CVS commit: pkgsrc/devel/cfitsio

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Fri Mar 11 11:56:06 UTC 2011

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

Log Message:
Update to 3.270, set LICENSE:

Version 3.27 - 3 March 2011

  Enhancements

    - added new routines fits_read_str and fits_delete_str which read or
      delete, respectively, a header keyword record that contains a specified
      character string.

    - added a new routine call fits_free_key_longstr which frees the memory
      that fits_read_key_longstr allocated for the long string keyword value.

    - enhanced the ffmkky routine in fitscore.c to not put a space before the
      equals sign when writing long string-valued keywords using the ESO
      HIERARCH keyword convension, if that extra character is needed to
      fit the length of the keyword name + value string within the 80-character
      FITS keyword record.

    - made small change to fits_translate_keyword to support translation of
      blank keywords (where the name = 8 blank chracters)

    - modified fpack so that it uses the minimum of the 2nd, 3rd, and 5th order
      MAD noise values when quantizing and compressing a floating point image.
      This is more conservative than just using the 3rd order MAD value alone.

    - added new routine imcomp_copy_prime2img to imcompress.c that is used by
      funpack to copy any keywords that may have been added to the primary
      array of the compressed image file (a null image) back into the header of
      the uncompressed image.

    - enhanced the fits_quantize_float and fits_quantize_double routines in
      quantize.c to also compress the tile if it is completely filled with
      null values.  Previously, this type of tile would have been written
      to the output compressed image without any compression.

    - enhanced imcomp_decompress_tile to support implicit datatype conversion
      when reading a losslessly compressed (with gzip) real*4 image into an
      array of real*8 values.

Version 3.26 - 30 December 2010

  Enhancements

   - defined 2 new macros in fitsio.h:
       #define CFITSIO_MAJOR 3
       #define CFITSIO_MINOR 26
     These may be used within other macros to detect the CFITSIO
     version number at compile time.

   - modified group.c to initialize the output URL to a null string in
     fits_url2relurl.  Also added more robust tests to see if 2 file
     pointers point to the same file.

   - enhanced the template keyword parsing code in grparser.c to support
     the 'D' exponent character in the ASCII representation of floating
     point keyword values (as in TVAL = 1.23D03).  Previously, the parser
     would have writen this keyword with a string value (TVAL = '1.23D03').

   - modified the low-level routines that write a keyword record to a FITS
     header so that they silently replace any illegal characters (ASCII
     values less than 32 or greater than 126) with an ASCII space character.
     Previously, these routines would have returned with an error when
     encountering these illegal characters in the keyword record (most commonly
     tab, carriage return, and line feed characters).

   - made substantial internal changes to imcompress.c in preparation for
     possible future support for compression methods for FITS tables analogous
     to the tiled image compression method.

   - replaced all the source code in CFITSIO that was distributed under the
     GNU General Public License with freely available code.  In particular,
     the  gzip file compression and uncompression code was replaced by the
     zlib compression library.  Thus, beginning with this version 3.26 of 
CFITSIO,
     other software applications may freely use CFITSIO without necessarily
     incurring any GNU licensing requirement.  See the License.txt file for
     the CFITSIO licensing requirements.

   - added support for using cfitsio in different 'locales' which use a
     comma, not a period, as the decimal point character in ASCII
     representation of a floating point number (e.g., France).  This
     affects how floating point keyword values and floating point numbers
     in ASCII tables are read and written with the 'printf' and 'strtod'
     functions.

   - added a new utility routine called fits_copy_rows/ffcprw that copies
     a specified range of rows from one table to another.

   - enhanced the test for illegal ASCII characters in a header (fftrec) to
     print out the name of the offending character (e.g TAB or Line Feed) as
     well as the Hex value of the chracter.

   - modified ffgtbc (in fitscore.c) to support nonstandard vector variable
     length array columns in binary tables (e.g. with TFORMn = 2000PE(500)').

   - modified the configure file to add "-lm" when linking CFITSIO on
     Solaris machines.

   - added new routine, fits_get_inttype, to parse an integer keyword value
     string and return the minimum integer datatype (TBYTE, TSHORT, TLONG,
     TLONGLONG) required to store the integer value.

   - added new routine, fits_convert_hdr2str, which is similar to fits_hdr2str
     except that if the input HDU is a tile compressed image (stored
     in a binary table) then it will first convert that header back to
     that of a normal uncompressed FITS image before concatenating the header
     keyword records.

   - modified the file template reading routine (ngp_line_from_file in
     grparser.c) so that it ignores any carriage return characters (\r)
     in the line, that might be present, e.g. if the file was created on a
     Windows machine that uses \r\n as end of line characters.

   - modified the ffoptplt routine in cfileio.c to check if the PCOUNT
     keyword in the template file has a non-zero value, and if so, resets
     it to zero in the newly created file.

   Bug Fixes

   - fixed a bug when uncompressing floating-point images that contain Nan
     values on some 64-bit platforms.

   - fixed a bug when updating the value of the CRPIXn world coordinate
     system keywords when extracting a subimage from larger FITS image, using 
the
     extended CFITSIO syntax (e.g.  myimage[1:500:2, 1:500:2]).  This bug only
     affects casee where the pixel increment value is not equal to 1, and caused
     the coordinate grid to be shifted by between 0.25 pixels (in the case of
     a pixel increment of 2) and 0.5 pixels (for large pixel increment values).

   - fixed a potential string buffer overflow error in the ffmkls routine
     that modifies the value and comment strings in a keyword that uses
     the HEASARC long string keyword convention.

   - fixed a bug in imcompress.c that could cause programs to abort on 64-bit
     machines when using gzip to tile-compress images.  Changed the declaration
     of clen in imcomp_compress_tile from int to size_t.

Version 3.25 - 9 June 2010

   - fixed bug that was introduced in version 3.13 that broke the ability
     to reverse an image section along the y-axis with an image section
     specifier like this: myimage.fits[*,-*].  This bug caused the output
     image to be filled with zeros.

   - fixed typo in the definition of the ftgprh Fortran wrapper routine
     in f77_wrap3.c.

   - modified the cfitsio.pc.in configuration file to make the lib path
     a variable instead of hard coding the path.   The provides more
     flexibility for projects such as suse and fedora when building CFITSIO.

   - fixed bug in imcomp_compress_tile in imcompress.c which caused
     null pixel values to be written incorrectly in the rare case where
     the floating-point tile of pixels could not be quantized into integers.

   - modified imcompress.c to add a new specialized routine to uncompress
     an input image and then write it to a output image on a tile by tile basis.
     This appears to be faster than the old method of uncompressing the
     whole image into memory before writing it out.  It also supports
     large images with more than 2**31 pixels.

   - made trivial changes to 2 statements in drvrfile.c to suppress
     nuisance compiler warnings.

   - some compilers define CLOCKS_PER_SEC as a double instead of an integer,
     so added an explicted integer type conversion to 2 statements in
     imcompress.c that used this macro.

   - removed debugging printf statements in drvrnet.c (15 July)

Version 3.24 - 26 January 2010

   - modified fits_translate_keywords so that it silently ignores any
     illegal ASCII characters in the value or comment fields of the input
     FITS file. Otherwise, fpack would abort without compressing input
     files that contained this minor violation of the FITS rules.

   - added support for Super H cpu in fitsio2.h

   - updated funpack to correctly handle the -S option, and to use a
     more robust algorithm for creating temporary output files.

   - modified the imcomp_compress_tile routine to support the NOCOMPRESS
     debugging option for real*4 images.

Version 3.23 - 7 January 2010

   - reduced the default value for the floating point image quantization
     parameter (q) from 16 to 4.  This parameter is used when tile compressing
     floating point images.  This change will increase the average compression
     ratio for floating point images from about 4.6 to about 6.5 without losing
     any significant information in the image.

   - enhanced the template keyword parsing routine to reject a header
     template string that only contains a sequence of dashes.

   - enhanced the ASCII region file reading routine to allow tabs as well
     as spaces between fields in the file.

   - got rid of bogus error message when calling fits_update_key_longstr

   - Made the error message more explicit when CFITSIO tries to write
     to a GZIP compressed file.  Instead of just stating "cannot write
     to a READONLY file", it will say "cannot write to a GZIP compressed
     file".

Version 3.22 - 28 October 2009

   - added an option (in imcompress.c) to losslessly compress floating
     point images, rather than using the default integer scaling method.
     This option is almost never useful in practice for astronomical
     images (because the amount of compression is so poor), but it has
     been added for test comparison purposes.

   - enhanced the dithering option when quantizing and compressing
     floating point images so that a random dithering starting point
     is used, so that the same dithering pattern does not get used for
     every image.

   - modified the architecture setup section of fitsio2.h to support the
     64-core 8x8-architecture Tile64 platform (thanks to Ken Mighell, NOAO)

   Fixes

   - fixed a problem that was introduced in version 3.13 of CFITSIO
     in cases where a program writes it own END keyword to the header
     instead of letting CFITSIO do it, as is strongly recommended.  In
     one case this caused CFITSIO to rewrite the END keyword and any
     blank fill keywords in the header many times, causing a
     noticeable slow-down in the FITS file writing speed.

Version 3.21 - 24 September 2009

   - fixed bug in cfileio.c  that caused CFITSIO to crash with a bus error
     on Mac OS X if CFITSIO was compiled with multi-threaded support (with
     the  --enable-reentrant configure option). The Mac requires an
     additional thread initialization step that is not required on Linux
     machines.  Even with this fix, occasional bus errors have been seen on
     some Mac platforms, The bus errors are seen when running the
     thread_test.c program.  The bus errors are very intermittent, and occur
     less than about 1% of the time, on the affected platforms.
     These bus errors have not been seen on Linux platforms.

   - fixed invalid C comment delimiter ("//*" should have been "/*")
     in imcompress.c.

   - Increased the CFITSIO version number string length
     in fpackutil.c, to fix problem on some platforms when running
     fpack -V or funpack -V.   Also modified the output format of the
     fpack -L command.

Version 3.20 - 31 August 2009

   - modified configure.in and configure so that it will build the Fortran
     interface routines by default, even if no Fortran compiler is found
     in the user's path. Building the interface routines may be disabled
     by specifying FC="none".  This was done at the request of users who
     obtained CFITSIO from some other standard linux distributions, where
     CFITSIO was apparently built in an environment that had no Fortran
     compiler and hence did not build the Fortran wrappers.

   - modified ffchdu (close HDU) so that it calls the routine to update
     the maximum length of variable length table columns in the TFORM
     values in all cases  where the values may have changed.  Previously
     it would not update the values if a value was already specified in
     the TFORM value.

   - added 2 new string manipulation functions to the CFITSIO parser
     (contributed by Craig Markwardt): strmid extracts a substring
     from a string, and strstr searches for a substring within a string.

   - removed the code in quantize.c that treated "floating-point integer"
     images as a special case (it would just do a datatype conversion from
     float to int, and not otherwise quantize the pixel values).  This
     caused complications with the new subtractive dithering feature.

   - enhanced the code for converting floating point images to quantized
     scaled integer prior to tile-compressing them, to apply a random
     subtractive dithering, which improves the photometric accuracy
     of the compressed images.

   - added new internal routine, iraf_delete_file, for use by fpack to
     delete a pair of IRAF format header and pixel files.

   - small change in cfileio.c in the way it recognizes an IRAF format
     .imh file.  Instead of just requiring that the filename contain the
     ".imh" string, that string must occur at the end of the file name.

   - fixed bug in the code that is used when tile-compressing real*4 FITS
     images, which quantizes the floating point pixel values into
     integer levels.  The bug would only appear in the fairly rare
     circumstance of tile compressing a floating point image that contains
     null pixels (NaNs) and only when using the lossy Hcompress algorithm
     (with the s parameter not equal to 1).  This could cause underflow of
     low valued pixels, causing them to appear as very large pixel values
     (e.g., > 10**30)  in the compressed image

   - changed the "if defined" blocks in fitsio.h, fitsio2.h and f77_wrap.h
     to correctly set the length of long variables on sparc64 machines.
     Patch contributed by Matthew Truch (U. Penn).

   - modified the HTTP file access code in drvrnet.c to support basic
     HTTP authentication, where the user supplies a user name and
     password.  The CFITSIO filename format in this case is:
     "http://username:password@hostname/...";
     Thanks to Jochen Liske (ESO) for the suggestion and the code.

Version 3.181 (BETA) - 12 May 2009

   - modified region.c and region.h to add support for additional
     types of region shapes that are supported by ds9: panda, epanda,
     and bpanda.

   - fixed compiler error when using the new _REENTRANT flag, having to
     do with the an attempted static definition of Fitsio_Lock in
     several source files, after declaring it to be non-static in fitsio2.h.

Version 3.18 (BETA) - 10 April 2009

   - Made extensive changes to make CFITSIO thread safe.  Previously,
     all opened FITS files shared a common pool of memory to store
     the most recently read or written FITS records in the files.
     In a multi-threaded environment different threads could
     simultaneously read or write to this common area causing
     unpredictable results. This was changed so that every opened
     FITS file has its own private memory area for buffering the
     file. Most of the changes were in buffers.c, fitsio.h, and
     fitsio2.h. Additional changes were made to cfileio.c, mainly
     to put locks around small sections of code when setting up the
     low-level drivers to read or write the FITS file.  Also, locks
     were needed around the GZIP compression and uncompression code
     in compress.c.,  the error message stack access routine in
     fitscore.c, the encode and decode routines in fits_hcompress.c
     and  fits_hdecompress.c, in ricecomp.c,  and  the table row
     selection and table calculator functions. Also, removed the
     'static' declaration of the local variables in pliocomp.c
     which did not appeared to be required and prevented the
     routines from being thread safe.

     As a consequence of having a separate memory buffer for every
     FITS file (by default, about 115 kB per file), CFITSIO may now
     allocate more memory than previously when an application
     program opens multiple FITS files at once.  The read and write
     speed may also be slightly faster, since the buffers are not
     shared between files.

   - Added new families of Fortran wrapper routines to read and
     write values to large tables that have more than 2**31 rows.
     The arguments that define the first row and first element to
     read or write must be I*8 integers, not ordinary I*4
     integers.  The names of these new routines have 'LL' appended
     to them, so for example, ftgcvb becomes ftgcvbll.

   Fixes

   - Corrected an obscure bug in imcompress.c that would have incorrectly
     written the null values only in the rare case of writing a signed
     byte array that is then tile compressed using the Hcompress or PLIO
     algorithm.

Version 3.14 - 18 March 2009

  Enhancements

   - modified the tiled-image compression and uncompression code to
     support compressing unsigned 16-bit integer images with PLIO.
     FITS unsigned integer arrays are offset by -32768, but the PLIO
     algorithm does not work with negative integer values.  In this
     case, an offset of 32768 is added to the array before compression,
     and then subtracted again when reading the compressed array.
     IMPORTANT NOTE:  This change is not backward compatible, so
     these PLIO compressed unsigned 16-bit integer images will not be
     read correctly by previous versions of CFITSIO; the pixel values
     will have an offset of +32768.

   - minor changes to the fpack utility to print out more complete
     version information with the -V option, and format the report
     produced by the -T option more compactly.

  Fixes

   - Modified imcomp_compress_image (which is called by fpack) so that
     it will preserve any null values (NaNs) if the input image has
     a floating point datatype (BITPIX = -32 or -64).  Null values in
     integer datatype images are handled correctly.

   - Modified imcomp_copy_comp2img so that it does not copy the
     ZBLANK keyword, if present, from the compressed image header
     when uncompressing the image.

   - Fixed typo in the Fortran wrapper macro for the ftexist function.

Version 3.13 -  5 January 2009

  Enhancements

   - updated the typedef of LONGLONG in fitsio.h and cfortran.h to
     support the Borland compiler which uses the  __int64 data type.

   - added new feature to the extended filename syntax so that when
     performing a filtering operation on specified HDU, if you add
     a '#' character after the name or number of the HDU, then ONLY
     that HDU (and the primary array if the HDU is a table) will be
     copied into the filtered version of the file in memory.  Otherwise,
     by default CFITSIO copies all the HDUs from the input file into
     memory.

   - when specifying a section, if the specified number of dimensions
     is less than the number of dimensions in the image, then CFITSIO
     will use the entire dimension, as if a '*' had been specified.
     Thus [1:100] is equivalent to [1:100,*] when specifying a section
     of 2 dimensional image.

   - modified fits_copy_image_section to read/write the section 1 row
     at a time, instead of the whole section, to reduce memory usage.

   - added new stream:// drivers for reading/writing to stdin/stdout.
     This driver is somewhat fragile, but for simple FITS read and
     write operations this driver streams the FITS file on stdin
     or stdout without first copying the entire file in memory, as is
     done when specifying the file name as "-".

   - slight modification to ffcopy to make sure that the END keyword
     is correctly written before copying the data.  This is required
     by the new stream driver.

   - modified ffgcprll, so that when writing data to an HDU, it first
     checks that the END keyword has been written to the correct place.
     This is required by the new stream driver.

  Fixes

   - fixed bug in ffgcls2 when reading an ASCII string column in binary
     tables in cases where the width of the column is greater than 2880
     characters and when reading more than 1 row at a time.  Similar
     change was made to ffpcls to fix same problem with writing to
     columns wider than 2880 characters.

   - updated the source files listed in makepc.bat so that it can be
     used to build CFITSIO with the Borland C++ compiler.

   - fixed overflow error in ffiblk that could cause writing to Large Files
     (> 2.1 GB) to fail with an error status.

   - fixed a bug in the spatial region code (region.c) with the annulus
     region.   This bug only affected specialized applications which
     directly use the internal region structure; it does not affect
     any CFITSIO functions directly.

   - fixed memory corruption bug in region.c that was triggered if the
     region file contained a large number of excluded regions.

   - got rid of a harmless error message that would appear if filtering
     a FITS table with a GTI file that has zero rows. (eval_f.c)

   - modified fits_read_rgnfile so that it removes the error messages
     from the error stack if it is unable to open the region file as
     a FITS file. (region.c)

Version 3.12 - 8 October 2008

   - modified the histogramming code so that the first pixel in the binned
     array is chosen as the reference pixel by default, if no other
     value is previously defined.

   - modified ffitab and ffibin to allow a null pointer to the
     EXTNAME string, when inserting a table with no name.

Version 3.11 - 19 September 2008

   - optimized the code when tile compressing real*4 images (which get
     scaled to integers).  This produced a modest speed increase.  For
     best performance, one must specify the absolute q quantization
     parameter, rather than relative to the noise in the tile (which
     is expensive to compute).

   - modified the FITS region file reading code to check for NaN values,
     which signify the end of the array of points in a polygon region.

   - removed the test for LONGSIZE == 64 from fitsio.h, since it may
     not be defined.

   - modified imcompress.c to support unconventional floating point FITS
     images that also have BSCALE and BZERO keywords.  The compressed
     floating point images are linearly scaled twice in this case.


To generate a diff of this commit:
cvs rdiff -u -r1.24 -r1.25 pkgsrc/devel/cfitsio/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/devel/cfitsio/distinfo
cvs rdiff -u -r1.3 -r1.4 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.