Mercurial > hg > minc-tools
view ChangeLog @ 2656:946695de0dca
EZ minc test implimentation
| author | Vladimir S. FONOV <vladimir.fonov@gmail.com> |
|---|---|
| date | Fri, 23 Mar 2012 16:41:29 -0400 |
| parents | aa328918dc06 |
| children | 6dae0da66b3c |
line wrap: on
line source
2012-03-14 Andrew L Janke <a.janke@gmail.com> * added progs/mincsample 2012-03-14 Andrew L Janke <a.janke@gmail.com> * added progs/mincmorph -- Release of minc 2.1.10 -- 2012-02-22 Andrew L Janke <a.janke@gmail.com> * added a patch from Steve Robbins that factors references to PATH_MAX out to fix a build problem on hurd 2011-12-20 Andrew L Janke <a.janke@gmail.com> * libsrc/netcdf_convenience.c: changed execute_decompress_command() to always decompress the whole file as the approach used for netCDF files for header_only does not work with HDF5 MINC2 files * merged Vlad's ezminc branch 2011-06-29 Andrew L Janke <a.janke@gmail.com> * configure.in: changed typo from enable to disable minc2 2011-05-30 Andrew L Janke <a.janke@gmail.com> * progs/minccalc: added imax() and imin() operators 2011-04-29 Andrew L Janke <a.janke@gmail.com> * libsrc2/volume.c: added minc_version global * libsrc/netcdf_convenience.c: added minc_version global 2011-02-17 Andrew L Janke <a.janke@gmail.com> * libsrc2/test/datatype-test.c: fixed a HDF5 bug in error output 2011-02-14 Andrew L Janke <a.janke@gmail.com> * progs/mincview/mincview: converted from csh to bash and changed from xv to display 2011-02-09 Andrew L Janke <a.janke@gmail.com> * libsrc/minc_compat.h: Added cplusplus extern to header 2011-01-19 Jim Nikelski <nikelski@bic.mni.mcgill.ca> * Fixed x86_64 ecattominc bug which resulted in a segmentation fault on 64-bit platforms. Change primarily required changing the type of the "dirblock" IO buffer from long to int32_t, reflecting the actual storage type in the ecat file. 2010-11-23 Claude Lepage <claude@bic.mni.mcgill.ca> * Fixed bug in dicom_to_minc.c for segmentation fault on undefined sequence (initialization of gi_ptr->cur_size) * Free some memory after usage 2010-11-23 Ilana Leppert <ilana@bic.mni.mcgill.ca> * Added b-matrix field for Siemens diffusion scans (version >= VB only). * Made changes to ordering of slices: e.g. a descending acquisition now has negative slice step. This was an issue with MOSAIC, in which the ordering of the slices in the MOSAIC image is ascending, even though the acquisition is descending (version >= VA25 and >= VB11). -- Release of minc 2.1.00 -- 2010-07-27 Andrew L Janke <a.janke@gmail.com> * conversion/micropet/upet2mnc.c: error bug squashed (John Cupitt) 2010-07-06 Claude Lepage <claude@bic.mni.mcgill.ca> * Improved convergence and accuracy for application of non-linear transformation (especially for 2-d slices) 2010-06-28 Andrew L Janke <a.janke@gmail.com> * Added progs/xfm/xfm2def.c and progs/xfm/xfm2def.man1 2010-05-23 Andrew L Janke <a.janke@gmail.com> * changed all calls to H5Acreate2 to the H5Acreate macro 2010-05-18 Steve M. Robbins <smr@sumost.ca> * libsrc/hdf_convenience.c: specify version 2 of H5Gopen, H5Acreate. * minc.h: ensure hdf5.h included before netcdf.h to avoid build error with netcdf 4.1.1 and openmpi 1.4.1. 2010-03-22 Andrew L Janke <a.janke@gmail.com> * added pod2man for manpage generation from scripts * shifted minchistory man to POD * conversion/vff2mnc/vff2mnc.c: added error checking for fgets * set default volume_io caching to none * added checks for outfiles in minccalc * removed outdated GETTING_STARTED file 2010-03-02 Andrew L Janke <a.janke@gmail.com> * Added minccmp (minccmp.c and minccmp.man1) * libsrc/hdf_convenience.c: removed spurious debug output * libsrc/minc.h: replaced MAX_NC_OPEN with 32 * libsrc/voxel_loop.c: replaced MAX_NC_OPEN with MI_MAX_NUM_ICV 2010-02-03 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincik: added -text_size option (Thanks Mishkin) * removed all non-quoted string barewords (hash refs) * added range calculation for anot bar if not defined 2009-11-13 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincpik: added -sagittal_offset_perc option 2009-11-06 Claude Lepage <claude@bic.mni.mcgill.ca> * volume_io/Volumes/output_mnc.c: fix output buffers for a slice as only first buffer would be written out 2009-08-11 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincpik: Added taking first time point for 4D files 2009-07-08 Andrew L Janke <a.janke@gmail.com> * Added minimum cmake version to CMakeLists.txt * Added libtoolize/glibtoolize logic in autogen.sh (thanks Sean) 2009-06-03 Claude Lepage <claude@bic.mni.mcgill.ca> * Fixed bug in multidim_array_is_alloced for correct check of memory allocation of image data. Return volume=NULL when memory allocation fails. -- Release of minc 2.0.18 -- 2009-04-29 Claude Lepage <claude@bic.mni.mcgill.ca> * Smarter utilization of buffer in input_mnc.c and output_mnc.c 2009-04-29 Andrew L Janke <a.janke@gmail.com> * progs/mincinfo/mincinfo.c: fixed a stack smash 2009-04-21 Claude Lepage <claude@bic.mni.mcgill.ca> * Fixed bug with chunking for internal file compression using hdf5 (now makes the code faster for large files) -- Release of minc 2.0.17 -- 2009-01-20 Andrew L Janke <a.janke@gmail.com> * Updated version in CMakeLists.txt * Note that with the bugfix in ParseArgv all other MINC programs that link against this will have to be rebuilt. * CMakeLists.txt: updated version Warning cleanups below * conversion/dcm2mnc/minc_file.c: fixed printf type * conversion/dcm2mnc/siemens_to_dicom.c: fixed printf type * conversion/ecattominc/machine_indep.c: added string.h and fixed 2 fprintf missing format args * conversion/micropet/upet2mnc.c: fixed two fprintf format args * conversion/minctoecat/ecat_write.c: added string.h * conversion/minctoecat/minctoecat.c: added missing argument to fprintf * conversion/nifti1/mnc2nii.c: fixed incorrect printf type * progs/mincview/invert_raw_image.c: added fwrite checking 2009-01-03 Steve M. Robbins <smr@sumost.ca> * testdir/run_test_progs.sh: New. Test that programs like mincheader and mincdiff work properly. * configure.in: Bump to version 2.0.17. * libsrc/ParseArgv.c (ParseArgv): Change ARGV_CONSTANT to treat src and dst and pointer to integer, as documented. Reverts change 6.9 of this file. * testdir/test_arg_parse.c: New. Test program for argument parsing (ParseArgv.[ch]). * testdir/run_test_arg_parse.sh: New. Test driver for above. * testdir/Makefile.am (TESTS): Add run_test_arg_parse.sh. * libsrc2/Makefile.am: Remove; the only content was SUBDIRS = test. * Makefile.am: Change SUBDIRS from libsrc2 to libsrc2/test. * configure.in: Remove libsrc2/Makefile output. * testdir/xfmconcat_01.sh: * testdir/xfmconcat_02.sh: Add -clobber to output-generating commands. * libsrc2/test/testminctools.sh: Add "set -e" to exit on any error. * configure.in: Remove AC_PROG_RANLIB, obsoleted by use of AC_PROG_LIBTOOL. 2008-10-12 Steve M. Robbins <smr@sumost.ca> * conversion/dcm2mnc/dcm2mnc.man1: * conversion/ecattominc/ecattominc.man1: * conversion/micropet/upet2mnc.man1: * conversion/minctoecat/minctoecat.man1: * conversion/nifti1/mnc2nii.man1: * conversion/nifti1/nii2mnc.man1: * conversion/vff2mnc/vff2mnc.man1: * progs/mincgen/mincgen.man1: Fix errors, mainly removing trailing TAB characters. -- Release of minc 2.0.16 -- 2008-09-04 Andrew L Janke <a.janke@gmail.com> * progs/xfm/xfmconcat.c: Added -verbose and -clobber options * progs/xfm/xfmconcat.man1: added -verbose and -clobber * progs/xfm/xfminvert.man1: added -verbose and -clobber 2008-08-13 Andrew L Janke <a.janke@gmail.com> * progs/rawtominc/rawtominc.c: changed to an enum for modalities to get around an esoteric bug with use of ParseArgv and strings passed by reference on 64 bit architectures 2008-08-11 Andrew L Janke <a.janke@gmail.com> * conversion/Acr_Nema: Many changes from Claude * conversion/dcm2mnc: Many changes for 64 bit and "new" DICOM types 2008-04-07 Andrew L Janke <a.janke@gmail.com> * conversion/ecattominc/ecattominc.c: added config.h * Makefile.am: removed minc_globdef.h * libsrc/minc_basic.h: rewrote error code to avoid global vars (Claude) * libsrc/minc_error.h: changes for error code (Claude) * libsrc/minc_error.c: changes for error code (Claude) 2008-03-08 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincpik: fixed a bug with bar width from Mike Ferreira 2008-03-07 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincpik: fixed two bugs with lookup triplanars 2008-02-28 Andrew L Janke <a.janke@gmail.com> * progs/mincpik/mincpik: added the -anot_bar option -- Release of minc 2.0.15 -- 2008-02-15 Andrew L Janke <a.janke@gmail.com> * Removed all fortran code (the subdirectory anyhow) * removed get_image_offset.c as it will not work with MINC2 * updated configure.in and Makefile.am to suit * changed --enable-minc2 to --disable-minc2 2008-01-24 Andrew L Janke <a.janke@gmail.com> * AUTHORS: added Claude Lepage * progs/xfm/xfmconcat.c: Added a history patch from Mishkin Derakhshan * conversion/nifti1/nii2mnc.c: Added a patch from Claude for patient names 2008-01-17 Andrew L Janke <a.janke@gmail.com> * libsrc/hdf_convenience.c (hdf_path_from_name): added NC_NAT to switch 2008-01-17 Steve M. Robbins <smr@sumost.ca> * testdir/test_speed.c (nctypename): Return "unknown" if no switch case used. * libsrc2/test/vector_dimension-test.c (create_test_file): * libsrc2/test/hyper-test-2.c (create_test_file): * conversion/dcm2mnc/dicom_to_minc.c (copy_element_properties): Change return type from int to void; no callers require a return value. * testdir/icv_fillvalue.c (main): * conversion/micropet/upet2mnc.c (main): Return 0 at end of function. 2008-01-17 Andrew L Janke <a.janke@gmail.com> * removed all rcsid's as they are not used * removed a bunch of ^L's that crept in somehow * removed old and out of date BUGS file 2008-01-13 Steve M. Robbins <smr@sumost.ca> * progs/mincreshape/mincreshape.h: * progs/mincreshape/mincreshape.c: * progs/mincreshape/copy_data.c: Move static function declarations from header file to .c files that define the function. Avoids compiler warnings. * progs/mincresample/mincresample.h: * progs/mincresample/mincresample.c: * progs/mincresample/resample_volumes.c: Move static function declarations from header file to .c files that define the function. Avoids compiler warnings. * progs/minccalc/minccalc.c (constant,constant2): Remove unushed variables. * libsrc/voxel_loop.c (get_output_filename): Remove unused function. * conversion/nifti1/nifti1_local.h: * conversion/nifti1/mnc2nii.c: Move definition of dimnames to .c file where it is used. Avoids compiler warning. * conversion/dcm2mnc/dicom_read.c: Don't declare or define convert_numa3_coordinate(), since the caller is #if 0'd out. 2008-01-12 Steve M. Robbins <smr@sumost.ca> * libsrc2/hyper.c (mirw_hyperslab_raw): * libsrc/hdf_convenience.c (hdf_varget): Use hsize_t rather than hssize_t for 3rd argument to H5Sselect_hyperslab(). * libsrc/voxel_loop.c: * progs/mincinfo/mincinfo.c: * progs/mincmath/mincmath.c: * progs/rawtominc/rawtominc.c: * testdir/icv.c: * testdir/icv_dim.c: * testdir/icv_dim1.c: * testdir/icv_fillvalue.c: * testdir/icv_range.c: * testdir/minc_types.c: Add braces around static initializers. 2008-01-11 Andrew L Janke <a.janke@gmail.com> * removed outdated TODO file * merged WHATSNEW-2.0 into NEWS/README 2008-01-09 Andrew L Janke <a.janke@gmail.com> * replaced mincedit with a complete rewrite in sh 2008-01-04 Andrew L Janke <a.janke@gmail.com> * mincheader: updated scripting style and replaced tmpdir code 2008-01-02 Steve M. Robbins <smr@sumost.ca> * testdir/run_tests.sh: * testdir/run_test2.sh: Quote the value assigned to variable tests, so that the scripts run. 2007-12-18 Jonathan Harlap <jharlap@bic.mni.mcgill.ca> * dcm2mnc: Restored dicom fields in minc headers. (conversion/dcm2mnc/minc_file.c) * dcm2mnc: Restored old name of acquisition comments attribute. (conversion/dcm2mnc/minc_file.c) 2007-12-06 Claude Lepage <claude@bic.mni.mcgill.ca> * Freed more memory in miicv_free (libsrc/image_conversion.c) * Added cubic interpolation in mincresample for x-y slices * Fixed seg fault bug with null history string (libsrc/minc_convenience.c) * Changed hard-coded strings for MIxspace (y,z) (libsrc2/volume.c and libsrc2/dimension.c) * Made global variables static in minccompress to avoid conflict with libz 2007-12-03 Andrew L Janke <a.janke@gmail.com> * changed all global variables to static in progs directory to avoid possible linker errors in the future. 2007-10-23 Andrew L Janke <a.janke@gmail.com> * Added most things needed for a CMake build * nii2mnc mnc2nii: Fixed a linking bug -- Release of minc 2.0.14 -- 2007-09-13 Andrew L Janke <a.janke@gmail.com> * Added a few more free's for memory thanks to Claude 2007-08-24 Andrew L Janke <a.janke@gmail.com> * added xfmflip and man page * fixed a bug in the build of minccalc * updated nifti library for nii2mnc 2007-08-08 Claude Lepage <claude@bic.mni.mcgill.ca> * Increased size of MI_MAX_VAR_BUFFER_SIZE and fix chunking for internal file compression using hdf5 * Modified mincconvert to use default chunking 2007-05-18 Andrew L Janke <a.janke@gmail.com> * Fixed up small problems with build process * replaced csh scripts with sh. (checks fail if no tcsh) * added libsrc2 to the INCLUDES. why this was not in before beats me 2006-09-01 Jonathan Harlap <jharlap@bic.mni.mcgill.ca> * conversion/Acr_nema - Fixed a bug causing dump_acr_nema to skip all elements with element number 0x0010 2006-05-31 Jonathan Harlap <jharlap@bic.mni.mcgill.ca> * Makefile.am - modified to build and install image_filters/extract and image_filters/byte_swap if the ACR NEMA tools are intstalled, as they are required by dicom_to_minc.pl 2006-05-18 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/various... added config.h to source files that need it for proper operation with MINC 2.0 2006-04-19 Claude Lepage <claude@bic.mni.mcgill.ca> * fix duplicate instances of solve_linear_system and scaled_maximal_pivoting_gaussian_elimination in volume_io/Geometry/gaussian.c and libsrc.2. Make static. This is to avoid linker problems with minc2. 2006-04-09 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc, conversion/Acr_nema - added general support for Siemens DTI sequences, inserting attributes according to Jennifer Campbell's conventions. 2006-03-27 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/nifti1/mnc2nii.c - Set time and vector dimensions "properly" for some versions of Analyze and NIfTI libraries. Also set the intent_code field to NIFTI_INTENT_VECTOR if the vector_dimension is set. Also fixed an issue with file names. 2006-03-10 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/Acr_nema/element.c - Modify acr_dump_element_list() to use helper function maybe_print_as_string() to print data with unknown VR as either ASCII or a string of hex bytes. 2006-02-28 Bert Vincent <bert@bic.mni.mcgill.ca> * libsrc/hdf_convenience.c - Modify the hdf_vardef() function to avoid errors in HDF5 1.6.5 2006-02-19 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * testdir/create_grid_xfm.c (main): Initialize variable mio before using. 2006-02-09 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc/dicom_to_minc.c, conversion/dcm2mnc/siemens_to_dicom.c - Deal more correctly with some odd cases in .IMA files. 2006-02-08 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/rawtominc/rawtominc.c, conversion/nifti1/nii2mnc.c, conversion/micropet/upet2mnc.c: Change fopen() parameter to "rb" to force correct operation on DOS/Windows. * libsrc2/volume.c: Allow signed as well as unsigned base types for labels. 2005-12-15 Bert Vincent <bert@bic.mni.mcgill.ca> * libsrc2/volume.c - set units field unconditionally in _miget_file_dimension() 2005-12-13 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc/dicom_to_minc.c: Ignore DICOM protocol errors. This change was necessitated by images from a Philips Intera scanner version 'NT 10.4.1\\PIIM V2.1.4.1 MIMIT MCS' that appears to set the DICOM length field incorrectly. 2005-12-03 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/micropet/upet2mnc.c - fix handling of single-frame data * progs/mincgen/main.c - make "-o" option imply "-b" 2005-11-22 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/mincgen/genlib.c - fix free() issue * progs/mincgen/load.c - #include config.h 2005-11-11 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc/dcm2mnc.h - fix definition of IMA_MAGIC_SIZE * conversion/dcm2mnc/dcm2mnc.c - fix test for is_ima_file() 2005-11-04 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc/dicom_to_minc.h - further relaxation of COORDINATE_EPSILON, now set to 0.005 * conversion/dcm2mnc/minc_file.c - combine cloned regular/irregular dimension checking code into new function, check_regular() * conversion/dcm2mnc/dcm2mnc.c - update version to 2.0.07 2005-10-26 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/dcm2mnc/dicom_to_minc.h - set COORDINATE_EPSILON to a fixed value of 0.0001 rather than 100*FLT_EPSILON to allow for more slop in coordinates. * conversion/nifti1/mnc2nii.c - handle missing value for spacetype. 2005-09-16 Bert Vincent <bert@bic.mni.mcgill.ca> * libsrc2/conversion/dcm2mnc/dicom_read.c - again change the handling of the slice thickness / slice spacing issue to accomodate Andrew Janke's Philips data. If both slice thickness and slice spacing are set, we select the maximum. For some reason I had been choosing the minimum, but logically the opposite seems more reasonable (and is certainly correct in Andrew's case). 2005-09-14 Bert Vincent <bert@bic.mni.mcgill.ca> * libsrc2/slice.c - in function mirw_slice_minmax(), properly reorient access for slice minimum and maximum if dimension order has been altered. * libsrc2/hyper.c - normalize data correctly in miget_real_value_hyperslab(). * progs/mincinfo/mincinfo.c - include config.h 2005-08-26 Bert Vincent <bert@bic.mni.mcgill.ca> * Implemented --enable-hdf5 option in ./configure script so that we can selectively enable or disable MINC2 support. This required changing the way we treat the MINC2 symbol, and being careful to include config.h in all files that call netCDF functions. * libsrc2/grpattr.c - Fixed issue in micreate_group() function - it would not function properly when a group already existed in the file. * conversion/dcm2mnc - Ported changes from MINC 1 branch. 2005-07-29 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/mincstats/mincstats.c: Add warning when mask file specified with no mask range option. 2005-07-28 Bert Vincent <bert@bic.mni.mcgill.ca> * conversion/nifti1/mnc2nii.c: Implement fix suggested by Hyun-Pil Kim to set unused dimension lengths to 1 rather than zero. 2005-07-25 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/mincstats/mincstats.c: Fix calculation of percent threshold to correctly account for non-zero histogram floor. 2005-07-15 Andrew Janke <a.janke@gmail.com> * added -auto_range option to mincpik (thanks to Jon Harlap) 2005-07-15 Bert Vincent <bert@bic.mni.mcgill.ca> * libsrc/hdf_convenience.c: Two minor fixes. First, when emulating 'signtype' attributes in MINC 2 files, comparisons with MI_SIGNED and MI_UNSIGNED should NOT depend on a properly- null-terminated attribute value. Second, suppress HDF5 errors in hdf_attdel() * progs/mincresample/mincresample.c * progs/mincresample/mincresample.h * progs/mincresample/mincresample.man1 * progs/mincresample/resample_volumes.c Support windowed sinc interpolation, as ported from 1.X branch. * progs/mincconcat/mincconcat.c: * progs/mincconcat/mincconcat.man1: Add support for -filestarts option, as ported from 1.X branch. 2005-07-04 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * Makefile.am: * progs/minchistory/minchistory.man1: New manual page for minchistory. 2005-07-03 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * configure.in: Check for sysconf(). * volume_io/Prog_utils/time.c (get_clock_ticks_per_second): Use POSIX sysconf() function, if available. 2005-06-22 Bert Vincent <bert@bic.mni.mcgill.ca> * Minor fix to ncgenyy.l to avoid compiler complaint on ia64. 2005-05-20 Bert Vincent <bert@bic.mni.mcgill.ca> * Update Makefile.msvc-win32 to build converters. * Declare restructure_array() in hyper.c to be MNCAPI so that nii2mnc can link to it. * Get rid of warnings in mincgen build. Affected files are progs/mincgen/ncgenyy.l and progs/mincgen/ncgentab.y * Replace direct usage of H5Fis_hdf5() function to avoid annoying error messages for nonexistant files. Instead there is now a function named hdf_access() that returns a boolean value TRUE if the file can be accessed and is in HDF5 format. This change affected the files libsrc/hdf_convenience.h, libsrc/hdf_convenience.c, and libsrc/netcdf_convenience.c * Remove and/or conditionalize some test code for memory-mapped files that should not have been checked in. Affected files are libsrc/netcdf_convenience.c, libsrc/hdf_convenience.c, and progs/mincstats/mincstats.c 2005-05-19 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix volume.c and m2util.c to be compatible with HDF5 1.6.3 and later. * Port nifti converter changes from MINC 1.X branch * Port dcm2mnc converter changes from MINC 1.X branch * Port build changes for dcm2mnc and ACR/NEMA library from MINC 1.X branch 2005-04-18 Bert Vincent <bert@bic.mni.mcgill.ca> * Move volume_io headers into Include/volume_io subdirectory. 2005-03-17 Andrew Janke <a.janke@gmail.com> * removed ':' from temporary filenames for windows compatibility 2005-03-11 Bert Vincent <bert@bic.mni.mcgill.ca> * Improve nii2mnc's support for functional (time-varying) data, and support qform as well as sform transforms in the header. 2005-01-28 Bert Vincent <bert@bic.mni.mcgill.ca> * Incorporate NIfTI-1 converters, nii2mnc and mnc2nii * Incorporate upet2mnc, converter for Concorde microPET data. * Copied fix for mincmakescalar to warn user if the vector_dimension is not the last dimension in the file. * Modify Leila's vector_dimension-test code to create its own data file, to avoid having to carry around a multi-megabyte test file as part of the distrbution. 2005-01-19 Bert Vincent <bert@bic.mni.mcgill.ca> * Incorporate Anthonin Reilhac's changes to ecattominc * Add ecattominc, mnc2nii, and nii2mnc to the automake files * Modify mincdump to print long attributes of type NC_BYTE as strings if all of the characters are printable. 2005-01-04 Bert Vincent <bert@bic.mni.mcgill.ca> * Adapt minc_simple.c to use Leila's revision of the restructure_array() parameters. This seems to work properly again. 2004-12-14 Bert Vincent <bert@bic.mni.mcgill.ca> * Got rid of lots of C99-related warnings * Added new biModalT algorithms to mincstats 2004-12-15 Andrew Janke <a.janke@gmail.com> * added epm-header.in, removed mni_minc.epm.header 2004-12-07 Andrew Janke <a.janke@gmail.com> * Squashed yet another bug with the BiModalT code aaargh! This should now replicate volume_stats even closer! 2004-10-18 Andrew Janke <a.janke@gmail.com> * Fixed bug in mincstats -BimodalT code to exactly replicate (within reason) volume_stats * Changed default # of int histogram bins from 10000 to 65536 2004-08-11 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix minc.h for netCDF 3.5.1 2004-08-03 Bert Vincent <bert@bic.mni.mcgill.ca> * Added new test cases to dimension-test.c * Fix bug(s) in volume.c * Correctly implement some of the conversion functions 2004-06-21 Bert Vincent <bert@bic.mni.mcgill.ca> * Updated mincgen man page * "Improve" Doxygen documentation 2004-06-16 Bert Vincent <bert@bic.mni.mcgill.ca> * Fixes and improvements for mincgen/mincdump * Emulate a vector_dimension for MINC 2.0 files with a compound datatype. * Move libsrc2 (MINC 2.0 API) files under the MINC hierarchy in CVS * Fix ordering of world coordinate values in miconvert_world_to_voxel and miconvert_voxel_to_world 2004-06-11 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix issue with minc_modify_header's new -sappend and -dappend options. * Add "mincgen" based upon "ncgen" for "mincedit" * Fix nasty minccalc bug. Minccalc would fail to work properly on any file with a vector_dimension of length greater than 1. 2004-06-09 Bert Vincent <bert@bic.mni.mcgill.ca> * Add netcdf and HDF5 versions to the -version list. 2004-06-08 Bert Vincent <bert@bic.mni.mcgill.ca> * Avoid printing HDF5 errors on excessively long attributes. Still have to decide how best to deal with this situations - truncate, drop, or somehow convert the attribute into a dataset? Right now we will drop excessively large attributes from HDF5 files, which is probably bad. * Fix bug (mentioned in previous entries) which caused mincdump (as derived from ncdump) to print zero-length attributes as an erroneous string of length one instead of as an empty string. * Eliminate bogus "not implemented yet" message from volume_io 2004-06-07 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix setting of length in hdf_vardef/hdf_dimdef * Handle zero-length character strings properly. There is actually a minor bug in "ncdump" which makes zero-length strings appear to have length one (the bogus character will appear to match the first character in the preceding string). 2004-06-04 Bert Vincent <bert@bic.mni.mcgill.ca> * Changed volume_io/Volumes/volume_cache.c to increase both the cache size and the default cached volume size (i.e. the size which turns on caching). 2004-06-01 Bert Vincent <bert@bic.mni.mcgill.ca> * Fixed endian-ness issues in MINC 2.0 format. 2004-05-25 Bert Vincent <bert@bic.mni.mcgill.ca> * Added -dappend, -sappend to minc_modify_header 2004-05-20 Bert Vincent <bert@bic.mni.mcgill.ca> * Revised man pages * Added -2 option to minclookup 2004-04-30 Bert Vincent <bert@bic.mni.mcgill.ca> * Further reduce compiler issues for IRIX MIPSpro compiler. * Tagged version 2.0.06 2004-04-29 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix compiler compatibility problem against IRIX MIPSpro compiler in netcdf_convenience.c 2004-04-22 Bert Vincent <bert@bic.mni.mcgill.ca> * Expanded test cases 2004-04-15 Bert Vincent <bert@bic.mni.mcgill.ca> * Add -DMINC2, #ifdef MINC2 to make most MINC2 additions and changes optional. * Expand minc2_uguide.tex 2004-04-08 Bert Vincent <bert@bic.mni.mcgill.ca> * Add mincdump command * Minor changes to increase portability, esp. to Windows. 2004-03-25 Bert Vincent <bert@bic.mni.mcgill.ca> * Add support for -compress and -chunk options to mincconvert * Some small library fixes * Fix handling of irregular dimension variables in emulation library. 2004-02-27 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix dimorder handling 2004-02-18 Bert Vincent <bert@bic.mni.mcgill.ca> * Fixed handling of "rootvariable" emulation in hdf_convenience.c and netcdf_convenience.c * Fixed behavior of some of the netCDF emulation attribute functions in hdf_convenience.c and minc_compat.c 2004-02-17 Bert Vincent <bert@bic.mni.mcgill.ca> * Fixed mincconvert - added ncendef() * Actually implemented MINC_COMPRESS MINC 1: 2004-03-24 Bert Vincent <bert@bic.mni.mcgill.ca> * Minor fix to miappend_history() in libsrc/minc_convenience.c 2004-03-23 Bert Vincent <bert@bic.mni.mcgill.ca> * Modify configure.in, libsrc/netcdf_convenience.c, volume_io/Prog_utils/files.c, and volume_io/Prog_utils/time.c to make MINC more portable, especially to Windows compilers. 2003-02-02 Bert Vincent <bert@bic.mni.mcgill.ca> * Added -version flag for all executables (or at least all "C" language executables). Implemented in ParseArgv() to make it universal, and applications can override their version number by adding a "ARGV_VERINFO" record to their argTable[]. * Created miget_version() and miappend_history() functions. 2003-12-05 Andrew L. Janke <a.janke@gmail.com> * Changes to mincpik: added -depth option (as per a diff supplied by Jonathan HARLAP); while at it, did a bit of clean-up including replacing home-grown tempdir cleanup with File::Temp; Added -clobber option so that mincpik more closely matches the other minc tools. 2003-11-23 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * configure.in: Set version to 1.3. Check for headers sys/stat.h, sys/wait.h, unistd.h; and for functions fork, system, and popen. * libsrc/netcdf_convenience.c: Use above checks for conditional inclusion of headers. (execute_decompress_command): Use fork or system to decompress file, if facility available. 2003-11-21 Steve ROBBINS <stever@bic.mni.mcgill.ca> * volume_io/Include/basic.h: Include <math.h> for M_PI definition. Build problem reported by Maxime Descoteaux <mdesco@cim.mcgill.ca>. 2003-11-14 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * Makefile.am (libvolume_io_la_LDFLAGS): (libminc_la_LDFLAGS): Update version-info. * progs/rawtominc/rawtominc.c: Include <unistd.h> for declaration of swab(). Cast void pointer "image" to unsigned char before adding integer size; otherwise IRIX CC fails. * progs/mincview/invert_raw_image.c (main): * progs/minc_modify_header/minc_modify_header.c (main): Specify return type. * libsrc/voxel_loop.c: * libsrc/value_conversion.c: * libsrc/dim_conversion.c: Include <math.h> for declaration of fabs(). 2003-11-13 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * progs/minchistory: * progs/mincpik: New. Perl scripts moved here from Andrew Janke's "minc_dev" tool set. * Makefile.am (dist_bin_SCRIPTS): Install minchistory and mincpik. * README: Mention minchistory, mincpik. Correct distribution URL. * mni_minc.epm.header: Update license, version. * Makefile.am (EXTRA_DIST): Distribute README.binary_packaging. * configure.in: Run autoupdate; change AM_CONFIG_HEADER to AC_CONFIG_HEADERS. * testdir/Makefile.am (INCLUDES): Add volume_io/Include. 2003-10-31 Bert Vincent <bert@bic.mni.mcgill.ca> * progs/rawtominc/rawtominc.c: Add options -dimorder and -swap_bytes. 2003-06-01 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * testdir/Makefile.am (script_tests): * Makefile.am (SUBDIRS): Process volume_io before testdir, because tests may link against volume_io. * volume_io/MNI_formats/gen_xf_io.c (output_one_transform): Update *volume_count after writing a grid transform (thanks, Peter Neelin). * testdir/create_grid_xfm.c: New. Utility to create grid transformation. * testdir/test_xfm.c: Copied from volume_io/Testing/test-xfm.c. * testdir/xfmconcat_01.sh: * testdir/xfmconcat_02.sh: New. Test concatenation of grid transformations. 2003-03-17 Bert Vincent <bert@bic.mni.mcgill.ca> * configure.in: added check for mkstemp(), tempnam(), and tmpnam() * libsrc/netcdf_convenience.c: added definition of micreate_tempfile() * libsrc/minc.h: added declaration of micreate_tempfile() * volume_io/Prog_utils/files.c: replaced uses of tmpnam() with micreate_tempfile(). * volume_io/Volumes/volume_cache.c: replaced use of tmpnam() with micreate_tempfile() 2003-02-14 Jason Lerch <jason@bic.mni.mcgill.ca> * configure.in: Set version to 1.1.1 * mni_minc.epm.header: added. * README.binary_packaging: added. 2003-01-17 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * configure.in: Set version to 1.2. 2003-01-17 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * MINC-1-1 tagged. * README.release: * INSTALL.minc: new. * AUTHORS: * GETTING_STARTED: * INSTALL: * README: Tune up for release. 2003-01-10 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * testdir/Makefile.am (INCLUDES): * volume_io/Testing/Makefile.am (INCLUDES): Set includes for test files. * Makefile.am (EXTRA_DIST, dist-hook): Distribute fortran subdirectory, sans the CVS files. * progs/mincstats/mincstats.man1: Document change of -max_bins to -int_max_bins. 2003-01-09 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * progs/rawtominc/rawtominc.man1: Document -skip option. * volume_io/Makefile.am: New. * volume_io/Documentation/Makefile.am: New. * volume_io/Testing/check_xfm.sh: * volume_io/Testing/test-xfm.c: * volume_io/Testing/t1.xfm: * volume_io/Testing/t2.xfm: * volume_io/Testing/t3.xfm: * volume_io/Testing/t3_grid_0.mnc: * volume_io/Testing/Makefile.am: New. * volume_io/Testing/test-xfm.c: Allow tolerance specified on command line. Exit with nonzero status if point out of tolerance. * Makefile.am (dist_man3_MANS): Distribute and install ParseArgv(3). (EXTRA_DIST): Distribute get_image_offset.c (not built). (noinst_HEADERS): Remove vax_conversions.h (not used). * doc/Makefile: Removed. * doc/Makefile.am: New. * testdir/run_tests.csh: Use -e flag to stop on error. Look for expected output files in $srcdir. * testdir/Makefile: Removed. * testdir/Makefile.am: New. * configure.in: * Makefile.am: Adjust for testdir/Makefile. 2003-01-07 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * autogen.sh: New. * Makefile.am: New. * configure.in: Updated to use automake, libtool. * AUTHORS: New. * LICENCE: Renamed to ... * COPYING: ... this. Makes automake happier. * progs/coordinates/voxeltoworld.man1: * progs/minccopy/minccopy.man1: * progs/mincdiff/mincdiff.man1: * progs/mincedit/mincedit.man1: * progs/mincextract/mincextract.man1: * progs/minctoraw/minctoraw.man1: * progs/mincview/invert_raw_image.man1: * progs/mincview/mincview.man1: * progs/mincwindow/mincwindow.man1: * progs/xfm/transformtags.man1: * progs/xfm/xfmconcat.man1: * progs/xfm/xfminvert.man1: New. 2002-12-11 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * progs/minccalc/gram.y: Insert missing semicolon at end of "exprlist" production. 2002-12-05 Steve Robbins <swmgr@shadow.bic.mni.mcgill.ca> * volume_io/Include/vol_io_prototypes.h: Add prototype for get_volume_translation(). 2002-11-05 Jason Lerch <jason@bic.mni.mcgill.ca> * progs/mincresample/mincresample.{c,h}: changed the setting of the interpolation type to go through an enum rather than directly to a function pointer, as that is the behaviour that ParseArgv expects and also makes mincresample 64 bit safe. 2002-10-30 Jason Lerch <jason@bic.mni.mcgill.ca> * libsrc/ParseArgv: added the ARGV_LONG argument type. * progs/mincresample/mincresample.c: changed the parsing of the nelements arguments to be ARGV_LONG. 2002-09-05 Andrew Janke <a.janke@gmail.com> * progs/mincstats/mincstats.c: Change command line option "-max_bins" to "-int_max_bins", to avoid clash with option "-max". 2002-09-03 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * CHANGES: Renamed ... * NEWS: ... to this. NEWS is the place to document important user-visible changes. The ChangeLog is the place for more detailed notes. See http://www.gnu.org/prep/standards.html. * volume_io/MNI_formats/gen_xfs.c (transform_or_invert_point): Do not flip inverse_flag when transform inverted. * volume_io/Testing/test-xfm.c: New. Regression tests for General_transforms. 2002-08-22 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * volume_io/Documentation/volume_io.tex (section{Volume Input}): Clarify notion of vector volume and vector-to-scalar conversion. * progs/minccalc/eval.c: * progs/minccalc/gram.y: * progs/minccalc/lex.l: * progs/minccalc/minccalc.man1: * progs/minccalc/node.c: * progs/minccalc/node.h: Add support for tan, asin, acos, and atan, courtesy of Andrew Janke. 2002-08-04 Peter Neelin <neelin@bic.mni.mcgill.ca> * progs/rawtominc/rawtominc.c: Add slightly modified code from Colin Holmes to support -skip option. 2002-04-08 John Sled <jgsled@bic.mni.mcgill.ca> * progs/mincstats/mincstats.c: Do not call fclose() on NULL file pointer. 2002-02-22 Steve M. Robbins <steve@nyongwa.montreal.qc.ca> * libsrc/ParseArgv.h: Declare code with "C" linkage when included by C++ compiler.