extname='mytable', write_bitcols=True)
+ write_success=True
+ except:
+ write_success=False
+
+ self.assertTrue(write_success,"testing write does not raise an error")
+ if not write_success:
+ self.skipTest("cannot test result if write failed")
+
+ d=fits[1].read()
+ self.compare_rec(self.bdata, d, "table read/write")
+
+ # now test read_column
+ with fitsio.FITS(fname) as fits:
+
+ for f in self.bdata.dtype.names:
+ d = fits[1].read_column(f)
+ self.compare_array(self.bdata[f], d, "table 1 single field read '%s'" % f)
+
+ # now list of columns
+ for cols in [['b1vec','b1arr']]:
+ d = fits[1].read(columns=cols)
+ for f in d.dtype.names:
+ self.compare_array(self.bdata[f][:], d[f], "test column list %s" % f)
+
+ rows = [1,3]
+ d = fits[1].read(columns=cols, rows=rows)
+ for f in d.dtype.names:
+ self.compare_array(self.bdata[f][rows], d[f], "test column list %s row subset" % f)
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableBitcolAppend(self):
+ """
+ Test creating a table with bitcol support and appending new rows.
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableAppendBitcol-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ # initial write
+ fits.write_table(self.bdata, extname='mytable', write_bitcols=True)
+
+ with fitsio.FITS(fname,'rw') as fits:
+ # now append
+ bdata2 = self.bdata.copy()
+ fits[1].append(bdata2)
+
+ d = fits[1].read()
+ self.assertEqual(d.size, self.bdata.size*2)
+
+ self.compare_rec(self.bdata, d[0:self.data.size], "Comparing initial write")
+ self.compare_rec(bdata2, d[self.data.size:], "Comparing appended data")
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def testTableBitcolInsert(self):
+ """
+ Test creating a table with bitcol support and appending new rows.
+ """
+
+ fname=tempfile.mktemp(prefix='fitsio-TableBitcolInsert-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+
+ # initial write
+ nrows=3
+ d = numpy.zeros(nrows, dtype=[('ra','f8')])
+ d['ra'] = range(d.size)
+ fits.write(d)
+
+ with fitsio.FITS(fname,'rw') as fits:
+ bcol = numpy.array([True,False,True])
+
+ # now append
+ fits[-1].insert_column('bscalar_inserted', bcol, write_bitcols=True)
+
+ d = fits[-1].read()
+ self.assertEqual(d.size, nrows,'read size equals')
+ self.compare_array(bcol, d['bscalar_inserted'], "inserted bitcol")
+
+ bvec = numpy.array([[True,False], [False,True], [True,True] ])
+
+ # now append
+ fits[-1].insert_column('bvec_inserted', bvec, write_bitcols=True)
+
+ d = fits[-1].read()
+ self.assertEqual(d.size, nrows,'read size equals')
+ self.compare_array(bvec, d['bvec_inserted'], "inserted bitcol")
+
+
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+
+ def _record_exists(self, header_records, key, value):
+ for rec in header_records:
+ if rec['name'] == key and rec['value'] == value:
+ return True
+
+ return False
+
+ def testReadCommentHistory(self):
+ fname=tempfile.mktemp(prefix='fitsio-TableBitcolInsert-',suffix='.fits')
+ try:
+ with fitsio.FITS(fname,'rw',clobber=True) as fits:
+ data = numpy.arange(100).reshape(10, 10)
+ fits.create_image_hdu(data)
+ hdu = fits[-1]
+ hdu.write_comment('A COMMENT 1')
+ hdu.write_comment('A COMMENT 2')
+ hdu.write_history('SOME HISTORY 1')
+ hdu.write_history('SOME HISTORY 2')
+ fits.close()
+
+ with fitsio.FITS(fname, 'r') as fits:
+ hdu = fits[-1]
+ header = hdu.read_header()
+ records = header.records()
+ self.assertTrue(self._record_exists(records, 'COMMENT', 'A COMMENT 1'))
+ self.assertTrue(self._record_exists(records, 'COMMENT', 'A COMMENT 2'))
+ self.assertTrue(self._record_exists(records, 'HISTORY', 'SOME HISTORY 1'))
+ self.assertTrue(self._record_exists(records, 'HISTORY', 'SOME HISTORY 2'))
+
+ finally:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+
+ def compare_names(self, read_names, true_names, lower=False, upper=False):
+ for nread,ntrue in zip(read_names,true_names):
+ if lower:
+ tname = ntrue.lower()
+ mess="lower: '%s' vs '%s'" % (nread,tname)
+ else:
+ tname = ntrue.upper()
+ mess="upper: '%s' vs '%s'" % (nread,tname)
+ self.assertEqual(nread, tname, mess)
+
+ def check_header(self, header, rh):
+ for k in header:
+ v = header[k]
+ rv = rh[k]
+ if isinstance(rv,str):
+ v = v.strip()
+ rv = rv.strip()
+ self.assertEqual(v,rv,"testing equal key '%s'" % k)
+
+
+ def compare_headerlist_header(self, header_list, header):
+ """
+ The first is a list of dicts, second a FITSHDR
+ """
+ for entry in header_list:
+ name=entry['name'].upper()
+ value=entry['value']
+ hvalue = header[name]
+ if isinstance(hvalue,str):
+ hvalue = hvalue.strip()
+ self.assertEqual(value,hvalue,"testing header key '%s'" % name)
+
+ if 'comment' in entry:
+ self.assertEqual(entry['comment'].strip(),
+ header.get_comment(name).strip(),
+ "testing comment for header key '%s'" % name)
+
+ def _cast_shape(self, shape):
+ if len(shape) == 2 and shape[1] == 1:
+ return (shape[0],)
+ elif shape == (1,):
+ return tuple()
+ else:
+ return shape
+
+ def compare_array_tol(self, arr1, arr2, tol, name):
+ self.assertEqual(arr1.shape, arr2.shape,
+ "testing arrays '%s' shapes are equal: "
+ "input %s, read: %s" % (name, arr1.shape, arr2.shape))
+
+ adiff = numpy.abs( (arr1-arr2)/arr1 )
+ maxdiff = adiff.max()
+ res=numpy.where(adiff > tol)
+ for i,w in enumerate(res):
+ self.assertEqual(w.size,0,
+ "testing array '%s' dim %d are "
+ "equal within tolerance %e, found "
+ "max diff %e" % (name,i,tol,maxdiff))
+
+ def compare_array_abstol(self, arr1, arr2, tol, name):
+ self.assertEqual(arr1.shape, arr2.shape,
+ "testing arrays '%s' shapes are equal: "
+ "input %s, read: %s" % (name, arr1.shape, arr2.shape))
+
+ adiff = numpy.abs(arr1-arr2)
+ maxdiff = adiff.max()
+ res=numpy.where(adiff > tol)
+ for i,w in enumerate(res):
+ self.assertEqual(w.size,0,
+ "testing array '%s' dim %d are "
+ "equal within tolerance %e, found "
+ "max diff %e" % (name,i,tol,maxdiff))
+
+
+ def compare_array(self, arr1, arr2, name):
+ arr1_shape = self._cast_shape(arr1.shape)
+ arr2_shape = self._cast_shape(arr2.shape)
+
+ self.assertEqual(arr1_shape, arr2_shape,
+ "testing arrays '%s' shapes are equal: "
+ "input %s, read: %s" % (name, arr1_shape, arr2_shape))
+
+ if sys.version_info >= (3, 0, 0) and arr1.dtype.char == 'S':
+ _arr1 = arr1.astype('U')
+ else:
+ _arr1 = arr1
+ res=numpy.where(_arr1 != arr2)
+ for i,w in enumerate(res):
+ self.assertEqual(w.size,0,"testing array '%s' dim %d are equal" % (name,i))
+
+ def compare_rec(self, rec1, rec2, name):
+ for f in rec1.dtype.names:
+ rec1_shape = self._cast_shape(rec1[f].shape)
+ rec2_shape = self._cast_shape(rec2[f].shape)
+ self.assertEqual(rec1_shape, rec2_shape,
+ "testing '%s' field '%s' shapes are equal: "
+ "input %s, read: %s" % (
+ name, f, rec1_shape, rec2_shape))
+
+ if sys.version_info >= (3, 0, 0) and rec1[f].dtype.char == 'S':
+ # for python 3, we get back unicode always
+ _rec1f = rec1[f].astype('U')
+ else:
+ _rec1f = rec1[f]
+
+ res=numpy.where(_rec1f != rec2[f])
+ for w in res:
+ self.assertEqual(w.size,0,"testing column %s" % f)
+
+ def compare_rec_subrows(self, rec1, rec2, rows, name):
+ for f in rec1.dtype.names:
+ rec1_shape = self._cast_shape(rec1[f][rows].shape)
+ rec2_shape = self._cast_shape(rec2[f].shape)
+
+ self.assertEqual(rec1_shape, rec2_shape,
+ "testing '%s' field '%s' shapes are equal: "
+ "input %s, read: %s" % (
+ name, f, rec1_shape, rec2_shape))
+
+ if sys.version_info >= (3, 0, 0) and rec1[f].dtype.char == 'S':
+ # for python 3, we get back unicode always
+ _rec1frows = rec1[f][rows].astype('U')
+ else:
+ _rec1frows = rec1[f][rows]
+
+ res=numpy.where(_rec1frows != rec2[f])
+ for w in res:
+ self.assertEqual(w.size,0,"testing column %s" % f)
+
+ #self.assertEqual(2,3,"on purpose error")
+
+ def compare_rec_with_var(self, rec1, rec2, name, rows=None):
+ """
+
+ First one *must* be the one with object arrays
+
+ Second can have fixed length
+
+ both should be same number of rows
+
+ """
+
+ if rows is None:
+ rows = arange(rec2.size)
+ self.assertEqual(rec1.size,rec2.size,
+ "testing '%s' same number of rows" % name)
+
+ # rec2 may have fewer fields
+ for f in rec2.dtype.names:
+
+ # f1 will have the objects
+ if fitsio.util.is_object(rec1[f]):
+ self.compare_object_array(rec1[f], rec2[f],
+ "testing '%s' field '%s'" % (name,f),
+ rows=rows)
+ else:
+ self.compare_array(rec1[f][rows], rec2[f],
+ "testing '%s' num field '%s' equal" % (name,f))
+
+ def compare_object_array(self, arr1, arr2, name, rows=None):
+ """
+ The first must be object
+ """
+ if rows is None:
+ rows = arange(arr1.size)
+
+ for i,row in enumerate(rows):
+ if (sys.version_info >= (3, 0, 0) and isinstance(arr2[i], bytes)) or isinstance(arr2[i], str):
+ if sys.version_info >= (3, 0, 0) and isinstance(arr1[row], bytes):
+ _arr1row = arr1[row].decode('ascii')
+ else:
+ _arr1row = arr1[row]
+ self.assertEqual(_arr1row,arr2[i],
+ "%s str el %d equal" % (name,i))
+ else:
+ delement = arr2[i]
+ orig = arr1[row]
+ s=len(orig)
+ self.compare_array(orig, delement[0:s],
+ "%s num el %d equal" % (name,i))
+
+ def compare_rec_with_var_subrows(self, rec1, rec2, name, rows):
+ """
+
+ Second one must be the one with object arrays
+
+ """
+ for f in rec1.dtype.names:
+ if fitsio.util.is_object(rec2[f]):
+
+ for i in xrange(rec2.size):
+ if isinstance(rec2[f][i],str):
+ self.assertEqual(rec1[f][i],rec2[f][i],
+ "testing '%s' str field '%s' el %d equal" % (name,f,i))
+ else:
+ delement = rec1[f][i]
+ orig = rec2[f][i]
+ s=orig.size
+ self.compare_array(orig, delement[0:s],
+ "testing '%s' num field '%s' el %d equal" % (name,f,i))
+ else:
+ self.compare_array(rec1[f], rec2[f],
+ "testing '%s' num field '%s' equal" % (name,f))
+
+
+
+
+
+if __name__ == '__main__':
+ test()
--- /dev/null
+"""
+utilities for the fits library
+"""
+import sys
+import numpy
+
+from . import _fitsio_wrap
+
+if sys.version_info >= (3, 0, 0):
+ IS_PY3 = True
+else:
+ IS_PY3 = False
+
+
+class FITSRuntimeWarning(RuntimeWarning):
+ pass
+
+
+def cfitsio_version(asfloat=False):
+ """
+ Return the cfitsio version as a string.
+ """
+ # use string version to avoid roundoffs
+ ver = '%0.3f' % _fitsio_wrap.cfitsio_version()
+ if asfloat:
+ return float(ver)
+ else:
+ return ver
+
+
+if sys.version_info > (3, 0, 0):
+ _itypes = (int,)
+ _stypes = (str, bytes)
+else:
+ _itypes = (int, long) # noqa - only for py2
+ _stypes = (basestring, unicode,) # noqa - only for py2
+
+_itypes += (numpy.uint8, numpy.int8,
+ numpy.uint16, numpy.int16,
+ numpy.uint32, numpy.int32,
+ numpy.uint64, numpy.int64)
+
+# different for py3
+_stypes += (numpy.string_, numpy.str_)
+
+# for header keywords
+_ftypes = (float, numpy.float32, numpy.float64)
+
+
+def isstring(arg):
+ return isinstance(arg, _stypes)
+
+
+def isinteger(arg):
+ return isinstance(arg, _itypes)
+
+
+def is_object(arr):
+ if arr.dtype.descr[0][1][1] == 'O':
+ return True
+ else:
+ return False
+
+
+def fields_are_object(arr):
+ isobj = numpy.zeros(len(arr.dtype.names), dtype=bool)
+ for i, name in enumerate(arr.dtype.names):
+ if is_object(arr[name]):
+ isobj[i] = True
+ return isobj
+
+
+def is_little_endian(array):
+ """
+ Return True if array is little endian, False otherwise.
+
+ Parameters
+ ----------
+ array: numpy array
+ A numerical python array.
+
+ Returns
+ -------
+ Truth value:
+ True for little-endian
+
+ Notes
+ -----
+ Strings are neither big or little endian. The input must be a simple numpy
+ array, not an array with fields.
+ """
+ if numpy.little_endian:
+ machine_little = True
+ else:
+ machine_little = False
+
+ byteorder = array.dtype.base.byteorder
+ return (byteorder == '<') or (machine_little and byteorder == '=')
+
+
+def array_to_native(array, inplace=False):
+ """
+ Convert an array to the native byte order.
+
+ NOTE: the inplace keyword argument is not currently used.
+ """
+ if numpy.little_endian:
+ machine_little = True
+ else:
+ machine_little = False
+
+ data_little = False
+ if array.dtype.names is None:
+
+ if array.dtype.base.byteorder == '|':
+ # strings and 1 byte integers
+ return array
+
+ data_little = is_little_endian(array)
+ else:
+ # assume all are same byte order: we only need to find one with
+ # little endian
+ for fname in array.dtype.names:
+ if is_little_endian(array[fname]):
+ data_little = True
+ break
+
+ if ((machine_little and not data_little)
+ or (not machine_little and data_little)):
+ output = array.byteswap(inplace)
+ else:
+ output = array
+
+ return output
+
+
+def array_to_native_c(array_in, inplace=False):
+ # copy only made if not C order
+ arr = numpy.array(array_in, order='C', copy=False)
+ return array_to_native(arr, inplace=inplace)
+
+
+def mks(val):
+ """
+ make sure the value is a string, paying mind to python3 vs 2
+ """
+ if sys.version_info > (3, 0, 0):
+ if isinstance(val, bytes):
+ sval = str(val, 'utf-8')
+ else:
+ sval = str(val)
+ else:
+ sval = str(val)
+
+ return sval
--- /dev/null
+# Patches for cfitsio
+
+This directory contains patches for the cfitsio build. These patches
+are applied before the library is compiled during the python package
+build step.
+
+The patches were generated with the script `build_cfitsio_patches.py` by
+Matthew Becker in December of 2018.
+
+## Adding New Patches
+
+To add new patches, you need to
+
+1. Make a copy of the file you want to patch.
+2. Modify it.
+3. Call `diff -u old_file new_file` to a get a unified format patch.
+4. Make sure the paths in the patch at the top look like this
+ ```
+ --- cfitsio<version>/<filename> 2018-03-01 10:28:51.000000000 -0600
+ +++ cfitsio<version>/<filename> 2018-12-14 08:39:20.000000000 -0600
+ ...
+ ```
+ where `<version>` and `<filename>` have the current cfitsio version and
+ file that is being patched.
+
+5. Commit the patch file in the patches directory with the name `<filename>.patch`.
--- /dev/null
+import os
+import sys
+import subprocess
+
+VERSION = '3.47'
+SRC_URL = (
+ "https://heasarc.gsfc.nasa.gov/FTP/software/"
+ "fitsio/c/cfitsio-%s.tar.gz" % VERSION)
+SRC_TARBALL = os.path.basename(SRC_URL)
+SRC_DIR = os.path.basename(SRC_URL).replace('.tar.gz', '')
+
+# download
+os.system(
+ 'rm -rf %s && rm -f %s && wget %s && tar xzvf %s && ls -alh' % (
+ SRC_DIR, SRC_TARBALL, SRC_URL, SRC_TARBALL))
+
+# diff src files
+# the sources are all at the top level
+os.makedirs('patches', exist_ok=True)
+
+for root, _, files in os.walk(SRC_DIR):
+ print(files)
+ for fname in files:
+ src = os.path.join(SRC_DIR, fname)
+ dst = os.path.join('cfitsio-%spatch' % VERSION, fname)
+ patch = os.path.join('patches', fname + '.patch')
+ os.system('diff -u %s %s > %s' % (src, dst, patch))
+ with open(patch, 'rb') as fp:
+ buff = fp.read()
+ if len(buff) == 0:
+ os.remove(patch)
+ break
+
+# clean up
+os.system('rm -rf %s && rm -f %s' % (SRC_DIR, SRC_TARBALL))
--- /dev/null
+--- cfitsio3470/configure.in 2018-03-01 10:28:51.000000000 -0600
++++ cfitsio3470/configure.in 2018-12-14 08:39:20.000000000 -0600
+@@ -42,6 +42,13 @@
+ [ if test $enableval = yes; then SSE_FLAGS="$SSE_FLAGS -mssse3"; fi ]
+ )
+
++AC_ARG_ENABLE(
++ standard_strings,
++ [AS_HELP_STRING([--enable-standard-strings],[Enable use of FITSIO standard string processing])],
++ [ if test $enableval = yes; then USE_STANDARD_STRINGS=yes; fi ]
++)
++
++
+ # Define BUILD_HERA when building for HERA project to activate code in
+ # drvrfile.c (by way of fitsio2.h):
+ AC_ARG_ENABLE(
+@@ -582,6 +589,14 @@
+ AC_CHECK_LIB([pthread],[main],[],[AC_MSG_ERROR(Unable to locate pthread library needed when enabling reentrant multithreading)])
+ fi
+
++# ------------------------------------------------------------------------------
++# Define FITS_USE_STANDARD_STRINGS
++# ------------------------------------------------------------------------------
++if test "x$USE_STANDARD_STRINGS" = xyes; then
++ AC_DEFINE(FITS_USE_STANDARD_STRINGS)
++fi
++
++
+ # -------------------------------------------------------------------------
+ # there are some idiosyncrasies with semun defs (used in semxxx). Solaris
+ # does not define it at all
--- /dev/null
+--- cfitsio3470/configure 2018-03-01 10:28:51.000000000 -0600
++++ cfitsio3470/configure 2018-12-14 08:39:20.000000000 -0600
+@@ -708,6 +708,7 @@
+ enable_reentrant
+ enable_sse2
+ enable_ssse3
++enable_standard_strings
+ enable_hera
+ with_gsiftp_flavour
+ with_gsiftp
+@@ -1339,6 +1340,8 @@
+ instruction set
+ --enable-ssse3 Enable use of instructions in the SSSE3 extended
+ instruction set
++ --enable-standard-strings
++ Enable use of FITSIO standard string processing
+ --enable-hera Build for HERA (ASD use only)
+
+ Optional Packages:
+@@ -2250,6 +2253,14 @@
+ fi
+
+
++# Check whether --enable-standard_strings was given.
++if test "${enable_standard_strings+set}" = set; then :
++ enableval=$enable_standard_strings; if test $enableval = yes; then USE_STANDARD_STRINGS=yes; fi
++
++fi
++
++
++
+ # Define BUILD_HERA when building for HERA project to activate code in
+ # drvrfile.c (by way of fitsio2.h):
+ # Check whether --enable-hera was given.
+@@ -5072,6 +5083,15 @@
+
+ fi
+
++# ------------------------------------------------------------------------------
++# Define FITS_USE_STANDARD_STRINGS
++# ------------------------------------------------------------------------------
++if test "x$USE_STANDARD_STRINGS" = xyes; then
++ $as_echo "#define FITS_USE_STANDARD_STRINGS 1" >>confdefs.h
++
++fi
++
++
+ # -------------------------------------------------------------------------
+ # there are some idiosyncrasies with semun defs (used in semxxx). Solaris
+ # does not define it at all
--- /dev/null
+--- drvrnet.c 2020-03-03 09:04:34.333712777 -0500
++++ drvrnet_new.c 2020-03-03 09:05:00.523143138 -0500
+@@ -1258,7 +1258,7 @@
+ if (urlname)
+ {
+ fprintf(stderr,"Downloading ");
+- fprintf(stderr,urlname);
++ fprintf(stderr,"%s",urlname);
+ fprintf(stderr,"...\n");
+ }
+ isFirst = 0;
--- /dev/null
+--- cfitsio3470/fitscore.c 2018-03-01 10:28:51.000000000 -0600
++++ cfitsio3470/fitscore.c 2018-12-14 08:39:20.000000000 -0600
+@@ -182,6 +182,19 @@
+
+ return(*version);
+ }
++
++/*
++ Return 1 if we are to treat strings per the FITS standard (not
++ replacing nulls with spaces, and not padding with spaces)
++*/
++int fits_use_standard_strings(void) {
++#ifdef FITS_USE_STANDARD_STRINGS
++ return 1;
++#else
++ return 0;
++#endif
++}
++
+ /*--------------------------------------------------------------------------*/
+ int ffflnm(fitsfile *fptr, /* I - FITS file pointer */
+ char *filename, /* O - name of the file */
--- /dev/null
+--- cfitsio3470/fitsio.h 2018-03-01 10:28:51.000000000 -0600
++++ cfitsio3470/fitsio.h 2018-12-14 08:39:20.000000000 -0600
+@@ -797,6 +797,7 @@
+ /*---------------- utility routines -------------*/
+
+ float CFITS_API ffvers(float *version);
++int CFITS_API fits_use_standard_strings(void);
+ void CFITS_API ffupch(char *string);
+ void CFITS_API ffgerr(int status, char *errtext);
+ void CFITS_API ffpmsg(const char *err_message);
--- /dev/null
+--- cfitsio3470/putcols.c 2018-03-01 10:28:51.000000000 -0600
++++ cfitsio3470/putcols.c 2018-12-14 08:39:20.000000000 -0600
+@@ -158,7 +158,16 @@
+
+ for (;jj < twidth; jj++) /* fill field with blanks, if needed */
+ {
+- *buffer = ' ';
++ if ( fits_use_standard_strings() ) {
++ if (snull[0] == ASCII_NULL_UNDEFINED) {
++ *buffer = ' ';
++ } else {
++ *buffer = '\0';
++ }
++ } else {
++ *buffer = ' ';
++ }
++
+ buffer++;
+ }
--- /dev/null
+[egg_info]
+tag_build =
+tag_date = 0
+
--- /dev/null
+#
+# setup script for fitsio, using setuptools
+#
+# c.f.
+# https://packaging.python.org/guides/distributing-packages-using-setuptools/
+
+from __future__ import print_function
+from setuptools import setup, Extension, find_packages
+from setuptools.command.build_ext import build_ext
+
+import os
+import subprocess
+from subprocess import Popen, PIPE
+import glob
+import shutil
+
+
+class build_ext_subclass(build_ext):
+ boolean_options = build_ext.boolean_options + ['use-system-fitsio']
+
+ user_options = build_ext.user_options + [
+ ('use-system-fitsio', None, "Use the cfitsio installed in the system"),
+ ('system-fitsio-includedir=', None,
+ "Path to look for cfitsio header; default is "
+ "the system search path."),
+ ('system-fitsio-libdir=', None,
+ "Path to look for cfitsio library; default is "
+ "the system search path."),
+ ]
+ cfitsio_version = '3490'
+ cfitsio_dir = 'cfitsio%s' % cfitsio_version
+
+ def initialize_options(self):
+ self.use_system_fitsio = False
+ self.system_fitsio_includedir = None
+ self.system_fitsio_libdir = None
+ build_ext.initialize_options(self)
+
+ def finalize_options(self):
+
+ build_ext.finalize_options(self)
+
+ self.cfitsio_build_dir = os.path.join(
+ self.build_temp, self.cfitsio_dir)
+ self.cfitsio_zlib_dir = os.path.join(
+ self.cfitsio_build_dir, 'zlib')
+ self.cfitsio_patch_dir = os.path.join(
+ self.build_temp, 'patches')
+
+ if self.use_system_fitsio:
+ if self.system_fitsio_includedir:
+ self.include_dirs.insert(0, self.system_fitsio_includedir)
+ if self.system_fitsio_libdir:
+ self.library_dirs.insert(0, self.system_fitsio_libdir)
+ else:
+ # We defer configuration of the bundled cfitsio to build_extensions
+ # because we will know the compiler there.
+ self.include_dirs.insert(0, self.cfitsio_build_dir)
+
+ def run(self):
+ # For extensions that require 'numpy' in their include dirs,
+ # replace 'numpy' with the actual paths
+ import numpy
+ np_include = numpy.get_include()
+
+ for extension in self.extensions:
+ if 'numpy' in extension.include_dirs:
+ idx = extension.include_dirs.index('numpy')
+ extension.include_dirs.insert(idx, np_include)
+ extension.include_dirs.remove('numpy')
+
+ build_ext.run(self)
+
+ def build_extensions(self):
+ if not self.use_system_fitsio:
+
+ # Use the compiler for building python to build cfitsio
+ # for maximized compatibility.
+
+ # there is some issue with non-aligned data with optimizations
+ # set to '-O3' on some versions of gcc. It appears to be
+ # a disagreement between gcc 4 and gcc 5
+
+ CCold = self.compiler.compiler
+ CC = []
+ for val in CCold:
+ if val == '-O3':
+ print("replacing '-O3' with '-O2' to address "
+ "gcc bug")
+ val = '-O2'
+ if val == 'ccache':
+ print("removing ccache from the compiler options")
+ continue
+
+ CC.append(val)
+
+ self.configure_cfitsio(
+ CC=CC,
+ ARCHIVE=self.compiler.archiver,
+ RANLIB=self.compiler.ranlib,
+ )
+
+ # If configure detected bzlib.h, we have to link to libbz2
+ with open(os.path.join(self.cfitsio_build_dir, 'Makefile')) as fp:
+ _makefile = fp.read()
+ if '-DHAVE_BZIP2=1' in _makefile:
+ self.compiler.add_library('bz2')
+ if '-DCFITSIO_HAVE_CURL=1' in _makefile:
+ self.compiler.add_library('curl')
+
+ self.compile_cfitsio()
+
+ # link against the .a library in cfitsio;
+ # It should have been a 'static' library of relocatable objects
+ # (-fPIC), since we use the python compiler flags
+
+ link_objects = glob.glob(
+ os.path.join(self.cfitsio_build_dir, '*.a'))
+
+ self.compiler.set_link_objects(link_objects)
+
+ # Ultimate hack: append the .a files to the dependency list
+ # so they will be properly rebuild if cfitsio source is updated.
+ for ext in self.extensions:
+ ext.depends += link_objects
+ else:
+ self.compiler.add_library('cfitsio')
+
+ # Check if system cfitsio was compiled with bzip2 and/or curl
+ if self.check_system_cfitsio_objects('bzip2'):
+ self.compiler.add_library('bz2')
+ if self.check_system_cfitsio_objects('curl_'):
+ self.compiler.add_library('curl')
+
+ # Make sure the external lib has the fits_use_standard_strings
+ # function. If not, then define a macro to tell the wrapper
+ # to always return False.
+ if not self.check_system_cfitsio_objects(
+ '_fits_use_standard_strings'):
+ self.compiler.define_macro(
+ 'FITSIO_PYWRAP_ALWAYS_NONSTANDARD_STRINGS')
+
+ # fitsio requires libm as well.
+ self.compiler.add_library('m')
+
+ # call the original build_extensions
+
+ build_ext.build_extensions(self)
+
+ def patch_cfitsio(self):
+ patches = glob.glob('%s/*.patch' % self.cfitsio_patch_dir)
+ for patch in patches:
+ fname = os.path.basename(patch.replace('.patch', ''))
+ try:
+ subprocess.check_call(
+ 'patch -N --dry-run %s/%s %s' % (
+ self.cfitsio_build_dir, fname, patch),
+ shell=True)
+ except subprocess.CalledProcessError:
+ pass
+ else:
+ subprocess.check_call(
+ 'patch %s/%s %s' % (
+ self.cfitsio_build_dir, fname, patch),
+ shell=True)
+
+ def configure_cfitsio(self, CC=None, ARCHIVE=None, RANLIB=None):
+
+ # prepare source code and run configure
+ def copy_update(dir1, dir2):
+ f1 = os.listdir(dir1)
+ for f in f1:
+ path1 = os.path.join(dir1, f)
+ path2 = os.path.join(dir2, f)
+
+ if os.path.isdir(path1):
+ if not os.path.exists(path2):
+ os.makedirs(path2)
+ copy_update(path1, path2)
+ else:
+ if not os.path.exists(path2):
+ shutil.copy(path1, path2)
+ else:
+ stat1 = os.stat(path1)
+ stat2 = os.stat(path2)
+ if (stat1.st_mtime > stat2.st_mtime):
+ shutil.copy(path1, path2)
+
+ if not os.path.exists('build'):
+ os.makedirs('build')
+
+ if not os.path.exists(self.cfitsio_build_dir):
+ os.makedirs(self.cfitsio_build_dir)
+
+ if not os.path.exists(self.cfitsio_patch_dir):
+ os.makedirs(self.cfitsio_patch_dir)
+
+ copy_update(self.cfitsio_dir, self.cfitsio_build_dir)
+ copy_update('patches', self.cfitsio_patch_dir)
+
+ # we patch the source in the buil dir to avoid mucking with the repo
+ self.patch_cfitsio()
+
+ makefile = os.path.join(self.cfitsio_build_dir, 'Makefile')
+
+ if os.path.exists(makefile):
+ # Makefile already there
+ return
+
+ args = ''
+ args += ' CC="%s"' % ' '.join(CC[:1])
+ args += ' CFLAGS="%s"' % ' '.join(CC[1:])
+
+ if ARCHIVE:
+ args += ' ARCHIVE="%s"' % ' '.join(ARCHIVE)
+ if RANLIB:
+ args += ' RANLIB="%s"' % ' '.join(RANLIB)
+
+ p = Popen(
+ "sh ./configure --with-bzip2 --enable-standard-strings " + args,
+ shell=True,
+ cwd=self.cfitsio_build_dir,
+ )
+ p.wait()
+ if p.returncode != 0:
+ raise ValueError(
+ "could not configure cfitsio %s" % self.cfitsio_version)
+
+ def compile_cfitsio(self):
+ p = Popen(
+ "make",
+ shell=True,
+ cwd=self.cfitsio_build_dir,
+ )
+ p.wait()
+ if p.returncode != 0:
+ raise ValueError(
+ "could not compile cfitsio %s" % self.cfitsio_version)
+
+ def check_system_cfitsio_objects(self, obj_name):
+ for lib_dir in self.library_dirs:
+ if os.path.isfile('%s/libcfitsio.a' % (lib_dir)):
+ p = Popen(
+ "nm -g %s/libcfitsio.a | grep %s" % (lib_dir, obj_name),
+ shell=True,
+ stdout=PIPE,
+ stderr=PIPE,
+ )
+ if len(p.stdout.read()) > 0:
+ return True
+ else:
+ return False
+
+
+sources = ["fitsio/fitsio_pywrap.c"]
+
+ext = Extension("fitsio._fitsio_wrap", sources, include_dirs=['numpy'])
+
+description = ("A full featured python library to read from and "
+ "write to FITS files.")
+
+with open(os.path.join(os.path.dirname(__file__), "README.md")) as fp:
+ long_description = fp.read()
+
+classifiers = [
+ "Development Status :: 5 - Production/Stable",
+ "License :: OSI Approved :: GNU General Public License (GPL)",
+ "Topic :: Scientific/Engineering :: Astronomy",
+ "Intended Audience :: Science/Research",
+]
+
+setup(
+ name="fitsio",
+ version="1.1.4",
+ description=description,
+ long_description=long_description,
+ long_description_content_type='text/markdown; charset=UTF-8; variant=GFM',
+ license="GPL",
+ classifiers=classifiers,
+ url="https://github.com/esheldon/fitsio",
+ author="Erin Scott Sheldon",
+ author_email="erin.sheldon@gmail.com",
+ setup_requires=['numpy'],
+ install_requires=['numpy'],
+ packages=find_packages(),
+ include_package_data=True,
+ ext_modules=[ext],
+ cmdclass={"build_ext": build_ext_subclass}
+)
projects / python-fitsio.git / commitdiff