| .. doctest-skip-all |
|
|
| astropy.io.fits History |
| *********************** |
|
|
| Prior to its inclusion in Astropy, the `astropy.io.fits` package was a stand- |
| alone package called `PyFITS`_. PyFITS is no longer actively maintained, and |
| its development is now solely in Astropy. |
| This page documents the release history of PyFITS prior to its merge into |
| Astropy. |
|
|
| .. contents:: PyFITS Changelog |
| :depth: 2 |
| :local: |
|
|
|
|
| 3.4.0 (2016-01-29) |
| ================== |
|
|
| This is the last released version of PyFITS as a standalone package. |
|
|
|
|
| 3.3.0 (2014-07-17) |
| ================== |
|
|
| New Features |
| ------------ |
|
|
| - Added new verification options ``fix+ignore``, ``fix+warn``, |
| ``fix+exception``, ``silentfix+ignore``, ``silentfix+warn``, and |
| ``silentfix+exception`` which give more control over how to report fixable |
| errors as opposed to unfixable errors. See the "Verification" section in |
| the PyFITS documentation for more details. |
|
|
| API Changes |
| ----------- |
|
|
| - The ``pyfits.new_table`` function is now fully deprecated (though will not |
| be removed for a long time, considering how widely it is used). |
|
|
| Instead please use the more explicit ``pyfits.BinTableHDU.from_columns`` to |
| create a new binary table HDU, and the similar |
| ``pyfits.TableHDU.from_columns`` to create a new ASCII table. These |
| otherwise accept the same arguments as ``pyfits.new_table`` which is now |
| just a wrapper for these. |
|
|
| - The ``.fromstring`` classmethod of each HDU type has been simplified such |
| that, true to its namesake, it only initializes an HDU from a string |
| containing its header *and* data. (spacetelescope/PyFITS#64) |
|
|
| - Fixed an issue where header wildcard matching (for example |
| ``header['DATE*']``) can be used to match *any* characters that might appear |
| in a keyword. Previously this only matched keywords containing characters |
| in the set ``[0-9A-Za-z_]``. Now this can also match a hyphen ``-`` and any |
| other characters, as some conventions like ``HIERARCH`` and record-valued |
| keyword cards allow a wider range of valid characters than standard FITS |
| keywords. |
|
|
| - This will be the *last* release to support the following APIs that have been |
| marked deprecated since PyFITS v3.1: |
|
|
| - The ``CardList`` class, which was part of the old header implementation. |
|
|
| - The ``Card.key`` attribute. Use ``Card.keyword`` instead. |
|
|
| - The ``Card.cardimage`` and ``Card.ascardimage`` attributes. Use simply |
| ``Card.image`` or ``str(card)`` instead. |
|
|
| - The ``create_card`` factory function. Simply use the normal ``Card`` |
| constructor instead. |
|
|
| - The ``create_card_from_string`` factory function. Use ``Card.fromstring`` |
| instead. |
|
|
| - The ``upper_key`` function. Use ``Card.normalize_keyword`` method instead |
| (this is not unlikely to be used outside of PyFITS itself, but it was |
| technically public API). |
|
|
| - The usage of ``Header.update`` with ``Header.update(keyword, value, |
| comment)`` arguments. ``Header.update`` should only be used analogously |
| to ``dict.update``. Use ``Header.set`` instead. |
|
|
| - The ``Header.ascard`` attribute. Use ``Header.cards`` instead for a list |
| of all the ``Card`` objects in the header. |
|
|
| - The ``Header.rename_key`` method. Use ``Header.rename_keyword`` instead. |
|
|
| - The ``Header.get_history`` method. Use ``header['HISTORY']`` instead |
| (normal keyword lookup). |
|
|
| - The ``Header.get_comment`` method. Use ``header['COMMENT']`` instead. |
|
|
| - The ``Header.toTxtFile`` method. Use ``header.totextfile`` instead. |
|
|
| - The ``Header.fromTxtFile`` method. Use ``Header.fromtextfile`` instead. |
|
|
| - The ``pyfits.tdump`` and ``tcreate`` functions. Use ``pyfits.tabledump`` |
| and ``pyfits.tableload`` respectively. |
|
|
| - The ``BinTableHDU.tdump`` and ``tcreate`` methods. Use |
| ``BinTableHDU.dump`` and ``BinTableHDU.load`` respectively. |
|
|
| - The ``txtfile`` argument to the ``Header`` constructor. Use |
| ``Header.fromfile`` instead. |
|
|
| - The ``startColumn`` and ``endColumn`` arguments to the ``FITS_record`` |
| constructor. These are unlikely to be used by any user code. |
|
|
| These deprecated interfaces will be removed from the development version of |
| PyFITS following the v3.3 release (they will still be available in any |
| v3.3.x bugfix releases, however). |
|
|
| Other Changes and Additions |
| --------------------------- |
|
|
| - PyFITS has switched to a unified code base which supports Python 2.5 through |
| 3.4 simultaneously without translation. This *shouldn't* have any |
| significant performance impacts, but please report if anything seems |
| noticeably slower. As a reminder, support for Python 2.5 will be ended |
| after PyFITS 3.3.x. |
| |
| - Warnings for deprecated APIs in PyFITS are now always displayed by default. |
| This is in line with a similar change made recently to Astropy: |
| https://github.com/astropy/astropy/pull/1871 |
| To disable PyFITS deprecation warnings in scripts one may call |
| ``pyfits.ignore_deprecation_warnings()`` after importing PyFITS. |
| |
| - ``Card`` objects have a new ``is_blank`` attribute which returns ``True`` if |
| the card represents a blank card (no keyword, value, or comment) and |
| ``False`` otherwise. |
| |
| Bug Fixes |
| --------- |
| |
| - Fixed a regression where it was not possible to save an empty "compressed" |
| image to a file (in this case there is nothing to compress, hence the |
| quotes, but trying to do so caused a crash). (spacetelescope/PyFITS#69) |
| |
| - Fixed a regression that may have been introduced in v3.2.1 with writing |
| compressed image HDUs, particularly compressed images using a non-empty |
| GZIP_COMPRESSED_DATA column. (spacetelescope/#71) |
| |
| |
| 3.2.4 (2014-06-02) |
| ================== |
| |
| - Fixed a regression where multiple consecutive calls of the ``writeto`` |
| method on the same HDU but to different files could lead to corrupt data or |
| crashes on the subsequent calls after the first. (spacetelescope/PyFITS#40) |
| |
| |
| 3.2.3 (2014-05-14) |
| ================== |
| |
| - Nominal support for Python 3.4. |
| |
| - Fixed a bug with using the ``tabledump`` and ``tableload`` functions with |
| tables containing array columns (columns in which each element is an array |
| instead of a single scalar value). (spacetelescope/PyFITS#22) |
| |
| - Fixed an issue where PyFITS allowed newline characters in header values and |
| comments. (spacetelescope/PyFITS#51) |
| |
| - Fixed pickling of ``FITS_rec`` (table data) objects. |
| (spacetelescope/PyFITS#53) |
| |
| - Improved behavior when writing large compressed images on OSX by removing an |
| unnecessary check for platform architecture. (spacetelescope/PyFITS#57) |
| |
| - Allow reading FITS files from file-like objects that do not have a |
| ``.closed`` attribute (and as such may not even have an "open" vs. "closed" |
| concept). (spacetelescope/PyFITS#56) |
| |
| - Fixed duplicate insertion of commentary keywords on compressed image |
| headers. (spacetelescope/PyFITS#58) |
| |
| - Fixed minor issue with comparison of header commentary card values. |
| (spacetelescope/PyFITS#59) |
| |
| |
| 3.1.6 (2014-05-14) |
| ================== |
| |
| - Nominal support for Python 3.4. |
| |
| - Fixed a bug with using the ``tabledump`` and ``tableload`` functions with |
| tables containing array columns (columns in which each element is an array |
| instead of a single scalar value). (Backported from 3.2.3) |
| |
| - Fixed an issue where PyFITS allowed newline characters in header values and |
| comments. (Backported from 3.2.3) |
| |
| - Fixed pickling of ``FITS_rec`` (table data) objects. |
| (Backported from 3.2.3) |
| |
| - Improved behavior when writing large compressed images on OSX by removing an |
| unnecessary check for platform architecture. (Backported from 3.2.3) |
| |
| - Allow reading FITS files from file-like objects that do not have a |
| ``.closed`` attribute (and as such may not even have an "open" vs. "closed" |
| concept). (Backported from 3.2.3) |
| |
| - Fixed minor issue with comparison of header commentary card values. |
| (Backported from 3.2.3) |
| |
| |
| 3.2.2 (2014-03-25) |
| ================== |
| |
| - Fixed a regression on deletion of record-valued keyword cards using |
| the Header wildcard syntax. This was intended to be fixed before the |
| v3.2.1 release. |
| |
| |
| 3.1.5 (2014-03-25) |
| ================== |
| |
| - Fixed a regression on deletion of record-valued keyword cards using |
| the Header wildcard syntax. This was intended to be fixed before the |
| v3.1.4 release. |
| |
| |
| 3.2.1 (2014-03-04) |
| ================== |
| |
| - Nominal support for the upcoming Python 3.4. |
| |
| - Added missing features from the ``Header.insert()`` method that were |
| intended for inclusion in the original 3.1 release: In addition to |
| accepting an integer index as the first argument, it also supports supplying |
| a keyword name as the first argument for insertion relative to a specific |
| keyword. It also now supports an optional ``after`` argument. If |
| ``after=True`` the insertion is made below the insertion point instead |
| of above it. (spacetelescope/PyFITS#12) |
| |
| - Fixed support for broadcasting of values assigned to table columns. |
| (spacetelescope/PyFITS#48) |
| |
| - A grab bag of minor performance improvements in headers. |
| (spacetelescope/PyFITS#46) |
| |
| - Fix an unrelated error that occurred when instantiating a ``ColDefs`` object |
| with invalid input. |
| |
| - Fixed an issue where opening an image containing pseudo-unsigned integers |
| and immediately writing it to a new file using the ``writeto`` method would |
| drop the scale factors that identified the data as unsigned. |
| |
| - Fixed a bug where writing a file with ``checksum=True`` did not add the |
| checksum on new files. (spacetelescope/PyFITS#8) |
| |
| - Fixed an issue where validating an HDU's checksums removed the checksum from |
| that HDU's header entirely (even if it was valid.) |
| |
| - Fixed checksums on compressed images, so that the ``ZHECKSUM`` and |
| ``ZDATASUM`` contain a checksum of the original image HDU, while |
| ``CHECKSUM`` and ``DATASUM`` contain checksums of the compressed image HDU. |
| This feature was supposed to be supported in 3.2, but the support was buggy. |
| |
| - Fixed an issue where the size of the heap was sometimes not computed |
| properly when writing an existing table containing variable-length array |
| columns to a new FITS file. This could result in corruption in the new FITS |
| file. (spacetelescope/PyFITS#47) |
| |
| - Fixed issue with updates to the header of ``CompImageHDU`` objects not being |
| preserved on save. (spacetelescope/PyFITS#23) |
| |
| - Fixed a bug where a boolean value of ``True`` in a header could not be |
| replaced with the integer 1, and likewise for ``False`` and 0 and vice |
| versa. |
| |
| - Fixed an issue similar to the above one but for numeric values--now |
| replacing a header value with an equivalent numeric value will up/downcast |
| that value. For example replacing '0' with '0.0' will write '0.0' to the |
| header so that it is returned as a floating point value. Likewise a float |
| can be downcast to an integer. (spacetelescope/PyFITS#49) |
| |
| - A handful of Python 3 compatibility fixes, especially for compatibility |
| with the upcoming Python 3.4. |
| |
| - Fixed unrelated crash when a header contains an invalid END card (for |
| example "END = "). This resulted in a cryptic traceback. Now headers like |
| this will detect "clearly intended" END cards and produce a warning about |
| their invalidity and fix them. (#217) |
| |
| - Allowed a sequence of ``Column`` objects to be passed in as the main |
| argument to ``FITS_rec.from_columns`` as the documentation suggests should |
| be possible. |
| |
| - Fixed a display formatting issue with fitsdiff where sometimes it did not |
| show the difference between two floating point numbers if they were the same |
| up to some low number of digits. (spacetelescope/PyFITS#21) |
| |
| - Fixed an issue where Python 2 sometimes allowed non-ASCII strings to be |
| assigned as header values if they were assigned as old-style ``str`` objects |
| and not ``unicode`` objects. (spacetelescope/PyFITS#37) |
| |
| |
| 3.1.4 (2014-03-04) |
| ================== |
| |
| - Added missing features from the ``Header.insert()`` method that were |
| intended for inclusion in the original 3.1 release: In addition to |
| accepting an integer index as the first argument, it also supports supplying |
| a keyword name as the first argument for insertion relative to a specific |
| keyword. It also now supports an optional ``after`` argument. If |
| ``after=True`` the insertion is made below the insertion point instead |
| of above it. (Backported from 3.2.1) |
| |
| - A grab bag of minor performance improvements in headers. |
| (Backported from 3.2.1) |
| |
| - Fixed an issue where opening an image containing pseudo-unsigned integers |
| and immediately writing it to a new file using the ``writeto`` method would |
| drop the scale factors that identified the data as unsigned. |
| (Backported from 3.2.1) |
| |
| - Fixed a bug where writing a file with ``checksum=True`` did not add the |
| checksum on new files. (Backported from 3.2.1) |
| |
| - Fixed an issue where validating an HDU's checksums removed the checksum from |
| that HDU's header entirely (even if it was valid.) |
| (Backported from 3.2.1) |
| |
| - Fixed an issue where the size of the heap was sometimes not computed |
| properly when writing an existing table containing variable-length array |
| columns to a new FITS file. This could result in corruption in the new FITS |
| file. (Backported from 3.2.1) |
| |
| - Fixed a bug where a boolean value of ``True`` in a header could not be |
| replaced with the integer 1, and likewise for ``False`` and 0 and vice |
| versa. (Backported from 3.2.1) |
| |
| - Fixed an issue similar to the above one but for numeric values--now |
| replacing a header value with an equivalent numeric value will up/downcast |
| that value. For example replacing '0' with '0.0' will write '0.0' to the |
| header so that it is returned as a floating point value. Likewise a float |
| can be downcast to an integer. (Backported from 3.2.1) |
| |
| - Fixed unrelated crash when a header contains an invalid END card (for |
| example "END = "). This resulted in a cryptic traceback. Now headers like |
| this will detect "clearly intended" END cards and produce a warning about |
| their invalidity and fix them. (Backported from 3.2.1) |
| |
| - Fixed a display formatting issue with fitsdiff where sometimes it did not |
| show the difference between two floating point numbers if they were the same |
| up to some low number of digits. (Backported from 3.2.1) |
| |
| - Fixed an issue where Python 2 sometimes allowed non-ASCII strings to be |
| assigned as header values if they were assigned as old-style ``str`` objects |
| and not ``unicode`` objects. (Backported from 3.2.1) |
| |
| |
| 3.0.13 (2014-03-04) |
| =================== |
| |
| - Fixed a bug where writing a file with ``checksum=True`` did not add the |
| checksum on new files. (Backported from 3.2.1) |
| |
| - Fixed an issue where validating an HDU's checksums removed the checksum from |
| that HDU's header entirely (even if it was valid.) |
| (Backported from 3.2.1) |
| |
| |
| 3.2 (2013-11-26) |
| ================ |
| |
| Highlights |
| ---------- |
| |
| - Rewrote CFITSIO-based backend for handling tile compression of FITS files. |
| It now uses a standard CFITSIO instead of heavily modified pieces of CFITSIO |
| as before. PyFITS ships with its own copy of CFITSIO v3.35 which supports |
| the latest version of the Tiled Image Convention (v2.3), but system |
| packagers may choose instead to strip this out in favor of a |
| system-installed version of CFITSIO. Earlier versions may work, but nothing |
| earlier than 3.28 has been tested yet. (#169) |
| |
| - Added support for reading and writing tables using the Q format for columns. |
| The Q format is identical to the P format (variable-length arrays) except |
| that it uses 64-bit integers for the data descriptors, allowing more than |
| 4 GB of variable-length array data in a single table. (#160) |
| |
| - Added initial support for table columns containing pseudo-unsigned integers. |
| This is currently enabled by using the ``uint=True`` option when opening |
| files; any table columns with the correct BZERO value will be interpreted |
| and returned as arrays of unsigned integers. |
| |
| - Some refactoring of the table and ``FITS_rec`` modules in order to better |
| separate the details of the FITS binary and ASCII table data structures from |
| the HDU data structures that encapsulate them. Most of these changes should |
| not be apparent to users (but see API Changes below). |
| |
| |
| API Changes |
| ----------- |
| |
| - Assigning to values in ``ColDefs.names``, ``ColDefs.formats``, |
| ``ColDefs.nulls`` and other attributes of ``ColDefs`` instances that return |
| lists of column properties is no longer supported. Assigning to those lists |
| will no longer update the corresponding columns. Instead, please just |
| modify the ``Column`` instances directly (``Column.name``, ``Column.null``, |
| etc.) |
| |
| - The ``pyfits.new_table`` function is marked "pending deprecation". This |
| does not mean it will be removed outright or that its functionality has |
| changed. It will likely be replaced in the future for a function with |
| similar, if not subtly different functionality. A better, if not slightly |
| more verbose approach is to use ``pyfits.FITS_rec.from_columns`` to create |
| a new ``FITS_rec`` table--this has the same interface as |
| ``pyfits.new_table``. The difference is that it returns a plan ``FITS_rec`` |
| array, and not an HDU instance. This ``FITS_rec`` object can then be used |
| as the data argument in the constructors for ``BinTableHDU`` (for binary |
| tables) or ``TableHDU`` (for ASCII tables). This is analogous to creating |
| an ``ImageHDU`` by passing in an image array. |
| ``pyfits.FITS_rec.from_columns`` is just a simpler way of creating a |
| FITS-compatible recarray from a FITS column specification. |
| |
| - The ``updateHeader``, ``updateHeaderData``, and ``updateCompressedData`` |
| methods of the ``CompDataHDU`` class are pending deprecation and moved to |
| internal methods. The operation of these methods depended too much on |
| internal state to be used safely by users; instead they are invoked |
| automatically in the appropriate places when reading/writing compressed image |
| HDUs. |
| |
| - The ``CompDataHDU.compData`` attribute is pending deprecation in favor of |
| the clearer and more PEP-8 compatible ``CompDataHDU.compressed_data``. |
| |
| - The constructor for ``CompDataHDU`` has been changed to accept new keyword |
| arguments. The new keyword arguments are essentially the same, but are in |
| underscore_separated format rather than camelCase format. The old arguments |
| are still pending deprecation. |
| |
| - The internal attributes of HDU classes ``_hdrLoc``, ``_datLoc``, and |
| ``_datSpan`` have been replaced with ``_header_offset``, ``_data_offset``, |
| and ``_data_size`` respectively. The old attribute names are still pending |
| deprecation. This should only be of interest to advanced users who have |
| created their own HDU subclasses. |
| |
| - The following previously deprecated functions and methods have been removed |
| entirely: ``createCard``, ``createCardFromString``, ``upperKey``, |
| ``ColDefs.data``, ``setExtensionNameCaseSensitive``, ``_File.getfile``, |
| ``_TableBaseHDU.get_coldefs``, ``Header.has_key``, ``Header.ascardlist``. |
| |
| If you run your code with a previous version of PyFITS (>= 3.0, < 3.2) with |
| the ``python -Wd`` argument, warnings for all deprecated interfaces still in |
| use will be displayed. |
| |
| - Interfaces that were pending deprecation are now fully deprecated. These |
| include: ``create_card``, ``create_card_from_string``, ``upper_key``, |
| ``Header.get_history``, and ``Header.get_comment``. |
| |
| - The ``.name`` attribute on HDUs is now directly tied to the HDU's header, so |
| that if ``.header['EXTNAME']`` changes so does ``.name`` and vice-versa. |
|
|
| - The ``pyfits.file.PYTHON_MODES`` constant dict was renamed to |
| ``pyfits.file.PYFITS_MODES`` which better reflects its purpose. This is |
| rarely used by client code, however. Support for the old name will be |
| removed by PyFITS 3.4. |
|
|
|
|
| Other Changes and Additions |
| --------------------------- |
|
|
| - The new compression code also adds support for the ZQUANTIZ and ZDITHER0 |
| keywords added in more recent versions of this FITS Tile Compression spec. |
| This includes support for lossless compression with GZIP. (#198) By default |
| no dithering is used, but the ``SUBTRACTIVE_DITHER_1`` and |
| ``SUBTRACTIVE_DITHER_2`` methods can be enabled by passing the correct |
| constants to the ``quantize_method`` argument to the ``CompImageHDU`` |
| constructor. A seed can be manually specified, or automatically generated |
| using either the system clock or checksum-based methods via the |
| ``dither_seed`` argument. See the documentation for ``CompImageHDU`` for |
| more details. (#198) (spacetelescope/PYFITS#32) |
|
|
| - Images compressed with the Tile Compression standard can now be larger than |
| 4 GB through support of the Q format. (#159) |
|
|
| - All HDUs now have a ``.ver`` ``.level`` attribute that returns the value of |
| the EXTVAL and EXTLEVEL keywords from that HDU's header, if the exist. This |
| was added for consistency with the ``.name`` attribute which returns the |
| EXTNAME value from the header. |
| |
| - Then ``Column`` and ``ColDefs`` classes have new ``.dtype`` attributes |
| which give the Numpy dtype for the column data in the first case, and the |
| full Numpy compound dtype for each table row in the latter case. |
| |
| - There was an issue where new tables created defaulted the values in all |
| string columns to '0.0'. Now string columns are filled with empty strings |
| by default--this seems a less surprising default, but it may cause |
| differences with tables created with older versions of PyFITS. |
| |
| - Improved round-tripping and preservation of manually assigned column |
| attributes (``TNULLn``, ``TSCALn``, etc.) in table HDU headers. |
| (astropy/astropy#996) |
| |
| |
| Bug Fixes |
| --------- |
| |
| - Binary tables containing compressed images may, optionally, contain other |
| columns unrelated to the tile compression convention. Although this is an |
| uncommon use case, it is permitted by the standard. (#159) |
| |
| - Reworked some of the file I/O routines to allow simpler, more consistent |
| mapping between OS-level file modes ('rb', 'wb', 'ab', etc.) and the more |
| "PyFITS-specific" modes used by PyFITS like "readonly" and "update". |
| That is, if reading a FITS file from an open file object, it doesn't matter |
| as much what "mode" it was opened in so long as it has the right |
| capabilities (read/write/etc.) Also works around bugs in the Python io |
| module in 2.6+ with regard to file modes. (spacetelescope/PyFITS#33) |
|
|
| - Fixed an obscure issue that can occur on systems that don't have flush to |
| memory-mapped files implemented (namely GNU Hurd). (astropy/astropy#968) |
| |
| |
| 3.1.3 (2013-11-26) |
| ================== |
| |
| - Disallowed assigning NaN and Inf floating point values as header values, |
| since the FITS standard does not define a way to represent them in. Because |
| this is undefined, the previous behavior did not make sense and produced |
| invalid FITS files. (spacetelescope/PyFITS#11) |
| |
| - Added a workaround for a bug in 64-bit OSX that could cause truncation when |
| writing files greater than 2^32 bytes in size. (spacetelescope/PyFITS#28) |
| |
| - Fixed a long-standing issue where writing binary tables did not correctly |
| write the TFORMn keywords for variable-length array columns (they omitted |
| the max array length parameter of the format). This was thought fixed in |
| v3.1.2, but it was only fixed there for compressed image HDUs and not for |
| binary tables in general. |
| |
| - Fixed an obscure issue that can occur on systems that don't have flush to |
| memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2) |
|
|
|
|
| 3.0.12 (2013-11-26) |
| =================== |
|
|
| - Disallowed assigning NaN and Inf floating point values as header values, |
| since the FITS standard does not define a way to represent them in. Because |
| this is undefined, the previous behavior did not make sense and produced |
| invalid FITS files. (Backported from 3.1.3) |
|
|
| - Added a workaround for a bug in 64-bit OSX that could cause truncation when |
| writing files greater than 2^32 bytes in size. (Backported from 3.1.3) |
|
|
| - Fixed a long-standing issue where writing binary tables did not correctly |
| write the TFORMn keywords for variable-length array columns (they omitted |
| the max array length parameter of the format). This was thought fixed in |
| v3.1.2, but it was only fixed there for compressed image HDUs and not for |
| binary tables in general. (Backported from 3.1.3) |
|
|
| - Fixed an obscure issue that can occur on systems that don't have flush to |
| memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2) |
| |
| |
| 3.1.3 (unreleased) |
| ================== |
| |
| - Disallowed assigning NaN and Inf floating point values as header values, |
| since the FITS standard does not define a way to represent them in. Because |
| this is undefined, the previous behavior did not make sense and produced |
| invalid FITS files. (spacetelescope/PyFITS#11) |
| |
| |
| 3.0.12 (unreleased) |
| =================== |
| |
| - Disallowed assigning NaN and Inf floating point values as header values, |
| since the FITS standard does not define a way to represent them in. Because |
| this is undefined, the previous behavior did not make sense and produced |
| invalid FITS files. (Backported from 3.1.3) |
| |
| - Added a workaround for a bug in 64-bit OSX that could cause truncation when |
| writing files greater than 2^32 bytes in size. (Backported from 3.1.3) |
| |
| |
| 3.1.2 (2013-04-22) |
| ================== |
| |
| - When an error occurs opening a file in fitsdiff the exception message will |
| now at least mention which file had the error. (#168) |
| |
| - Fixed support for opening gzipped FITS files by filename in a writeable mode |
| (PyFITS has supported writing to gzip files for some time now, but only |
| enabled it when GzipFile objects were passed to ``pyfits.open()`` due to |
| some legacy code preventing full gzip support. (#195) |
| |
| - Added a more helpful error message in the case of malformatted FITS files |
| that contain non-float NULL values in an ASCII table but are missing the |
| required TNULLn keywords in the header. (#197) |
| |
| - Fixed an (apparently long-standing) issue where writing compressed images |
| did not correctly write the TFORMn keywords for variable-length array |
| columns (they omitted the max array length parameter of the format). (#199) |
| |
| - Slightly refactored how tables containing variable-length array columns are |
| handled to add two improvements: Fixes an issue where accessing the data |
| after a call to the ``pyfits.getdata`` convenience function caused an |
| exception, and allows the VLA data to be read from an existing mmap of the |
| FITS file. (#200) |
| |
| - Fixed a bug that could occur when opening a table containing |
| multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it |
| out to a new file. (#201) |
| |
| - Added use of the console_scripts entry point to install the fitsdiff and |
| fitscheck scripts, which if nothing else provides better Windows support. |
| The generated scripts now override the ones explicitly defined in the |
| scripts/ directory (which were just trivial stubs to begin with). (#202) |
| |
| - Fixed a bug on Python 3 where attempting to open a non-existent file on |
| Python 3 caused a seemingly unrelated traceback. (#203) |
| |
| - Fixed a bug in fitsdiff that reported two header keywords containing NaN |
| as value as different. (#204) |
| |
| - Fixed an issue in the tests that caused some tests to fail if pyfits is |
| installed with read-only permissions. (#208) |
| |
| - Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array |
| containing boolean fields converted all the values to ``False``. (#215) |
| |
| - Fixed an issue where passing an array of integers into the constructor of |
| ``Column()`` when the column type is floats of the same byte width caused the |
| column array to become garbled. (#218) |
| |
| - Fixed inconsistent behavior in creating CONTINUE cards from byte strings |
| versus Unicode strings in Python 2--CONTINUE cards can now be created |
| properly from Unicode strings (so long as they are convertible to ASCII). |
| (spacetelescope/PyFITS#1) |
| |
| - Fixed a couple cases where creating a new table using TDIMn in some of the |
| columns could caused a crash. (spacetelescope/PyFITS#3) |
| |
| - Fixed a bug in parsing HIERARCH keywords that do not have a space after |
| the first equals sign (before the value). (spacetelescope/PyFITS#5) |
| |
| - Prevented extra leading whitespace on HIERARCH keywords from being treated |
| as part of the keyword. (spacetelescope/PyFITS#6) |
| |
| - Fixed a bug where HIERARCH keywords containing lower-case letters was |
| mistakenly marked as invalid during header validation. |
| (spacetelescope/PyFITS#7) |
| |
| - Fixed an issue that was ancillary to (spacetelescope/PyFITS#7) where the |
| ``Header.index()`` method did not work correctly with HIERARCH keywords |
| containing lower-case letters. |
| |
| |
| 3.0.11 (2013-04-17) |
| =================== |
| |
| - Fixed support for opening gzipped FITS files by filename in a writeable mode |
| (PyFITS has supported writing to gzip files for some time now, but only |
| enabled it when GzipFile objects were passed to ``pyfits.open()`` due to |
| some legacy code preventing full gzip support. Backported from 3.1.2. (#195) |
| |
| - Added a more helpful error message in the case of malformatted FITS files |
| that contain non-float NULL values in an ASCII table but are missing the |
| required TNULLn keywords in the header. Backported from 3.1.2. (#197) |
| |
| - Fixed an (apparently long-standing) issue where writing compressed images did |
| not correctly write the TFORMn keywords for variable-length array columns |
| (they omitted the max array length parameter of the format). Backported from |
| 3.1.2. (#199) |
| |
| - Slightly refactored how tables containing variable-length array columns are |
| handled to add two improvements: Fixes an issue where accessing the data |
| after a call to the ``pyfits.getdata`` convenience function caused an |
| exception, and allows the VLA data to be read from an existing mmap of the |
| FITS file. Backported from 3.1.2. (#200) |
| |
| - Fixed a bug that could occur when opening a table containing |
| multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it |
| out to a new file. Backported from 3.1.2. (#201) |
| |
| - Fixed a bug on Python 3 where attempting to open a non-existent file on |
| Python 3 caused a seemingly unrelated traceback. Backported from 3.1.2. |
| (#203) |
| |
| - Fixed a bug in fitsdiff that reported two header keywords containing NaN |
| as value as different. Backported from 3.1.2. (#204) |
| |
| - Fixed an issue in the tests that caused some tests to fail if pyfits is |
| installed with read-only permissions. Backported from 3.1.2. (#208) |
| |
| - Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array |
| containing boolean fields converted all the values to ``False``. Backported |
| from 3.1.2. (#215) |
| |
| - Fixed an issue where passing an array of integers into the constructor of |
| ``Column()`` when the column type is floats of the same byte width caused the |
| column array to become garbled. Backported from 3.1.2. (#218) |
| |
| - Fixed a couple cases where creating a new table using TDIMn in some of the |
| columns could caused a crash. Backported from 3.1.2. |
| (spacetelescope/PyFITS#3) |
| |
| |
| 3.1.1 (2013-01-02) |
| ================== |
| |
| This is a bug fix release for the 3.1.x series. |
| |
| Bug Fixes |
| --------- |
| |
| - Improved handling of scaled images and pseudo-unsigned integer images in |
| compressed image HDUs. They now work more transparently like normal image |
| HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options, |
| as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method |
| works better too. (#88) |
| |
| - Permits non-string values for the EXTNAME keyword when reading in a file, |
| rather than throwing an exception due to the malformatting. Added |
| verification for the format of the EXTNAME keyword when writing. (#96) |
| |
| - Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME |
| is specified in the header, it will also be reflected in the ``.name`` |
| attribute and in ``pyfits.info()``. These keywords used to be verboten in |
| PRIMARY HDUs, but the latest version of the FITS standard allows them. |
| (#151) |
| |
| - HCOMPRESS can again be used to compress data cubes (and higher-dimensional |
| arrays) so long as the tile size is effectively 2-dimensional. In fact, |
| PyFITS will automatically use compatible tile sizes even if they're not |
| explicitly specified. (#171) |
|
|
| - Added support for the optional ``endcard`` parameter in the |
| ``Header.fromtextfile()`` and ``Header.totextfile()`` methods. Although |
| ``endcard=False`` was a reasonable default assumption, there are still text |
| dumps of FITS headers that include the END card, so this should have been |
| more flexible. (#176) |
|
|
| - Fixed a crash when running fitsdiff on two empty (that is, zero row) tables. |
| (#178) |
|
|
| - Fixed an issue where opening files containing random groups HDUs in update |
| mode could cause an unnecessary rewrite of the file even if none of the |
| data is modified. (#179) |
|
|
| - Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS |
| is used with Numpy 1.7 in some cases. (#180) |
|
|
| - Fixed a crash when generating diff reports from diffs using the |
| ``ignore_comments`` options. (#181) |
|
|
| - Fixed some bugs with FITS WCS distortion paper record-valued keyword cards: |
|
|
| - Cards that looked kind of like RVKCs but were not intended to be were |
| over-permissively treated as such--commentary keywords like COMMENT and |
| HISTORY were particularly affected. (#183) |
|
|
| - Looking up a card in a header by its standard FITS keyword only should |
| always return the raw value of that card. That way cards containing |
| values that happen to valid RVKCs but were not intended to be will still |
| be treated like normal cards. (#184) |
|
|
| - Looking up a RVKC in a header with only part of the field-specifier (for |
| example "DP1.AXIS" instead of "DP1.AXIS.1") was implicitly treated as a |
| wildcard lookup. (#184) |
|
|
| - Fixed a crash when diffing two FITS files where at least one contains a |
| compressed image HDU which was not recognized as an image instead of a |
| table. (#187) |
|
|
| - Fixed bugs in the backwards compatibility layer for the ``CardList.index`` |
| and ``CardList.count`` methods. (#190) |
|
|
| - Improved ``__repr__`` and text file representation of cards with long values |
| that are split into CONTINUE cards. (#193) |
|
|
| - Fixed a crash when trying to assign a long (> 72 character) value to blank |
| ('') keywords. This also changed how blank keywords are represented--there |
| are still exactly 8 spaces before any commentary content can begin; this |
| *may* affect the exact display of header cards that assumed there could be |
| fewer spaces in a blank keyword card before the content begins. However, the |
| current approach is more in line with the requirements of the FITS standard. |
| (#194) |
|
|
|
|
| 3.0.10 (2013-01-02) |
| =================== |
|
|
| - Improved handling of scaled images and pseudo-unsigned integer images in |
| compressed image HDUs. They now work more transparently like normal image |
| HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options, |
| as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method |
| works better too. Backported from 3.1.1. (#88) |
|
|
| - Permits non-string values for the EXTNAME keyword when reading in a file, |
| rather than throwing an exception due to the malformatting. Added |
| verification for the format of the EXTNAME keyword when writing. Backported |
| from 3.1.1. (#96) |
|
|
| - Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME |
| is specified in the header, it will also be reflected in the ``.name`` |
| attribute and in ``pyfits.info()``. These keywords used to be verbotten in |
| PRIMARY HDUs, but the latest version of the FITS standard allows them. |
| Backported from 3.1.1. (#151) |
|
|
| - HCOMPRESS can again be used to compress data cubes (and higher-dimensional |
| arrays) so long as the tile size is effectively 2-dimensional. In fact, |
| PyFITS will not automatically use compatible tile sizes even if they're not |
| explicitly specified. Backported from 3.1.1. (#171) |
|
|
| - Fixed a bug when writing out files containing zero-width table columns, |
| where the TFIELDS keyword would be updated incorrectly, leaving the table |
| largely unreadable. Backported from 3.1.0. (#174) |
|
|
| - Fixed an issue where opening files containing random groups HDUs in update |
| mode could cause an unnecessary rewrite of the file even if none of the |
| data is modified. Backported from 3.1.1. (#179) |
|
|
| - Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS |
| is used with Numpy 1.7 in some cases. Backported from 3.1.1. (#180) |
|
|
|
|
| 3.1 (2012-08-08) |
| ================ |
|
|
| Highlights |
| ---------- |
|
|
| - The ``Header`` object has been significantly reworked, and ``CardList`` |
| objects are now deprecated (their functionality folded into the ``Header`` |
| class). See API Changes below for more details. |
|
|
| - Memory maps are now used by default to access HDU data. See API Changes |
| below for more details. |
|
|
| - Now includes a new version of the ``fitsdiff`` program for comparing two |
| FITS files, and a new FITS comparison API used by ``fitsdiff``. See New |
| Features below. |
|
|
| API Changes |
| ----------- |
|
|
| - The ``Header`` class has been rewritten, and the ``CardList`` class is |
| deprecated. Most of the basic details of working with FITS headers are |
| unchanged, and will not be noticed by most users. But there are differences |
| in some areas that will be of interest to advanced users, and to application |
| developers. For full details of the changes, see the "Header Interface |
| Transition Guide" section in the PyFITS documentation. See ticket #64 on |
| the PyFITS Trac for further details and background. Some highlights are |
| listed below: |
|
|
| * The Header class now fully implements the Python dict interface, and can |
| be used interchangeably with a dict, where the keys are header keywords. |
|
|
| * New keywords can be added to the header using normal keyword assignment |
| (previously it was necessary to use ``Header.update`` to add new |
| keywords). For example:: |
|
|
| >>> header['NAXIS'] = 2 |
|
|
| will update the existing 'FOO' keyword if it already exists, or add a new |
| one if it doesn't exist, just like a dict. |
| |
| * It is possible to assign both a value and a comment at the same time using |
| a tuple:: |
| |
| >>> header['NAXIS'] = (2, 'Number of axes') |
| |
| * To add/update a new card and ensure it's added in a specific location, use |
| ``Header.set()``:: |
|
|
| >>> header.set('NAXIS', 2, 'Number of axes', after='BITPIX') |
|
|
| This works the same as the old ``Header.update()``. ``Header.update()`` |
| still works in the old way too, but is deprecated. |
|
|
| * Although ``Card`` objects still exist, it generally is not necessary to |
| work with them directly. ``Header.ascardlist()``/``Header.ascard`` are |
| deprecated and should not be used. To directly access the ``Card`` |
| objects in a header, use ``Header.cards``. |
|
|
| * To access card comments, it is still possible to either go through the |
| card itself, or through ``Header.comments``. For example:: |
|
|
| >>> header.cards['NAXIS'].comment |
| Number of axes |
| >>> header.comments['NAXIS'] |
| Number of axes |
|
|
| * ``Card`` objects can now be used interchangeably with |
| ``(keyword, value, comment)`` 3-tuples. They still have ``.value`` and |
| ``.comment`` attributes as well. The ``.key`` attribute has been renamed |
| to ``.keyword`` for consistency, though ``.key`` is still supported (but |
| deprecated). |
|
|
| - Memory mapping is now used by default to access HDU data. That is, |
| ``pyfits.open()`` uses ``memmap=True`` as the default. This provides better |
| performance in the majority of use cases--there are only some I/O intensive |
| applications where it might not be desirable. Enabling mmap by default also |
| enabled finding and fixing a large number of bugs in PyFITS' handling of |
| memory-mapped data (most of these bug fixes were backported to PyFITS |
| 3.0.5). (#85) |
| |
| * A new ``pyfits.USE_MEMMAP`` global variable was added. Set |
| ``pyfits.USE_MEMMAP = False`` to change the default memmap setting for |
| opening files. This is especially useful for controlling the behavior in |
| applications where pyfits is deeply embedded. |
| |
| * Likewise, a new ``PYFITS_USE_MEMMAP`` environment variable is supported. |
| Set ``PYFITS_USE_MEMMAP = 0`` in your environment to change the default |
| behavior. |
| |
| - The ``size()`` method on HDU objects is now a ``.size`` property--this |
| returns the size in bytes of the data portion of the HDU, and in most cases |
| is equivalent to ``hdu.data.nbytes`` (#83) |
| |
| - ``BinTableHDU.tdump`` and ``BinTableHDU.tcreate`` are deprecated--use |
| ``BinTableHDU.dump`` and ``BinTableHDU.load`` instead. The new methods |
| output the table data in a slightly different format from previous versions, |
| which places quotes around each value. This format is compatible with data |
| dumps from previous versions of PyFITS, but not vice-versa due to a parsing |
| bug in older versions. |
| |
| - Likewise the ``pyfits.tdump`` and ``pyfits.tcreate`` convenience function |
| versions of these methods have been renamed ``pyfits.tabledump`` and |
| ``pyfits.tableload``. The old deprecated, but currently retained for |
| backwards compatibility. (r1125) |
| |
| - A new global variable ``pyfits.EXTENSION_NAME_CASE_SENSITIVE`` was added. |
| This serves as a replacement for ``pyfits.setExtensionNameCaseSensitive`` |
| which is not deprecated and may be removed in a future version. To enable |
| case-sensitivity of extension names (i.e. treat 'sci' as distinct from 'SCI') |
| set ``pyfits.EXTENSION_NAME_CASE_SENSITIVE = True``. The default is |
| ``False``. (r1139) |
| |
| - A new global configuration variable ``pyfits.STRIP_HEADER_WHITESPACE`` was |
| added. By default, if a string value in a header contains trailing |
| whitespace, that whitespace is automatically removed when the value is read. |
| Now if you set ``pyfits.STRIP_HEADER_WHITESPACE = False`` all whitespace is |
| preserved. (#146) |
| |
| - The old ``classExtensions`` extension mechanism (which was deprecated in |
| PyFITS 3.0) is removed outright. To our knowledge it was no longer used |
| anywhere. (r1309) |
| |
| - Warning messages from PyFITS issued through the Python warnings API are now |
| output to stderr instead of stdout, as is the default. PyFITS no longer |
| modifies the default behavior of the warnings module with respect to which |
| stream it outputs to. (r1319) |
| |
| - The ``checksum`` argument to ``pyfits.open()`` now accepts a value of |
| 'remove', which causes any existing CHECKSUM/DATASUM keywords to be ignored, |
| and removed when the file is saved. |
| |
| New Features |
| ------------ |
| |
| - Added support for the proposed "FITS" extension HDU type. FITS |
| HDUs contain an entire FITS file embedded in their data section. ``FitsHDU`` |
| objects work like other HDU types in PyFITS. Their ``.data`` attribute |
| returns the raw data array. However, they have a special ``.hdulist`` |
| attribute which processes the data as a FITS file and returns it as an |
| in-memory HDUList object. FitsHDU objects also support a |
| ``FitsHDU.fromhdulist()`` classmethod which returns a new ``FitsHDU`` object |
| that embeds the supplied HDUList. (#80) |
| |
| - Added a new ``.is_image`` attribute on HDU objects, which is True if the HDU |
| data is an 'image' as opposed to a table or something else. Here the |
| meaning of 'image' is fairly loose, and mostly just means a Primary or Image |
| extension HDU, or possibly a compressed image HDU (#71) |
| |
| - Added an ``HDUList.fromstring`` classmethod which can parse a FITS file |
| already in memory and instantiate and ``HDUList`` object from it. This |
| could be useful for integrating PyFITS with other libraries that work on |
| FITS file, such as CFITSIO. It may also be useful in streaming |
| applications. The name is a slight misnomer, in that it actually accepts |
| any Python object that implements the buffer interface, which includes |
| ``bytes``, ``bytearray``, ``memoryview``, ``numpy.ndarray``, etc. (#90) |
| |
| - Added a new ``pyfits.diff`` module which contains facilities for comparing |
| FITS files. One can use the ``pyfits.diff.FITSDiff`` class to compare two |
| FITS files in their entirety. There is also a ``pyfits.diff.HeaderDiff`` |
| class for just comparing two FITS headers, and other similar interfaces. |
| See the PyFITS Documentation for more details on this interface. The |
| ``pyfits.diff`` module powers the new ``fitsdiff`` program installed with |
| PyFITS. After installing PyFITS, run ``fitsdiff --help`` for usage details. |
| |
| - ``pyfits.open()`` now accepts a ``scale_back`` argument. If set to |
| ``True``, this automatically scales the data using the original BZERO and |
| BSCALE parameters the file had when it was first opened, if any, as well as |
| the original BITPIX. For example, if the original BITPIX were 16, this |
| would be equivalent to calling ``hdu.scale('int16', 'old')`` just before |
| calling ``flush()`` or ``close()`` on the file. This option applies to all |
| HDUs in the file. (#120) |
| |
| - ``pyfits.open()`` now accepts a ``save_backup`` argument. If set to |
| ``True``, this automatically saves a backup of the original file before |
| flushing any changes to it (this of course only applies to update and append |
| mode). This may be especially useful when working with scaled image data. |
| (#121) |
| |
| Changes in Behavior |
| ------------------- |
| |
| - Warnings from PyFITS are not output to stderr by default, instead of stdout |
| as it has been for some time. This is contrary to most users' expectations |
| and makes it more difficult for them to separate output from PyFITS from the |
| desired output for their scripts. (r1319) |
|
|
| Bug Fixes |
| --------- |
|
|
| - Fixed ``pyfits.tcreate()`` (now ``pyfits.tableload()``) to be more robust |
| when encountering blank lines in a column definition file (#14) |
|
|
| - Fixed a fairly rare crash that could occur in the handling of CONTINUE cards |
| when using Numpy 1.4 or lower (though 1.4 is the oldest version supported by |
| PyFITS). (r1330) |
|
|
| - Fixed ``_BaseHDU.fromstring`` to actually correctly instantiate an HDU |
| object from a string/buffer containing the header and data of that HDU. |
| This allowed for the implementation of ``HDUList.fromstring`` described |
| above. (#90) |
|
|
| - Fixed a rare corner case where, in some use cases, (mildly, recoverable) |
| malformatted float values in headers were not properly returned as floats. |
| (#137) |
|
|
| - Fixed a corollary to the previous bug where float values with a leading zero |
| before the decimal point had the leading zero unnecessarily removed when |
| saving changes to the file (eg. "0.001" would be written back as ".001" even |
| if no changes were otherwise made to the file). (#137) |
|
|
| - When opening a file containing CHECKSUM and/or DATASUM keywords in update |
| mode, the CHECKSUM/DATASUM are updated and preserved even if the file was |
| opened with checksum=False. This change in behavior prevents checksums from |
| being unintentionally removed. (#148) |
|
|
| - Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it |
| was not restoring the image to its original BSCALE and BZERO values. (#162) |
| |
| - Fixed a bug when writing out files containing zero-width table columns, |
| where the TFIELDS keyword would be updated incorrectly, leaving the table |
| largely unreadable. This fix will be backported to the 3.0.x series in |
| version 3.0.10. (#174) |
| |
| |
| 3.0.9 (2012-08-06) |
| ================== |
| |
| This is a bug fix release for the 3.0.x series. |
| |
| Bug Fixes |
| --------- |
| |
| - Fixed ``Header.values()``/``Header.itervalues()`` and ``Header.items()``/ |
| ``Header.iteritems()`` to correctly return the different values for |
| duplicate keywords (particularly commentary keywords like HISTORY and |
| COMMENT). This makes the old Header implementation slightly more compatible |
| with the new implementation in PyFITS 3.1. (#127) |
| |
| .. note:: |
| This fix did not change the existing behavior from earlier PyFITS |
| versions where ``Header.keys()`` returns all keywords in the header with |
| duplicates removed. PyFITS 3.1 changes that behavior, so that |
| ``Header.keys()`` includes duplicates. |
| |
| - Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it |
| was not restoring the image to its original BSCALE and BZERO values. (#162) |
|
|
| - Fixed a bug where opening a file containing compressed image HDUs in |
| 'update' mode and then immediately closing it without making any changes |
| caused the file to be rewritten unnecessarily. (#167) |
|
|
| - Fixed two memory leaks that could occur when writing compressed image data, |
| or in some cases when opening files containing compressed image HDUs in |
| 'update' mode. (#168) |
|
|
|
|
| 3.0.8 (2012-06-04) |
| ================== |
|
|
| Changes in Behavior |
| ------------------- |
|
|
| - Prior to this release, image data sections did not work with scaled |
| data--that is, images with non-trivial BSCALE and/or BZERO values. |
| Previously, in order to read such images in sections, it was necessary to |
| manually apply the BSCALE+BZERO to each section. It's worth noting that |
| sections *did* support pseudo-unsigned ints (flakily). This change just |
| extends that support for general BSCALE+BZERO values. |
| |
| Bug Fixes |
| --------- |
| |
| - Fixed a bug that prevented updates to values in boolean table columns from |
| being saved. This turned out to be a symptom of a deeper problem that could |
| prevent other table updates from being saved as well. (#139) |
| |
| - Fixed a corner case in which a keyword comment ending with the string "END" |
| could, in some circumstances, cause headers (and the rest of the file after |
| that point) to be misread. (#142) |
| |
| - Fixed support for scaled image data and pseudo-unsigned ints in image data |
| sections (``hdu.section``). Previously this was not supported at all. At |
| some point support was supposedly added, but it was buggy and incomplete. |
| Now the feature seems to work much better. (#143) |
| |
| - Fixed the documentation to point out that image data sections *do* support |
| non-contiguous slices (and have for a long time). The documentation was |
| never updated to reflect this, and misinformed users that only contiguous |
| slices were supported, leading to some confusion. (#144) |
| |
| - Fixed a bug where creating an ``HDUList`` object containing multiple PRIMARY |
| HDUs caused an infinite recursion when validating the object prior to |
| writing to a file. (#145) |
| |
| - Fixed a rare but serious case where saving an update to a file that |
| previously had a CHECKSUM and/or DATASUM keyword, but removed the checksum |
| in saving, could cause the file to be slightly corrupted and unreadable. |
| (#147) |
| |
| - Fixed problems with reading "non-standard" FITS files with primary headers |
| containing SIMPLE = F. PyFITS has never made many guarantees as to how such |
| files are handled. But it should at least be possible to read their |
| headers, and the data if possible. Saving changes to such a file should not |
| try to prepend an unwanted valid PRIMARY HDU. (#157) |
| |
| - Fixed a bug where opening an image with ``disable_image_compression = True`` |
| caused compression to be disabled for all subsequent ``pyfits.open()`` calls. |
| (r1651) |
| |
| |
| 3.0.7 (2012-04-10) |
| ================== |
| |
| Changes in Behavior |
| ------------------- |
| |
| - Slices of GroupData objects now return new GroupData objects instead of |
| extended multi-row _Group objects. This is analogous to how PyFITS 3.0 fixed |
| FITS_rec slicing, and should have been fixed for GroupData at the same time. |
| The old behavior caused bugs where functions internal to Numpy expected that |
| slicing an ndarray would return a new ndarray. As this is a rare use case |
| with a rare feature most users are unlikely to be affected by this change. |
| |
| - The previously internal _Group object for representing individual group |
| records in a GroupData object are renamed Group and are now a public |
| interface. However, there's almost no good reason to create Group objects |
| directly, so it shouldn't be considered a "new feature". |
| |
| - An annoyance from PyFITS 3.0.6 was fixed, where the value of the EXTEND |
| keyword was always being set to F if there are not actually any extension |
| HDUs. It was unnecessary to modify this value. |
| |
| Bug Fixes |
| --------- |
| |
| - Fixed GroupData objects to return new GroupData objects when sliced instead |
| of _Group record objects. See "Changes in behavior" above for more details. |
| |
| - Fixed slicing of Group objects--previously it was not possible to slice |
| slice them at all. |
| |
| - Made it possible to assign ``np.bool_`` objects as header values. (#123) |
| |
| - Fixed overly strict handling of the EXTEND keyword; see "Changes in |
| behavior" above. (#124) |
| |
| - Fixed many cases where an HDU's header would be marked as "modified" by |
| PyFITS and rewritten, even when no changes to the header are necessary. |
| (#125) |
|
|
| - Fixed a bug where the values of the PTYPEn keywords in a random groups HDU |
| were forced to be all lower-case when saving the file. (#130) |
|
|
| - Removed an unnecessary inline import in ``ExtensionHDU.__setattr__`` that was |
| causing some slowdown when opening files containing a large number of |
| extensions, plus a few other small (but not insignificant) performance |
| improvements thanks to Julian Taylor. (#133) |
|
|
| - Fixed a regression where header blocks containing invalid end-of-header |
| padding (i.e. null bytes instead of spaces) couldn't be parsed by PyFITS. |
| Such headers can be parsed again, but a warning is raised, as such headers |
| are not valid FITS. (#136) |
| |
| - Fixed a memory leak where table data in random groups HDUs weren't being |
| garbage collected. (#138) |
|
|
|
|
| 3.0.6 (2012-02-29) |
| ================== |
|
|
| Highlights |
| ---------- |
|
|
| The main reason for this release is to fix an issue that was introduced in |
| PyFITS 3.0.5 where merely opening a file containing scaled data (that is, with |
| non-trivial BSCALE and BZERO keywords) in 'update' mode would cause the data |
| to be automatically rescaled--possibly converting the data from ints to |
| floats--as soon as the file is closed, even if the application did not touch |
| the data. Now PyFITS will only rescale the data in an extension when the data |
| is actually accessed by the application. So opening a file in 'update' mode |
| in order to modify the header or append new extensions will not cause any |
| change to the data in existing extensions. |
|
|
| This release also fixes a few Windows-specific bugs found through more |
| extensive Windows testing, and other miscellaneous bugs. |
|
|
| Bug Fixes |
| --------- |
|
|
| - More accurate error messages when opening files containing invalid header |
| cards. (#109) |
|
|
| - Fixed a possible reference cycle/memory leak that was caught through more |
| extensive testing on Windows. (#112) |
|
|
| - Fixed 'ostream' mode to open the underlying file in 'wb' mode instead of 'w' |
| mode. (#112) |
|
|
| - Fixed a Windows-only issue where trying to save updates to a resized FITS |
| file could result in a crash due to there being open mmaps on that file. |
| (#112) |
|
|
| - Fixed a crash when trying to create a FITS table (i.e. with new_table()) |
| from a Numpy array containing bool fields. (#113) |
|
|
| - Fixed a bug where manually initializing an ``HDUList`` with a list of of |
| HDUs wouldn't set the correct EXTEND keyword value on the primary HDU. |
| (#114) |
| |
| - Fixed a crash that could occur when trying to deepcopy a Header in Python < |
| 2.7. (#115) |
| |
| - Fixed an issue where merely opening a scaled image in 'update' mode would |
| cause the data to be converted to floats when the file is closed. (#119) |
| |
| |
| 3.0.5 (2012-01-30) |
| ================== |
| |
| - Fixed a crash that could occur when accessing image sections of files |
| opened with memmap=True. (r1211) |
| |
| - Fixed the inconsistency in the behavior of files opened in 'readonly' mode |
| when memmap=True vs. when memmap=False. In the latter case, although |
| changes to array data were not saved to disk, it was possible to update the |
| array data in memory. On the other hand with memmap=True, 'readonly' mode |
| prevented even in-memory modification to the data. This is what |
| 'copyonwrite' mode was for, but difference in behavior was confusing. Now |
| 'readonly' is equivalent to 'copyonwrite' when using memmap. If the old |
| behavior of denying changes to the array data is necessary, a new |
| 'denywrite' mode may be used, though it is only applicable to files opened |
| with memmap. (r1275) |
| |
| - Fixed an issue where files opened with memmap=True would return image data |
| as a raw numpy.memmap object, which can cause some unexpected |
| behaviors--instead memmap object is viewed as a numpy.ndarray. (r1285) |
| |
| - Fixed an issue in Python 3 where a workaround for a bug in Numpy on Python 3 |
| interacted badly with some other software, namely to vo.table package (and |
| possibly others). (r1320, r1337, and #110) |
| |
| - Fixed buggy behavior in the handling of SIGINTs (i.e. Ctrl-C keyboard |
| interrupts) while flushing changes to a FITS file. PyFITS already prevented |
| SIGINTs from causing an incomplete flush, but did not clean up the signal |
| handlers properly afterwards, or reraise the keyboard interrupt once the |
| flush was complete. (r1321) |
| |
| - Fixed a crash that could occur in Python 3 when opening files with checksum |
| checking enabled. (r1336) |
| |
| - Fixed a small bug that could cause a crash in the ``StreamingHDU`` interface |
| when using Numpy below version 1.5. |
| |
| - Fixed a crash that could occur when creating a new ``CompImageHDU`` from an |
| array of big-endian data. (#104) |
| |
| - Fixed a crash when opening a file with extra zero padding at the end. |
| Though FITS files should not have such padding, it's not explicitly forbidden |
| by the format either, and PyFITS shouldn't stumble over it. (#106) |
| |
| - Fixed a major slowdown in opening tables containing large columns of string |
| values. (#111) |
| |
| |
| 3.0.4 (2011-11-22) |
| ================== |
| |
| - Fixed a crash when writing HCOMPRESS compressed images that could happen on |
| Python 2.5 and 2.6. (r1217) |
| |
| - Fixed a crash when slicing an table in a file opened in 'readonly' mode with |
| memmap=True. (r1230) |
| |
| - Writing changes to a file or writing to a new file verifies the output in |
| 'fix' mode by default instead of 'exception'--that is, PyFITS will |
| automatically fix common FITS format errors rather than raising an |
| exception. (r1243) |
| |
| - Fixed a bug where convenience functions such as getval() and getheader() |
| crashed when specifying just 'PRIMARY' as the extension to use (r1263). |
| |
| - Fixed a bug that prevented passing keyword arguments (beyond the standard |
| data and header arguments) as positional arguments to the constructors of |
| extension HDU classes. |
| |
| - Fixed some tests that were failing on Windows--in this case the tests |
| themselves failed to close some temp files and Windows refused to delete them |
| while there were still open handles on them. (r1295) |
| |
| - Fixed an issue with floating point formatting in header values on Python 2.5 |
| for Windows (and possibly other platforms). The exponent was zero-padded to |
| 3 digits; although the FITS standard makes no specification on this, the |
| formatting is now normalized to always pad the exponent to two digits. |
| (r1295) |
| |
| - Fixed a bug where long commentary cards (such as HISTORY and COMMENT) were |
| broken into multiple CONTINUE cards. However, commentary cards are not |
| expected to be found in CONTINUE cards. Instead these long cards are broken |
| into multiple commentary cards. (#97) |
| |
| - GZIP/ZIP-compressed FITS files can be detected and opened regardless of |
| their filename extension. (#99) |
| |
| - Fixed a serious bug where opening scaled images in 'update' mode and then |
| closing the file without touching the data would cause the file to be |
| corrupted. (#101) |
| |
| |
| 3.0.3 (2011-10-05) |
| ================== |
| |
| - Fixed several small bugs involving corner cases in record-valued keyword |
| cards (#70) |
| |
| - In some cases HDU creation failed if the first keyword value in the header |
| was not a string value (#89) |
| |
| - Fixed a crash when trying to compute the HDU checksum when the data array |
| contains an odd number of bytes (#91) |
| |
| - Disabled an unnecessary warning that was displayed on opening compressed |
| HDUs with disable_image_compression = True (#92) |
| |
| - Fixed a typo in code for handling HCOMPRESS compressed images. |
| |
| |
| 3.0.2 (2011-09-23) |
| ================== |
| |
| - The ``BinTableHDU.tcreate`` method and by extension the ``pyfits.tcreate`` |
| function don't get tripped up by blank lines anymore (#14) |
|
|
| - The presence, value, and position of the EXTEND keyword in Primary HDUs is |
| verified when reading/writing a FITS file (#32) |
|
|
| - Improved documentation (in warning messages as well as in the handbook) that |
| PyFITS uses zero-based indexing (as one would expect for C/Python code, but |
| contrary to the PyFITS standard which was written with FORTRAN in mind) |
| (#68) |
|
|
| - Fixed a bug where updating a header card comment could cause the value to be |
| lost if it had not already been read from the card image string. |
|
|
| - Fixed a related bug where changes made directly to Card object in a header |
| (i.e. assigning directly to card.value or card.comment) would not propagate |
| when flushing changes to the file (#69) [Note: This and the bug above it |
| were originally reported as being fixed in version 3.0.1, but the fix was |
| never included in the release.] |
|
|
| - Improved file handling, particularly in Python 3 which had a few small file |
| I/O-related bugs (#76) |
|
|
| - Fixed a bug where updating a FITS file would sometimes cause it to lose its |
| original file permissions (#79) |
|
|
| - Fixed the handling of TDIMn keywords; 3.0 added support for them, but got |
| the axis order backwards (they were treated as though they were row-major) |
| (#82) |
|
|
| - Fixed a crash when a FITS file containing scaled data is opened and |
| immediately written to a new file without explicitly viewing the data first |
| (#84) |
|
|
| - Fixed a bug where creating a table with columns named either 'names' or |
| 'formats' resulted in an infinite recursion (#86) |
|
|
|
|
| 3.0.1 (2011-09-12) |
| ================== |
|
|
| - Fixed a bug where updating a header card comment could cause the value to be |
| lost if it had not already been read from the card image string. |
|
|
| - Changed ``_TableBaseHDU.data`` so that if the data contain an empty table a |
| ``FITS_rec`` object with zero rows is returned rather than ``None``. |
|
|
| - The ``.key`` attribute of ``RecordValuedKeywordCards`` now returns the full |
| keyword+field-specifier value, instead of just the plain keyword (#46) |
|
|
| - Fixed a related bug where changes made directly to Card object in a header |
| (i.e. assigning directly to card.value or card.comment) would not propagate |
| when flushing changes to the file (#69) |
|
|
| - Fixed a bug where writing a table with zero rows could fail in some cases |
| (#72) |
|
|
| - Miscellaneous small bug fixes that were causing some tests to fail, |
| particularly on Python 3 (#74, #75) |
|
|
| - Fixed a bug where creating a table column from an array in non-native byte |
| order would not preserve the byte order, thus interpreting the column array |
| using the wrong byte order (#77) |
|
|
|
|
| 3.0.0 (2011-08-23) |
| ==================== |
|
|
| - Contains major changes, bumping the version to 3.0 |
|
|
| - Large amounts of refactoring and reorganization of the code; tried to |
| preserve public API backwards-compatibility with older versions (private API |
| has many changes and is not guaranteed to be backwards-compatible). There |
| are a few small public API changes to be aware of: |
|
|
| * The pyfits.rec module has been removed completely. If your version of |
| numpy does not have the numpy.core.records module it is too old to be used |
| with PyFITS. |
|
|
| * The ``Header.ascardlist()`` method is deprecated--use the ``.ascard`` |
| attribute instead. |
|
|
| * ``Card`` instances have a new ``.cardimage`` attribute that should be used |
| rather than ``.ascardimage()``, which may become deprecated. |
|
|
| * The ``Card.fromstring()`` method is now a classmethod. It returns a new |
| ``Card`` instance rather than modifying an existing instance. |
|
|
| * The ``req_cards()`` method on HDU instances has changed: The ``pos`` |
| argument is not longer a string. It is either an integer value (meaning |
| the card's position must match that value) or it can be a function that |
| takes the card's position as it's argument, and returns True if the |
| position is valid. Likewise, the ``test`` argument no longer takes a |
| string, but instead a function that validates the card's value and returns |
| True or False. |
|
|
| * The ``get_coldefs()`` method of table HDUs is deprecated. Use the |
| ``.columns`` attribute instead. |
|
|
| * The ``ColDefs.data`` attribute is deprecated--use ``ColDefs.columns`` |
| instead (though in general you shouldn't mess with it directly--it might |
| become internal at some point). |
|
|
| * ``FITS_record`` objects take ``start`` and ``end`` as arguments instead of |
| ``startColumn`` and ``endColumn`` (these are rarely created manually, so |
| it's unlikely that this change will affect anyone). |
|
|
| * ``BinTableHDU.tcreate()`` is now a classmethod, and returns a new |
| ``BinTableHDU`` instance. |
|
|
| * Use ``ExtensionHDU`` and ``NonstandardExtHDU`` for making new extension HDU |
| classes. They are now public interfaces, wheres previously they were |
| private and prefixed with underscores. |
|
|
| * Possibly others--please report if you find any changes that cause |
| difficulties. |
|
|
| - Calls to deprecated functions will display a Deprecation warning. However, |
| in Python 2.7 and up Deprecation warnings are ignored by default, so run |
| Python with the ``-Wd`` option to see if you're using any deprecated |
| functions. If we get close to actually removing any functions, we might |
| make the Deprecation warnings display by default. |
|
|
| - Added basic Python 3 support |
|
|
| - Added support for multi-dimensional columns in tables as specified by the |
| TDIMn keywords (#47) |
|
|
| - Fixed a major memory leak that occurred when creating new tables with the |
| ``new_table()`` function (#49) |
| be padded with zero-bytes) vs ASCII tables (where strings are padded with |
| spaces) (#15) |
|
|
| - Fixed a bug in which the case of Random Access Group parameters names was not |
| preserved when writing (#41) |
|
|
| - Added support for binary table fields with zero width (#42) |
|
|
| - Added support for wider integer types in ASCII tables; although this is non- |
| standard, some GEIS images require it (#45) |
|
|
| - Fixed a bug that caused the index_of() method of HDULists to crash when the |
| HDUList object is created from scratch (#48) |
|
|
| - Fixed the behavior of string padding in binary tables (where strings should |
| be padded with nulls instead of spaces) |
|
|
| - Fixed a rare issue that caused excessive memory usage when computing |
| checksums using a non-standard block size (see r818) |
|
|
| - Add support for forced uint data in image sections (#53) |
|
|
| - Fixed an issue where variable-length array columns were not extended when |
| creating a new table with more rows than the original (#54) |
|
|
| - Fixed tuple and list-based indexing of FITS_rec objects (#55) |
|
|
| - Fixed an issue where BZERO and BSCALE keywords were appended to headers in |
| the wrong location (#56) |
|
|
| - ``FITS_record`` objects (table rows) have full slicing support, including |
| stepping, etc. (#59) |
|
|
| - Fixed a bug where updating multiple files simultaneously (such as when |
| running parallel processes) could lead to a race condition with mktemp() |
| (#61) |
|
|
| - Fixed a bug where compressed image headers were not in the order expected by |
| the funpack utility (#62) |
|
|
|
|
| 2.4.0 (2011-01-10) |
| ==================== |
| The following enhancements were added: |
|
|
| - Checksum support now correctly conforms to the FITS standard. pyfits |
| supports reading and writing both the old checksums and new |
| standard-compliant checksums. The ``fitscheck`` command-line utility is |
| provided to verify and update checksums. |
|
|
| - Added a new optional keyword argument ``do_not_scale_image_data`` |
| to the ``pyfits.open`` convenience function. When this argument |
| is provided as True, and an ImageHDU is read that contains scaled |
| data, the data is not automatically scaled when it is read. This |
| option may be used when opening a fits file for update, when you only |
| want to update some header data. Without the use of this argument, if |
| the header updates required the size of the fits file to change, then |
| when writing the updated information, the data would be read, scaled, |
| and written back out in its scaled format (usually with a different |
| data type) instead of in its non-scaled format. |
|
|
| - Added a new optional keyword argument ``disable_image_compression`` to the |
| ``pyfits.open`` function. When ``True``, any compressed image HDU's will |
| be read in like they are binary table HDU's. |
|
|
| - Added a ``verify`` keyword argument to the ``pyfits.append`` function. When |
| ``False``, ``append`` will assume the existing FITS file is already valid |
| and simply append new content to the end of the file, resulting in a large |
| speed up appending to large files. |
|
|
| - Added HDU methods ``update_ext_name`` and ``update_ext_version`` for |
| updating the name and version of an HDU. |
|
|
| - Added HDU method ``filebytes`` to calculate the number of bytes that will be |
| written to the file associated with the HDU. |
|
|
| - Enhanced the section class to allow reading non-contiguous image data. |
| Previously, the section class could only be used to read contiguous data. |
| (CNSHD781626) |
|
|
| - Added method ``HDUList.fileinfo()`` that returns a dictionary with |
| information about the location of header and data in the file associated |
| with the HDU. |
|
|
| The following bugs were fixed: |
|
|
| - Reading in some malformed FITS headers would cause a ``NameError`` |
| exception, rather than information about the cause of the error. |
|
|
| - pyfits can now handle non-compliant ``CONTINUE`` cards produced by Java |
| FITS. |
|
|
| - ``BinTable`` columns with ``TSCALn`` are now byte-swapped correctly. |
|
|
| - Ensure that floating-point card values are no longer than 20 characters. |
|
|
| - Updated ``flush`` so that when the data has changed in an HDU for a file |
| opened in update mode, the header will be updated to match the changed data |
| before writing out the HDU. |
|
|
| - Allow ``HIERARCH`` cards to contain a keyword and value whose total |
| character length is 69 characters. Previous length was limited at 68 |
| characters. |
|
|
| - Calls to ``FITS_rec['columnName']`` now return an ``ndarray``. exactly the |
| same as a call to ``FITS_rec.field('columnName')`` or |
| ``FITS_rec.columnName``. Previously, ``FITS_rec['columnName']`` returned a |
| much less useful ``fits_record`` object. (CNSHD789053) |
|
|
| - Corrected the ``append`` convenience function to eliminate the reading of |
| the HDU data from the file that is being appended to. (CNSHD794738) |
|
|
| - Eliminated common symbols between the pyfitsComp module and the cfitsio and |
| zlib libraries. These can cause problems on systems that use both PyFITS |
| and cfitsio or zlib. (CNSHD795046) |
|
|
|
|
| 2.3.1 (2010-06-03) |
| ==================== |
|
|
| The following bugs were fixed: |
|
|
| - Replaced code in the Compressed Image HDU extension which was covered under |
| a GNU General Public License with code that is covered under a BSD License. |
| This change allows the distribution of pyfits under a BSD License. |
|
|
|
|
| 2.3 (2010-05-11) |
| ================== |
|
|
| The following enhancements were made: |
|
|
| - Completely eliminate support for numarray. |
|
|
| - Rework pyfits documentation to use Sphinx. |
|
|
| - Support python 2.6 and future division. |
|
|
| - Added a new method to get the file name associated with an HDUList object. |
| The method HDUList.filename() returns the name of an associated file. It |
| returns None if no file is associated with the HDUList. |
|
|
| - Support the python 2.5 'with' statement when opening fits files. |
| (CNSHD766308) It is now possible to use the following construct: |
|
|
| >>> from __future__ import with_statement import pyfits |
| >>> with pyfits.open("input.fits") as hdul: |
| ... #process hdul |
| >>> |
|
|
| - Extended the support for reading unsigned integer 16 values from an ImageHDU |
| to include unsigned integer 32 and unsigned integer 64 values. ImageHDU |
| data is considered to be unsigned integer 16 when the data type is signed |
| integer 16 and BZERO is equal to 2**15 (32784) and BSCALE is equal to 1. |
| ImageHDU data is considered to be unsigned integer 32 when the data type is |
| signed integer 32 and BZERO is equal to 2**31 and BSCALE is equal to 1. |
| ImageHDU data is considered to be unsigned integer 64 when the data type is |
| signed integer 64 and BZERO is equal to 2**63 and BSCALE is equal to 1. An |
| optional keyword argument (uint) was added to the open convenience function |
| for this purpose. Supplying a value of True for this argument will cause |
| data of any of these types to be read in and scaled into the appropriate |
| unsigned integer array (uint16, uint32, or uint64) instead of into the |
| normal float 32 or float 64 array. If an HDU associated with a file that |
| was opened with the 'int' option and containing unsigned integer 16, 32, or |
| 64 data is written to a file, the data will be reverse scaled into a signed |
| integer 16, 32, or 64 array and written out to the file along with the |
| appropriate BSCALE/BZERO header cards. Note that for backward |
| compatibility, the 'uint16' keyword argument will still be accepted in the |
| open function when handling unsigned integer 16 conversion. |
|
|
| - Provided the capability to access the data for a column of a fits table by |
| indexing the table using the column name. This is consistent with Record |
| Arrays in numpy (array with fields). (CNSHD763378) The following example |
| will illustrate this: |
|
|
| >>> import pyfits |
| >>> hdul = pyfits.open('input.fits') |
| >>> table = hdul[1].data |
| >>> table.names |
| ['c1','c2','c3','c4'] |
| >>> print table.field('c2') # this is the data for column 2 |
| ['abc' 'xy'] |
| >>> print table['c2'] # this is also the data for column 2 |
| array(['abc', 'xy '], dtype='|S3') |
| >>> print table[1] # this is the data for row 1 |
| (2, 'xy', 6.6999997138977054, True) |
|
|
| - Provided capabilities to create a BinaryTableHDU directly from a numpy |
| Record Array (array with fields). The new capabilities include table |
| creation, writing a numpy Record Array directly to a fits file using the |
| pyfits.writeto and pyfits.append convenience functions. Reading the data |
| for a BinaryTableHDU from a fits file directly into a numpy Record Array |
| using the pyfits.getdata convenience function. (CNSHD749034) Thanks to |
| Erin Sheldon at Brookhaven National Laboratory for help with this. |
|
|
| The following should illustrate these new capabilities: |
|
|
| >>> import pyfits |
| >>> import numpy |
| >>> t=numpy.zeros(5,dtype=[('x','f4'),('y','2i4')]) \ |
| ... # Create a numpy Record Array with fields |
| >>> hdu = pyfits.BinTableHDU(t) \ |
| ... # Create a Binary Table HDU directly from the Record Array |
| >>> print hdu.data |
| [(0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32))] |
| >>> hdu.writeto('test1.fits',clobber=True) \ |
| ... # Write the HDU to a file |
| >>> pyfits.info('test1.fits') |
| Filename: test1.fits |
| No. Name Type Cards Dimensions Format |
| 0 PRIMARY PrimaryHDU 4 () uint8 |
| 1 BinTableHDU 12 5R x 2C [E, 2J] |
| >>> pyfits.writeto('test.fits', t, clobber=True) \ |
| ... # Write the Record Array directly to a file |
| >>> pyfits.append('test.fits', t) \ |
| ... # Append another Record Array to the file |
| >>> pyfits.info('test.fits') |
| Filename: test.fits |
| No. Name Type Cards Dimensions Format |
| 0 PRIMARY PrimaryHDU 4 () uint8 |
| 1 BinTableHDU 12 5R x 2C [E, 2J] |
| 2 BinTableHDU 12 5R x 2C [E, 2J] |
| >>> d=pyfits.getdata('test.fits',ext=1) \ |
| ... # Get the first extension from the file as a FITS_rec |
| >>> print type(d) |
| <class 'pyfits.core.FITS_rec'> |
| >>> print d |
| [(0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32)) |
| (0.0, array([0, 0], dtype=int32))] |
| >>> d=pyfits.getdata('test.fits',ext=1,view=numpy.ndarray) \ |
| ... # Get the first extension from the file as a numpy Record |
| Array |
| >>> print type(d) |
| <type 'numpy.ndarray'> |
| >>> print d |
| [(0.0, [0, 0]) (0.0, [0, 0]) (0.0, [0, 0]) (0.0, [0, 0]) |
| (0.0, [0, 0])] |
| >>> print d.dtype |
| [('x', '>f4'), ('y', '>i4', 2)] |
| >>> d=pyfits.getdata('test.fits',ext=1,upper=True, |
| ... view=pyfits.FITS_rec) \ |
| ... # Force the Record Array field names to be in upper case |
| regardless of how they are stored in the file |
| >>> print d.dtype |
| [('X', '>f4'), ('Y', '>i4', 2)] |
|
|
| - Provided support for writing fits data to file-like objects that do not |
| support the random access methods seek() and tell(). Most pyfits functions |
| or methods will treat these file-like objects as an empty file that cannot |
| be read, only written. It is also expected that the file-like object is in |
| a writable condition (ie. opened) when passed into a pyfits function or |
| method. The following methods and functions will allow writing to a |
| non-random access file-like object: HDUList.writeto(), HDUList.flush(), |
| pyfits.writeto(), and pyfits.append(). The pyfits.open() convenience |
| function may be used to create an HDUList object that is associated with the |
| provided file-like object. (CNSHD770036) |
|
|
| An illustration of the new capabilities follows. In this example fits data |
| is written to standard output which is associated with a file opened in |
| write-only mode: |
|
|
| >>> import pyfits |
| >>> import numpy as np |
| >>> import sys |
| >>> |
| >>> hdu = pyfits.PrimaryHDU(np.arange(100,dtype=np.int32)) |
| >>> hdul = pyfits.HDUList() |
| >>> hdul.append(hdu) |
| >>> tmpfile = open('tmpfile.py','w') |
| >>> sys.stdout = tmpfile |
| >>> hdul.writeto(sys.stdout, clobber=True) |
| >>> sys.stdout = sys.__stdout__ |
| >>> tmpfile.close() |
| >>> pyfits.info('tmpfile.py') |
| Filename: tmpfile.py |
| No. Name Type Cards Dimensions Format |
| 0 PRIMARY PrimaryHDU 5 (100,) int32 |
| >>> |
|
|
| - Provided support for slicing a FITS_record object. The FITS_record object |
| represents the data from a row of a table. Pyfits now supports the slice |
| syntax to retrieve values from the row. The following illustrates this new |
| syntax: |
|
|
| >>> hdul = pyfits.open('table.fits') |
| >>> row = hdul[1].data[0] |
| >>> row |
| ('clear', 'nicmos', 1, 30, 'clear', 'idno= 100') |
| >>> a, b, c, d, e = row[0:5] |
| >>> a |
| 'clear' |
| >>> b |
| 'nicmos' |
| >>> c |
| 1 |
| >>> d |
| 30 |
| >>> e |
| 'clear' |
| >>> |
|
|
| - Allow the assignment of a row value for a pyfits table using a tuple or a |
| list as input. The following example illustrates this new feature: |
|
|
| >>> c1=pyfits.Column(name='target',format='10A') |
| >>> c2=pyfits.Column(name='counts',format='J',unit='DN') |
| >>> c3=pyfits.Column(name='notes',format='A10') |
| >>> c4=pyfits.Column(name='spectrum',format='5E') |
| >>> c5=pyfits.Column(name='flag',format='L') |
| >>> coldefs=pyfits.ColDefs([c1,c2,c3,c4,c5]) |
| >>> |
| >>> tbhdu=pyfits.new_table(coldefs, nrows = 5) |
| >>> |
| >>> # Assigning data to a table's row using a tuple |
| >>> tbhdu.data[2] = ('NGC1',312,'A Note', |
| ... num.array([1.1,2.2,3.3,4.4,5.5],dtype=num.float32), |
| ... True) |
| >>> |
| >>> # Assigning data to a tables row using a list |
| >>> tbhdu.data[3] = ['JIM1','33','A Note', |
| ... num.array([1.,2.,3.,4.,5.],dtype=num.float32),True] |
| |
| - Allow the creation of a Variable Length Format (P format) column from a list |
| of data. The following example illustrates this new feature: |
| |
| >>> a = [num.array([7.2e-20,7.3e-20]),num.array([0.0]), |
| ... num.array([0.0])] |
| >>> acol = pyfits.Column(name='testa',format='PD()',array=a) |
| >>> acol.array |
| _VLF([[ 7.20000000e-20 7.30000000e-20], [ 0.], [ 0.]], |
| dtype=object) |
| >>> |
| |
| - Allow the assignment of multiple rows in a table using the slice syntax. The |
| following example illustrates this new feature: |
| |
| >>> counts = num.array([312,334,308,317]) |
| >>> names = num.array(['NGC1','NGC2','NGC3','NCG4']) |
| >>> c1=pyfits.Column(name='target',format='10A',array=names) |
| >>> c2=pyfits.Column(name='counts',format='J',unit='DN', |
| ... array=counts) |
| >>> c3=pyfits.Column(name='notes',format='A10') |
| >>> c4=pyfits.Column(name='spectrum',format='5E') |
| >>> c5=pyfits.Column(name='flag',format='L',array=[1,0,1,1]) |
| >>> coldefs=pyfits.ColDefs([c1,c2,c3,c4,c5]) |
| >>> |
| >>> tbhdu1=pyfits.new_table(coldefs) |
| >>> |
| >>> counts = num.array([112,134,108,117]) |
| >>> names = num.array(['NGC5','NGC6','NGC7','NCG8']) |
| >>> c1=pyfits.Column(name='target',format='10A',array=names) |
| >>> c2=pyfits.Column(name='counts',format='J',unit='DN', |
| ... array=counts) |
| >>> c3=pyfits.Column(name='notes',format='A10') |
| >>> c4=pyfits.Column(name='spectrum',format='5E') |
| >>> c5=pyfits.Column(name='flag',format='L',array=[0,1,0,0]) |
| >>> coldefs=pyfits.ColDefs([c1,c2,c3,c4,c5]) |
| >>> |
| >>> tbhdu=pyfits.new_table(coldefs) |
| >>> tbhdu.data[0][3] = num.array([1.,2.,3.,4.,5.], |
| ... dtype=num.float32) |
| >>> |
| >>> tbhdu2=pyfits.new_table(tbhdu1.data, nrows=9) |
| >>> |
| >>> # Assign the 4 rows from the second table to rows 5 thru |
| ... 8 of the new table. Note that the last row of the new |
| ... table will still be initialized to the default values. |
| >>> tbhdu2.data[4:] = tbhdu.data |
| >>> |
| >>> print tbhdu2.data |
| [ ('NGC1', 312, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), True) |
| ('NGC2', 334, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), False) |
| ('NGC3', 308, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), True) |
| ('NCG4', 317, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), True) |
| ('NGC5', 112, '0.0', array([ 1., 2., 3., 4., 5.], |
| dtype=float32), False) |
| ('NGC6', 134, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), True) |
| ('NGC7', 108, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), False) |
| ('NCG8', 117, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), False) |
| ('0.0', 0, '0.0', array([ 0., 0., 0., 0., 0.], |
| dtype=float32), False)] |
| >>> |
| |
| The following bugs were fixed: |
| |
| - Corrected bugs in HDUList.append and HDUList.insert to correctly handle the |
| situation where you want to insert or append a Primary HDU as something |
| other than the first HDU in an HDUList and the situation where you want to |
| insert or append an Extension HDU as the first HDU in an HDUList. |
| |
| - Corrected a bug involving scaled images (both compressed and not compressed) |
| that include a BLANK, or ZBLANK card in the header. When the image values |
| match the BLANK or ZBLANK value, the value should be replaced with NaN after |
| scaling. Instead, pyfits was scaling the BLANK or ZBLANK value and |
| returning it. (CNSHD766129) |
| |
| - Corrected a byteswapping bug that occurs when writing certain column data. |
| (CNSHD763307) |
| |
| - Corrected a bug that occurs when creating a column from a chararray when one |
| or more elements are shorter than the specified format length. The bug |
| wrote nulls instead of spaces to the file. (CNSHD695419) |
| |
| - Corrected a bug in the HDU verification software to ensure that the header |
| contains no NAXISn cards where n > NAXIS. |
| |
| - Corrected a bug involving reading and writing compressed image data. When |
| written, the header keyword card ZTENSION will always have the value 'IMAGE' |
| and when read, if the ZTENSION value is not 'IMAGE' the user will receive a |
| warning, but the data will still be treated as image data. |
| |
| - Corrected a bug that restricted the ability to create a custom HDU class and |
| use it with pyfits. The bug fix will allow something like this: |
| |
| >>> import pyfits |
| >>> class MyPrimaryHDU(pyfits.PrimaryHDU): |
| ... def __init__(self, data=None, header=None): |
| ... pyfits.PrimaryHDU.__init__(self, data, header) |
| ... def _summary(self): |
| ... """ |
| ... Reimplement a method of the class. |
| ... """ |
| ... s = pyfits.PrimaryHDU._summary(self) |
| ... # change the behavior to suit me. |
| ... s1 = 'MyPRIMARY ' + s[11:] |
| ... return s1 |
| ... |
| >>> hdul=pyfits.open("pix.fits", |
| ... classExtensions={pyfits.PrimaryHDU: MyPrimaryHDU}) |
| >>> hdul.info() |
| Filename: pix.fits |
| No. Name Type Cards Dimensions Format |
| 0 MyPRIMARY MyPrimaryHDU 59 (512, 512) int16 |
| >>> |
| |
| - Modified ColDefs.add_col so that instead of returning a new ColDefs object |
| with the column added to the end, it simply appends the new column to the |
| current ColDefs object in place. (CNSHD768778) |
| |
| - Corrected a bug in ColDefs.del_col which raised a KeyError exception when |
| deleting a column from a ColDefs object. |
| |
| - Modified the open convenience function so that when a file is opened in |
| readonly mode and the file contains no HDU's an IOError is raised. |
|
|
| - Modified _TableBaseHDU to ensure that all locations where data is referenced |
| in the object actually reference the same ndarray, instead of copies of the |
| array. |
|
|
| - Corrected a bug in the Column class that failed to initialize data when the |
| data is a boolean array. (CNSHD779136) |
|
|
| - Corrected a bug that caused an exception to be raised when creating a |
| variable length format column from character data (PA format). |
|
|
| - Modified installation code so that when installing on Windows, when a C++ |
| compiler compatible with the Python binary is not found, the installation |
| completes with a warning that all optional extension modules failed to |
| build. Previously, an Error was issued and the installation stopped. |
|
|
|
|
| 2.2.2 (2009-10-12) |
| ==================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following bugs were fixed: |
|
|
| - Corrected a bug that caused an exception to be raised when creating a |
| CompImageHDU using an initial header that does not match the image data in |
| terms of the number of axis. |
|
|
|
|
| 2.2.1 (2009-10-06) |
| ==================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following bugs were fixed: |
|
|
| - Corrected a bug that prevented the opening of a fits file where a header |
| contained a CHECKSUM card but no DATASUM card. |
|
|
| - Corrected a bug that caused NULLs to be written instead of blanks when an |
| ASCII table was created using a numpy chararray in which the original data |
| contained trailing blanks. (CNSHD695419) |
|
|
|
|
| 2.2 (2009-09-23) |
| ================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following enhancements were made: |
|
|
| - Provide support for the FITS Checksum Keyword Convention. (CNSHD754301) |
|
|
| - Adding the checksum=True keyword argument to the open convenience function |
| will cause checksums to be verified on file open: |
|
|
| >>> hdul=pyfits.open('in.fits', checksum=True) |
|
|
| - On output, CHECKSUM and DATASUM cards may be output to all HDU's in a fits |
| file by using the keyword argument checksum=True in calls to the writeto |
| convenience function, the HDUList.writeto method, the writeto methods of all |
| of the HDU classes, and the append convenience function: |
| |
| >>> hdul.writeto('out.fits', checksum=True) |
| |
| - Implemented a new insert method to the HDUList class that allows for the |
| insertion of a HDU into a HDUList at a given index: |
| |
| >>> hdul.insert(2,hdu) |
| |
| - Provided the capability to handle Unicode input for file names. |
| |
| - Provided support for integer division required by Python 3.0. |
| |
| The following bugs were fixed: |
| |
| - Corrected a bug that caused an index out of bounds exception to be raised |
| when iterating over the rows of a binary table HDU using the syntax "for |
| row in tbhdu.data: ". (CNSHD748609) |
| |
| - Corrected a bug that prevented the use of the writeto convenience function |
| for writing table data to a file. (CNSHD749024) |
| |
| - Modified the code to raise an IOError exception with the comment "Header |
| missing END card." when pyfits can't find a valid END card for a header when |
| opening a file. |
|
|
| - This change addressed a problem with a non-standard fits file that |
| contained several new-line characters at the end of each header and at the |
| end of the file. However, since some people want to be able to open these |
| non-standard files anyway, an option was added to the open convenience |
| function to allow these files to be opened without exception: |
|
|
| >>> pyfits.open('infile.fits',ignore_missing_end=True) |
|
|
| - Corrected a bug that prevented the use of StringIO objects as fits files |
| when reading and writing table data. Previously, only image data was |
| supported. (CNSHD753698) |
|
|
| - Corrected a bug that caused a bus error to be generated when compressing |
| image data using GZIP_1 under the Solaris operating system. |
|
|
| - Corrected bugs that prevented pyfits from properly reading Random Groups |
| HDU's using numpy. (CNSHD756570) |
| |
| - Corrected a bug that can occur when writing a fits file. (CNSHD757508) |
| |
| - If no default SIGINT signal handler has not been assigned, before the |
| write, a TypeError exception is raised in the _File.flush() method when |
| attempting to return the signal handler to its previous state. Notably |
| this occurred when using mod_python. The code was changed to use SIG_DFL |
| when no old handler was defined. |
| |
| - Corrected a bug in CompImageHDU that prevented rescaling the image data |
| using hdu.scale(option='old'). |
| |
| |
| 2.1.1 (2009-04-22) |
| =================== |
| |
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
| |
| The following bugs were fixed: |
| |
| - Corrected a bug that caused an exception to be raised when closing a file |
| opened for append, where an HDU was appended to the file, after data was |
| accessed from the file. This exception was only raised when running on a |
| Windows platform. |
| |
| - Updated the installation scripts, compression source code, and benchmark |
| test scripts to properly install, build, and execute on a Windows platform. |
| |
| |
| 2.1 (2009-04-14) |
| ================== |
| |
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
| |
| The following enhancements were made: |
| |
| - Added new tdump and tcreate capabilities to pyfits. |
| |
| - The new tdump convenience function allows the contents of a binary table |
| HDU to be dumped to a set of three files in ASCII format. One file will |
| contain column definitions, the second will contain header parameters, and |
| the third will contain header data. |
| |
| - The new tcreate convenience function allows the creation of a binary table |
| HDU from the three files dumped by the tdump convenience function. |
| |
| - The primary use for the tdump/tcreate methods are to allow editing in a |
| standard text editor of the binary table data and parameters. |
| |
| - Added support for case sensitive values of the EXTNAME card in an extension |
| header. (CNSHD745784) |
| |
| - By default, pyfits converts the value of EXTNAME cards to upper case when |
| reading from a file. A new convenience function |
| (setExtensionNameCaseSensitive) was implemented to allow a user to |
| circumvent this behavior so that the EXTNAME value remains in the same |
| case as it is in the file. |
| |
| - With the following function call, pyfits will maintain the case of all |
| characters in the EXTNAME card values of all extension HDU's during the |
| entire python session, or until another call to the function is made: |
|
|
| >>> import pyfits |
| >>> pyfits.setExtensionNameCaseSensitive() |
|
|
| - The following function call will return pyfits to its default (all upper |
| case) behavior: |
|
|
| >>> pyfits.setExtensionNameCaseSensitive(False) |
|
|
|
|
| - Added support for reading and writing FITS files in which the value of the |
| first card in the header is 'SIMPLE=F'. In this case, the pyfits open |
| function returns an HDUList object that contains a single HDU of the new |
| type _NonstandardHDU. The header for this HDU is like a normal header (with |
| the exception that the first card contains SIMPLE=F instead of SIMPLE=T). |
| Like normal HDU's the reading of the data is delayed until actually |
| requested. The data is read from the file into a string starting from the |
| first byte after the header END card and continuing till the end of the |
| file. When written, the header is written, followed by the data string. No |
| attempt is made to pad the data string so that it fills into a standard 2880 |
| byte FITS block. (CNSHD744730) |
| |
| - Added support for FITS files containing extensions with unknown XTENSION |
| card values. (CNSHD744730) Standard FITS files support extension HDU's of |
| types TABLE, IMAGE, BINTABLE, and A3DTABLE. Accessing a nonstandard |
| extension from a FITS file will now create a _NonstandardExtHDU object. |
| Accessing the data of this object will cause the data to be read from the |
| file into a string. If the HDU is written back to a file the string data is |
| written after the Header and padded to fill a standard 2880 byte FITS block. |
|
|
| The following bugs were fixed: |
|
|
| - Extensive changes were made to the tiled image compression code to support |
| the latest enhancements made in CFITSIO version 3.13 to support this |
| convention. |
|
|
| - Eliminated a memory leak in the tiled image compression code. |
|
|
| - Corrected a bug in the FITS_record.__setitem__ method which raised a |
| NameError exception when attempting to set a value in a FITS_record object. |
| (CNSHD745844) |
|
|
| - Corrected a bug that caused a TypeError exception to be raised when reading |
| fits files containing large table HDU's (>2Gig). (CNSHD745522) |
| |
| - Corrected a bug that caused a TypeError exception to be raised for all calls |
| to the warnings module when running under Python 2.6. The formatwarning |
| method in the warnings module was changed in Python 2.6 to include a new |
| argument. (CNSHD746592) |
| |
| - Corrected the behavior of the membership (in) operator in the Header class |
| to check against header card keywords instead of card values. (CNSHD744730) |
| |
| - Corrected the behavior of iteration on a Header object. The new behavior |
| iterates over the unique card keywords instead of the card values. |
| |
| |
| 2.0.1 (2009-02-03) |
| ==================== |
| |
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
| |
| The following bugs were fixed: |
| |
| - Eliminated a memory leak when reading Table HDU's from a fits file. |
| (CNSHD741877) |
|
|
|
|
| 2.0 (2009-01-30) |
| ================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following enhancements were made: |
|
|
| - Provide initial support for an image compression convention known as the |
| "Tiled Image Compression Convention" `[1]`_. |
|
|
| - The principle used in this convention is to first divide the n-dimensional |
| image into a rectangular grid of subimages or "tiles". Each tile is then |
| compressed as a continuous block of data, and the resulting compressed |
| byte stream is stored in a row of a variable length column in a FITS |
| binary table. Several commonly used algorithms for compressing image |
| tiles are supported. These include, GZIP, RICE, H-Compress and IRAF pixel |
| list (PLIO). |
|
|
| - Support for compressed image data is provided using the optional |
| "pyfitsComp" module contained in a C shared library (pyfitsCompmodule.so). |
|
|
| - The header of a compressed image HDU appears to the user like any image |
| header. The actual header stored in the FITS file is that of a binary |
| table HDU with a set of special keywords, defined by the convention, to |
| describe the structure of the compressed image. The conversion between |
| binary table HDU header and image HDU header is all performed behind the |
| scenes. Since the HDU is actually a binary table, it may not appear as a |
| primary HDU in a FITS file. |
|
|
| - The data of a compressed image HDU appears to the user as standard |
| uncompressed image data. The actual data is stored in the fits file as |
| Binary Table data containing at least one column (COMPRESSED_DATA). Each |
| row of this variable-length column contains the byte stream that was |
| generated as a result of compressing the corresponding image tile. |
| Several optional columns may also appear. These include, |
| UNCOMPRESSED_DATA to hold the uncompressed pixel values for tiles that |
| cannot be compressed, ZSCALE and ZZERO to hold the linear scale factor and |
| zero point offset which may be needed to transform the raw uncompressed |
| values back to the original image pixel values, and ZBLANK to hold the |
| integer value used to represent undefined pixels (if any) in the image. |
|
|
| - To create a compressed image HDU from scratch, simply construct a |
| CompImageHDU object from an uncompressed image data array and its |
| associated image header. From there, the HDU can be treated just like any |
| image HDU: |
|
|
| >>> hdu=pyfits.CompImageHDU(imageData,imageHeader) |
| >>> hdu.writeto('compressed_image.fits') |
|
|
| - The signature for the CompImageHDU initializer method describes the |
| possible options for constructing a CompImageHDU object:: |
|
|
| def __init__(self, data=None, header=None, name=None, |
| compressionType='RICE_1', |
| tileSize=None, |
| hcompScale=0., |
| hcompSmooth=0, |
| quantizeLevel=16.): |
| """ |
| data: data of the image |
| header: header to be associated with the |
| image |
| name: the EXTNAME value; if this value |
| is None, then the name from the |
| input image header will be used; |
| if there is no name in the input |
| image header then the default name |
| 'COMPRESSED_IMAGE' is used |
| compressionType: compression algorithm 'RICE_1', |
| 'PLIO_1', 'GZIP_1', 'HCOMPRESS_1' |
| tileSize: compression tile sizes default |
| treats each row of image as a tile |
| hcompScale: HCOMPRESS scale parameter |
| hcompSmooth: HCOMPRESS smooth parameter |
| quantizeLevel: floating point quantization level; |
| """ |
|
|
| - Added two new convenience functions. The setval function allows the setting |
| of the value of a single header card in a fits file. The delval function |
| allows the deletion of a single header card in a fits file. |
|
|
| - A modification was made to allow the reading of data from a fits file |
| containing a Table HDU that has duplicate field names. It is normally a |
| requirement that the field names in a Table HDU be unique. Prior to this |
| change a ValueError was raised, when the data was accessed, to indicate that |
| the HDU contained duplicate field names. Now, a warning is issued and the |
| field names are made unique in the internal record array. This will not |
| change the TTYPEn header card values. You will be able to get the data from |
| all fields using the field name, including the first field containing the |
| name that is duplicated. To access the data of the other fields with the |
| duplicated names you will need to use the field number instead of the field |
| name. (CNSHD737193) |
|
|
| - An enhancement was made to allow the reading of unsigned integer 16 values |
| from an ImageHDU when the data is signed integer 16 and BZERO is equal to |
| 32784 and BSCALE is equal to 1 (the standard way for scaling unsigned |
| integer 16 data). A new optional keyword argument (uint16) was added to the |
| open convenience function. Supplying a value of True for this argument will |
| cause data of this type to be read in and scaled into an unsigned integer 16 |
| array, instead of a float 32 array. If a HDU associated with a file that |
| was opened with the uint16 option and containing unsigned integer 16 data is |
| written to a file, the data will be reverse scaled into an integer 16 array |
| and written out to the file and the BSCALE/BZERO header cards will be |
| written with the values 1 and 32768 respectively. (CHSHD736064) Reference |
| the following example: |
|
|
| >>> import pyfits |
| >>> hdul=pyfits.open('o4sp040b0_raw.fits',uint16=1) |
| >>> hdul[1].data |
| array([[1507, 1509, 1505, ..., 1498, 1500, 1487], |
| [1508, 1507, 1509, ..., 1498, 1505, 1490], |
| [1505, 1507, 1505, ..., 1499, 1504, 1491], |
| ..., |
| [1505, 1506, 1507, ..., 1497, 1502, 1487], |
| [1507, 1507, 1504, ..., 1495, 1499, 1486], |
| [1515, 1507, 1504, ..., 1492, 1498, 1487]], dtype=uint16) |
| >>> hdul.writeto('tmp.fits') |
| >>> hdul1=pyfits.open('tmp.fits',uint16=1) |
| >>> hdul1[1].data |
| array([[1507, 1509, 1505, ..., 1498, 1500, 1487], |
| [1508, 1507, 1509, ..., 1498, 1505, 1490], |
| [1505, 1507, 1505, ..., 1499, 1504, 1491], |
| ..., |
| [1505, 1506, 1507, ..., 1497, 1502, 1487], |
| [1507, 1507, 1504, ..., 1495, 1499, 1486], |
| [1515, 1507, 1504, ..., 1492, 1498, 1487]], dtype=uint16) |
| >>> hdul1=pyfits.open('tmp.fits') |
| >>> hdul1[1].data |
| array([[ 1507., 1509., 1505., ..., 1498., 1500., 1487.], |
| [ 1508., 1507., 1509., ..., 1498., 1505., 1490.], |
| [ 1505., 1507., 1505., ..., 1499., 1504., 1491.], |
| ..., |
| [ 1505., 1506., 1507., ..., 1497., 1502., 1487.], |
| [ 1507., 1507., 1504., ..., 1495., 1499., 1486.], |
| [ 1515., 1507., 1504., ..., 1492., 1498., 1487.]], dtype=float32) |
|
|
| - Enhanced the message generated when a ValueError exception is raised when |
| attempting to access a header card with an unparsable value. The message |
| now includes the Card name. |
|
|
| The following bugs were fixed: |
|
|
| - Corrected a bug that occurs when appending a binary table HDU to a fits |
| file. Data was not being byteswapped on little endian machines. |
| (CNSHD737243) |
|
|
| - Corrected a bug that occurs when trying to write an ImageHDU that is missing |
| the required PCOUNT card in the header. An UnboundLocalError exception |
| complaining that the local variable 'insert_pos' was referenced before |
| assignment was being raised in the method _ValidHDU.req_cards. The code was |
| modified so that it would properly issue a more meaningful ValueError |
| exception with a description of what required card is missing in the header. |
|
|
| - Eliminated a redundant warning message about the PCOUNT card when validating |
| an ImageHDU header with a PCOUNT card that is missing or has a value other |
| than 0. |
|
|
| .. _[1]: https://fits.gsfc.nasa.gov/registry/tilecompression.html |
|
|
|
|
| 1.4.1 (2008-11-04) |
| ==================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following enhancements were made: |
|
|
| - Enhanced the way import errors are reported to provide more information. |
|
|
| The following bugs were fixed: |
|
|
| - Corrected a bug that occurs when a card value is a string and contains a |
| colon but is not a record-valued keyword card. |
|
|
| - Corrected a bug where pyfits fails to properly handle a record-valued |
| keyword card with values using exponential notation and trailing blanks. |
|
|
|
|
| 1.4 (2008-07-07) |
| ================== |
|
|
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
|
|
| The following enhancements were made: |
|
|
| - Added support for file objects and file like objects. |
|
|
| - All convenience functions and class methods that take a file name will now |
| also accept a file object or file like object. File like objects |
| supported are StringIO and GzipFile objects. Other file like objects will |
| work only if they implement all of the standard file object methods. |
|
|
| - For the most part, file or file like objects may be either opened or |
| closed at function call. An opened object must be opened with the proper |
| mode depending on the function or method called. Whenever possible, if |
| the object is opened before the method is called, it will remain open |
| after the call. This will not be possible when writing a HDUList that has |
| been resized or when writing to a GzipFile object regardless of whether it |
| is resized. If the object is closed at the time of the function call, |
| only the name from the object is used, not the object itself. The pyfits |
| code will extract the file name used by the object and use that to create |
| an underlying file object on which the function will be performed. |
|
|
| - Added support for record-valued keyword cards as introduced in the "FITS WCS |
| proposal for representing a more general distortion model". |
|
|
| - Record-valued keyword cards are string-valued cards where the string is |
| interpreted as a definition giving a record field name, and its floating |
| point value. In a FITS header they have the following syntax:: |
|
|
| keyword= 'field-specifier: float' |
|
|
| where keyword is a standard eight-character FITS keyword name, float is |
| the standard FITS ASCII representation of a floating point number, and |
| these are separated by a colon followed by a single blank. |
|
|
| The grammar for field-specifier is:: |
|
|
| field-specifier: |
| field |
| field-specifier.field |
|
|
| field: |
| identifier |
| identifier.index |
|
|
| where identifier is a sequence of letters (upper or lower case), |
| underscores, and digits of which the first character must not be a digit, |
| and index is a sequence of digits. No blank characters may occur in the |
| field-specifier. The index is provided primarily for defining array |
| elements though it need not be used for that purpose. |
|
|
| Multiple record-valued keywords of the same name but differing values may |
| be present in a FITS header. The field-specifier may be viewed as part of |
| the keyword name. |
|
|
| Some examples follow:: |
|
|
| DP1 = 'NAXIS: 2' |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
| DP1 = 'NAUX: 2' |
| DP1 = 'AUX.1.COEFF.0: 0' |
| DP1 = 'AUX.1.POWER.0: 1' |
| DP1 = 'AUX.1.COEFF.1: 0.00048828125' |
| DP1 = 'AUX.1.POWER.1: 1' |
|
|
| - As with standard header cards, the value of a record-valued keyword card |
| can be accessed using either the index of the card in a HDU's header or |
| via the keyword name. When accessing using the keyword name, the user may |
| specify just the card keyword or the card keyword followed by a period |
| followed by the field-specifier. Note that while the card keyword is case |
| insensitive, the field-specifier is not. Thus, hdu['abc.def'], |
| hdu['ABC.def'], or hdu['aBc.def'] are all equivalent but hdu['ABC.DEF'] is |
| not. |
| |
| - When accessed using the card index of the HDU's header the value returned |
| will be the entire string value of the card. For example: |
|
|
| >>> print hdr[10] |
| NAXIS: 2 |
| >>> print hdr[11] |
| AXIS.1: 1 |
|
|
| - When accessed using the keyword name exclusive of the field-specifier, the |
| entire string value of the header card with the lowest index having that |
| keyword name will be returned. For example: |
|
|
| >>> print hdr['DP1'] |
| NAXIS: 2 |
|
|
| - When accessing using the keyword name and the field-specifier, the value |
| returned will be the floating point value associated with the |
| record-valued keyword card. For example: |
|
|
| >>> print hdr['DP1.NAXIS'] |
| 2.0 |
|
|
| - Any attempt to access a non-existent record-valued keyword card value will |
| cause an exception to be raised (IndexError exception for index access or |
| KeyError for keyword name access). |
|
|
| - Updating the value of a record-valued keyword card can also be |
| accomplished using either index or keyword name. For example: |
|
|
| >>> print hdr['DP1.NAXIS'] |
| 2.0 |
| >>> hdr['DP1.NAXIS'] = 3.0 |
| >>> print hdr['DP1.NAXIS'] |
| 3.0 |
|
|
| - Adding a new record-valued keyword card to an existing header is |
| accomplished using the Header.update() method just like any other card. |
| For example: |
|
|
| >>> hdr.update('DP1', 'AXIS.3: 1', 'a comment', after='DP1.AXIS.2') |
|
|
| - Deleting a record-valued keyword card from an existing header is |
| accomplished using the standard list deletion syntax just like any other |
| card. For example: |
|
|
| >>> del hdr['DP1.AXIS.1'] |
|
|
| - In addition to accessing record-valued keyword cards individually using a |
| card index or keyword name, cards can be accessed in groups using a set of |
| special pattern matching keys. This access is made available via the |
| standard list indexing operator providing a keyword name string that |
| contains one or more of the special pattern matching keys. Instead of |
| returning a value, a CardList object will be returned containing shared |
| instances of the Cards in the header that match the given keyword |
| specification. |
|
|
| - There are three special pattern matching keys. The first key '*' will |
| match any string of zero or more characters within the current level of |
| the field-specifier. The second key '?' will match a single character. |
| The third key '...' must appear at the end of the keyword name string and |
| will match all keywords that match the preceding pattern down all levels |
| of the field-specifier. All combinations of ?, \*, and ... are permitted |
| (though ... is only permitted at the end). Some examples follow: |
|
|
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> print cl |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
| >>> cl=hdr['DP1.*'] |
| >>> print cl |
| DP1 = 'NAXIS: 2' |
| DP1 = 'NAUX: 2' |
| >>> cl=hdr['DP1.AUX...'] |
| >>> print cl |
| DP1 = 'AUX.1.COEFF.0: 0' |
| DP1 = 'AUX.1.POWER.0: 1' |
| DP1 = 'AUX.1.COEFF.1: 0.00048828125' |
| DP1 = 'AUX.1.POWER.1: 1' |
| >>> cl=hdr['DP?.NAXIS'] |
| >>> print cl |
| DP1 = 'NAXIS: 2' |
| DP2 = 'NAXIS: 2' |
| DP3 = 'NAXIS: 2' |
| >>> cl=hdr['DP1.A*S.*'] |
| >>> print cl |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
|
|
| - The use of the special pattern matching keys for adding or updating header |
| cards in an existing header is not allowed. However, the deletion of |
| cards from the header using the special keys is allowed. For example: |
|
|
| >>> del hdr['DP3.A*...'] |
|
|
| - As noted above, accessing pyfits Header object using the special pattern |
| matching keys will return a CardList object. This CardList object can |
| itself be searched in order to further refine the list of Cards. For |
| example: |
|
|
| >>> cl=hdr['DP1...'] |
| >>> print cl |
| DP1 = 'NAXIS: 2' |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
| DP1 = 'NAUX: 2' |
| DP1 = 'AUX.1.COEFF.1: 0.000488' |
| DP1 = 'AUX.2.COEFF.2: 0.00097656' |
| >>> cl1=cl['*.*AUX...'] |
| >>> print cl1 |
| DP1 = 'NAUX: 2' |
| DP1 = 'AUX.1.COEFF.1: 0.000488' |
| DP1 = 'AUX.2.COEFF.2: 0.00097656' |
|
|
| - The CardList keys() method will allow the retrieval of all of the key |
| values in the CardList. For example: |
|
|
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> print cl |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
| >>> cl.keys() |
| ['DP1.AXIS.1', 'DP1.AXIS.2'] |
|
|
| - The CardList values() method will allow the retrieval of all of the values |
| in the CardList. For example: |
|
|
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> print cl |
| DP1 = 'AXIS.1: 1' |
| DP1 = 'AXIS.2: 2' |
| >>> cl.values() |
| [1.0, 2.0] |
|
|
| - Individual cards can be retrieved from the list using standard list |
| indexing. For example: |
|
|
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> c=cl[0] |
| >>> print c |
| DP1 = 'AXIS.1: 1' |
| >>> c=cl['DP1.AXIS.2'] |
| >>> print c |
| DP1 = 'AXIS.2: 2' |
|
|
| - Individual card values can be retrieved from the list using the value |
| attribute of the card. For example: |
|
|
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> cl[0].value |
| 1.0 |
|
|
| - The cards in the CardList are shared instances of the cards in the source |
| header. Therefore, modifying a card in the CardList also modifies it in |
| the source header. However, making an addition or a deletion to the |
| CardList will not affect the source header. For example: |
|
|
| >>> hdr['DP1.AXIS.1'] |
| 1.0 |
| >>> cl=hdr['DP1.AXIS.*'] |
| >>> cl[0].value = 4.0 |
| >>> hdr['DP1.AXIS.1'] |
| 4.0 |
| >>> del cl[0] |
| >>> print cl['DP1.AXIS.1'] |
| Traceback (most recent call last): |
| ... |
| KeyError: "Keyword 'DP1.AXIS.1' not found." |
| >>> hdr['DP1.AXIS.1'] |
| 4.0 |
|
|
| - A FITS header consists of card images. In pyfits each card image is |
| manifested by a Card object. A pyfits Header object contains a list of |
| Card objects in the form of a CardList object. A record-valued keyword |
| card image is represented in pyfits by a RecordValuedKeywordCard object. |
| This object inherits from a Card object and has all of the methods and |
| attributes of a Card object. |
|
|
| - A new RecordValuedKeywordCard object is created with the |
| RecordValuedKeywordCard constructor: RecordValuedKeywordCard(key, value, |
| comment). The key and value arguments may be specified in two ways. The |
| key value may be given as the 8 character keyword only, in which case the |
| value must be a character string containing the field-specifier, a colon |
| followed by a space, followed by the actual value. The second option is |
| to provide the key as a string containing the keyword and field-specifier, |
| in which case the value must be the actual floating point value. For |
| example: |
|
|
| >>> c1 = pyfits.RecordValuedKeywordCard('DP1', 'NAXIS: 2', 'Number of variables') |
| >>> c2 = pyfits.RecordValuedKeywordCard('DP1.AXIS.1', 1.0, 'Axis number') |
|
|
| - RecordValuedKeywordCards have attributes .key, .field_specifier, .value, |
| and .comment. Both .value and .comment can be changed but not .key or |
| .field_specifier. The constructor will extract the field-specifier from |
| the input key or value, whichever is appropriate. The .key attribute is |
| the 8 character keyword. |
|
|
| - Just like standard Cards, a RecordValuedKeywordCard may be constructed |
| from a string using the fromstring() method or verified using the verify() |
| method. For example: |
|
|
| >>> c1 = pyfits.RecordValuedKeywordCard().fromstring( |
| "DP1 = 'NAXIS: 2' / Number of independent variables") |
| >>> c2 = pyfits.RecordValuedKeywordCard().fromstring( |
| "DP1 = 'AXIS.1: X' / Axis number") |
| >>> print c1; print c2 |
| DP1 = 'NAXIS: 2' / Number of independent variables |
| DP1 = 'AXIS.1: X' / Axis number |
| >>> c2.verify() |
| Output verification result: |
| Card image is not FITS standard (unparsable value string). |
|
|
| - A standard card that meets the criteria of a RecordValuedKeywordCard may |
| be turned into a RecordValuedKeywordCard using the class method coerce. |
| If the card object does not meet the required criteria then the original |
| card object is just returned. |
|
|
| >>> c1 = pyfits.Card('DP1','AUX: 1','comment') |
| >>> c2 = pyfits.RecordValuedKeywordCard.coerce(c1) |
| >>> print type(c2) |
| <'pyfits.NP_pyfits.RecordValuedKeywordCard'> |
|
|
| - Two other card creation methods are also available as |
| RecordVauedKeywordCard class methods. These are createCard() which will |
| create the appropriate card object (Card or RecordValuedKeywordCard) given |
| input key, value, and comment, and createCardFromString which will create |
| the appropriate card object given an input string. These two methods are |
| also available as convenience functions: |
|
|
| >>> c1 = pyfits.RecordValuedKeywordCard.createCard('DP1','AUX: 1','comment') |
|
|
| or |
|
|
| >>> c1 = pyfits.createCard('DP1','AUX: 1','comment') |
| >>> print type(c1) |
| <'pyfits.NP_pyfits.RecordValuedKeywordCard'> |
|
|
| >>> c1 = pyfits.RecordValuedKeywordCard.createCard('DP1','AUX 1','comment') |
|
|
| or |
|
|
| >>> c1 = pyfits.createCard('DP1','AUX 1','comment') |
| >>> print type(c1) |
| <'pyfits.NP_pyfits.Card'> |
|
|
| >>> c1 = pyfits.RecordValuedKeywordCard.createCardFromString \ |
| ("DP1 = 'AUX: 1.0' / comment") |
|
|
| or |
|
|
| >>> c1 = pyfits.createCardFromString("DP1 = 'AUX: 1.0' / comment") |
| >>> print type(c1) |
| <'pyfits.NP_pyfits.RecordValuedKeywordCard'> |
|
|
| The following bugs were fixed: |
|
|
| - Corrected a bug that occurs when writing a HDU out to a file. During the |
| write, any Keyboard Interrupts are trapped so that the write completes |
| before the interrupt is handled. Unfortunately, the Keyboard Interrupt was |
| not properly reinstated after the write completed. This was fixed. |
| (CNSHD711138) |
|
|
| - Corrected a bug when using ipython, where temporary files created with the |
| tempFile.NamedTemporaryFile method are not automatically removed. This can |
| happen for instance when opening a Gzipped fits file or when open a fits |
| file over the internet. The files will now be removed. (CNSHD718307) |
|
|
| - Corrected a bug in the append convenience function's call to the writeto |
| convenience function. The classExtensions argument must be passed as a |
| keyword argument. |
| |
| - Corrected a bug that occurs when retrieving variable length character arrays |
| from binary table HDUs (PA() format) and using slicing to obtain rows of |
| data containing variable length arrays. The code issued a TypeError |
| exception. The data can now be accessed with no exceptions. (CNSHD718749) |
| |
| - Corrected a bug that occurs when retrieving data from a fits file opened in |
| memory map mode when the file contains multiple image extensions or ASCII |
| table or binary table HDUs. The code issued a TypeError exception. The |
| data can now be accessed with no exceptions. (CNSHD707426) |
| |
| - Corrected a bug that occurs when attempting to get a subset of data from a |
| Binary Table HDU and then use the data to create a new Binary Table HDU |
| object. A TypeError exception was raised. The data can now be subsetted |
| and used to create a new HDU. (CNSHD723761) |
| |
| - Corrected a bug that occurs when attempting to scale an Image HDU back to |
| its original data type using the _ImageBaseHDU.scale method. The code was |
| not resetting the BITPIX header card back to the original data type. This |
| has been corrected. |
| |
| - Changed the code to issue a KeyError exception instead of a NameError |
| exception when accessing a non-existent field in a table. |
| |
| |
| 1.3 (2008-02-22) |
| ================== |
| |
| Updates described in this release are only supported in the NUMPY version of |
| pyfits. |
| |
| The following enhancements were made: |
| |
| - Provided support for a new extension to pyfits called *stpyfits*. |
| |
| - The *stpyfits* module is a wrapper around pyfits. It provides all of the |
| features and functions of pyfits along with some STScI specific features. |
| Currently, the only new feature supported by stpyfits is the ability to |
| read and write fits files that contain image data quality extensions with |
| constant data value arrays. See stpyfits `[2]`_ for more details on |
| stpyfits. |
| |
| - Added a new feature to allow trailing HDUs to be deleted from a fits file |
| without actually reading the data from the file. |
| |
| - This supports a JWST requirement to delete a trailing HDU from a file |
| whose primary Image HDU is too large to be read on a 32 bit machine. |
| |
| - Updated pyfits to use the warnings module to issue warnings. All warnings |
| will still be issued to stdout, exactly as they were before, however, you |
| may now suppress warnings with the -Wignore command line option. For |
| example, to run a script that will ignore warnings use the following command |
| line syntax: |
| |
| python -Wignore yourscript.py |
| |
| - Updated the open convenience function to allow the input of an already |
| opened file object in place of a file name when opening a fits file. |
| |
| - Updated the writeto convenience function to allow it to accept the |
| output_verify option. |
| |
| - In this way, the user can use the argument output_verify='fix' to allow |
| pyfits to correct any errors it encounters in the provided header before |
| writing the data to the file. |
| |
| - Updated the verification code to provide additional detail with a |
| VerifyError exception. |
| |
| - Added the capability to create a binary table HDU directly from a |
| numpy.ndarray. This may be done using either the new_table convenience |
| function or the BinTableHDU constructor. |
| |
| |
| The following performance improvements were made: |
| |
| - Modified the import logic to dramatically decrease the time it takes to |
| import pyfits. |
| |
| - Modified the code to provide performance improvements when copying and |
| examining header cards. |
| |
| The following bugs were fixed: |
| |
| - Corrected a bug that occurs when reading the data from a fits file that |
| includes BZERO/BSCALE scaling. When the data is read in from the file, |
| pyfits automatically scales the data using the BZERO/BSCALE values in the |
| header. In the previous release, pyfits created a 32 bit floating point |
| array to hold the scaled data. This could cause a problem when the value of |
| BZERO is so large that the scaled value will not fit into the float 32. For |
| this release, when the input data is 32 bit integer, a 64 bit floating point |
| array is used for the scaled data. |
| |
| - Corrected a bug that caused an exception to be raised when attempting to |
| scale image data using the ImageHDU.scale method. |
| |
| - Corrected a bug in the new_table convenience function that occurred when a |
| binary table was created using a ColDefs object as input and supplying an |
| nrows argument for a number of rows that is greater than the number of rows |
| present in the input ColDefs object. The previous version of pyfits failed |
| to allocate the necessary memory for the additional rows. |
| |
| - Corrected a bug in the new_table convenience function that caused an |
| exception to be thrown when creating an ASCII table. |
| |
| - Corrected a bug in the new_table convenience function that will allow the |
| input of a ColDefs object that was read from a file as a binary table with a |
| data value equal to None. |
| |
| - Corrected a bug in the construction of ASCII tables from Column objects that |
| are created with noncontinuous start columns. |
| |
| - Corrected bugs in a number of areas that would sometimes cause a failure to |
| improperly raise an exception when an error occurred. |
| |
| - Corrected a bug where attempting to open a non-existent fits file on a |
| windows platform using a drive letter in the file specification caused a |
| misleading IOError exception to be raised. |
| |
| .. _[2]: https://stscitools.readthedocs.io/en/latest/stpyfits.html |
| |
| |
| 1.1 (2007-06-15) |
| ================== |
| |
| - Modified to use either NUMPY or NUMARRAY. |
| |
| - New file writing modes have been provided to allow streaming data to |
| extensions without requiring the whole output extension image in memory. See |
| documentation on StreamingHDU. |
| |
| - Improvements to minimize byteswapping and memory usage by byteswapping in |
| place. |
| |
| - Now supports ':' characters in filenames. |
| |
| - Handles keyboard interrupts during long operations. |
| |
| - Preserves the byte order of the input image arrays. |
| |
| |
| 1.0.1 (2006-03-24) |
| ==================== |
| |
| The changes to PyFITS were primarily to improve the docstrings and to |
| reclassify some public functions and variables as private. Readgeis and |
| fitsdiff which were distributed with PyFITS in previous releases were moved to |
| pytools. This release of PyFITS is v1.0.1. The next release of PyFITS will |
| support both numarray and numpy (and will be available separately from |
| stsci_python, as are all the python packages contained within stsci_python). |
| An alpha release for PyFITS numpy support will be made around the time of this |
| stsci_python release. |
| |
| - Updated docstrings for public functions. |
| |
| - Made some previously public functions private. |
| |
| |
| 1.0 (2005-11-01) |
| ================== |
| |
| Major Changes since v0.9.6: |
| |
| - Added support for the HIERARCH convention |
| |
| - Added support for iteration and slicing for HDU lists |
| |
| - PyFITS now uses the standard setup.py installation script |
| |
| - Add utility functions at the module level, they include: |
| |
| - getheader |
| - getdata |
| - getval |
| - writeto |
| - append |
| - update |
| - info |
| |
| Minor changes since v0.9.6: |
| |
| - Fix a bug to make single-column ASCII table work. |
| |
| - Fix a bug so a new table constructed from an existing table with X-formatted |
| columns will work. |
| |
| - Fix a problem in verifying HDUList right after the open statement. |
| |
| - Verify that elements in an HDUList, besides the first one, are ExtensionHDU. |
| |
| - Add output verification in methods flush() and close(). |
| |
| - Modify the design of the open() function to remove the output_verify |
| argument. |
| |
| - Remove the groups argument in GroupsHDU's constructor. |
|
|
| - Redesign the column definition class to make its column components more |
| accessible. Also to make it conducive for higher level functionalities, |
| e.g. combining two column definitions. |
|
|
| - Replace the Boolean class with the Python Boolean type. The old TRUE/FALSE |
| will still work. |
|
|
| - Convert classes to the new style. |
|
|
| - Better format when printing card or card list. |
|
|
| - Add the optional argument clobber to all writeto() functions and methods. |
|
|
| - If adding a blank card, will not use existing blank card's space. |
| |
| PyFITS Version 1.0 REQUIRES Python 2.3 or later. |
| |
| |
| 0.9.6 (2004-11-11) |
| ==================== |
| |
| Major changes since v0.9.3: |
| |
| - Support for variable length array tables. |
| |
| - Support for writing ASCII table extensions. |
| |
| - Support for random groups, both reading and writing. |
| |
| Some minor changes: |
| |
| - Support for numbers with leading zeros in an ASCII table extension. |
| |
| - Changed scaled columns' data type from Float32 to Float64 to preserve |
| precision. |
|
|
| - Made Column constructor more flexible in accepting format specification. |
|
|
|
|
| 0.9.3 (2004-07-02) |
| ==================== |
|
|
| Changes since v0.9.0: |
|
|
| - Lazy instantiation of full Headers/Cards for all HDU's when the file is |
| opened. At the open, only extracts vital info (e.g. NAXIS's) from the |
| header parts. This change will speed up the performance if the user only |
| needs to access one extension in a multi-extension FITS file. |
|
|
| - Support the X format (bit flags) columns, both reading and writing, in a |
| binary table. At the user interface, they are converted to Boolean arrays |
| for easy manipulation. For example, if the column's TFORM is "11X", |
| internally the data is stored in 2 bytes, but the user will see, at each row |
| of this column, a Boolean array of 11 elements. |
| |
| - Fix a bug such that when a table extension has no data, it will not try to |
| scale the data when updating/writing the HDU list. |
| |
| |
| 0.9 (2004-04-27) |
| ================== |
| |
| Changes since v0.8.0: |
| |
| - Rewriting of the Card class to separate the parsing and verification of |
| header cards |
| |
| - Restructure the keyword indexing scheme which speed up certain applications |
| (update large number of new keywords and reading a header with larger |
| numbers of cards) by a factor of 30 or more |
| |
| - Change the default to be lenient FITS standard checking on input and strict |
| FITS standard checking on output |
| |
| - Support CONTINUE cards, both reading and writing |
| |
| - Verification can now be performed at any of the HDUList, HDU, and Card |
| levels |
| |
| - Support (contiguous) subsection (attribute .section) of images to reduce |
| memory usage for large images |
| |
| |
| 0.8.0 (2003-08-19) |
| ==================== |
| |
| **NOTE:** This version will only work with numarray Version 0.6. In addition, |
| earlier versions of PyFITS will not work with numarray 0.6. Therefore, both |
| must be updated simultaneously. |
| |
| Changes since 0.7.6: |
| |
| - Compatible with numarray 0.6/records 2.0 |
| |
| - For binary tables, now it is possible to update the original array if a |
| scaled field is updated. |
| |
| - Support of complex columns |
| |
| - Modify the __getitem__ method in FITS_rec. In order to make sure the scaled |
| quantities are also viewing the same data as the original FITS_rec, all |
| fields need to be "touched" when __getitem__ is called. |
| |
| - Add a new attribute mmobject for HDUList, and close the memmap object when |
| close HDUList object. Earlier version does not close memmap object and can |
| cause memory lockup. |
| |
| - Enable 'update' as a legitimate memmap mode. |
| |
| - Do not print message when closing an HDUList object which is not created |
| from reading a FITS file. Such message is confusing. |
| |
| - remove the internal attribute "closed" and related method (__getattr__ in |
| HDUList). It is redundant. |
| |
| |
| 0.7.6 (2002-11-22) |
| |
| **NOTE:** This version will only work with numarray Version 0.4. |
| |
| Changes since 0.7.5: |
| |
| - Change x*=n to numarray.multiply(x, n, x) where n is a floating number, in |
| order to make pyfits to work under Python 2.2. (2 occurrences) |
| |
| - Modify the "update" method in the Header class to use the "fixed-format" |
| card even if the card already exists. This is to avoid the mis-alignment as |
| shown below: |
| |
| After running drizzle on ACS images it creates a CD matrix whose elements |
| have very many digits, *e.g.*: |
| |
| CD1_1 = 1.1187596304411E-05 / partial of first axis coordinate w.r.t. x |
| CD1_2 = -8.502767249350019E-06 / partial of first axis coordinate w.r.t. y |
| |
| with pyfits, an "update" on these header items and write in new values which |
| has fewer digits, *e.g.*: |
| |
| CD1_1 = 1.0963011E-05 / partial of first axis coordinate w.r.t. x |
| CD1_2 = -8.527229E-06 / partial of first axis coordinate w.r.t. y |
| |
| - Change some internal variables to make their appearance more consistent: |
| |
| old name new name |
| |
| __octalRegex _octalRegex |
| __readblock() _readblock() |
| __formatter() _formatter(). |
| __value_RE _value_RE |
| __numr _numr |
| __comment_RE _comment_RE |
| __keywd_RE _keywd_RE |
| __number_RE _number_RE. |
| tmpName() _tmpName() |
| dimShape _dimShape |
| ErrList _ErrList |
| |
| - Move up the module description. Move the copyright statement to the bottom |
| and assign to the variable __credits__. |
| |
| - change the following line: |
| |
| self.__dict__ = input.__dict__ |
| |
| to |
| |
| self.__setstate__(input.__getstate__()) |
| |
| in order for pyfits to run under numarray 0.4. |
| |
| - edit _readblock to add the (optional) firstblock argument and raise IOError |
| if the first 8 characters in the first block is not 'SIMPLE ' or |
| 'XTENSION'. Edit the function open to check for IOError to skip the last |
| null filled block(s). Edit readHDU to add the firstblock argument. |
| |
| |
| 0.7.5 (2002-08-16) |
| ==================== |
| |
| Changes since v0.7.3: |
| |
| - Memory mapping now works for readonly mode, both for images and binary |
| tables. |
| |
| Usage: pyfits.open('filename', memmap=1) |
| |
| - Edit the field method in FITS_rec class to make the column scaling for |
| numbers use less temporary memory. (does not work under 2.2, due to Python |
| "bug" of array \*=) |
| |
| - Delete bscale/bzero in the ImageBaseHDU constructor. |
| |
| - Update bitpix in BaseImageHDU.__getattr__ after deleting bscale/bzero. (bug |
| fix) |
| |
| - In BaseImageHDU.__getattr__ point self.data to raw_data if float and if not |
| memmap. (bug fix). |
| |
| - Change the function get_tbdata() to private: _get_tbdata(). |
| |
| |
| 0.7.3 (2002-07-12) |
| ==================== |
| |
| Changes since v0.7.2: |
| |
| - It will scale all integer image data to Float32, if BSCALE/BZERO != 1/0. It |
| will also expunge the BSCALE/BZERO keywords. |
| |
| - Add the scale() method for ImageBaseHDU, so data can be scaled just before |
| being written to the file. It has the following arguments: |
| |
| type: destination data type (string), e.g. Int32, Float32, UInt8, etc. |
| |
| option: scaling scheme. if 'old', use the old BSCALE/BZERO values. if |
| 'minmax', use the data range to fit into the full range of specified integer |
| type. Float destination data type will not be scaled for this option. |
| |
| bscale/bzero: user specifiable BSCALE/BZERO values. They overwrite the |
| "option". |
| |
| - Deal with data area resizing in 'update' mode. |
| |
| - Make the data scaling (both input and output) faster and use less memory. |
| |
| - Bug fix to make column name change takes effect for field. |
| |
| - Bug fix to avoid exception if the key is not present in the header already. |
| This affects (fixes) add_history(), add_comment(), and add_blank(). |
| |
| - Bug fix in __getattr__() in Card class. The change made in 0.7.2 to rstrip |
| the comment must be string type to avoid exception. |
| |
| 0.7.2.1 (2002-06-25) |
| ====================== |
| |
| A couple of bugs were addressed in this version. |
| |
| - Fix a bug in _add_commentary(). Due to a change in index_of() during version |
| 0.6.5.5, _add_commentary needs to be modified to avoid exception if the key |
| is not present in the header already. This affects (fixes) add_history(), |
| add_comment(), and add_blank(). |
| |
| - Fix a bug in __getattr__() in Card class. The change made in 0.7.2 to rstrip |
| the comment must be string type to avoid exception. |
| |
| |
| 0.7.2 (2002-06-19) |
| ==================== |
| |
| The two major improvements from Version 0.6.2 are: |
| |
| - support reading tables with "scaled" columns (e.g. tscal/tzero, Boolean, |
| and ASCII tables) |
| |
| - a prototype output verification. |
| |
| This version of PyFITS requires numarray version 0.3.4. |
| |
| Other changes include: |
| |
| - Implement the new HDU hierarchy proposed earlier this year. This in turn |
| reduces some of the redundant methods common to several HDU classes. |
| |
| - Add 3 new methods to the Header class: add_history, add_comment, and |
| add_blank. |
| |
| - The table attributes _columns are now .columns and the attributes in ColDefs |
| are now all without the underscores. So, a user can get a list of column |
| names by: hdu.columns.names. |
| |
| - The "fill" argument in the new_table method now has a new meaning:<br> If |
| set to true (=1), it will fill the entire new table with zeros/blanks. |
| Otherwise (=0), just the extra rows/cells are filled with zeros/blanks. |
| Fill values other than zero/blank are now not possible. |
| |
| - Add the argument output_verify to the open method and writeto method. Not |
| in the flush or close methods yet, due to possible complication. |
| |
| - A new copy method for tables, the copy is totally independent from the table |
| it copies from. |
| |
| - The tostring() call in writeHDUdata takes up extra space to store the string |
| object. Use tofile() instead, to save space. |
| |
| - Make changes from _byteswap to _byteorder, following corresponding changes |
| in numarray and recarray. |
| |
| - Insert(update) EXTEND in PrimaryHDU only when header is None. |
| |
| - Strip the trailing blanks for the comment value of a card. |
| |
| - Add seek(0) right after the __buildin__.open(0), because for the 'ab+' mode, |
| the pointer is at the end after open in Linux, but it is at the beginning in |
| Solaris. |
| |
| - Add checking of data against header, update header keywords (NAXIS's, |
| BITPIX) when they don't agree with the data. |
| |
| - change version to __version__. |
| |
| There are also many other minor internal bug fixes and |
| technical changes. |
| |
| |
| 0.6.2 (2002-02-12) |
| ==================== |
| |
| This version requires numarray version 0.2. |
| |
| Things not yet supported but are part of future development: |
| |
| - Verification and/or correction of FITS objects being written to disk so that |
| they are legal FITS. This is being added now and should be available in |
| about a month. Currently, one may construct FITS headers that are |
| inconsistent with the data and write such FITS objects to disk. Future |
| versions will provide options to either a) correct discrepancies and warn, |
| b) correct discrepancies silently, c) throw a Python exception, or d) write |
| illegal FITS (for test purposes!). |
| |
| - Support for ascii tables or random groups format. Support for ASCII tables |
| will be done soon (~1 month). When random group support is added is |
| uncertain. |
| |
| - Support for memory mapping FITS data (to reduce memory demands). We expect |
| to provide this capability in about 3 months. |
| |
| - Support for columns in binary tables having scaled values (e.g. BSCALE or |
| BZERO) or boolean values. Currently booleans are stored as Int8 arrays and |
| users must explicitly convert them into a boolean array. Likewise, scaled |
| columns must be copied with scaling and offset by testing for those |
| attributes explicitly. Future versions will produce such copies |
| automatically. |
| |
| - Support for tables with TNULL values. This awaits an enhancement to numarray |
| to support mask arrays (planned). (At least a couple of months off). |
| |
| .. _PyFITS: https://github.com/spacetelescope/pyfits |
| |