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ENH: Update external libminc to write backward-compatible HDF5 1.8.x files #53

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ENH: Update external libminc to write backward-compatible HDF5 1.8.x files #53

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3bae44c
MINC 2018-08-09 (ce4333ca)
vfonov Aug 9, 2018
178437b
Merge branch 'upstream-minc' into update-minc
gdevenyi Aug 9, 2018
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2 changes: 1 addition & 1 deletion Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ PROJECT(LIBMINC)

SET(LIBMINC_PACKAGE_VERSION_MAJOR 2)
SET(LIBMINC_PACKAGE_VERSION_MINOR 4)
SET(LIBMINC_PACKAGE_VERSION_PATCH 02)
SET(LIBMINC_PACKAGE_VERSION_PATCH 03)

SET(LIBMINC_SOVERSION "5.2.0")

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3 changes: 1 addition & 2 deletions Modules/ThirdParty/MINC/src/libminc/README
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Expand Up @@ -86,7 +86,7 @@ MINC_MAX_FILE_BUFFER_KB = <N>
#
MINC_MAX_MEMORY_KB = <N>

# FILE cache, used in some minc programs
# Memory cache for MINC2 files, per open file
#
MINC_FILE_CACHE_MB = <N>

Expand All @@ -107,4 +107,3 @@ DOCUMENTATION
-------------

http://en.wikibooks.org/wiki/MINC

17 changes: 9 additions & 8 deletions Modules/ThirdParty/MINC/src/libminc/libsrc/hdf_convenience.c
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Expand Up @@ -13,9 +13,9 @@
#define MI2_LENGTH "length"
#define MI2_CLASS "class"

/* So we build with 1.8.4 */
#ifndef H5F_LIBVER_18
#define H5F_LIBVER_18 H5F_LIBVER_LATEST
/* Make 1.8.x compatible files if building with 1.10.x */
#if (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR<10)
#define H5F_LIBVER_V18 H5F_LIBVER_LATEST
#endif

/************************************************************************
Expand Down Expand Up @@ -2218,6 +2218,8 @@ hdf_open(const char *path, int mode)

/*Set cachine parameters*/
fpid=H5Pcreate( H5P_FILE_ACCESS );
/* Limit file compatability to 1.8.x */
H5Pset_libver_bounds (fpid, H5F_LIBVER_V18, H5F_LIBVER_V18);

/*setup a bigger cache to work with typical chunking ( MI_MAX_VAR_BUFFER_SIZE )*/
H5Pset_cache(fpid, 0, 2503, miget_cfg_present(MICFG_MINC_FILE_CACHE)?miget_cfg_int(MICFG_MINC_FILE_CACHE)*100000:MI_MAX_VAR_BUFFER_SIZE*10, 1.0);
Expand All @@ -2228,6 +2230,7 @@ hdf_open(const char *path, int mode)
hid_t prp_id;

prp_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_libver_bounds (prp_id, H5F_LIBVER_V18, H5F_LIBVER_V18);
H5Pset_fapl_mmap(prp_id, 8192, 1);
file_id = H5Fopen(path, mode & 0x7FFF, prp_id);
H5Pclose(prp_id);
Expand Down Expand Up @@ -2326,10 +2329,11 @@ hdf_create(const char *path, int cmode, struct mi2opts *opts_ptr)

/*Set cachine parameters*/
fpid = H5Pcreate (H5P_FILE_ACCESS);
/* Limit file compatability to 1.8.x */
H5Pset_libver_bounds (fpid, H5F_LIBVER_V18, H5F_LIBVER_V18);

/*setup a bigger cache to work with typical chunking ( MI_MAX_VAR_BUFFER_SIZE )*/
H5Pset_cache(fpid, 0, 2503, miget_cfg_present(MICFG_MINC_FILE_CACHE)?miget_cfg_int(MICFG_MINC_FILE_CACHE)*100000:MI_MAX_VAR_BUFFER_SIZE*10, 1.0);

H5Pset_cache(fpid, 0, 2503, miget_cfg_present(MICFG_MINC_FILE_CACHE)?miget_cfg_int(MICFG_MINC_FILE_CACHE)*100000:MI_MAX_VAR_BUFFER_SIZE*10, 1.0);

/* Convert the MINC (NetCDF) mode to a HDF5 mode.
*/
Expand All @@ -2340,9 +2344,6 @@ hdf_create(const char *path, int cmode, struct mi2opts *opts_ptr)
cmode = H5F_ACC_TRUNC;
}

/*VF use all the features of new HDF5 1.8*/
H5Pset_libver_bounds (fpid, H5F_LIBVER_18, H5F_LIBVER_18);

H5E_BEGIN_TRY {
file_id = H5Fcreate(path, cmode, H5P_DEFAULT, fpid);
} H5E_END_TRY;
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4 changes: 2 additions & 2 deletions Modules/ThirdParty/MINC/src/libminc/libsrc/voxel_loop.c
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Expand Up @@ -1120,7 +1120,7 @@ PRIVATE void setup_variables(int inmincid, int outmincid,
}
else {
set_ncopts(0);
(void) ncattdel(outmincid, outimgid, MIvalid_range); /*VF: why is this needed?*/
(void) ncattdel(outmincid, outimgid, MIvalid_range); /*VF: needed for MINC v2 and not for MINC v1*/
set_ncopts(NC_OPTS_VAL);
}
}
Expand Down Expand Up @@ -1669,7 +1669,6 @@ PRIVATE int do_voxel_loop(Loop_Options *loop_options,
if( loop_options->is_labels )
{
/*Have to write out global valid range and global image range*/

if ((global_minimum[ofile] == DBL_MAX) &&
(global_maximum[ofile] == -DBL_MAX)) {
global_minimum[ofile] = 0.0;
Expand All @@ -1689,6 +1688,7 @@ PRIVATE int do_voxel_loop(Loop_Options *loop_options,
}
(void) mivarput1(outmincid, minid, 0, NC_DOUBLE, NULL, &valid_range[0]);
(void) mivarput1(outmincid, maxid, 0, NC_DOUBLE, NULL, &valid_range[1]);
/*VF: if MINC2 this works, if MINC1 - variables are not updated?*/
(void) miset_valid_range(outmincid, imgid, valid_range);
}
}
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11 changes: 6 additions & 5 deletions Modules/ThirdParty/MINC/src/libminc/libsrc2/volume.c
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Expand Up @@ -32,9 +32,9 @@
#include "minc2.h"
#include "minc2_private.h"

/* So we build with 1.8.4 */
#ifndef H5F_LIBVER_18
#define H5F_LIBVER_18 H5F_LIBVER_LATEST
/* Build with 1.8.x support if using 1.10.x */
#if (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR<10)
#define H5F_LIBVER_V18 H5F_LIBVER_LATEST
#endif

/*Used to optimize chunking size for faster MINC1 API access*/
Expand Down Expand Up @@ -117,6 +117,7 @@ static hid_t _hdf_open(const char *path, int mode)
int ndims;*/

prp_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_libver_bounds(prp_id, H5F_LIBVER_V18, H5F_LIBVER_V18);
H5Pset_cache(prp_id, 0, 2503, miget_cfg_present(MICFG_MINC_FILE_CACHE)?miget_cfg_int(MICFG_MINC_FILE_CACHE)*100000:_MI1_MAX_VAR_BUFFER_SIZE*10, 1.0);

H5E_BEGIN_TRY {
Expand Down Expand Up @@ -218,8 +219,8 @@ static hid_t _hdf_create(const char *path, int cmode)

fpid = H5Pcreate (H5P_FILE_ACCESS);

/*VF use all the features of new HDF5 1.8*/
H5Pset_libver_bounds (fpid, H5F_LIBVER_18, H5F_LIBVER_18);
/* Limit filetype to 1.8.x */
H5Pset_libver_bounds(fpid, H5F_LIBVER_V18, H5F_LIBVER_V18);

H5Pset_cache(fpid, 0, 2503, miget_cfg_present(MICFG_MINC_FILE_CACHE)?miget_cfg_int(MICFG_MINC_FILE_CACHE)*100000:_MI1_MAX_VAR_BUFFER_SIZE*100, 1.0);

Expand Down