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ChangeLog
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2015-08-06 Robert D. Vincent <robert.d.vincent@mcgill.ca>
* progs/mincstats/mincstats.c: Incorporate Claude's suggested changes to
the otsu_threshold() function.
* {various}: Corrected many warnings.
2015-08-06 Andrew Janke <a.janke@gmail.com>
* progs/mincstats/mincstats.man1: Add documentation of new command line
options.
2015-08-05 Robert D. Vincent <robert.d.vincent@mcgill.ca>
* progs/mincstats/mincstats.c: Add -skewness and -kurtosis options.
2015-07-09 Robert D. Vincent <robert.d.vincent@mcgill.ca>
* Testing/{mincstats-test.pl, mincinfo-test.pl}: Added test scripts for
mincstats and mincinfo.
2015-06-26 Robert D. Vincent <robert.d.vincent@mcgill.ca>
* progs/mincstats/mincstats.c: Fix potential memory error and removed some warnings.
* conversion/dcm2mnc/*: Many changes to improve robustness of DICOM conversion.
* conversion/nifti1/mnc2nii.c: Use new restructure_array() and restructure.h.
* progs/mincmorph/*: Fix a number of memory issues and odd use
of pointers.
* progs/mincconvert/mincconvert.c: Allow conversion from MINC2 to MINC2.
* mincextract.c, mincreshape.c, rawtominc.c: Use new ParseLong() function
rather than strtol() to avoid interpreting numbers with leading zeros
in octal.
* Testing/: added tests for mincreshape, mincresample, minccalc, and
mincaverage.
* conversion/nifti1/: Moved nifti1_io.c, znzlib.c and headers to libminc.
* progs/mincresample/mincresample.c: Warn before doing incorrect things
with non-monotonic irregular dimensions.
* progs/minccmp/minccmp.c: Add support for confusion matrix statistics
(e.g. Dice statistics) with discrete volumes.
* progs/mincdump/mincdump.c: Expand legal character set in text, fix usage
message.
* progs/mincresample/resample_volumes.c: Fix issue with -keep_real_range
(see Github issue #21).
* conversion/nifti1/mnc2nii.c: Fix a number of bugs.
* progs/mincextract/mincextract.c, progs/minctoraw/minctoraw.c: Provide for
creation of either big-endian or little-endian data.
* progs/minccalc/{minccalc.c, sym.c}: Fix minor memory leak, incorrect
modification of symbol values in ranges (see Github issue #18).
* progs/minccmp/minccmp.c: Print results for all volumes, not just the
first (see Github issue #9).
* progs/mincaverage/mincaverage.c: Fix incorrect normalized average when
mean is less than zero (bug reported by Alex Z.).
-- Release of minc 2.2.00 --
2012-09-24 Andrew L Janke <a.janke@gmail.com>
* added make_mincmorph_kernel.pl
* merged changed from develop branch
* added -size arguments to mincresample
2012-08-03 Andrew L Janke <a.janke@gmail.com>
* progs/mincheader/mincheader: fixed to handle files with spaces
2012-06-21 Andrew L Janke <a.janke@gmail.com>
* added mincblob.man1 and updated configure.ac and Makefile.am
2012-05-16 Andrew L Janke <a.janke@gmail.com>
* added patches from Jordi Gutiérrez Hermoso
* libsrc/hdf_convenience.c: added default switch case
* libsrc/ParseArgv.c: added intptr_t casts
* conversion/dcm2mnc/dicom_to_minc.c: added initialisation of tmp_offset
2012-04-10 Andrew L Janke <a.janke@gmail.com>
* libsrc2/grpattr.c: added a history patch from Leila
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