CVS commit: pkgsrc/devel/cfitsio

["Hiramatsu Yoshifumi" <hiramatsu%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   hiramatsu
Date:           Wed Apr  8 16:23:28 UTC 2015

Modified Files:
        pkgsrc/devel/cfitsio: Makefile PLIST distinfo
        pkgsrc/devel/cfitsio/patches: patch-aa

Log Message:
Update devel/cfitsio to 3.37.

Changes from previous:
----------------------
Version 3.37 - 3 June 2014

   - added configure options to support reading bzip2 compressed FITS files.
     This depends on having the bzlib library installed on the local machine.
     Patch submitted by Dustin Lang.

   - replaced the random Gaussian and Poissonian distribution functions with
     new code written by Craig Markwardt derived from public domain C++ functions
     written by John D Cook.

   - patched fitsio2.h to support CFITSIO on AArch64 (64-bit ARM)
     architecture (both big and little endian).  Supplied by
     Marcin Juszkiewicz and Sergio Pascual Ramirez, with further update
     by Michel Normand.

   - fixed bug in fpackutil.c that caused fpack to exit prematurely if
     the FZALGOR directive keyword was present in the HDU header.

Version 3.36 - 6 December 2013

   - added 9 Dec: small change to the fileseek function in drvrfile.c to
     support large files > 2 GB when building CFITSIO with MinGW on Windows

   - reorganized the CFITSIO code directory structure; added a 'docs'
     subdirectory for all the documentation, and a 'zlib' directory
     for the zlib/gzip file compression code.

   - made major changes to the compression code for FITS binary table
     to support all types of columns, including variable-length arrays.
     This code is mainly used via the fpack and funpack programs.

   - increased the number of FITS files that can be opened as one
     time to 1000, as defined by NMAXFILES in fitsio2.h.

   - made small configuration changes to configure.in, configure,
     fitsio.h, and drvrfile.c to support large files (64-bit file
     offsets} when using the mingw-w64 compiler (provided by
     Benjamin Gilbert).

   - made small change to fits_delete_file to more completely ignore
     any non-zero input status value.

   - fixed a logic error in a 'if' test when parsing a keyword name
     in the ngp_keyword_is_write function in grparser.c (provided
     by David Binderman).

   - when specifying the image compression parameters as part of the
     compressed image file name (using the "[compress]" qualifier
     after the name of the file), the quantization level value, if
     specified, was not being recognized by the CFITSIO compression
     routines. The image would always be compressed with the default
     quantization level of 4.0, regardless of what was specified.  This
     affected the imcopy program, and potentially other user-generated
     application programs that used this method to specify the
     compression parameters.  This bug did not affect fpack or
     funpack.   This was fixed in the imcomp_get_compressed_image_par
     routine in the imcompress.c file. (reported by Sean Peters)

   - defined a new CFITS_API macro in fitsio.h which is used to export the
     public symbols when building CFITSIO on Windows systems with CMake. This
     works in conjunction with the new Windows CMake build procedure that
     is described in the README.win32 file. This complete revamping of the
     way CFITSIO is built under Windows now supports building 64-bit
     versions of the library.  Thanks to Daniel Kaneider (Luminance HDR
     Team) for providing these new  CMake build procedures.

   - modified the way that the low-level file_create routine works when
     running in the Hera environment to ensure that the FITS file that is
     created is within the allow user data disk area.

   - modified fits_get_compression_type so that it does not return an error
     if the HDU is a normal FITS IMAGE extension, and is not a tile-compressed
     image.

   - modified the low-level ffgcl* and ffpcl* routines to ensure that they
     never try ro read or write more than 2**31 bytes from disk at one time,
     as might happen with very large images, to avoid integer overflow errors.
     Fix kindly provided by Fred Gutsche at NanoFocus AG (www.nanofocus.de).

   - modified Makefile.in so that doing 'make distclean' does not delete
     new config.sub and config.guess files that were recently added.

   - adopted a patch from Debian in zcompress.c to "define" the values of
     GZBUFSIZE and BUFFINCR, instead of exporting the symbols as 'int's.

Version 3.35 - 26 June 2013  (1st beta release was on 24 May)

   - fixed problem with the default tile size when compressing images with
     fpack using the Hcompress algorithm.

   - fixed returned value ("status" instead of "*status")

   - in imcompress.c, declared some arrays that are used to store the dimensions
     of the image from 'int' to 'long', to support very large images (at least
     on systems where sizeof(long) = 8),

   - modified the routines that convert a string value to a float or double
     to prevent them from returning a NaN or Inf value if the
     string is "NaN" or "Inf" (as can happen with gcc implementation of the
     strtod function).

   - removed/replaced the use of the assert() functions when locking or
     unlocking threads because they did not work correctly if NDEBUG is
     defined.

   - made modifications to the way the command-line file filters are parsed to
     1) remove the 1024-character limit when specifying a column filter,
     2) fixed a potential character buffer-overflow risk in fits_get_token, and
     3) improved the parsing logic to remove any possible of confusing
     2 slash characters ("//") in the string as the beginning of a
     comment string.

   - modified configure and Makefile.in so that when building CFITSIO
     as a shared library on linux or Mac platforms, it will use the SONAME
     convention to indicate whether each new release of the CFITSIO
     library is binary-compatible with the previous version.  Application
     programs that link with the shared library will not need to be
     recompiled as long as the versions are compatible.  In practice,
     this means that the shared library binary file that is created (on
     Linux systems) will have a name like 'libcfitsio.so.I.J.K', where I is the
     SONAME version number, J is the major CFITSIO version number (e.g. 3),
     and K is the minor CFITSIO version number (e.g., 34).  Two link
     files will also be created such that
       libcfitsio.so -> libcfitsio.so.I, and
       libcfitsio.so.I -> libcfitsio.I.J.K
     Application programs will still run correctly with the new version of
     CFITSIO as long as the 'I' version number remains the same, but the
     applications will fail to run if the 'I' number changes, thus alerting
     the user that the application must be rebuilt.

   - fixed bug in fits_insert_col when computing the new table row width
     when inserting a '1Q' variable length array column.

  - modified the image compression routines so that the output compressed
     image (stored in a FITS binary table) uses the '1Q' variable length
     array format (instead of '1P') when the input file is larger than 4 GB.

   - added support for "compression directive" keywords which indicate how
     that HDU should be compressed (e.g., which compression algorithm to use,
     what tiling pattern to use, etc.).  The values of these keywords will
     override the compression parameters that were specified on the command
     line when running the fpack FITS file compression program.

   - globally changed the variable and/or subroutine name "dither_offset"
     to "dither_seed" and "quantize_dither" to "quantize_method" so
     that the names more accurately reflects their purpose.

   - added support for a new SUBTRACTIVE_DITHER_2 method when compressing
     floating point images.  The only difference with the previous method
     is that pixels with a value exactly equal to 0.0 will not be dithered,
     and instead will be exactly preserved when the image is compressed.

   - added support for an alias of "RICE_ONE" for "RICE_1" as the value
     of the ZCMPTYPE keyword, which gives the name of the image compression
     algorithm.  This alias is used if the new SUBTRACTIVE_DITHER_2 option
     is used, to prevent old versions of funpack from creating a corrupted
     uncompressed image file.  Only newer versions of funpack will recognize
     this alias and be able to uncompress the image.

   - made performance improvement to fits_read_compressed_img so that
     when reading a section of an compressed image that includes only
     every nth pixel in some dimension, it will only uncompressed a tile
     if there are actually any pixels of interest in that tile.

   - fixed several issues with the beta FITS binary table compression code
     that is used by fpack:  added support for zero-length vector columns,
     made improvements to the output report when using the -T option in fpack,
     changed the default table compression method to 'Rice' instead of
     'Best', and now writes the 'ZTILELEN' keyword to document the number
     of table rows in each tile.

   - fixed error in ffbinit in calculating the total length of the binary
     table extension if the THEAP keyword was used to override the
     default starting location of the heap.

Version 3.34 - 20 March 2013

   - modified configure and configure.in to support cross-compiled cfitsio
     as a static library for Windows on a Linux platform using MXE
     (http://mxe.cc) - a build environment for mingw32. (contributed by
     Niels Kristian Bech Jensen)

   - added conditional compilation statementsfor the mingw32 environment in
     drvrfile.c because mingw32 does not include the ftello and fseeko functions.
     (contributed by Niels Kristian Bech Jensen)

   - fixed a potential bug in ffcpcl (routine to copy a column from one table
     to another table) when dealing with the rare case of a '0X' column (zero
     length bit column).

   - fixed an issue in the routines that update or modify string-valued
     keyword values, as a result of the change to ffc2s in the previous
     release.  These routines would exit with a 204 error status if the
     current value of the keyword to be updated or modified is null.

   - fixed typo in the previous modification that was intended to ignore
     numerical overflows in Hcompress when decompressing an image.

   - moved the 'startcol' static variable out of the ffgcnn routine and
     instead added it as a member of the 'FITSfile' structure that is defined
     in fitsio.h.  This removes a possible race condition in ffgcnn in
     multi-threaded environments.

Version 3.33 - 14 Feb 2013

   - modified the imcomp_decompress_tile routine to ignore any numerical
     overflows that might occur when using Hcompress to decompress the
     image.  If Hcompress is used in its 'lossy' mode, the uncompressed
     image pixel values may slightly exceed the range of an integer*2
     variable. This is generally of no consequence, so we can safely ignore
     any overflows in this case and just clip the values to the legal range.

   - the default tiling pattern when writing a tile-compressed image
     has been changed.  The old behavior was to compress the whole image
     as one single large tile.  This is often not optimal when dealing
     with large images, so the new default behavior is to treat each
     row of the image as one tile.  This is the same default behavior
     as in the standalone fpack program.  The default tile size can
     be overridden by calling fits_set_tile_dim.

   - fixed bug that resulted in a corrupted output FITS image when
     attempting to write a float or double array of values to a
     tile-compressed integer data type image.  CFITSIO does not support
     implicit data type conversion in this case and now correctly
     returns an appropriate error status.

   - modified ricecomp.c to define the nonzero_count lookup table as an
     external variable, rather then dynamically allocating it within the
     3 routines that use it.  This simplifies the code and eliminates the
     need for special thread locking and unlocking statements. (Thanks to
     Lars Kr. Lundin for this suggestion).

   - modified how the uncompressed size of a gzipped file is computed in the
     mem_compress_open routine in drvrmem.c.  Since gzip only uses 4 bytes
     in the compressed file header to store the original file size, one may
     need to apply a modulo 2^32 byte correction in some cases.  The logic
     here was modified to allow for corner cases (e.g., very small files, and
     when running on 32-bit platforms that do not support files larger than
     2^31 bytes in size).

   - added new public routine to construct a 80 keyword record from the 3 input
     component strings, i.e, the keyword name string, the value string, and
     the comment string: fits_make_key/ffmkky.  (This was already an undocumented
     internal routine in previous versions of CFITSIO).

   - modified ffc2s so that if the input keyword value string is a null string,
     then it will return a VALUE_UNDEFINED (204) status value.  This makes it
     consistent with the behavior when attempting to read a null keyword
     (which has no value) as a logical or as a number (which also returns
     the 204 error).  This should only affect cases where the header keyword
     does not have an equal sign followed by a space character in columns 9
     and 10 of the header record.

   - Changed the "char *" parameter declarations to "const char *" in many
     of the routines (mainly the routines that modify or update keywords) to
     avoid compiler warnings or errors from C++ programs that tend to be more
     rigorous about using "const char *" when appropriate.

   - added support for caching uncompressed image tiles, so that the tile does
     not need to be uncompressed again if the application program wants
     to read more data from the same tile. This required changes to the
     main FITS file structure that is defined in fitsio.h, as well as
     changes to imcompress.c.

   - enhanced the previous modification to drvrfile.c to handle additional user
     cases when running in the HEASARC's Hera environment.

Version 3.32 - Oct 2012

   - fixed flaw in the way logical columns (TFORM = 'L') in binary tables
     were read which caused an illegal value of 1 in the column to be interpreted
     as a 'T' (TRUE) value.

   - extended the column filtering syntax in the CFITSIO file name parser to
     enable users and scripts to append new COMMENT or HISTORY keyword into the
     header of the filtered file (provided by Craig Markwardt).  For example,
     fcopy "infile.fits[col #HISTORY='Processed on 2012-10-05']" outfile.fits
     will append this header keyword: "HISTORY Processed on 2012-10-05"

   - small change to the code that opens and reads an ASCII region file to
     return an error if the file is empty.

   - fixed obscure sign propagation error when attempting to read the
     uncompressed size of a gzipped FITS file.  This resulted in a memory
     allocation error if the gzipped file had an uncompressed file
     size between 2^31 and 2^32 bytes.  Fix supplied by Gudlaugur Johannesson
     (Stanford).

Version 3.31 - 18 July 2012

   - enhanced the CFITSIO column filtering syntax to allow the comma, in addition
     to the semi-colon, to be used to separate clauses, for example:
     [col X,Y;Z = max(X,Y)].  This was done because users are not allowed to
     enter the semi-colon character in the on-line Hera data processing
     system due to computer security concerns.

   - enhanced the CFITSIO extended filename syntax to allow specifying image
     compression parameters (e.g. '[compress Rice]') when opening an existing
     FITS file with write access.  The specified compression parameters will
     be used by default if more images are appended to the existing file.

   - modified drvrfile.c to do additional file security checks when CFITSIO
     is running within the HEASARC's Hera software system.  In this case
     CFITSIO will not allow FITS files to be created outside of the user's
     individual Hera data directory area.

   - fixed an issue in fpack and funpack on Windows machines, caused by
     the fact that the 'rename' function behaves differently on Windows
     in that it does not clobber an existing file, as it does on Unix
     platforms.

   - fixed bug in the way byte-swapping was being performed when writing
     integer*8 null values to an image or binary table column.

   - added the missing macro definition for fffree to fitsio.h.

   - modified the low level table read and write functions in getcol*.c and
     putcol*.c to remove the 32-bit limitation on the number of elements.
     These routines now support reading and writing more than 2**31 elements
     at one time. Thanks to Keh-Cheng Chu (Stanford U.) for the patch.

   - modified Makefile.in so that the shared libcfitsio.so is linked against
     pthreads and libm.

Version 3.30 - 11 April 2012

  Enhancements

   - Added new routine called fits_is_reentrant which returns 1 or 0 depending on
     whether or not CFITSIO was compiled with the -D_REENTRANT directive.  This can
     be used to determine if it is safe to use CFITSIO in multi-threaded programs.

   - Implemented much faster byte-swapping algorithms in swapproc.c based on code
     provided by Julian Taylor at ESO, Garching.  These routines significantly
     improve the FITS image read and write speed (by more than a factor of 2 in
     some cases) on little-endian machines (e.g., Linux and Microsoft Windows and
     Macs running on x86 CPUs) where byte-swapping is required when reading and
     writing data in FITS files.  This has no effect on big-endian machines
     (e.g. Motorola CPUs and some IBM systems).  Even faster byte-swapping
     performance can be achieved in some cases by invoking the new "--enable-sse2"
     or "--enable-ssse3" configure options when building CFITSIO on machines that
     have CPUs and compilers that support the SSE2 and SSSE3 machine instructions.

   - added additional support for implicit data type conversion in cases where
     the floating point image has been losslessly compressed with gzip.  The
     pixels in these compressed images can now be read back as arrays of short,
     int, and long integers as well as single and double precision floating-point.

   - modified fitsio2.h and f77_wrap.h to recognize IBM System z mainframes by
     testing if __s390x__ or __s390__ is defined.

   - small change to ffgcrd in getkey.c so that it supports reading a blank
     keyword (e.g., a keyword whose name simply contains 8 space characters).

   Bug Fixes

   - fixed a bug in imcomp_decompress_tile that caused the tile-compressed image
     to be uncompressed incorrectly (even though the tile-compressed image itself
     was written correctly) under the following specific conditions:
      - the original FITS image has a "float" datatype (R*4)
      - one or more of the image tiles cannot be compressed using the standard
        quantization method  and instead are losslessly compressed with gzip
      - the pixels in these tiles are not all equal to zero (this bug does
        affect tiles where all the pixels are equal to zero)
      - the program that is reading the compressed image uses CFITSIO's
        "implicit datatype conversion" feature to read the "float" image
        back into an array of "double" pixel values.
      If all these conditions are met, then the returned pixel values in the
      affected image tiles will be garbage, with values often ranging
      up to 10**34.  Note that this bug does not affect the fpack/funpack
      programs, because funpack does not use CFITSIO's implicit datatype
      conversion feature when uncompressing the image.


To generate a diff of this commit:
cvs rdiff -u -r1.28 -r1.29 pkgsrc/devel/cfitsio/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/devel/cfitsio/PLIST
cvs rdiff -u -r1.11 -r1.12 pkgsrc/devel/cfitsio/distinfo
cvs rdiff -u -r1.4 -r1.5 pkgsrc/devel/cfitsio/patches/patch-aa

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.