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ChangeLog
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-- Release of minc 2.3.00 --
2015-09-11 Robert D. Vincent <[email protected]>
* Remove autoconf/automake support.
2015-08-24 Robert D. Vincent <[email protected]>
* libsrc/netcdf_convenience.c: Changed the logic in miopen() to
explicitly differentiate netCDF vs. HDF5 files. This was needed
because ncopen() in netCDF 4.4 successfully opens HDF5 files, so
the old logic no longer worked.
2015-08-13 Robert D. Vincent <[email protected]>
* volume_io/Volumes/input_nifti.c: Fix loading of dynamic scans, handle
NIfTI units.
2015-06-11 Robert D. Vincent <[email protected]>
* libsrc/minc.h, libsrc2/minc2_defs.h: Increase MI_MAX_NUM_ICV from 32
to 1000. This should improve the behavior of voxel_loop programs
when used with a large number of input files.
2015-05-28 Robert D. Vincent <[email protected]>
* libsrc/ParseArgv.c: Added ParseLong() function to handle numeric
command-line parameters. This eliminates the questionable support
for octal values. We now support only decimal (with optional
leading zeros) and hex (with a leading "0x").
2015-04-23 Robert D. Vincent <[email protected]>
* Support for loading FreeSurfer and NIfTI-1 format files in volume_io.
(volume_io/Volumes/{input_mgh.c, input_nifti.c, input_volume.c})
* Added set_volume_n_dimensions() function.
(volume_io/Volumes/volumes.c)
(volume_io/Volumes/Include/volume_io/vol_io_prototypes.h)
* Incorporated public NIfTI-1 library code in new "nifti" subdirectory.
(nifti/*)
2015-04-20 Robert D. Vincent <[email protected]>
* Allow the current_realtime_seconds() function to return fractional seconds.
(volume_io/Prog_utils/time.c)
2015-04-20 Robert D. Vincent <[email protected]>
* Fix some warnings through use of "const" where appropriate.
(libsrc/ParseArgv.c, libsrc/ParseArgv.h, libsrc/image_conversion.c)
(libsrc/minc.h)
* Added range checks to catch edge cases in ICV code.
(libsrc/image_conversion.c, libsrc/dim_conversion.c)
2014-08-05 Vladimir S. FONOV <[email protected]>
* Merged changes from Steven M. Robbins
2014-04-12 Andrew L Janke <[email protected]>
* Updated README.release for CMake build instructions
* Release handover to Matthijs van Eede <[email protected]>
2014-04-09 Vladimir S Fonov
* Incorporated multiple bug fixes from Sean McBride
* Added some info in NEWS
2013-11-28 Vladimir S Fonov
* Removed autoconf/automake files
* MINC2 file format now can store long attributes, but uses HDF5 1.8 features
* MINC2 API can now read MINC1 files, by creating a temporary MINC2 file first, beware of huge files
* This is a pre-release of minc 2.3.00
* volume_io can now read and write files in MINC2 format using MINC2 API
* MINC2 library can be compiled without netcdf library
2013-07-09 Vladimir S Fonov
* Lots of bug fixes in minc2
* Joining of volume_io into main library
2012-09-25 Andrew L Janke <[email protected]> + Vladimir S Fonov
* split libminc from minc-tools
* started build of minc2 only for ITK
-- Release of minc 2.2.00 --
2012-09-24 Andrew L Janke <[email protected]>
* added make_mincmorph_kernel.pl
* merged changed from develop branch
* added -size arguments to mincresample
2012-08-03 Andrew L Janke <[email protected]>
* progs/mincheader/mincheader: fixed to handle files with spaces
2012-06-21 Andrew L Janke <[email protected]>
* added mincblob.man1 and updated configure.ac and Makefile.am
2012-05-16 Andrew L Janke <[email protected]>
* 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 <[email protected]>
* libsrc2/grpattr.c: added a history patch from Leila
2012-03-14 Andrew L Janke <[email protected]>
* added progs/mincsample
2012-03-14 Andrew L Janke <[email protected]>
* added progs/mincmorph
-- Release of minc 2.1.10 --
2012-02-22 Andrew L Janke <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* configure.in: changed typo from enable to disable minc2
2011-05-30 Andrew L Janke <[email protected]>
* progs/minccalc: added imax() and imin() operators
2011-04-29 Andrew L Janke <[email protected]>
* libsrc2/volume.c: added minc_version global
* libsrc/netcdf_convenience.c: added minc_version global
2011-02-17 Andrew L Janke <[email protected]>
* libsrc2/test/datatype-test.c: fixed a HDF5 bug in error output
2011-02-14 Andrew L Janke <[email protected]>
* progs/mincview/mincview: converted from csh to bash and changed
from xv to display
2011-02-09 Andrew L Janke <[email protected]>
* libsrc/minc_compat.h: Added cplusplus extern to header
2011-01-19 Jim Nikelski <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* conversion/micropet/upet2mnc.c: error bug squashed (John Cupitt)
2010-07-06 Claude Lepage <[email protected]>
* Improved convergence and accuracy for application of non-linear
transformation (especially for 2-d slices)
2010-06-28 Andrew L Janke <[email protected]>
* Added progs/xfm/xfm2def.c and progs/xfm/xfm2def.man1
2010-05-23 Andrew L Janke <[email protected]>
* changed all calls to H5Acreate2 to the H5Acreate macro
2010-05-18 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* progs/mincpik/mincpik: added -sagittal_offset_perc option
2009-11-06 Claude Lepage <[email protected]>
* 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 <[email protected]>
* progs/mincpik/mincpik: Added taking first time point for 4D files
2009-07-08 Andrew L Janke <[email protected]>
* Added minimum cmake version to CMakeLists.txt
* Added libtoolize/glibtoolize logic in autogen.sh (thanks Sean)
2009-06-03 Claude Lepage <[email protected]>
* 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 <[email protected]>
* Smarter utilization of buffer in input_mnc.c and output_mnc.c
2009-04-29 Andrew L Janke <[email protected]>
* progs/mincinfo/mincinfo.c: fixed a stack smash
2009-04-21 Claude Lepage <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* conversion/Acr_Nema: Many changes from Claude
* conversion/dcm2mnc: Many changes for 64 bit and "new" DICOM types
2008-04-07 Andrew L Janke <[email protected]>
* 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 <[email protected]>
* progs/mincpik/mincpik: fixed a bug with bar width from Mike Ferreira
2008-03-07 Andrew L Janke <[email protected]>
* progs/mincpik/mincpik: fixed two bugs with lookup triplanars
2008-02-28 Andrew L Janke <[email protected]>
* progs/mincpik/mincpik: added the -anot_bar option
-- Release of minc 2.0.15 --
2008-02-15 Andrew L Janke <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* libsrc/hdf_convenience.c (hdf_path_from_name): added NC_NAT to switch
2008-01-17 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* removed outdated TODO file
* merged WHATSNEW-2.0 into NEWS/README
2008-01-09 Andrew L Janke <[email protected]>
* replaced mincedit with a complete rewrite in sh
2008-01-04 Andrew L Janke <[email protected]>
* mincheader: updated scripting style and replaced tmpdir code
2008-01-02 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* changed all global variables to static in progs directory to
avoid possible linker errors in the future.
2007-10-23 Andrew L Janke <[email protected]>
* 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 <[email protected]>
* Added a few more free's for memory thanks to Claude
2007-08-24 Andrew L Janke <[email protected]>
* added xfmflip and man page
* fixed a bug in the build of minccalc
* updated nifti library for nii2mnc
2007-08-08 Claude Lepage <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* conversion/Acr_nema - Fixed a bug causing dump_acr_nema to skip
all elements with element number 0x0010
2006-05-31 Jonathan Harlap <[email protected]>
* 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 <[email protected]>
* progs/various... added config.h to source files that need it for
proper operation with MINC 2.0
2006-04-19 Claude Lepage <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* libsrc/hdf_convenience.c - Modify the hdf_vardef() function
to avoid errors in HDF5 1.6.5
2006-02-19 Steve M. Robbins <[email protected]>
* testdir/create_grid_xfm.c (main): Initialize variable
mio before using.
2006-02-09 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* libsrc2/volume.c - set units field unconditionally in
_miget_file_dimension()
2005-12-13 Bert Vincent <[email protected]>
* 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 <[email protected]>
* conversion/micropet/upet2mnc.c - fix handling of single-frame data
* progs/mincgen/main.c - make "-o" option imply "-b"
2005-11-22 Bert Vincent <[email protected]>
* progs/mincgen/genlib.c - fix free() issue
* progs/mincgen/load.c - #include config.h
2005-11-11 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* progs/mincstats/mincstats.c: Add warning when mask file
specified with no mask range option.
2005-07-28 Bert Vincent <[email protected]>
* 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 <[email protected]>
* progs/mincstats/mincstats.c: Fix calculation of percent
threshold to correctly account for non-zero histogram floor.
2005-07-15 Andrew Janke <[email protected]>
* added -auto_range option to mincpik (thanks to Jon Harlap)
2005-07-15 Bert Vincent <[email protected]>
* 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 <[email protected]>
* Makefile.am:
* progs/minchistory/minchistory.man1: New manual page for
minchistory.
2005-07-03 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* Minor fix to ncgenyy.l to avoid compiler complaint on ia64.
2005-05-20 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Move volume_io headers into Include/volume_io subdirectory.
2005-03-17 Andrew Janke <[email protected]>
* removed ':' from temporary filenames for windows compatibility
2005-03-11 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Got rid of lots of C99-related warnings
* Added new biModalT algorithms to mincstats
2004-12-15 Andrew Janke <[email protected]>
* added epm-header.in, removed mni_minc.epm.header
2004-12-07 Andrew Janke <[email protected]>
* Squashed yet another bug with the BiModalT code
aaargh! This should now replicate volume_stats even closer!
2004-10-18 Andrew Janke <[email protected]>
* 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 <[email protected]>
* Fix minc.h for netCDF 3.5.1
2004-08-03 Bert Vincent <[email protected]>
* 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 <[email protected]>
* Updated mincgen man page
* "Improve" Doxygen documentation
2004-06-16 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Add netcdf and HDF5 versions to the -version list.
2004-06-08 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Fixed endian-ness issues in MINC 2.0 format.
2004-05-25 Bert Vincent <[email protected]>
* Added -dappend, -sappend to minc_modify_header
2004-05-20 Bert Vincent <[email protected]>
* Revised man pages
* Added -2 option to minclookup
2004-04-30 Bert Vincent <[email protected]>
* Further reduce compiler issues for IRIX MIPSpro compiler.
* Tagged version 2.0.06
2004-04-29 Bert Vincent <[email protected]>
* Fix compiler compatibility problem against IRIX MIPSpro compiler
in netcdf_convenience.c
2004-04-22 Bert Vincent <[email protected]>
* Expanded test cases
2004-04-15 Bert Vincent <[email protected]>
* Add -DMINC2, #ifdef MINC2 to make most MINC2
additions and changes optional.
* Expand minc2_uguide.tex
2004-04-08 Bert Vincent <[email protected]>
* Add mincdump command
* Minor changes to increase portability, esp. to Windows.
2004-03-25 Bert Vincent <[email protected]>
* 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 <[email protected]>
* Fix dimorder handling
2004-02-18 Bert Vincent <[email protected]>
* 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 <[email protected]>
* Fixed mincconvert - added ncendef()
* Actually implemented MINC_COMPRESS
MINC 1:
2004-03-24 Bert Vincent <[email protected]>
* Minor fix to miappend_history() in libsrc/minc_convenience.c
2004-03-23 Bert Vincent <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* volume_io/Include/basic.h: Include <math.h> for M_PI definition.
Build problem reported by Maxime Descoteaux
2003-11-14 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* progs/rawtominc/rawtominc.c: Add options -dimorder and -swap_bytes.
2003-06-01 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* configure.in: Set version to 1.1.1
* mni_minc.epm.header: added.
* README.binary_packaging: added.
2003-01-17 Steve M. Robbins <[email protected]>
* configure.in: Set version to 1.2.
2003-01-17 Steve M. Robbins <[email protected]>
* MINC-1-1 tagged.
* README.release:
* INSTALL.minc: new.
* AUTHORS:
* GETTING_STARTED:
* INSTALL:
* README: Tune up for release.
2003-01-10 Steve M. Robbins <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* progs/minccalc/gram.y: Insert missing semicolon at end
of "exprlist" production.
2002-12-05 Steve Robbins <[email protected]>
* volume_io/Include/vol_io_prototypes.h: Add prototype
for get_volume_translation().