c_nifti 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +37 -0
- data/.rspec +2 -0
- data/.ruby-gemset +1 -0
- data/.ruby-version +1 -0
- data/COPYING +621 -0
- data/COPYING.lesser +166 -0
- data/Gemfile +4 -0
- data/README.md +117 -0
- data/Rakefile +6 -0
- data/c_nifti.gemspec +31 -0
- data/ext/nifticlib/extconf.rb +30 -0
- data/ext/nifticlib/include/nifti_image.h +2 -0
- data/ext/nifticlib/include/nifti_image_converters.h +3 -0
- data/ext/nifticlib/include/nifti_image_dimensions.h +1 -0
- data/ext/nifticlib/include/nifti_image_intents.h +1 -0
- data/ext/nifticlib/include/nifti_image_metadata.h +1 -0
- data/ext/nifticlib/include/nifti_image_quaternions.h +1 -0
- data/ext/nifticlib/include/nifti_image_spacings.h +1 -0
- data/ext/nifticlib/include/nifti_image_timings.h +1 -0
- data/ext/nifticlib/include/nifti_image_transforms.h +1 -0
- data/ext/nifticlib/nifti_image.c +169 -0
- data/ext/nifticlib/nifti_image_converters.c +65 -0
- data/ext/nifticlib/nifti_image_dimensions.c +113 -0
- data/ext/nifticlib/nifti_image_intents.c +45 -0
- data/ext/nifticlib/nifti_image_metadata.c +133 -0
- data/ext/nifticlib/nifti_image_quaternions.c +59 -0
- data/ext/nifticlib/nifti_image_spacings.c +87 -0
- data/ext/nifticlib/nifti_image_timings.c +66 -0
- data/ext/nifticlib/nifti_image_transforms.c +38 -0
- data/ext/nifticlib/nifticlib-2.0.0/CMakeLists.txt +140 -0
- data/ext/nifticlib/nifticlib-2.0.0/CTestConfig.cmake +13 -0
- data/ext/nifticlib/nifticlib-2.0.0/LICENSE +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Makefile +265 -0
- data/ext/nifticlib/nifticlib-2.0.0/Makefile.cross_mingw32 +94 -0
- data/ext/nifticlib/nifticlib-2.0.0/README +79 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/CMakeLists.txt +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/Makefile +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/README_regress +50 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@show.diffs +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@test +80 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/CMakeLists.txt +47 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/bricks_test.sh +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/comment_test.sh +65 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dci_test.sh +46 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dsets_test.sh +61 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dts_test.sh +75 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/fetch_data_test.sh +45 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/mod_header_test.sh +60 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/newfiles_test.sh +36 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c01.versions +10 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c02.nt.help +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c03.hist +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c04.disp.anat0.info +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c05.mod.hdr +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c06.add.ext +22 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c07.cbl.4bricks +8 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c08.dts.19.36.11 +4 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c09.dts4.compare +9 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c10.dci.ts4 +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c10a.dci.run.210 +16 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c11.add.comment +8 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c12.check.comments +7 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c13.check.hdrs +5 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c14.make.dsets +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c15.new.files +21 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c16.rand.swap +35 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c17.file.case +34 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/CMakeLists.txt +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/nifti_test.c +690 -0
- data/ext/nifticlib/nifticlib-2.0.0/Testing/niftilib/nifti_test2.c +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/Updates.txt +110 -0
- data/ext/nifticlib/nifticlib-2.0.0/bin/.gitkeep +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/docs/Doxy_nifti.txt +123 -0
- data/ext/nifticlib/nifticlib-2.0.0/docs/Doxyfile.ORIG +746 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/CMakeLists.txt +15 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/Makefile +48 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/clib_01_read_write.c +94 -0
- data/ext/nifticlib/nifticlib-2.0.0/examples/fsl_api_driver.c +142 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/CMakeLists.txt +32 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/Makefile +29 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/fslio.c +2426 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/fslio.tcl +83 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imcp +65 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imglob +59 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imln +37 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/immv +64 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imrm +29 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imtest +53 -0
- data/ext/nifticlib/nifticlib-2.0.0/fsliolib/remove_ext +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/include/.gitkeep +0 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/CMakeLists.txt +28 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/Makefile +28 -0
- data/ext/nifticlib/nifticlib-2.0.0/nifticdf/nifticdf.c +11107 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/CMakeLists.txt +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/Makefile +31 -0
- data/ext/nifticlib/nifticlib-2.0.0/niftilib/nifti1_io.c +7509 -0
- data/ext/nifticlib/nifticlib-2.0.0/packaging/DevPackage.template +18 -0
- data/ext/nifticlib/nifticlib-2.0.0/packaging/nifticlib.spec +62 -0
- data/ext/nifticlib/nifticlib-2.0.0/real_easy/nifti1_read_write.c +361 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/CMakeLists.txt +73 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/Makefile +55 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti1_test.c +95 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_stats.c +95 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_tool.c +4193 -0
- data/ext/nifticlib/nifticlib-2.0.0/utils/nifti_tool.h +163 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/CMakeLists.txt +31 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/Makefile +33 -0
- data/ext/nifticlib/nifticlib-2.0.0/znzlib/znzlib.c +322 -0
- data/ext/nifticlib/nifticlib.c +107 -0
- data/ext/nifticlib/patches/nifticlib_fpic.patch +13 -0
- data/features/read_modify_write.feature +11 -0
- data/features/step_definitions/nifti_image_steps.rb +16 -0
- data/features/support/env.rb +14 -0
- data/features/support/fixtures/sample.nii.gz +0 -0
- data/lib/c_nifti.rb +9 -0
- data/lib/c_nifti/data.rb +70 -0
- data/lib/c_nifti/header.rb +16 -0
- data/lib/c_nifti/header_element.rb +13 -0
- data/lib/c_nifti/header_element/datatype.rb +49 -0
- data/lib/c_nifti/header_element/datatype/base.rb +9 -0
- data/lib/c_nifti/header_element/datatype/binary.rb +11 -0
- data/lib/c_nifti/header_element/datatype/double.rb +11 -0
- data/lib/c_nifti/header_element/datatype/float.rb +11 -0
- data/lib/c_nifti/header_element/datatype/long_double.rb +11 -0
- data/lib/c_nifti/header_element/datatype/long_long.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_char.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_int.rb +11 -0
- data/lib/c_nifti/header_element/datatype/signed_short.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_char.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_int.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_long_long.rb +11 -0
- data/lib/c_nifti/header_element/datatype/unsigned_short.rb +11 -0
- data/lib/c_nifti/header_element/dimensions.rb +53 -0
- data/lib/c_nifti/header_element/intents.rb +25 -0
- data/lib/c_nifti/header_element/metadata.rb +49 -0
- data/lib/c_nifti/header_element/miscellaneous.rb +25 -0
- data/lib/c_nifti/header_element/quaternions.rb +33 -0
- data/lib/c_nifti/header_element/spacings.rb +45 -0
- data/lib/c_nifti/header_element/timings.rb +37 -0
- data/lib/c_nifti/header_element/transforms.rb +21 -0
- data/lib/c_nifti/image.rb +31 -0
- data/lib/c_nifti/version.rb +3 -0
- data/lib/nifticlib.rb +1 -0
- data/spec/data_spec.rb +112 -0
- data/spec/factories/nifti_images.rb +9 -0
- data/spec/header_element/datatype/base_spec.rb +9 -0
- data/spec/header_element/datatype/binary_spec.rb +9 -0
- data/spec/header_element/datatype/double_spec.rb +9 -0
- data/spec/header_element/datatype/float_spec.rb +9 -0
- data/spec/header_element/datatype/long_double_spec.rb +9 -0
- data/spec/header_element/datatype/long_long_spec.rb +9 -0
- data/spec/header_element/datatype/signed_char_spec.rb +9 -0
- data/spec/header_element/datatype/signed_int_spec.rb +9 -0
- data/spec/header_element/datatype/signed_short_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_char_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_int_spec.rb +9 -0
- data/spec/header_element/datatype/unsigned_long_long.rb +9 -0
- data/spec/header_element/datatype/unsigned_short_spec.rb +9 -0
- data/spec/header_element/datatype_spec.rb +109 -0
- data/spec/header_element/dimensions_spec.rb +105 -0
- data/spec/header_element/intents_spec.rb +48 -0
- data/spec/header_element/metadata_spec.rb +96 -0
- data/spec/header_element/miscellaneous_spec.rb +48 -0
- data/spec/header_element/quaternions_spec.rb +64 -0
- data/spec/header_element/spacings_spec.rb +88 -0
- data/spec/header_element/timings_spec.rb +72 -0
- data/spec/header_element/transforms_spec.rb +64 -0
- data/spec/image_spec.rb +39 -0
- data/spec/spec_helper.rb +85 -0
- metadata +363 -0
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CC = gcc
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CFLAGS = -ansi -pedantic
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FSLIO_INCS = -I../include
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NIFTI_INCS = -I../include
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ZNZ_INCS = -I/usr/include
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FSLIO_LIBS = -L../lib -lfslio
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NIFTI_LIBS = -L../lib -lniftiio
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NIFTICDF_LIBS = -L../lib -lnifticdf
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ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
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##############################################################
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# platform specific redefines (to use, set ARCH appropriately)
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## ARCH = X86_64
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ifeq ($(ARCH),SGI) ## SGI 32bit
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ZNZ_INCS = -I/usr/freeware/include
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ZNZ_LIBS = -L/usr/freeware/lib32 -L../lib -lznz -lm -lz
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else
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ifeq ($(ARCH),I386) ## 32-bit Linux
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ZNZ_INCS = -I/usr/include
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ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
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else
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ifeq ($(ARCH),X86_64) ## 64-bit Linux
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ZNZ_INCS =
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ZNZ_LIBS = -L../lib -lznz -lm -lz
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endif
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endif
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endif
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####################################################
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UTILS_PROGS = nifti_stats nifti_tool nifti1_test
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all: $(UTILS_PROGS)
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clean:
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rm -f $(UTILS_PROGS)
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nifti_stats: nifti_stats.c
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$(CC) $(CFLAGS) -o nifti_stats nifti_stats.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTICDF_LIBS) $(NIFTI_LIBS) $(ZNZ_LIBS)
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nifti_tool: nifti_tool.c nifti_tool.h
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$(CC) $(CFLAGS) -Wall -o nifti_tool nifti_tool.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS)
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nifti1_test: nifti1_test.c
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$(CC) $(CFLAGS) -o nifti1_test nifti1_test.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS)
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#include <nifti1_io.h> /* directly include I/O library functions */
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/*-----------------------------------------------*/
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/* cc -o nifti1_test -O2 nifti1_test.c -lm */
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/*-----------------------------------------------*/
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/****************************************************************************/
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int main( int argc , char *argv[] )
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{
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nifti_image *nim ;
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int iarg=1 , outmode=1 , ll , argn=1, usegzip=0;
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char *tmpstr;
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if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
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printf("Usage: nifti1_test [-n2|-n1|-na|-a2] infile [prefix]\n"
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"\n"
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" If prefix is given, then the options mean:\n"
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" -a2 ==> write an ANALYZE 7.5 file pair: prefix.hdr/prefix.img\n"
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" -n2 ==> write a NIFTI-1 file pair: prefix.hdr/prefix.img\n"
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" -n1 ==> write a NIFTI-1 single file: prefix.nii\n"
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" -na ==> write a NIFTI-1 ASCII+binary file: prefix.nia\n");
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printf(" -za2 => write an ANALYZE 7.5 file pair:\n"
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" prefix.hdr.gz/prefix.img.gz\n"
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" -zn2 => write a NIFTI-1 file pair: prefix.hdr.gz/prefix.img.gz\n"
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" -zn1 => write a NIFTI-1 single file: prefix.nii.gz\n");
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printf(" The default is '-n1'.\n"
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"\n"
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" If prefix is not given, then the header info from infile\n"
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" file is printed to stdout.\n"
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"\n"
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" Please note that the '.nia' format is NOT part of the\n"
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" NIFTI-1 specification, but is provided mostly for ease\n"
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" of visualization (e.g., you can edit a .nia file and\n"
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" change some header fields, then rewrite it as .nii)\n"
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) ;
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printf("\nsizeof(nifti_1_header)=%u\n",
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(unsigned int)sizeof(nifti_1_header)) ;
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exit(0) ;
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}
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if( argv[1][0] == '-' ){
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argn=1;
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if (argv[1][1] == 'z' ) {
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usegzip = 1;
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argn=2;
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}
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if( argv[1][argn] == 'a' ){
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outmode = 0 ;
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} else if( argv[1][argn] == 'n' ){
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switch( argv[1][argn+1] ){
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case '1': outmode = 1 ; break ;
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default: outmode = 2 ; break ;
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case 'a': outmode = 3 ; break ;
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}
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}
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iarg++ ;
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}
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if( iarg >= argc ){
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fprintf(stderr,"** ERROR: no input file on command line!?\n"); exit(1);
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}
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nim = nifti_image_read( argv[iarg++] , 1 ) ;
|
65
|
+
if( nim == NULL ) exit(1) ;
|
66
|
+
|
67
|
+
if( iarg >= argc ){ nifti_image_infodump(nim); exit(0); }
|
68
|
+
|
69
|
+
nim->nifti_type = outmode ;
|
70
|
+
if( nim->fname != NULL ) free(nim->fname) ;
|
71
|
+
if( nim->iname != NULL ) free(nim->iname) ;
|
72
|
+
|
73
|
+
ll = strlen(argv[iarg]) ;
|
74
|
+
tmpstr = nifti_makebasename(argv[iarg]);
|
75
|
+
nim->fname = (char *)calloc(1,ll+8) ; strcpy(nim->fname,tmpstr) ;
|
76
|
+
nim->iname = (char *)calloc(1,ll+8) ; strcpy(nim->iname,tmpstr) ;
|
77
|
+
free(tmpstr);
|
78
|
+
if( nim->nifti_type == 1 ){
|
79
|
+
strcat(nim->fname,".nii") ;
|
80
|
+
strcat(nim->iname,".nii") ;
|
81
|
+
} else if ( nim->nifti_type == 3 ){
|
82
|
+
strcat(nim->fname,".nia") ;
|
83
|
+
strcat(nim->iname,".nia") ;
|
84
|
+
} else {
|
85
|
+
strcat(nim->fname,".hdr") ;
|
86
|
+
strcat(nim->iname,".img") ;
|
87
|
+
}
|
88
|
+
if (usegzip) {
|
89
|
+
strcat(nim->fname,".gz");
|
90
|
+
strcat(nim->iname,".gz");
|
91
|
+
}
|
92
|
+
nifti_image_write( nim ) ;
|
93
|
+
nifti_image_free( nim ) ;
|
94
|
+
exit(0) ;
|
95
|
+
}
|
@@ -0,0 +1,95 @@
|
|
1
|
+
#include "nifti1.h" /* for the NIFTI_INTENT_* constants */
|
2
|
+
#include "nifticdf.h"
|
3
|
+
#include <stdio.h>
|
4
|
+
#include <stdlib.h>
|
5
|
+
#include <math.h>
|
6
|
+
#include <string.h>
|
7
|
+
|
8
|
+
int main( int argc , char *argv[] )
|
9
|
+
{
|
10
|
+
double val , p , p1=0.0,p2=0.0,p3=0.0 ;
|
11
|
+
double vbot,vtop,vdel ;
|
12
|
+
int code , iarg=1 , doq=0 , dod=0 , doi=0 , doz=0 , doh=0 ;
|
13
|
+
|
14
|
+
/*-- print some help for the pitiful user --*/
|
15
|
+
|
16
|
+
if( argc < 3 || strstr(argv[1],"help") != NULL ){
|
17
|
+
int ii ;
|
18
|
+
printf("\n") ;
|
19
|
+
printf("Demo program for computing NIfTI statistical functions.\n") ;
|
20
|
+
printf("Usage: nifti_stats [-q|-d|-1|-z] val CODE [p1 p2 p3]\n") ;
|
21
|
+
printf(" val can be a single number or in the form bot:top:step.\n") ;
|
22
|
+
printf(" default ==> output p = Prob(statistic < val).\n") ;
|
23
|
+
printf(" -q ==> output is 1-p.\n") ;
|
24
|
+
printf(" -d ==> output is density.\n") ;
|
25
|
+
printf(" -1 ==> output is x such that Prob(statistic < x) = val.\n") ;
|
26
|
+
printf(" -z ==> output is z such that Normal cdf(z) = p(val).\n") ;
|
27
|
+
printf(" -h ==> output is z such that 1/2-Normal cdf(z) = p(val).\n");
|
28
|
+
printf(" Allowable CODEs:\n") ;
|
29
|
+
for( ii=NIFTI_FIRST_STATCODE ; ii <= NIFTI_LAST_STATCODE ; ii++ ){
|
30
|
+
printf(" %-10s",inam[ii]); if((ii-NIFTI_FIRST_STATCODE)%6==5)printf("\n");
|
31
|
+
}
|
32
|
+
printf("\n") ;
|
33
|
+
printf(" Following CODE are distributional parameters, as needed.\n");
|
34
|
+
printf("\n") ;
|
35
|
+
printf("Results are written to stdout, 1 number per output line.\n") ;
|
36
|
+
printf("Example (piping output into AFNI program 1dplot):\n") ;
|
37
|
+
printf(" nifti_stats -d 0:4:.001 INVGAUSS 1 3 | 1dplot -dx 0.001 -stdin\n");
|
38
|
+
printf("\n") ;
|
39
|
+
printf("Author - RW Cox - SSCC/NIMH/NIH/DHHS/USA/EARTH - March 2004\n") ;
|
40
|
+
printf("\n") ;
|
41
|
+
exit(0) ;
|
42
|
+
}
|
43
|
+
|
44
|
+
/*-- check first arg to see if it is an output option;
|
45
|
+
if so, set the appropriate output flag to determine what to compute --*/
|
46
|
+
|
47
|
+
if( strcmp(argv[iarg],"-q") == 0 ){ doq = 1 ; iarg++ ; }
|
48
|
+
else if( strcmp(argv[iarg],"-d") == 0 ){ dod = 1 ; iarg++ ; }
|
49
|
+
else if( strcmp(argv[iarg],"-1") == 0 ){ doi = 1 ; iarg++ ; }
|
50
|
+
else if( strcmp(argv[iarg],"-z") == 0 ){ doz = 1 ; iarg++ ; }
|
51
|
+
else if( strcmp(argv[iarg],"-h") == 0 ){ doh = 1 ; iarg++ ; }
|
52
|
+
|
53
|
+
/*-- get the value(s) to process --*/
|
54
|
+
|
55
|
+
vbot=vtop=vdel = 0.0 ;
|
56
|
+
sscanf( argv[iarg++] , "%lf:%lf:%lf" , &vbot,&vtop,&vdel ) ;
|
57
|
+
if( vbot >= vtop ) vdel = 0.0 ;
|
58
|
+
if( vdel <= 0.0 ) vtop = vbot ;
|
59
|
+
|
60
|
+
/*-- decode the CODE into the integer signifying the distribution --*/
|
61
|
+
|
62
|
+
code = nifti_intent_code(argv[iarg++]) ;
|
63
|
+
if( code < 0 ){ fprintf(stderr,"illegal code=%s\n",argv[iarg-1]); exit(1); }
|
64
|
+
|
65
|
+
/*-- get the parameters, if present (defaults are 0) --*/
|
66
|
+
|
67
|
+
if( argc > iarg ) p1 = strtod(argv[iarg++],NULL) ;
|
68
|
+
if( argc > iarg ) p2 = strtod(argv[iarg++],NULL) ;
|
69
|
+
if( argc > iarg ) p3 = strtod(argv[iarg++],NULL) ;
|
70
|
+
|
71
|
+
/*-- loop over input value(s), compute output, write to stdout --*/
|
72
|
+
|
73
|
+
for( val=vbot ; val <= vtop ; val += vdel ){
|
74
|
+
if( doq ) /* output = 1-cdf */
|
75
|
+
p = nifti_stat2rcdf( val , code,p1,p2,p3 ) ;
|
76
|
+
else if( dod ) /* output = density */
|
77
|
+
p = 1000.0*( nifti_stat2cdf(val+.001,code,p1,p2,p3)
|
78
|
+
-nifti_stat2cdf(val ,code,p1,p2,p3)) ;
|
79
|
+
else if( doi ) /* output = inverse */
|
80
|
+
p = nifti_cdf2stat( val , code,p1,p2,p3 ) ;
|
81
|
+
else if( doz ) /* output = z score */
|
82
|
+
p = nifti_stat2zscore( val , code,p1,p2,p3 ) ;
|
83
|
+
else if( doh ) /* output = halfz score */
|
84
|
+
p = nifti_stat2hzscore( val , code,p1,p2,p3 ) ;
|
85
|
+
else /* output = cdf */
|
86
|
+
p = nifti_stat2cdf( val , code,p1,p2,p3 ) ;
|
87
|
+
|
88
|
+
printf("%.9g\n",p) ;
|
89
|
+
if( vdel <= 0.0 ) break ; /* the case of just 1 value */
|
90
|
+
}
|
91
|
+
|
92
|
+
/*-- terminus est --*/
|
93
|
+
|
94
|
+
exit(0) ;
|
95
|
+
}
|
@@ -0,0 +1,4193 @@
|
|
1
|
+
/*--------------------------------------------------------------------------*/
|
2
|
+
/*! \file nifti_tool.c
|
3
|
+
* \brief a tool for nifti file perusal, manipulation and copying
|
4
|
+
* written by Rick Reynolds, SSCC, NIMH, January 2005
|
5
|
+
* <pre>
|
6
|
+
*
|
7
|
+
* usage: nifti_tool [options] -infiles files...
|
8
|
+
*
|
9
|
+
* Via this tool, one should be able to:
|
10
|
+
*
|
11
|
+
* - copy a set of volumes (sub-bricks) from one dataset to another
|
12
|
+
* - copy a dataset, restricting some dimensions to given indices
|
13
|
+
*
|
14
|
+
* - display the contents of a nifti_image (or various fields)
|
15
|
+
* - display the contents of a nifti1_header (or various fields)
|
16
|
+
* - display AFNI extensions (they are text)
|
17
|
+
* - display the time series at coordinates i,j,k
|
18
|
+
* - display the data from any collapsed image
|
19
|
+
*
|
20
|
+
* - do a diff on two nifti_image structs (or various fields)
|
21
|
+
* - do a diff on two nifti1_header structs (or various fields)
|
22
|
+
*
|
23
|
+
* - add an AFNI extension
|
24
|
+
* - remove any extension
|
25
|
+
*
|
26
|
+
* - modify any field(s) of a nifti_image
|
27
|
+
* - modify any field(s) of a nifti1_struct
|
28
|
+
*
|
29
|
+
* usage forms:
|
30
|
+
*
|
31
|
+
* nifti_tool -help
|
32
|
+
* nifti_tool -help_hdr
|
33
|
+
* nifti_tool -help_nim
|
34
|
+
* nifti_tool -help_ana
|
35
|
+
* nifti_tool -help_datatypes
|
36
|
+
* nifti_tool -hist
|
37
|
+
* nifti_tool -ver
|
38
|
+
* nifti_tool -nifti_hist
|
39
|
+
* nifti_tool -nifti_ver
|
40
|
+
* nifti_tool -with_zlib
|
41
|
+
*
|
42
|
+
* nifti_tool -check_hdr -infiles f1 ...
|
43
|
+
* nifti_tool -check_nim -infiles f1 ...
|
44
|
+
|
45
|
+
* nifti_tool -disp_exts -infiles f1 ...
|
46
|
+
* nifti_tool -disp_hdr [-field fieldname] [...] -infiles f1 ...
|
47
|
+
* nifti_tool -disp_nim [-field fieldname] [...] -infiles f1 ...
|
48
|
+
* nifti_tool -disp_ana [-field fieldname] [...] -infiles f1 ...
|
49
|
+
* nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
|
50
|
+
* nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
|
51
|
+
*
|
52
|
+
* nifti_tool -diff_hdr [-field fieldname] [...] -infiles f1 f2
|
53
|
+
* nifti_tool -diff_nim [-field fieldname] [...] -infiles f1 f2
|
54
|
+
*
|
55
|
+
* nifti_tool -add_afni_ext "extension in quotes" -infiles f1 ...
|
56
|
+
* nifti_tool -add_comment_ext "extension in quotes" -infiles f1 ...
|
57
|
+
* nifti_tool -rm_ext ext_index -infiles f1 ...
|
58
|
+
*
|
59
|
+
* nifti_tool -mod_hdr [-mod_field fieldname new_val] [...] -infiles f1 ...
|
60
|
+
* nifti_tool -mod_nim [-mod_field fieldname new_val] [...] -infiles f1 ...
|
61
|
+
*
|
62
|
+
* </pre> */
|
63
|
+
/*-------------------------------------------------------------------------*/
|
64
|
+
|
65
|
+
/*! module history */
|
66
|
+
static char * g_history[] =
|
67
|
+
{
|
68
|
+
"----------------------------------------------------------------------\n"
|
69
|
+
"nifti_tool modification history:\n"
|
70
|
+
"\n",
|
71
|
+
"0.1 30 December 2004 [rickr]\n"
|
72
|
+
" (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
|
73
|
+
" - skeleton version: options read and printed\n"
|
74
|
+
"\n",
|
75
|
+
"1.0 07 January 2005 [rickr]\n"
|
76
|
+
" - initial release version\n"
|
77
|
+
"\n",
|
78
|
+
"1.1 14 January 2005 [rickr]\n"
|
79
|
+
" - changed all non-error/non-debug output from stderr to stdout\n"
|
80
|
+
" note: creates a mis-match between normal output and debug messages\n"
|
81
|
+
" - modified act_diff_hdrs and act_diff_nims to do the processing in\n"
|
82
|
+
" lower-level functions\n",
|
83
|
+
" - added functions diff_hdrs, diff_hdrs_list, diff_nims, diff_nims_list\n"
|
84
|
+
" - added function get_field, to return a struct pointer via a fieldname\n"
|
85
|
+
" - made 'quiet' output more quiet (no description on output)\n"
|
86
|
+
" - made hdr and nim_fields arrays global, so do not pass in main()\n"
|
87
|
+
" - return (from main()) after first act_diff() difference\n"
|
88
|
+
"\n",
|
89
|
+
"1.2 9 February 2005 [rickr] - minor\n"
|
90
|
+
" - defined a local NTL_FERR macro (so it does not come from nifti1_io.h)\n"
|
91
|
+
" - added new set_byte_order parameter to nifti_set_filenames\n"
|
92
|
+
"\n",
|
93
|
+
"1.3 23 February 2005 [rickr] - sourceforge.net merge\n"
|
94
|
+
" - moved to utils directory\n"
|
95
|
+
" - added simple casts of 3 pointers for -pedantic warnings\n"
|
96
|
+
" - added a doxygen comment for the file\n"
|
97
|
+
"\n",
|
98
|
+
"1.4 02 March 2005 [rickr] - small update\n"
|
99
|
+
" - no validation in nifti_read_header calls\n"
|
100
|
+
"\n",
|
101
|
+
"1.5 05 April 2005 [rickr] - small update\n"
|
102
|
+
" - refuse mod_hdr for gzipped files (we cannot do partial overwrites)\n"
|
103
|
+
"\n",
|
104
|
+
"1.6 08 April 2005 [rickr] - added cbl, cci and dts functionality\n"
|
105
|
+
" - added -cbl: 'copy brick list' dataset copy functionality\n"
|
106
|
+
" - added -ccd: 'copy collapsed data' dataset copy functionality\n"
|
107
|
+
" - added -disp_ts: 'disp time series' data display functionality\n"
|
108
|
+
" - moved raw data display to disp_raw_data()\n"
|
109
|
+
"\n",
|
110
|
+
"1.7 14 April 2005 [rickr] - added data display functionality\n"
|
111
|
+
" - added -dci: 'display collapsed image' functionality\n"
|
112
|
+
" - modified -dts to use -dci\n"
|
113
|
+
" - modified and updated the help in use_full()\n"
|
114
|
+
" - changed copy_collapsed_dims to copy_collapsed_image, etc.\n",
|
115
|
+
" - fixed problem in disp_raw_data() for printing NT_DT_CHAR_PTR\n"
|
116
|
+
" - modified act_disp_ci():\n"
|
117
|
+
" o was act_disp_ts(), now displays arbitrary collapsed image data\n"
|
118
|
+
" o added missed debug filename act_disp_ci()\n"
|
119
|
+
" o can now save free() of data pointer for end of file loop\n",
|
120
|
+
" - modified disp_raw_data()\n"
|
121
|
+
" o takes a flag for whether to print newline\n"
|
122
|
+
" o trailing spaces and zeros are removed from printing floats\n"
|
123
|
+
" - added clear_float_zeros(), to remove trailing zeros\n"
|
124
|
+
"\n",
|
125
|
+
"1.8 19 April 2005 [rickr] - COMMENT extensions\n"
|
126
|
+
" - added int_list struct, and keep_hist,etypes,command fields to nt_opts\n"
|
127
|
+
" - added -add_comment_ext action\n"
|
128
|
+
" - allowed for removal of multiple extensions, including option of ALL\n"
|
129
|
+
" - added -keep_hist option, to store the command as a COMMENT extension\n",
|
130
|
+
" (includes fill_cmd_string() and add_int(), is done for all actions)\n"
|
131
|
+
" - added remove_ext_list(), for removing a list of extensions by indices\n"
|
132
|
+
" - added -strip action, to strip all extensions and descrip fields\n"
|
133
|
+
"\n",
|
134
|
+
"1.9 25 Aug 2005 [rickr] - const/string cleanup for warnings\n",
|
135
|
+
"1.10 18 Nov 2005 [rickr] - added check_hdr and check_nim actions\n",
|
136
|
+
"1.11 31 Jan 2006 [rickr] - check for new vox_offset in act_mod_hdrs\n",
|
137
|
+
"1.12 02 Mar 2006 [rickr]\n"
|
138
|
+
" - in act_cbl(), check for nt = 0 because of niftilib update 1.17\n",
|
139
|
+
"1.13 24 Apr 2006 [rickr] - act_disp_ci(): remove time series length check\n",
|
140
|
+
"1.14 04 Jun 2007 [rickr] - free_opts_mem(), to appease valgrind\n",
|
141
|
+
"1.15 05 Jun 2007 [rickr] - act_check_hdrs: free(nim)->nifti_image_free()\n",
|
142
|
+
"1.16 12 Jun 2007 [rickr] - allow creation of datasets via MAKE_IM\n",
|
143
|
+
" - added nt_image_read, nt_read_header and nt_read_bricks\n"
|
144
|
+
" to wrap nifti read functions, allowing creation of new datasets\n"
|
145
|
+
" - added -make_im, -new_dim, -new_datatype and -copy_im\n"
|
146
|
+
"1.17 13 Jun 2007 [rickr] - added help for -copy_im, enumerate examples\n",
|
147
|
+
"1.18 23 Jun 2007 [rickr] - main returns 0 on -help, -hist, -ver\n"
|
148
|
+
"1.19 28 Nov 2007 [rickr] - added -help_datatypes\n",
|
149
|
+
"1.20 13 Jun 2008 [rickr]\n"
|
150
|
+
" - added -with_zlib\n"
|
151
|
+
" - added ability to create extension from text file (for J. Gunter)\n",
|
152
|
+
"1.21 03 Aug 2008 [rickr] - ANALYZE 7.5 support\n"
|
153
|
+
" - added -help_ana, -disp_ana,\n"
|
154
|
+
" -swap_as_analyze, -swap_as_nifti, -swap_as_old\n"
|
155
|
+
"1.22 08 Oct 2008 [rickr] - allow cbl with indices in 0..nt*nu*nv*nw-1\n"
|
156
|
+
"1.23 06 Jul 2010 [rickr]\n",
|
157
|
+
" - in nt_read_bricks, bsize computation should allow for large integers\n"
|
158
|
+
"----------------------------------------------------------------------\n"
|
159
|
+
};
|
160
|
+
static char g_version[] = "version 1.23 (July 6, 2010)";
|
161
|
+
static int g_debug = 1;
|
162
|
+
|
163
|
+
#define _NIFTI_TOOL_C_
|
164
|
+
#include "nifti1_io.h"
|
165
|
+
#include "nifti_tool.h"
|
166
|
+
|
167
|
+
/* local prototypes */
|
168
|
+
static int free_opts_mem(nt_opts * nopt);
|
169
|
+
static int num_volumes(nifti_image * nim);
|
170
|
+
static char * read_file_text(char * filename, int * length);
|
171
|
+
|
172
|
+
#define NTL_FERR(func,msg,file) \
|
173
|
+
fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file)
|
174
|
+
|
175
|
+
/* val may be a function call, so evalulate first, and return result */
|
176
|
+
#define FREE_RETURN(val) \
|
177
|
+
do{ int tval=(val); free_opts_mem(&opts); return tval; } while(0)
|
178
|
+
|
179
|
+
/* these are effectively constant, and are built only for verification */
|
180
|
+
field_s g_hdr_fields[NT_HDR_NUM_FIELDS]; /* nifti_1_header fields */
|
181
|
+
field_s g_ana_fields[NT_ANA_NUM_FIELDS]; /* nifti_analyze75 */
|
182
|
+
field_s g_nim_fields[NT_NIM_NUM_FIELDS]; /* nifti_image fields */
|
183
|
+
|
184
|
+
int main( int argc, char * argv[] )
|
185
|
+
{
|
186
|
+
nt_opts opts;
|
187
|
+
int rv;
|
188
|
+
|
189
|
+
if( (rv = process_opts(argc, argv, &opts)) != 0) /* then return */
|
190
|
+
{
|
191
|
+
if( rv < 0 ) FREE_RETURN(1); /* free opts memory, and return */
|
192
|
+
else FREE_RETURN(0); /* valid usage */
|
193
|
+
}
|
194
|
+
|
195
|
+
if( (rv = verify_opts(&opts, argv[0])) != 0 )
|
196
|
+
FREE_RETURN(rv);
|
197
|
+
|
198
|
+
/* now perform the requested action(s) */
|
199
|
+
|
200
|
+
if( (rv = fill_hdr_field_array(g_hdr_fields)) != 0 )
|
201
|
+
FREE_RETURN(rv);
|
202
|
+
|
203
|
+
if( (rv = fill_nim_field_array(g_nim_fields)) != 0 )
|
204
|
+
FREE_RETURN(rv);
|
205
|
+
|
206
|
+
if( (rv = fill_ana_field_array(g_ana_fields)) != 0 )
|
207
|
+
FREE_RETURN(rv);
|
208
|
+
|
209
|
+
/* 'check' functions, first */
|
210
|
+
if( opts.check_hdr || opts.check_nim ) /* allow for both */
|
211
|
+
FREE_RETURN( act_check_hdrs(&opts) );
|
212
|
+
|
213
|
+
/* copy or dts functions -- do not continue after these */
|
214
|
+
if( opts.cbl ) FREE_RETURN( act_cbl(&opts) );
|
215
|
+
if( opts.cci ) FREE_RETURN( act_cci(&opts) );
|
216
|
+
if( opts.dts || opts.dci ) FREE_RETURN( act_disp_ci(&opts) );
|
217
|
+
|
218
|
+
/* perform modifications early, in case we allow multiple actions */
|
219
|
+
if( opts.strip && ((rv = act_strip (&opts)) != 0) ) FREE_RETURN(rv);
|
220
|
+
|
221
|
+
if( opts.add_exts && ((rv = act_add_exts (&opts)) != 0) ) FREE_RETURN(rv);
|
222
|
+
if( opts.rm_exts && ((rv = act_rm_ext (&opts)) != 0) ) FREE_RETURN(rv);
|
223
|
+
|
224
|
+
if( opts.mod_hdr && ((rv = act_mod_hdrs (&opts)) != 0) ) FREE_RETURN(rv);
|
225
|
+
if( opts.mod_nim && ((rv = act_mod_nims (&opts)) != 0) ) FREE_RETURN(rv);
|
226
|
+
|
227
|
+
if((opts.swap_hdr || opts.swap_ana || opts.swap_old )
|
228
|
+
&& ((rv = act_swap_hdrs (&opts)) != 0) ) FREE_RETURN(rv);
|
229
|
+
|
230
|
+
/* if a diff, return wither a difference exists (like the UNIX command) */
|
231
|
+
if( opts.diff_hdr && ((rv = act_diff_hdrs(&opts)) != 0) ) FREE_RETURN(rv);
|
232
|
+
if( opts.diff_nim && ((rv = act_diff_nims(&opts)) != 0) ) FREE_RETURN(rv);
|
233
|
+
|
234
|
+
/* last action type is display */
|
235
|
+
if( opts.disp_exts && ((rv = act_disp_exts(&opts)) != 0) ) FREE_RETURN(rv);
|
236
|
+
if( opts.disp_hdr && ((rv = act_disp_hdrs(&opts)) != 0) ) FREE_RETURN(rv);
|
237
|
+
if( opts.disp_nim && ((rv = act_disp_nims(&opts)) != 0) ) FREE_RETURN(rv);
|
238
|
+
if( opts.disp_ana && ((rv = act_disp_anas(&opts)) != 0) ) FREE_RETURN(rv);
|
239
|
+
|
240
|
+
FREE_RETURN(0);
|
241
|
+
}
|
242
|
+
|
243
|
+
/*----------------------------------------------------------------------
|
244
|
+
* process user options, return 0 on success
|
245
|
+
*----------------------------------------------------------------------*/
|
246
|
+
int process_opts( int argc, char * argv[], nt_opts * opts )
|
247
|
+
{
|
248
|
+
int ac;
|
249
|
+
|
250
|
+
memset(opts, 0, sizeof(*opts));
|
251
|
+
|
252
|
+
opts->prefix = NULL;
|
253
|
+
opts->debug = 1; /* init debug level to basic output */
|
254
|
+
|
255
|
+
/* init options for creating a new dataset via "MAKE_IM" */
|
256
|
+
opts->new_datatype = NIFTI_TYPE_INT16;
|
257
|
+
opts->new_dim[0] = 3;
|
258
|
+
opts->new_dim[1] = 1; opts->new_dim[2] = 1; opts->new_dim[3] = 1;
|
259
|
+
|
260
|
+
if( argc < 2 ) return usage(argv[0], USE_FULL);
|
261
|
+
|
262
|
+
/* terminal options are first, the rest are sorted */
|
263
|
+
for( ac = 1; ac < argc; ac++ )
|
264
|
+
{
|
265
|
+
if( ! strncmp(argv[ac], "-help_datatypes", 9) )
|
266
|
+
{
|
267
|
+
ac++;
|
268
|
+
if( ac >= argc )
|
269
|
+
nifti_disp_type_list(3); /* show all types */
|
270
|
+
else if( argv[ac][0] == 'd' || argv[ac][0] == 'D' )
|
271
|
+
nifti_disp_type_list(1); /* show DT_* types */
|
272
|
+
else if( argv[ac][0] == 't' || argv[ac][0] == 'T' )
|
273
|
+
nifti_test_datatype_sizes(1); /* test each nbyper and swapsize */
|
274
|
+
else
|
275
|
+
nifti_disp_type_list(2); /* show NIFTI_* types */
|
276
|
+
return 1;
|
277
|
+
}
|
278
|
+
else if( ! strncmp(argv[ac], "-help_hdr", 9) )
|
279
|
+
return usage(argv[0], USE_FIELD_HDR);
|
280
|
+
else if( ! strncmp(argv[ac], "-help_nim", 9) )
|
281
|
+
return usage(argv[0], USE_FIELD_NIM);
|
282
|
+
else if( ! strncmp(argv[ac], "-help_ana", 9) )
|
283
|
+
return usage(argv[0], USE_FIELD_ANA);
|
284
|
+
else if( ! strncmp(argv[ac], "-help", 5) )
|
285
|
+
return usage(argv[0], USE_FULL);
|
286
|
+
else if( ! strncmp(argv[ac], "-hist", 5) )
|
287
|
+
return usage(argv[0], USE_HIST);
|
288
|
+
else if( ! strncmp(argv[ac], "-ver", 2) )
|
289
|
+
return usage(argv[0], USE_VERSION);
|
290
|
+
else if( ! strncmp(argv[ac], "-nifti_hist", 11) )
|
291
|
+
{
|
292
|
+
nifti_disp_lib_hist();
|
293
|
+
return 1;
|
294
|
+
}
|
295
|
+
else if( ! strncmp(argv[ac], "-nifti_ver", 10) )
|
296
|
+
{
|
297
|
+
nifti_disp_lib_version();
|
298
|
+
return 1;
|
299
|
+
}
|
300
|
+
else if( ! strncmp(argv[ac], "-with_zlib", 5) ) {
|
301
|
+
printf("Was NIfTI library compiled with zlib? %s\n",
|
302
|
+
nifti_compiled_with_zlib() ? "YES" : "NO");
|
303
|
+
return 1;
|
304
|
+
}
|
305
|
+
|
306
|
+
/* begin normal execution options... */
|
307
|
+
else if( ! strncmp(argv[ac], "-add_afni_ext", 9) )
|
308
|
+
{
|
309
|
+
ac++;
|
310
|
+
CHECK_NEXT_OPT(ac, argc, "-add_afni_ext");
|
311
|
+
if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */
|
312
|
+
if( add_int(&opts->etypes, NIFTI_ECODE_AFNI) ) return -1;
|
313
|
+
opts->add_exts = 1;
|
314
|
+
}
|
315
|
+
else if( ! strncmp(argv[ac], "-add_comment_ext", 9) )
|
316
|
+
{
|
317
|
+
ac++;
|
318
|
+
CHECK_NEXT_OPT(ac, argc, "-add_comment_ext");
|
319
|
+
if( add_string(&opts->elist, argv[ac]) ) return -1; /* add extension */
|
320
|
+
if( add_int(&opts->etypes, NIFTI_ECODE_COMMENT) ) return -1;
|
321
|
+
opts->add_exts = 1;
|
322
|
+
}
|
323
|
+
else if( ! strncmp(argv[ac], "-check_hdr", 10) )
|
324
|
+
opts->check_hdr = 1;
|
325
|
+
else if( ! strncmp(argv[ac], "-check_nim", 10) )
|
326
|
+
opts->check_nim = 1;
|
327
|
+
else if( ! strncmp(argv[ac], "-copy_brick_list", 11) ||
|
328
|
+
! strncmp(argv[ac], "-copy_im", 10) ||
|
329
|
+
! strncmp(argv[ac], "-cbl", 4) )
|
330
|
+
{
|
331
|
+
opts->cbl = 1;
|
332
|
+
}
|
333
|
+
else if( ! strncmp(argv[ac], "-copy_collapsed_image", 10) ||
|
334
|
+
! strncmp(argv[ac], "-cci", 4) )
|
335
|
+
{
|
336
|
+
/* we need to read in the 7 dimension values */
|
337
|
+
int index;
|
338
|
+
opts->ci_dims[0] = 0;
|
339
|
+
for( index = 1; index < 8; index++ )
|
340
|
+
{
|
341
|
+
ac++;
|
342
|
+
CHECK_NEXT_OPT_MSG(ac,argc,"-cci","7 dimension values are requred");
|
343
|
+
if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
|
344
|
+
fprintf(stderr,"** -cci param %d (= '%s') is not a valid\n"
|
345
|
+
" consider: 'nifti_tool -help'\n",index,argv[ac]);
|
346
|
+
return -1;
|
347
|
+
}
|
348
|
+
opts->ci_dims[index] = atoi(argv[ac]);
|
349
|
+
}
|
350
|
+
|
351
|
+
opts->cci = 1;
|
352
|
+
}
|
353
|
+
else if( ! strncmp(argv[ac], "-debug", 6) )
|
354
|
+
{
|
355
|
+
ac++;
|
356
|
+
CHECK_NEXT_OPT(ac, argc, "-debug");
|
357
|
+
opts->debug = atoi(argv[ac]);
|
358
|
+
}
|
359
|
+
else if( ! strncmp(argv[ac], "-diff_hdr", 8) )
|
360
|
+
opts->diff_hdr = 1;
|
361
|
+
else if( ! strncmp(argv[ac], "-diff_nim", 8) )
|
362
|
+
opts->diff_nim = 1;
|
363
|
+
else if( ! strncmp(argv[ac], "-disp_exts", 7) )
|
364
|
+
opts->disp_exts = 1;
|
365
|
+
else if( ! strncmp(argv[ac], "-disp_hdr", 8) )
|
366
|
+
opts->disp_hdr = 1;
|
367
|
+
else if( ! strncmp(argv[ac], "-disp_nim", 8) )
|
368
|
+
opts->disp_nim = 1;
|
369
|
+
else if( ! strncmp(argv[ac], "-disp_ana", 8) )
|
370
|
+
opts->disp_ana = 1;
|
371
|
+
else if( ! strncmp(argv[ac], "-dci_lines", 6) || /* before -dts */
|
372
|
+
! strncmp(argv[ac], "-dts_lines", 6) )
|
373
|
+
{
|
374
|
+
opts->dci_lines = 1;
|
375
|
+
}
|
376
|
+
else if( ! strncmp(argv[ac], "-disp_collapsed_image", 10) ||
|
377
|
+
! strncmp(argv[ac], "-disp_ci", 8) )
|
378
|
+
{
|
379
|
+
/* we need to read in the 7 dimension values */
|
380
|
+
int index;
|
381
|
+
opts->ci_dims[0] = 0;
|
382
|
+
for( index = 1; index < 8; index++ )
|
383
|
+
{
|
384
|
+
ac++;
|
385
|
+
CHECK_NEXT_OPT_MSG(ac,argc,"-disp_ci",
|
386
|
+
"7 dimension values are requred");
|
387
|
+
if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
|
388
|
+
fprintf(stderr,"** -disp_ci param %d (= '%s') is not a valid\n"
|
389
|
+
" consider: 'nifti_tool -help'\n",index,argv[ac]);
|
390
|
+
return -1;
|
391
|
+
}
|
392
|
+
opts->ci_dims[index] = atoi(argv[ac]);
|
393
|
+
}
|
394
|
+
|
395
|
+
opts->dci = 1;
|
396
|
+
}
|
397
|
+
else if( ! strncmp(argv[ac], "-disp_ts", 10) ||
|
398
|
+
! strncmp(argv[ac], "-dts", 4) )
|
399
|
+
{
|
400
|
+
/* we need to read in the ijk indices into the ci_dims array */
|
401
|
+
int index;
|
402
|
+
for( index = 1; index <= 3; index++ )
|
403
|
+
{
|
404
|
+
ac++;
|
405
|
+
CHECK_NEXT_OPT_MSG(ac,argc,"-dts","i,j,k indices are requied\n");
|
406
|
+
if( ! isdigit(argv[ac][0]) ){
|
407
|
+
fprintf(stderr,"** -dts param %d (= '%s') is not a number\n"
|
408
|
+
" consider: 'nifti_tool -help'\n",index,argv[ac]);
|
409
|
+
return -1;
|
410
|
+
}
|
411
|
+
opts->ci_dims[index] = atoi(argv[ac]);
|
412
|
+
}
|
413
|
+
/* and fill the rest of the array */
|
414
|
+
opts->ci_dims[0] = 0;
|
415
|
+
for( index = 4; index < 8; index++ ) opts->ci_dims[index] = -1;
|
416
|
+
|
417
|
+
opts->dts = 1;
|
418
|
+
}
|
419
|
+
else if( ! strncmp(argv[ac], "-field", 2) )
|
420
|
+
{
|
421
|
+
ac++;
|
422
|
+
CHECK_NEXT_OPT(ac, argc, "-field");
|
423
|
+
if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */
|
424
|
+
}
|
425
|
+
else if( ! strncmp(argv[ac], "-infiles", 3) )
|
426
|
+
{
|
427
|
+
int count;
|
428
|
+
/* for -infiles, get all next arguments until a '-' or done */
|
429
|
+
ac++;
|
430
|
+
for( count = 0; (ac < argc) && (argv[ac][0] != '-'); ac++, count++ )
|
431
|
+
if( add_string(&opts->infiles, argv[ac]) ) return -1;/* add field */
|
432
|
+
if( count > 0 && ac < argc ) ac--; /* more options to process */
|
433
|
+
if( g_debug > 2 ) fprintf(stderr,"+d have %d file names\n", count);
|
434
|
+
}
|
435
|
+
else if( ! strncmp(argv[ac], "-make_image", 8) )
|
436
|
+
{
|
437
|
+
opts->make_im = 1; /* will setup later, as -cbl and MAKE_IM */
|
438
|
+
}
|
439
|
+
else if( ! strncmp(argv[ac], "-mod_field", 6) )
|
440
|
+
{
|
441
|
+
ac++;
|
442
|
+
CHECK_NEXT_OPT(ac, argc, "-mod_field");
|
443
|
+
if( add_string(&opts->flist, argv[ac]) ) return -1; /* add field */
|
444
|
+
ac++;
|
445
|
+
CHECK_NEXT_OPT(ac, argc, "-mod_field (2)");
|
446
|
+
if( add_string(&opts->vlist, argv[ac]) ) return -1; /* add value */
|
447
|
+
}
|
448
|
+
else if( ! strncmp(argv[ac], "-mod_hdr", 7) )
|
449
|
+
opts->mod_hdr = 1;
|
450
|
+
else if( ! strncmp(argv[ac], "-mod_nim", 7) )
|
451
|
+
opts->mod_nim = 1;
|
452
|
+
else if( ! strncmp(argv[ac], "-keep_hist", 5) )
|
453
|
+
opts->keep_hist = 1;
|
454
|
+
else if( ! strncmp(argv[ac], "-new_dim", 8) )
|
455
|
+
{
|
456
|
+
/* we need to read in the 8 dimension values */
|
457
|
+
int index;
|
458
|
+
for( index = 0; index < 8; index++ )
|
459
|
+
{
|
460
|
+
ac++;
|
461
|
+
CHECK_NEXT_OPT_MSG(ac,argc,"-new_dim","8 dim values are requred");
|
462
|
+
if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
|
463
|
+
fprintf(stderr,"** -new_dim param %d (= '%s') is not a valid\n"
|
464
|
+
" consider: 'nifti_tool -help'\n",index,argv[ac]);
|
465
|
+
return -1;
|
466
|
+
}
|
467
|
+
opts->new_dim[index] = atoi(argv[ac]);
|
468
|
+
}
|
469
|
+
}
|
470
|
+
else if( ! strncmp(argv[ac], "-new_datatype", 10) )
|
471
|
+
{
|
472
|
+
ac++;
|
473
|
+
CHECK_NEXT_OPT(ac, argc, "-new_datatype");
|
474
|
+
opts->new_datatype = atoi(argv[ac]);
|
475
|
+
}
|
476
|
+
else if( ! strncmp(argv[ac], "-overwrite", 6) )
|
477
|
+
opts->overwrite = 1;
|
478
|
+
else if( ! strncmp(argv[ac], "-prefix", 4) )
|
479
|
+
{
|
480
|
+
ac++;
|
481
|
+
CHECK_NEXT_OPT(ac, argc, "-prefix");
|
482
|
+
opts->prefix = argv[ac];
|
483
|
+
}
|
484
|
+
else if( ! strncmp(argv[ac], "-quiet", 3) )
|
485
|
+
opts->debug = 0;
|
486
|
+
else if( ! strncmp(argv[ac], "-rm_ext", 7) )
|
487
|
+
{
|
488
|
+
ac++;
|
489
|
+
CHECK_NEXT_OPT(ac, argc, "-rm_ext");
|
490
|
+
if( strcmp(argv[ac],"ALL") == 0 ) /* special case, pass -1 */
|
491
|
+
{
|
492
|
+
if( add_string(&opts->elist, "-1") ) return -1;
|
493
|
+
}
|
494
|
+
else
|
495
|
+
{
|
496
|
+
int index = atoi(argv[ac]);
|
497
|
+
if( (index != -1) && ((index > 1000) || !isdigit(*argv[ac])) ){
|
498
|
+
fprintf(stderr,
|
499
|
+
"** '-rm_ext' requires an extension index (read '%s')\n",
|
500
|
+
argv[ac]);
|
501
|
+
return -1;
|
502
|
+
}
|
503
|
+
if( add_string(&opts->elist, argv[ac]) ) return -1;
|
504
|
+
}
|
505
|
+
opts->rm_exts = 1;
|
506
|
+
}
|
507
|
+
else if( ! strncmp(argv[ac], "-strip_extras", 6) )
|
508
|
+
opts->strip = 1;
|
509
|
+
else if( ! strncmp(argv[ac], "-swap_as_analyze", 12) )
|
510
|
+
opts->swap_ana = 1;
|
511
|
+
else if( ! strncmp(argv[ac], "-swap_as_nifti", 12) )
|
512
|
+
opts->swap_hdr = 1;
|
513
|
+
else if( ! strncmp(argv[ac], "-swap_as_old", 12) )
|
514
|
+
opts->swap_old = 1;
|
515
|
+
else
|
516
|
+
{
|
517
|
+
fprintf(stderr,"** unknown option: '%s'\n", argv[ac]);
|
518
|
+
return -1;
|
519
|
+
}
|
520
|
+
}
|
521
|
+
|
522
|
+
if( opts->make_im )
|
523
|
+
{
|
524
|
+
if( opts->infiles.len > 0 )
|
525
|
+
{
|
526
|
+
fprintf(stderr,"** -infiles is invalid when using -make_im\n");
|
527
|
+
return -1;
|
528
|
+
}
|
529
|
+
/* apply -make_im via -cbl and "MAKE_IM" */
|
530
|
+
opts->cbl = 1;
|
531
|
+
if( add_string(&opts->infiles, NT_MAKE_IM_NAME) ) return -1;
|
532
|
+
}
|
533
|
+
|
534
|
+
/* verify for programming purposes */
|
535
|
+
if( opts->add_exts && ( opts->elist.len != opts->etypes.len ) )
|
536
|
+
{
|
537
|
+
fprintf(stderr,"** ext list length (%d) != etype length (%d)\n",
|
538
|
+
opts->elist.len, opts->etypes.len);
|
539
|
+
return -1;
|
540
|
+
}
|
541
|
+
|
542
|
+
g_debug = opts->debug;
|
543
|
+
nifti_set_debug_level(g_debug);
|
544
|
+
|
545
|
+
fill_cmd_string(opts, argc, argv); /* copy this command */
|
546
|
+
|
547
|
+
if( g_debug > 2 ) disp_nt_opts("options read: ", opts);
|
548
|
+
|
549
|
+
return 0;
|
550
|
+
}
|
551
|
+
|
552
|
+
|
553
|
+
/*----------------------------------------------------------------------
|
554
|
+
* verify that the options make sense
|
555
|
+
*----------------------------------------------------------------------*/
|
556
|
+
int verify_opts( nt_opts * opts, char * prog )
|
557
|
+
{
|
558
|
+
int ac, errs = 0; /* number of requested action types */
|
559
|
+
|
560
|
+
/* check that only one of disp, diff, mod or add_*_ext is used */
|
561
|
+
ac = (opts->check_hdr || opts->check_nim ) ? 1 : 0;
|
562
|
+
ac += (opts->diff_hdr || opts->diff_nim ) ? 1 : 0;
|
563
|
+
ac += (opts->disp_hdr || opts->disp_nim ||
|
564
|
+
opts->disp_ana || opts->disp_exts ) ? 1 : 0;
|
565
|
+
ac += (opts->mod_hdr || opts->mod_nim ) ? 1 : 0;
|
566
|
+
ac += (opts->swap_hdr || opts->swap_ana || opts->swap_old ) ? 1 : 0;
|
567
|
+
ac += (opts->add_exts || opts->rm_exts ) ? 1 : 0;
|
568
|
+
ac += (opts->strip ) ? 1 : 0;
|
569
|
+
ac += (opts->cbl ) ? 1 : 0;
|
570
|
+
ac += (opts->cci ) ? 1 : 0;
|
571
|
+
ac += (opts->dts || opts->dci ) ? 1 : 0;
|
572
|
+
|
573
|
+
if( ac < 1 )
|
574
|
+
{
|
575
|
+
fprintf(stderr,
|
576
|
+
"** no action option, so nothing to do...\n"
|
577
|
+
" (try one of '-add...', '-diff...', '-disp...' or '-mod...')\n"
|
578
|
+
" (see '%s -help' for details)\n", prog);
|
579
|
+
return 1;
|
580
|
+
}
|
581
|
+
else if( ac > 1 )
|
582
|
+
{
|
583
|
+
fprintf(stderr,
|
584
|
+
"** only one action option is allowed, please use only one of:\n"
|
585
|
+
" '-add_...', '-check_...', '-diff_...', '-disp_...',\n"
|
586
|
+
" '-mod_...', '-strip', '-dts', '-cbl' or '-cci'\n"
|
587
|
+
" (see '%s -help' for details)\n", prog);
|
588
|
+
return 1;
|
589
|
+
}
|
590
|
+
|
591
|
+
/* can modify nifti_1_header or nifti_image, but not both */
|
592
|
+
if( opts->mod_hdr && opts->mod_nim )
|
593
|
+
{
|
594
|
+
fprintf(stderr,"** cannot use both '-mod_hdr' and '-mod_nim'\n");
|
595
|
+
return 1;
|
596
|
+
}
|
597
|
+
|
598
|
+
/* can add or remove extensions, but not both */
|
599
|
+
if( opts->add_exts && opts->rm_exts )
|
600
|
+
{
|
601
|
+
fprintf(stderr,"** cannot use both '-add_*_ext' and '-rm_ext'\n");
|
602
|
+
return 1;
|
603
|
+
}
|
604
|
+
if( (opts->add_exts || opts->rm_exts) && opts->elist.len <= 0 )
|
605
|
+
{
|
606
|
+
fprintf(stderr,"** missing extensions to add or remove\n");
|
607
|
+
return 1;
|
608
|
+
}
|
609
|
+
|
610
|
+
/* if modify, then we need fields and corresponding values */
|
611
|
+
if( opts->mod_hdr || opts->mod_nim )
|
612
|
+
{
|
613
|
+
if( opts->flist.len <= 0 )
|
614
|
+
{
|
615
|
+
fprintf(stderr,"** missing field to modify (need '-mod_field' opt)\n");
|
616
|
+
return 1;
|
617
|
+
}
|
618
|
+
if( opts->flist.len != opts->vlist.len )
|
619
|
+
{
|
620
|
+
fprintf(stderr,"** error: modifying %d fields with %d values\n",
|
621
|
+
opts->flist.len, opts->vlist.len);
|
622
|
+
return 1;
|
623
|
+
}
|
624
|
+
}
|
625
|
+
|
626
|
+
/* verify the number of files given for each of 4 action types */
|
627
|
+
|
628
|
+
/* -diff_... : require nfiles == 2 */
|
629
|
+
if( opts->diff_hdr || opts->diff_nim )
|
630
|
+
{
|
631
|
+
if( opts->infiles.len != 2 )
|
632
|
+
{
|
633
|
+
fprintf(stderr,"** '-diff_XXX' options require exactly 2 inputs files\n");
|
634
|
+
return 1;
|
635
|
+
}
|
636
|
+
}
|
637
|
+
/* if we are making changes, but not overwriting... */
|
638
|
+
else if( (opts->elist.len > 0 || opts->mod_hdr || opts->mod_nim ||
|
639
|
+
opts->swap_hdr || opts->swap_ana || opts->swap_old ) &&
|
640
|
+
!opts->overwrite )
|
641
|
+
{
|
642
|
+
if( opts->infiles.len > 1 )
|
643
|
+
{
|
644
|
+
fprintf(stderr,"** without -overwrite, only one input file may be"
|
645
|
+
" modified at a time\n");
|
646
|
+
errs++;
|
647
|
+
}
|
648
|
+
else if( ! opts->prefix )
|
649
|
+
{
|
650
|
+
fprintf(stderr,"** missing -prefix for output file\n");
|
651
|
+
errs++;
|
652
|
+
}
|
653
|
+
}
|
654
|
+
|
655
|
+
if( opts->dci_lines && ! opts->dts && ! opts->dci )
|
656
|
+
{
|
657
|
+
fprintf(stderr,"** option '-dci_lines' must only be used with '-dts'\n");
|
658
|
+
errs++;
|
659
|
+
}
|
660
|
+
|
661
|
+
if( opts->infiles.len <= 0 ) /* in any case */
|
662
|
+
{
|
663
|
+
fprintf(stderr,"** missing input files (see -infiles option)\n");
|
664
|
+
errs++;
|
665
|
+
}
|
666
|
+
|
667
|
+
if ( opts->overwrite && opts->prefix )
|
668
|
+
{
|
669
|
+
fprintf(stderr, "** please specify only one of -prefix and -overwrite\n");
|
670
|
+
errs++;
|
671
|
+
}
|
672
|
+
|
673
|
+
if( errs ) return 1;
|
674
|
+
|
675
|
+
if( g_debug > 1 ) fprintf(stderr,"+d options seem valid\n");
|
676
|
+
|
677
|
+
return 0;
|
678
|
+
}
|
679
|
+
|
680
|
+
|
681
|
+
/*----------------------------------------------------------------------
|
682
|
+
* re-assemble the command string into opts->command
|
683
|
+
*----------------------------------------------------------------------*/
|
684
|
+
int fill_cmd_string( nt_opts * opts, int argc, char * argv[])
|
685
|
+
{
|
686
|
+
char * cp;
|
687
|
+
int len, remain = NT_CMD_LEN; /* NT_CMD_LEN is max command len */
|
688
|
+
int c, ac;
|
689
|
+
int has_space; /* arguments containing space must be quoted */
|
690
|
+
int skip = 0; /* counter to skip some of the arguments */
|
691
|
+
|
692
|
+
/* get the first argument separately */
|
693
|
+
len = sprintf( opts->command, "\n command: %s", argv[0] );
|
694
|
+
cp = opts->command + len;
|
695
|
+
remain -= len;
|
696
|
+
|
697
|
+
/* get the rest, with special attention to input files */
|
698
|
+
for( ac = 1; ac < argc; ac++ )
|
699
|
+
{
|
700
|
+
if( skip ){ skip--; continue; } /* then skip these arguments */
|
701
|
+
|
702
|
+
len = strlen(argv[ac]);
|
703
|
+
if( len + 3 >= remain ) { /* extra 3 for space and possible '' */
|
704
|
+
fprintf(stderr,"FCS: no space remaining for command, continuing...\n");
|
705
|
+
return 1;
|
706
|
+
}
|
707
|
+
|
708
|
+
/* put the argument in, possibly with '' */
|
709
|
+
|
710
|
+
has_space = 0;
|
711
|
+
for( c = 0; c < len-1; c++ )
|
712
|
+
if( isspace(argv[ac][c]) ){ has_space = 1; break; }
|
713
|
+
if( has_space ) len = sprintf(cp, " '%s'", argv[ac]);
|
714
|
+
else len = sprintf(cp, " %s", argv[ac]);
|
715
|
+
|
716
|
+
remain -= len;
|
717
|
+
|
718
|
+
/* infiles is okay, but after the *next* argument, we may skip files */
|
719
|
+
/* (danger, will robinson! hack alert!) */
|
720
|
+
if( !strncmp(argv[ac-1],"-infiles",3) )
|
721
|
+
{
|
722
|
+
/* if more than 4 (just to be arbitrary) input files,
|
723
|
+
include only the first and last */
|
724
|
+
if( opts->infiles.len > 4 )
|
725
|
+
skip = opts->infiles.len - 2;
|
726
|
+
}
|
727
|
+
|
728
|
+
cp += len;
|
729
|
+
}
|
730
|
+
|
731
|
+
if( g_debug > 1 ){
|
732
|
+
fprintf(stderr,"+d filled command string, %d args, %d bytes\n",
|
733
|
+
argc, (int)(cp - opts->command));
|
734
|
+
if( g_debug > 2 ) fprintf(stderr,"%s\n", opts->command);
|
735
|
+
}
|
736
|
+
|
737
|
+
return 0;
|
738
|
+
}
|
739
|
+
|
740
|
+
|
741
|
+
/*----------------------------------------------------------------------
|
742
|
+
* - only bother to alloc one pointer at a time (don't need efficiency here)
|
743
|
+
* - return 0 on success
|
744
|
+
*----------------------------------------------------------------------*/
|
745
|
+
int add_int(int_list * ilist, int val)
|
746
|
+
{
|
747
|
+
if( ilist->len == 0 ) ilist->list = NULL; /* just to be safe */
|
748
|
+
ilist->len++;
|
749
|
+
ilist->list = (int *)realloc(ilist->list,ilist->len*sizeof(int));
|
750
|
+
if( ! ilist->list ){
|
751
|
+
fprintf(stderr,"** failed to alloc %d (int *) elements\n",ilist->len);
|
752
|
+
return -1;
|
753
|
+
}
|
754
|
+
|
755
|
+
ilist->list[ilist->len-1] = val;
|
756
|
+
|
757
|
+
return 0;
|
758
|
+
}
|
759
|
+
|
760
|
+
|
761
|
+
/*----------------------------------------------------------------------
|
762
|
+
* - do not duplicate the string
|
763
|
+
* - only bother to alloc one pointer at a time (don't need efficiency here)
|
764
|
+
* - return 0 on success
|
765
|
+
*----------------------------------------------------------------------*/
|
766
|
+
int add_string(str_list * slist, char * str)
|
767
|
+
{
|
768
|
+
if( slist->len == 0 ) slist->list = NULL; /* just to be safe */
|
769
|
+
slist->len++;
|
770
|
+
slist->list = (char **)realloc(slist->list,slist->len*sizeof(char *));
|
771
|
+
if( ! slist->list ){
|
772
|
+
fprintf(stderr,"** failed to alloc %d (char *) elements\n",slist->len);
|
773
|
+
return -1;
|
774
|
+
}
|
775
|
+
|
776
|
+
slist->list[slist->len-1] = str;
|
777
|
+
|
778
|
+
return 0;
|
779
|
+
}
|
780
|
+
|
781
|
+
|
782
|
+
/*----------------------------------------------------------------------
|
783
|
+
* display information on using the program
|
784
|
+
*----------------------------------------------------------------------*/
|
785
|
+
int usage(char * prog, int level)
|
786
|
+
{
|
787
|
+
int c, len;
|
788
|
+
if( level == USE_SHORT )
|
789
|
+
{
|
790
|
+
fprintf(stdout,"usage %s [options] -infiles files...\n", prog);
|
791
|
+
fprintf(stdout,"usage %s -help\n", prog);
|
792
|
+
return -1;
|
793
|
+
}
|
794
|
+
else if( level == USE_FULL )
|
795
|
+
use_full("nifti_tool"); /* let's not allow paths in here */
|
796
|
+
else if( level == USE_HIST )
|
797
|
+
{
|
798
|
+
len = sizeof(g_history)/sizeof(char *);
|
799
|
+
for( c = 0; c < len; c++)
|
800
|
+
fputs(g_history[c], stdout);
|
801
|
+
}
|
802
|
+
else if( level == USE_FIELD_HDR )
|
803
|
+
{
|
804
|
+
field_s nhdr_fields[NT_HDR_NUM_FIELDS]; /* just do it all here */
|
805
|
+
|
806
|
+
fill_hdr_field_array(nhdr_fields);
|
807
|
+
disp_field_s_list("nifti_1_header: ", nhdr_fields, NT_HDR_NUM_FIELDS);
|
808
|
+
}
|
809
|
+
else if( level == USE_FIELD_ANA )
|
810
|
+
{
|
811
|
+
field_s nhdr_fields[NT_ANA_NUM_FIELDS]; /* just do it all here */
|
812
|
+
|
813
|
+
fill_ana_field_array(nhdr_fields);
|
814
|
+
disp_field_s_list("nifti_analyze75: ",nhdr_fields,NT_ANA_NUM_FIELDS);
|
815
|
+
}
|
816
|
+
else if( level == USE_FIELD_NIM )
|
817
|
+
{
|
818
|
+
field_s nim_fields[NT_NIM_NUM_FIELDS];
|
819
|
+
|
820
|
+
fill_nim_field_array(nim_fields);
|
821
|
+
disp_field_s_list("nifti_image: ", nim_fields, NT_NIM_NUM_FIELDS);
|
822
|
+
}
|
823
|
+
else if( level == USE_VERSION )
|
824
|
+
fprintf(stdout, "%s, %s\n", prog, g_version);
|
825
|
+
else {
|
826
|
+
fprintf(stdout,"** illegal level for usage(): %d\n", level);
|
827
|
+
return -1;
|
828
|
+
}
|
829
|
+
|
830
|
+
return 1;
|
831
|
+
}
|
832
|
+
|
833
|
+
|
834
|
+
/*----------------------------------------------------------------------
|
835
|
+
* full usage
|
836
|
+
*----------------------------------------------------------------------*/
|
837
|
+
int use_full(char * prog)
|
838
|
+
{
|
839
|
+
printf(
|
840
|
+
"nifti_tool\n"
|
841
|
+
"\n"
|
842
|
+
" - display, modify or compare nifti structures in datasets\n"
|
843
|
+
" - copy a dataset by selecting a list of volumes from the original\n"
|
844
|
+
" - copy a dataset, collapsing any dimensions, each to a single index\n"
|
845
|
+
" - display a time series for a voxel, or more generally, the data\n"
|
846
|
+
" from any collapsed image, in ASCII text\n");
|
847
|
+
printf(
|
848
|
+
"\n"
|
849
|
+
" This program can be used to display information from nifti datasets,\n"
|
850
|
+
" to modify information in nifti datasets, to look for differences\n"
|
851
|
+
" between two nifti datasets (like the UNIX 'diff' command), and to copy\n"
|
852
|
+
" a dataset to a new one, either by restricting any dimensions, or by\n"
|
853
|
+
" copying a list of volumes (the time dimension) from a dataset.\n"
|
854
|
+
"\n");
|
855
|
+
printf(
|
856
|
+
" Only one action type is allowed, e.g. one cannot modify a dataset\n"
|
857
|
+
" and then take a 'diff'.\n"
|
858
|
+
"\n");
|
859
|
+
printf(
|
860
|
+
" one can display - any or all fields in the nifti_1_header structure\n"
|
861
|
+
" - any or all fields in the nifti_image structure\n"
|
862
|
+
" - any or all fields in the nifti_analyze75 structure\n"
|
863
|
+
" - the extensions in the nifti_image structure\n"
|
864
|
+
" - the time series from a 4-D dataset, given i,j,k\n"
|
865
|
+
" - the data from any collapsed image, given dims. list\n"
|
866
|
+
"\n");
|
867
|
+
printf(
|
868
|
+
" one can check - perform internal check on the nifti_1_header struct\n"
|
869
|
+
" (by nifti_hdr_looks_good())\n"
|
870
|
+
" - perform internal check on the nifti_image struct\n"
|
871
|
+
" (by nifti_nim_is_valid())\n"
|
872
|
+
"\n");
|
873
|
+
printf(
|
874
|
+
" one can modify - any or all fields in the nifti_1_header structure\n"
|
875
|
+
" - any or all fields in the nifti_image structure\n"
|
876
|
+
" - swap all fields in NIFTI or ANALYZE header structure\n"
|
877
|
+
" add/rm - any or all extensions in the nifti_image structure\n"
|
878
|
+
" remove - all extensions and descriptions from the datasets\n"
|
879
|
+
"\n");
|
880
|
+
printf(
|
881
|
+
" one can compare - any or all field pairs of nifti_1_header structures\n"
|
882
|
+
" - any or all field pairs of nifti_image structures\n"
|
883
|
+
"\n"
|
884
|
+
" one can copy - an arbitrary list of dataset volumes (time points)\n"
|
885
|
+
" - a dataset, collapsing across arbitrary dimensions\n"
|
886
|
+
" (restricting those dimensions to the given indices)\n"
|
887
|
+
"\n"
|
888
|
+
" one can create - a new dataset out of nothing\n"
|
889
|
+
"\n");
|
890
|
+
printf(
|
891
|
+
" Note: to learn about which fields exist in either of the structures,\n"
|
892
|
+
" or to learn a field's type, size of each element, or the number\n"
|
893
|
+
" of elements in the field, use either the '-help_hdr' option, or\n"
|
894
|
+
" the '-help_nim' option. No further options are required.\n"
|
895
|
+
" ------------------------------\n");
|
896
|
+
printf(
|
897
|
+
"\n"
|
898
|
+
" usage styles:\n"
|
899
|
+
"\n"
|
900
|
+
" nifti_tool -help : show this help\n"
|
901
|
+
" nifti_tool -help_hdr : show nifti_1_header field info\n"
|
902
|
+
" nifti_tool -help_nim : show nifti_image field info\n"
|
903
|
+
" nifti_tool -help_ana : show nifti_analyze75 field info\n"
|
904
|
+
" nifti_tool -help_datatypes : show datatype table\n"
|
905
|
+
"\n");
|
906
|
+
printf(
|
907
|
+
" nifti_tool -ver : show the current version\n"
|
908
|
+
" nifti_tool -hist : show the modification history\n"
|
909
|
+
" nifti_tool -nifti_ver : show the nifti library version\n"
|
910
|
+
" nifti_tool -nifti_hist : show the nifti library history\n"
|
911
|
+
" nifti_tool -with_zlib : was library compiled with zlib\n"
|
912
|
+
"\n"
|
913
|
+
"\n");
|
914
|
+
printf(
|
915
|
+
" nifti_tool -check_hdr -infiles f1 ...\n"
|
916
|
+
" nifti_tool -check_nim -infiles f1 ...\n"
|
917
|
+
"\n");
|
918
|
+
printf(
|
919
|
+
" nifti_tool -copy_brick_list -infiles f1'[indices...]'\n"
|
920
|
+
" nifti_tool -copy_collapsed_image I J K T U V W -infiles f1\n"
|
921
|
+
" nifti_tool -copy_im -infiles f1\n"
|
922
|
+
"\n");
|
923
|
+
printf(
|
924
|
+
" nifti_tool -make_im -prefix new_im.nii\n"
|
925
|
+
"\n");
|
926
|
+
printf(
|
927
|
+
" nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...\n"
|
928
|
+
" nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...\n"
|
929
|
+
" nifti_tool -disp_ana [-field FIELDNAME] [...] -infiles f1 ...\n"
|
930
|
+
" nifti_tool -disp_exts -infiles f1 ...\n"
|
931
|
+
" nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...\n"
|
932
|
+
" nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...\n"
|
933
|
+
"\n");
|
934
|
+
printf(
|
935
|
+
" nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n"
|
936
|
+
" nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n"
|
937
|
+
"\n"
|
938
|
+
" nifti_tool -swap_as_nifti -overwrite -infiles f1\n"
|
939
|
+
" nifti_tool -swap_as_analyze -overwrite -infiles f1\n"
|
940
|
+
" nifti_tool -swap_as_old -overwrite -infiles f1\n"
|
941
|
+
"\n");
|
942
|
+
printf(
|
943
|
+
" nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1\n"
|
944
|
+
" nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1\n"
|
945
|
+
" nifti_tool -add_comment_ext 'file:FILENAME' [...] -infiles f1\n"
|
946
|
+
" nifti_tool -rm_ext INDEX [...] -infiles f1 ...\n"
|
947
|
+
" nifti_tool -strip_extras -infiles f1 ...\n"
|
948
|
+
"\n");
|
949
|
+
printf(
|
950
|
+
" nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2\n"
|
951
|
+
" nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2\n"
|
952
|
+
"\n"
|
953
|
+
" ------------------------------\n");
|
954
|
+
|
955
|
+
printf(
|
956
|
+
"\n"
|
957
|
+
" selected examples:\n"
|
958
|
+
"\n"
|
959
|
+
" A. checks header (for problems):\n"
|
960
|
+
"\n"
|
961
|
+
" 1. nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n"
|
962
|
+
" 2. nifti_tool -check_hdr -infiles *.nii *.hdr\n"
|
963
|
+
" 3. nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n"
|
964
|
+
"\n");
|
965
|
+
printf(
|
966
|
+
" B. show header differences:\n"
|
967
|
+
"\n"
|
968
|
+
" 1. nifti_tool -diff_hdr -field dim -field intent_code \\\n"
|
969
|
+
" -infiles dset0.nii dset1.nii \n"
|
970
|
+
" 2. nifti_tool -diff_hdr -new_dims 3 10 20 30 0 0 0 0 \\\n"
|
971
|
+
" -infiles my_dset.nii MAKE_IM \n"
|
972
|
+
"\n"
|
973
|
+
" C. display structures or fields:\n"
|
974
|
+
"\n");
|
975
|
+
printf(
|
976
|
+
" 1. nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n"
|
977
|
+
" 2. nifti_tool -disp_hdr -field dim -field descrip -infiles dset.nii\n"
|
978
|
+
" 3. nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n"
|
979
|
+
" 4. nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n"
|
980
|
+
" 5. nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n"
|
981
|
+
"\n");
|
982
|
+
printf(
|
983
|
+
" 6. nifti_tool -disp_ana -infiles analyze.hdr\n"
|
984
|
+
" 7. nifti_tool -disp_nim -infiles nifti.nii\n"
|
985
|
+
"\n");
|
986
|
+
printf(
|
987
|
+
" D. create a new dataset from nothing:\n"
|
988
|
+
"\n"
|
989
|
+
" 1. nifti_tool -make_im -prefix new_im.nii \n"
|
990
|
+
" 2. nifti_tool -make_im -prefix float_im.nii \\\n"
|
991
|
+
" -new_dims 3 10 20 30 0 0 0 0 -new_datatype 16\n");
|
992
|
+
printf(
|
993
|
+
" 3. nifti_tool -mod_hdr -mod_field descrip 'dataset with mods' \\\n"
|
994
|
+
" -new_dims 3 10 20 30 0 0 0 0 \\\n"
|
995
|
+
" -prefix new_desc.nii -infiles MAKE_IM\n"
|
996
|
+
"\n");
|
997
|
+
printf(
|
998
|
+
" E. copy dataset, brick list or collapsed image:\n"
|
999
|
+
"\n"
|
1000
|
+
" 1. nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n"
|
1001
|
+
" 2. nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n"
|
1002
|
+
" 3. nifti_tool -cbl -prefix new_partial.nii \\\n"
|
1003
|
+
" -infiles dset0.nii'[3..$(2)]'\n"
|
1004
|
+
"\n"
|
1005
|
+
" 4. nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n"
|
1006
|
+
" 5. nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n"
|
1007
|
+
" -prefix new_5_0_17_2.nii\n"
|
1008
|
+
"\n");
|
1009
|
+
printf(
|
1010
|
+
" F. modify the header (modify fields or swap entire header):\n"
|
1011
|
+
"\n"
|
1012
|
+
" 1. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1013
|
+
" -mod_field dim '4 64 64 20 30 1 1 1 1'\n"
|
1014
|
+
" 2. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1015
|
+
" -mod_field descrip 'beer, brats and cheese, mmmmm...'\n"
|
1016
|
+
);
|
1017
|
+
printf(
|
1018
|
+
" 3. cp old_dset.hdr nifti_swap.hdr \n"
|
1019
|
+
" nifti_tool -swap_as_nifti -overwrite -infiles nifti_swap.hdr\n"
|
1020
|
+
" 4. cp old_dset.hdr analyze_swap.hdr \n"
|
1021
|
+
" nifti_tool -swap_as_analyze -overwrite -infiles analyze_swap.hdr\n"
|
1022
|
+
" 5. nifti_tool -swap_as_old -prefix old_swap.hdr -infiles old_dset.hdr\n"
|
1023
|
+
" nifti_tool -diff_hdr -infiles nifti_swap.hdr old_swap.hdr\n"
|
1024
|
+
"\n");
|
1025
|
+
printf(
|
1026
|
+
" G. strip, add or remove extensions:\n"
|
1027
|
+
" (in example #3, the extension is copied from a text file)\n"
|
1028
|
+
"\n"
|
1029
|
+
"\n"
|
1030
|
+
" 1. nifti_tool -strip -overwrite -infiles *.nii\n"
|
1031
|
+
" 2. nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n"
|
1032
|
+
" -prefix dnew -infiles dset0.nii\n"
|
1033
|
+
);
|
1034
|
+
printf(
|
1035
|
+
" 3. nifti_tool -add_comment 'file:my.extension.txt' \\\n"
|
1036
|
+
" -prefix dnew -infiles dset0.nii\n"
|
1037
|
+
" 4. nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n"
|
1038
|
+
" 5. nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n"
|
1039
|
+
" -infiles dset0.nii\n"
|
1040
|
+
"\n"
|
1041
|
+
" ------------------------------\n");
|
1042
|
+
printf(
|
1043
|
+
"\n"
|
1044
|
+
" options for check actions:\n"
|
1045
|
+
"\n");
|
1046
|
+
printf(
|
1047
|
+
" -check_hdr : check for a valid nifti_1_header struct\n"
|
1048
|
+
"\n"
|
1049
|
+
" This action is used to check the nifti_1_header structure for\n"
|
1050
|
+
" problems. The nifti_hdr_looks_good() function is used for the\n"
|
1051
|
+
" test, and currently checks:\n"
|
1052
|
+
" \n"
|
1053
|
+
" dim[], sizeof_hdr, magic, datatype\n"
|
1054
|
+
" \n"
|
1055
|
+
" More tests can be requested of the author.\n"
|
1056
|
+
"\n");
|
1057
|
+
printf(
|
1058
|
+
" e.g. perform checks on the headers of some datasets\n"
|
1059
|
+
" nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n"
|
1060
|
+
" nifti_tool -check_hdr -infiles *.nii *.hdr\n"
|
1061
|
+
" \n"
|
1062
|
+
" e.g. add the -quiet option, so that only erros are reported\n"
|
1063
|
+
" nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n"
|
1064
|
+
"\n");
|
1065
|
+
printf(
|
1066
|
+
" -check_nim : check for a valid nifti_image struct\n"
|
1067
|
+
"\n"
|
1068
|
+
" This action is used to check the nifti_image structure for\n"
|
1069
|
+
" problems. This is tested via both nifti_convert_nhdr2nim()\n"
|
1070
|
+
" and nifti_nim_is_valid(), though other functions are called\n"
|
1071
|
+
" below them, of course. Current checks are:\n"
|
1072
|
+
"\n");
|
1073
|
+
printf(
|
1074
|
+
" dim[], sizeof_hdr, datatype, fname, iname, nifti_type\n"
|
1075
|
+
" \n"
|
1076
|
+
" Note that creation of a nifti_image structure depends on good\n"
|
1077
|
+
" header fields. So errors are terminal, meaning this check would\n"
|
1078
|
+
" probably report at most one error, even if more exist. The\n"
|
1079
|
+
" -check_hdr action is more complete.\n"
|
1080
|
+
"\n");
|
1081
|
+
printf(
|
1082
|
+
" More tests can be requested of the author.\n"
|
1083
|
+
"\n");
|
1084
|
+
printf(
|
1085
|
+
" e.g. nifti_tool -check_nim -infiles dset0.nii dset1.nii\n"
|
1086
|
+
" e.g. nifti_tool -check_nim -infiles *.nii *.hdr\n"
|
1087
|
+
"\n");
|
1088
|
+
printf(
|
1089
|
+
" ------------------------------\n");
|
1090
|
+
|
1091
|
+
printf(
|
1092
|
+
"\n"
|
1093
|
+
" options for create action:\n"
|
1094
|
+
"\n");
|
1095
|
+
printf(
|
1096
|
+
" -make_im : create a new dataset from nothing\n"
|
1097
|
+
"\n"
|
1098
|
+
" With this the user can create a new dataset of a basic style,\n"
|
1099
|
+
" which can then be modified with other options. This will create\n"
|
1100
|
+
" zero-filled data of the appropriate size.\n"
|
1101
|
+
" \n");
|
1102
|
+
printf(
|
1103
|
+
" The default is a 1x1x1 image of shorts. These settings can be\n"
|
1104
|
+
" modified with the -new_dim option, to set the 8 dimension values,\n"
|
1105
|
+
" and the -new_datatype, to provide the integral type for the data.\n"
|
1106
|
+
"\n");
|
1107
|
+
printf(
|
1108
|
+
" See -new_dim, -new_datatype and -infiles for more information.\n"
|
1109
|
+
" \n"
|
1110
|
+
" Note that any -infiles dataset of the name MAKE_IM will also be\n"
|
1111
|
+
" created on the fly.\n"
|
1112
|
+
"\n");
|
1113
|
+
printf(
|
1114
|
+
" -new_dim D0 .. D7 : specify the dim array for the a new dataset.\n"
|
1115
|
+
"\n"
|
1116
|
+
" e.g. -new_dim 4 64 64 27 120 0 0 0\n"
|
1117
|
+
"\n"
|
1118
|
+
" This dimension list will apply to any dataset created via\n"
|
1119
|
+
" MAKE_IM or -make_im. All 8 values are required. Recall that\n"
|
1120
|
+
" D0 is the number of dimensions, and D1 through D7 are the sizes.\n"
|
1121
|
+
" \n");
|
1122
|
+
printf(
|
1123
|
+
" -new_datatype TYPE : specify the dim array for the a new dataset.\n"
|
1124
|
+
"\n"
|
1125
|
+
" e.g. -new_datatype 16\n"
|
1126
|
+
" default: -new_datatype 4 (short)\n"
|
1127
|
+
"\n"
|
1128
|
+
" This dimension list will apply to any dataset created via\n"
|
1129
|
+
" MAKE_IM or -make_im. TYPE should be one of the NIFTI_TYPE_*\n"
|
1130
|
+
" numbers, from nifti1.h.\n"
|
1131
|
+
" \n");
|
1132
|
+
printf(
|
1133
|
+
" ------------------------------\n");
|
1134
|
+
printf(
|
1135
|
+
"\n"
|
1136
|
+
" options for copy actions:\n"
|
1137
|
+
"\n"
|
1138
|
+
" -copy_brick_list : copy a list of volumes to a new dataset\n"
|
1139
|
+
" -cbl : (a shorter, alternative form)\n"
|
1140
|
+
" -copy_im : (a shorter, alternative form)\n"
|
1141
|
+
"\n");
|
1142
|
+
printf(
|
1143
|
+
" This action allows the user to copy a list of volumes (over time)\n"
|
1144
|
+
" from one dataset to another. The listed volumes can be in any\n"
|
1145
|
+
" order and contain repeats, but are of course restricted to\n"
|
1146
|
+
" the set of values {1, 2, ..., nt-1}, from dimension 4.\n"
|
1147
|
+
"\n");
|
1148
|
+
printf(
|
1149
|
+
" This option is a flag. The index list is specified with the input\n"
|
1150
|
+
" dataset, contained in square brackets. Note that square brackets\n"
|
1151
|
+
" are special to most UNIX shells, so they should be contained\n"
|
1152
|
+
" within single quotes. Syntax of an index list:\n"
|
1153
|
+
"\n"
|
1154
|
+
" notes:\n"
|
1155
|
+
"\n");
|
1156
|
+
printf(
|
1157
|
+
" - indices start at zero\n"
|
1158
|
+
" - indices end at nt-1, which has the special symbol '$'\n"
|
1159
|
+
" - single indices should be separated with commas, ','\n"
|
1160
|
+
" e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'\n"
|
1161
|
+
" - ranges may be specified using '..' or '-' \n");
|
1162
|
+
printf(
|
1163
|
+
" e.g. -infiles dset0.nii'[2..95]'\n"
|
1164
|
+
" e.g. -infiles dset0.nii'[2..$]'\n"
|
1165
|
+
" - ranges may have step values, specified in ()\n"
|
1166
|
+
" example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}\n"
|
1167
|
+
" e.g. -infiles dset0.nii'[2..95(3)]'\n"
|
1168
|
+
"\n");
|
1169
|
+
printf(
|
1170
|
+
" This functionality applies only to 3 or 4-dimensional datasets.\n"
|
1171
|
+
"\n"
|
1172
|
+
" e.g. to copy a dataset:\n"
|
1173
|
+
" nifti_tool -copy_im -prefix new.nii -infiles dset0.nii\n"
|
1174
|
+
"\n");
|
1175
|
+
printf(
|
1176
|
+
" e.g. to copy sub-bricks 0 and 7:\n"
|
1177
|
+
" nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n"
|
1178
|
+
"\n"
|
1179
|
+
" e.g. to copy an entire dataset:\n"
|
1180
|
+
" nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'\n"
|
1181
|
+
"\n");
|
1182
|
+
printf(
|
1183
|
+
" e.g. to copy every other time point, skipping the first three:\n"
|
1184
|
+
" nifti_tool -cbl -prefix new_partial.nii \\\n"
|
1185
|
+
" -infiles dset0.nii'[3..$(2)]'\n"
|
1186
|
+
"\n"
|
1187
|
+
"\n"
|
1188
|
+
" -copy_collapsed_image ... : copy a list of volumes to a new dataset\n"
|
1189
|
+
" -cci I J K T U V W : (a shorter, alternative form)\n"
|
1190
|
+
"\n");
|
1191
|
+
printf(
|
1192
|
+
" This action allows the user to copy a collapsed dataset, where\n"
|
1193
|
+
" some dimensions are collapsed to a given index. For instance, the\n"
|
1194
|
+
" X dimension could be collapsed to i=42, and the time dimensions\n"
|
1195
|
+
" could be collapsed to t=17. To collapse a dimension, set Di to\n"
|
1196
|
+
" the desired index, where i is in {0..ni-1}. Any dimension that\n"
|
1197
|
+
" should not be collapsed must be listed as -1.\n"
|
1198
|
+
"\n");
|
1199
|
+
printf(
|
1200
|
+
" Any number (of valid) dimensions can be collapsed, even down to a\n"
|
1201
|
+
" a single value, by specifying enough valid indices. The resulting\n"
|
1202
|
+
" dataset will then have a reduced number of non-trivial dimensions.\n"
|
1203
|
+
"\n"
|
1204
|
+
" Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.\n"
|
1205
|
+
" Note that this is a 4-dimensional dataset.\n"
|
1206
|
+
"\n");
|
1207
|
+
printf(
|
1208
|
+
" e.g. copy the time series for voxel i,j,k = 5,4,17\n"
|
1209
|
+
" nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n"
|
1210
|
+
"\n"
|
1211
|
+
" e.g. read the single volume at time point 26\n"
|
1212
|
+
" nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii\n"
|
1213
|
+
"\n");
|
1214
|
+
printf(
|
1215
|
+
" Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.\n"
|
1216
|
+
" Note that this is a 6-dimensional dataset.\n"
|
1217
|
+
"\n"
|
1218
|
+
" e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2\n"
|
1219
|
+
" (and add the command to the history)\n"
|
1220
|
+
" nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n"
|
1221
|
+
" -prefix new_5_0_17_2.nii\n"
|
1222
|
+
"\n");
|
1223
|
+
printf(
|
1224
|
+
" e.g. copy all data where i=3, j=19 and v=2\n"
|
1225
|
+
" (I do not claim to know a good reason to do this)\n"
|
1226
|
+
" nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii\n"
|
1227
|
+
"\n"
|
1228
|
+
" See '-disp_ci' for more information (which displays/prints the\n"
|
1229
|
+
" data, instead of copying it to a new dataset).\n"
|
1230
|
+
"\n"
|
1231
|
+
" ------------------------------\n");
|
1232
|
+
|
1233
|
+
printf(
|
1234
|
+
"\n"
|
1235
|
+
" options for display actions:\n"
|
1236
|
+
"\n"
|
1237
|
+
" -disp_hdr : display nifti_1_header fields for datasets\n"
|
1238
|
+
"\n"
|
1239
|
+
" This flag means the user wishes to see some of the nifti_1_header\n"
|
1240
|
+
" fields in one or more nifti datasets. The user may want to specify\n"
|
1241
|
+
" mutliple '-field' options along with this. This option requires\n"
|
1242
|
+
" one or more files input, via '-infiles'.\n"
|
1243
|
+
"\n");
|
1244
|
+
printf(
|
1245
|
+
" If no '-field' option is present, all fields will be displayed.\n"
|
1246
|
+
"\n"
|
1247
|
+
" e.g. to display the contents of all fields:\n"
|
1248
|
+
" nifti_tool -disp_hdr -infiles dset0.nii\n"
|
1249
|
+
" nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n"
|
1250
|
+
"\n"
|
1251
|
+
" e.g. to display the contents of select fields:\n"
|
1252
|
+
" nifti_tool -disp_hdr -field dim -infiles dset0.nii\n"
|
1253
|
+
" nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii\n"
|
1254
|
+
"\n");
|
1255
|
+
printf(
|
1256
|
+
" -disp_nim : display nifti_image fields for datasets\n"
|
1257
|
+
"\n"
|
1258
|
+
" This flag option works the same way as the '-disp_hdr' option,\n"
|
1259
|
+
" except that the fields in question are from the nifti_image\n"
|
1260
|
+
" structure.\n"
|
1261
|
+
"\n");
|
1262
|
+
printf(
|
1263
|
+
" -disp_ana : display nifti_analyze75 fields for datasets\n"
|
1264
|
+
"\n"
|
1265
|
+
" This flag option works the same way as the '-disp_hdr' option,\n"
|
1266
|
+
" except that the fields in question are from the nifti_analyze75\n"
|
1267
|
+
" structure.\n"
|
1268
|
+
"\n");
|
1269
|
+
printf(
|
1270
|
+
" -disp_exts : display all AFNI-type extensions\n"
|
1271
|
+
"\n"
|
1272
|
+
" This flag option is used to display all nifti_1_extension data,\n"
|
1273
|
+
" for only those extensions of type AFNI (code = 4). The only\n"
|
1274
|
+
" other option used will be '-infiles'.\n"
|
1275
|
+
"\n");
|
1276
|
+
printf(
|
1277
|
+
" e.g. to display the extensions in datasets:\n"
|
1278
|
+
" nifti_tool -disp_exts -infiles dset0.nii\n"
|
1279
|
+
" nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n"
|
1280
|
+
"\n");
|
1281
|
+
printf(
|
1282
|
+
" -disp_ts I J K : display ASCII time series at i,j,k = I,J,K\n"
|
1283
|
+
"\n"
|
1284
|
+
" This option is used to display the time series data for the voxel\n"
|
1285
|
+
" at i,j,k indices I,J,K. The data is displayed in text, either all\n"
|
1286
|
+
" on one line (the default), or as one number per line (via the\n"
|
1287
|
+
" '-dci_lines' option).\n"
|
1288
|
+
"\n");
|
1289
|
+
printf(
|
1290
|
+
" Notes:\n"
|
1291
|
+
"\n"
|
1292
|
+
" o This function applies only to 4-dimensional datasets.\n"
|
1293
|
+
" o The '-quiet' option can be used to suppress the text header,\n"
|
1294
|
+
" leaving only the data.\n"
|
1295
|
+
" o This option is short for using '-disp_ci' (display collapsed\n"
|
1296
|
+
" image), restricted to 4-dimensional datasets. i.e. :\n"
|
1297
|
+
" -disp_ci I J K -1 -1 -1 -1\n"
|
1298
|
+
"\n");
|
1299
|
+
printf(
|
1300
|
+
" e.g. to display the time series at voxel 23, 0, 172:\n"
|
1301
|
+
" nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n"
|
1302
|
+
" nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii\n"
|
1303
|
+
" nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii\n"
|
1304
|
+
"\n");
|
1305
|
+
printf(
|
1306
|
+
" -disp_collapsed_image : display ASCII values for collapsed dataset\n"
|
1307
|
+
" -disp_ci I J K T U V W : (a shorter, alternative form)\n"
|
1308
|
+
"\n"
|
1309
|
+
" This option is used to display all of the data from a collapsed\n"
|
1310
|
+
" image, given the dimension list. The data is displayed in text,\n"
|
1311
|
+
" either all on one line (the default), or as one number per line\n"
|
1312
|
+
" (by using the '-dci_lines' flag).\n"
|
1313
|
+
"\n");
|
1314
|
+
printf(
|
1315
|
+
" The '-quiet' option can be used to suppress the text header.\n"
|
1316
|
+
"\n"
|
1317
|
+
" e.g. to display the time series at voxel 23, 0, 172:\n"
|
1318
|
+
" nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n"
|
1319
|
+
"\n"
|
1320
|
+
" e.g. to display z-slice 14, at time t=68:\n"
|
1321
|
+
" nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii\n"
|
1322
|
+
"\n"
|
1323
|
+
" See '-ccd' for more information, which copies such data to a new\n"
|
1324
|
+
" dataset, instead of printing it to the terminal window.\n"
|
1325
|
+
"\n"
|
1326
|
+
" ------------------------------\n");
|
1327
|
+
printf(
|
1328
|
+
"\n"
|
1329
|
+
" options for modification actions:\n"
|
1330
|
+
"\n"
|
1331
|
+
" -mod_hdr : modify nifti_1_header fields for datasets\n"
|
1332
|
+
"\n"
|
1333
|
+
" This action is used to modify some of the nifti_1_header fields in\n"
|
1334
|
+
" one or more datasets. The user must specify a list of fields to\n"
|
1335
|
+
" modify via one or more '-mod_field' options, which include field\n"
|
1336
|
+
" names, along with the new (set of) values.\n"
|
1337
|
+
"\n");
|
1338
|
+
printf(
|
1339
|
+
" The user can modify a dataset in place, or use '-prefix' to\n"
|
1340
|
+
" produce a new dataset, to which the changes have been applied.\n"
|
1341
|
+
" It is recommended to normally use the '-prefix' option, so as not\n"
|
1342
|
+
" to ruin a dataset.\n"
|
1343
|
+
"\n");
|
1344
|
+
printf(
|
1345
|
+
" Note that some fields have a length greater than 1, meaning that\n"
|
1346
|
+
" the field is an array of numbers, or a string of characters. In\n"
|
1347
|
+
" order to modify an array of numbers, the user must provide the\n"
|
1348
|
+
" correct number of values, and contain those values in quotes, so\n"
|
1349
|
+
" that they are seen as a single option.\n"
|
1350
|
+
"\n");
|
1351
|
+
printf(
|
1352
|
+
" To modify a string field, put the string in quotes.\n"
|
1353
|
+
"\n"
|
1354
|
+
" The '-mod_field' option takes a field_name and a list of values.\n"
|
1355
|
+
"\n"
|
1356
|
+
" e.g. to modify the contents of various fields:\n"
|
1357
|
+
"\n");
|
1358
|
+
printf(
|
1359
|
+
" nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1360
|
+
" -mod_field qoffset_x -17.325\n"
|
1361
|
+
" nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1362
|
+
" -mod_field dim '4 64 64 20 30 1 1 1 1'\n"
|
1363
|
+
" nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1364
|
+
" -mod_field descrip 'beer, brats and cheese, mmmmm...'\n"
|
1365
|
+
"\n");
|
1366
|
+
printf(
|
1367
|
+
" e.g. to modify the contents of multiple fields:\n"
|
1368
|
+
" nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
|
1369
|
+
" -mod_field qoffset_x -17.325 -mod_field slice_start 1\n"
|
1370
|
+
"\n"
|
1371
|
+
" e.g. to modify the contents of multiple files (must overwrite):\n"
|
1372
|
+
" nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \\\n"
|
1373
|
+
" -infiles dset0.nii dset1.nii\n"
|
1374
|
+
"\n");
|
1375
|
+
printf(
|
1376
|
+
" -mod_nim : modify nifti_image fields for datasets\n"
|
1377
|
+
"\n"
|
1378
|
+
" This action option is used the same way that '-mod_hdr' is used,\n"
|
1379
|
+
" except that the fields in question are from the nifti_image\n"
|
1380
|
+
" structure.\n"
|
1381
|
+
"\n");
|
1382
|
+
printf(
|
1383
|
+
" -strip_extras : remove extensions and descriptions from datasets\n"
|
1384
|
+
"\n"
|
1385
|
+
" This action is used to attempt to 'clean' a dataset of general\n"
|
1386
|
+
" text, in order to make it more anonymous. Extensions and the\n"
|
1387
|
+
" nifti_image descrip field are cleared by this action.\n"
|
1388
|
+
"\n");
|
1389
|
+
printf(
|
1390
|
+
" e.g. to strip all *.nii datasets in this directory:\n"
|
1391
|
+
" nifti_tool -strip -overwrite -infiles *.nii\n"
|
1392
|
+
"\n");
|
1393
|
+
printf(
|
1394
|
+
" -swap_as_nifti : swap the header according to nifti_1_header\n"
|
1395
|
+
"\n"
|
1396
|
+
" Perhaps a NIfTI header is mal-formed, and the user explicitly\n"
|
1397
|
+
" wants to swap it before performing other operations. This action\n"
|
1398
|
+
" will swap the field bytes under the assumption that the header is\n"
|
1399
|
+
" in the NIfTI format.\n"
|
1400
|
+
"\n");
|
1401
|
+
printf(
|
1402
|
+
" ** The recommended course of action is to make a copy of the\n"
|
1403
|
+
" dataset and overwrite the header via -overwrite. If the header\n"
|
1404
|
+
" needs such an operation, it is likely that the data would not\n"
|
1405
|
+
" otherwise be read in correctly.\n"
|
1406
|
+
"\n");
|
1407
|
+
printf(
|
1408
|
+
" -swap_as_analyze : swap the header according to nifti_analyze75\n"
|
1409
|
+
"\n"
|
1410
|
+
" Perhaps an ANALYZE header is mal-formed, and the user explicitly\n"
|
1411
|
+
" wants to swap it before performing other operations. This action\n"
|
1412
|
+
" will swap the field bytes under the assumption that the header is\n"
|
1413
|
+
" in the ANALYZE 7.5 format.\n"
|
1414
|
+
"\n");
|
1415
|
+
printf(
|
1416
|
+
" ** The recommended course of action is to make a copy of the\n"
|
1417
|
+
" dataset and overwrite the header via -overwrite. If the header\n"
|
1418
|
+
" needs such an operation, it is likely that the data would not\n"
|
1419
|
+
" otherwise be read in correctly.\n"
|
1420
|
+
"\n");
|
1421
|
+
printf(
|
1422
|
+
" -swap_as_old : swap the header using the old method\n"
|
1423
|
+
"\n"
|
1424
|
+
" As of library version 1.35 (3 Aug, 2008), nifticlib now swaps all\n"
|
1425
|
+
" fields of a NIfTI dataset (including UNUSED ones), and it swaps\n"
|
1426
|
+
" ANALYZE datasets according to the nifti_analyze75 structure.\n"
|
1427
|
+
" This is a significant different in the case of ANALYZE datasets.\n"
|
1428
|
+
"\n");
|
1429
|
+
printf(
|
1430
|
+
" The -swap_as_old option was added to compare the results of the\n"
|
1431
|
+
" swapping methods, or to undo one swapping method and replace it\n"
|
1432
|
+
" with another (such as to undo the old method and apply the new).\n"
|
1433
|
+
"\n");
|
1434
|
+
printf(" ------------------------------\n");
|
1435
|
+
printf(
|
1436
|
+
"\n"
|
1437
|
+
" options for adding/removing extensions:\n"
|
1438
|
+
"\n"
|
1439
|
+
" -add_afni_ext EXT : add an AFNI extension to the dataset\n"
|
1440
|
+
"\n"
|
1441
|
+
" This option is used to add AFNI-type extensions to one or more\n"
|
1442
|
+
" datasets. This option may be used more than once to add more than\n"
|
1443
|
+
" one extension.\n"
|
1444
|
+
"\n"
|
1445
|
+
" If EXT is of the form 'file:FILENAME', then the extension will\n"
|
1446
|
+
" be read from the file, FILENAME.\n"
|
1447
|
+
"\n");
|
1448
|
+
printf(
|
1449
|
+
" The '-prefix' option is recommended, to create a new dataset.\n"
|
1450
|
+
" In such a case, only a single file may be taken as input. Using\n"
|
1451
|
+
" '-overwrite' allows the user to overwrite the current file, or\n"
|
1452
|
+
" to add the extension(s) to multiple files, overwriting them.\n"
|
1453
|
+
"\n");
|
1454
|
+
printf(
|
1455
|
+
" e.g. to add a generic AFNI extension:\n"
|
1456
|
+
" nifti_tool -add_afni_ext 'wow, my first extension' -prefix dnew \\\n"
|
1457
|
+
" -infiles dset0.nii\n"
|
1458
|
+
"\n"
|
1459
|
+
" e.g. to add multiple AFNI extensions:\n"
|
1460
|
+
" nifti_tool -add_afni_ext 'wow, my first extension :)' \\\n"
|
1461
|
+
" -add_afni_ext 'look, my second...' \\\n"
|
1462
|
+
" -prefix dnew -infiles dset0.nii\n"
|
1463
|
+
"\n");
|
1464
|
+
printf(
|
1465
|
+
" e.g. to add an extension, and overwrite the dataset:\n"
|
1466
|
+
" nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \\\n"
|
1467
|
+
" -infiles dset0.nii dset1.nii \n"
|
1468
|
+
"\n");
|
1469
|
+
printf(
|
1470
|
+
" -add_comment_ext EXT : add a COMMENT extension to the dataset\n"
|
1471
|
+
"\n"
|
1472
|
+
" This option is used to add COMMENT-type extensions to one or more\n"
|
1473
|
+
" datasets. This option may be used more than once to add more than\n"
|
1474
|
+
" one extension. This option may also be used with '-add_afni_ext'.\n"
|
1475
|
+
"\n"
|
1476
|
+
" If EXT is of the form 'file:FILENAME', then the extension will\n"
|
1477
|
+
" be read from the file, FILENAME.\n"
|
1478
|
+
"\n");
|
1479
|
+
printf(
|
1480
|
+
" The '-prefix' option is recommended, to create a new dataset.\n"
|
1481
|
+
" In such a case, only a single file may be taken as input. Using\n"
|
1482
|
+
" '-overwrite' allows the user to overwrite the current file, or\n"
|
1483
|
+
" to add the extension(s) to multiple files, overwriting them.\n"
|
1484
|
+
"\n");
|
1485
|
+
printf(
|
1486
|
+
" e.g. to add a comment about the dataset:\n"
|
1487
|
+
" nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n"
|
1488
|
+
" -prefix dnew \\\n"
|
1489
|
+
" -infiles dset0.nii\n"
|
1490
|
+
"\n");
|
1491
|
+
printf(
|
1492
|
+
" e.g. to add multiple extensions:\n"
|
1493
|
+
" nifti_tool -add_comment 'add a comment extension' \\\n"
|
1494
|
+
" -add_afni_ext 'and an AFNI XML style extension' \\\n"
|
1495
|
+
" -add_comment 'dataset copied from dset0.nii' \\\n"
|
1496
|
+
" -prefix dnew -infiles dset0.nii\n"
|
1497
|
+
"\n");
|
1498
|
+
printf(
|
1499
|
+
" -rm_ext INDEX : remove the extension given by INDEX\n"
|
1500
|
+
"\n"
|
1501
|
+
" This option is used to remove any single extension from the\n"
|
1502
|
+
" dataset. Multiple extensions require multiple options.\n"
|
1503
|
+
"\n"
|
1504
|
+
" notes - extension indices begin with 0 (zero)\n"
|
1505
|
+
" - to view the current extensions, see '-disp_exts'\n"
|
1506
|
+
" - all exensions can be removed using ALL or -1 for INDEX\n"
|
1507
|
+
"\n");
|
1508
|
+
printf(
|
1509
|
+
" e.g. to remove the extension #0:\n"
|
1510
|
+
" nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii\n"
|
1511
|
+
"\n"
|
1512
|
+
" e.g. to remove ALL extensions:\n"
|
1513
|
+
" nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n"
|
1514
|
+
" nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii\n"
|
1515
|
+
"\n");
|
1516
|
+
printf(
|
1517
|
+
" e.g. to remove the extensions #2, #3 and #5:\n"
|
1518
|
+
" nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n"
|
1519
|
+
" -infiles dset0.nii\n"
|
1520
|
+
"\n"
|
1521
|
+
" ------------------------------\n");
|
1522
|
+
|
1523
|
+
printf(
|
1524
|
+
"\n"
|
1525
|
+
" options for showing differences:\n"
|
1526
|
+
"\n"
|
1527
|
+
" -diff_hdr : display header field diffs between two datasets\n"
|
1528
|
+
"\n"
|
1529
|
+
" This option is used to find differences between two datasets.\n"
|
1530
|
+
" If any fields are different, the contents of those fields is\n"
|
1531
|
+
" displayed (unless the '-quiet' option is used).\n"
|
1532
|
+
"\n");
|
1533
|
+
printf(
|
1534
|
+
" A list of fields can be specified by using multiple '-field'\n"
|
1535
|
+
" options. If no '-field' option is given, all fields will be\n"
|
1536
|
+
" checked.\n"
|
1537
|
+
"\n"
|
1538
|
+
" Exactly two dataset names must be provided via '-infiles'.\n"
|
1539
|
+
"\n"
|
1540
|
+
" e.g. to display all nifti_1_header field differences:\n"
|
1541
|
+
" nifti_tool -diff_hdr -infiles dset0.nii dset1.nii\n"
|
1542
|
+
"\n");
|
1543
|
+
printf(
|
1544
|
+
" e.g. to display selected nifti_1_header field differences:\n"
|
1545
|
+
" nifti_tool -diff_hdr -field dim -field intent_code \\\n"
|
1546
|
+
" -infiles dset0.nii dset1.nii \n"
|
1547
|
+
"\n"
|
1548
|
+
" -diff_nim : display nifti_image field diffs between datasets\n"
|
1549
|
+
"\n"
|
1550
|
+
" This option works the same as '-diff_hdr', except that the fields\n"
|
1551
|
+
" in question are from the nifti_image structure.\n"
|
1552
|
+
"\n"
|
1553
|
+
" ------------------------------\n");
|
1554
|
+
|
1555
|
+
printf(
|
1556
|
+
"\n"
|
1557
|
+
" miscellaneous options:\n"
|
1558
|
+
"\n"
|
1559
|
+
" -debug LEVEL : set the debugging level\n"
|
1560
|
+
"\n"
|
1561
|
+
" Level 0 will attempt to operate with no screen output, but errors.\n"
|
1562
|
+
" Level 1 is the default.\n"
|
1563
|
+
" Levels 2 and 3 give progressively more infomation.\n"
|
1564
|
+
"\n"
|
1565
|
+
" e.g. -debug 2\n"
|
1566
|
+
"\n");
|
1567
|
+
printf(
|
1568
|
+
" -field FIELDNAME : provide a field to work with\n"
|
1569
|
+
"\n"
|
1570
|
+
" This option is used to provide a field to display, modify or\n"
|
1571
|
+
" compare. This option can be used along with one of the action\n"
|
1572
|
+
" options presented above.\n"
|
1573
|
+
"\n"
|
1574
|
+
" See '-disp_hdr', above, for complete examples.\n"
|
1575
|
+
"\n"
|
1576
|
+
" e.g. nifti_tool -field descrip\n"
|
1577
|
+
" e.g. nifti_tool -field descrip -field dim\n"
|
1578
|
+
"\n");
|
1579
|
+
printf(
|
1580
|
+
" -infiles file0... : provide a list of files to work with\n"
|
1581
|
+
"\n"
|
1582
|
+
" This parameter is required for any of the actions, in order to\n"
|
1583
|
+
" provide a list of files to process. If input filenames do not\n"
|
1584
|
+
" have an extension, the directory we be searched for any\n"
|
1585
|
+
" appropriate files (such as .nii or .hdr).\n"
|
1586
|
+
"\n");
|
1587
|
+
printf(
|
1588
|
+
" Note: if the filename has the form MAKE_IM, then a new dataset\n"
|
1589
|
+
" will be created, without the need for file input.\n"
|
1590
|
+
"\n");
|
1591
|
+
printf(
|
1592
|
+
" See '-mod_hdr', above, for complete examples.\n"
|
1593
|
+
"\n"
|
1594
|
+
" e.g. nifti_tool -infiles file0.nii\n"
|
1595
|
+
" e.g. nifti_tool -infiles file1.nii file2 file3.hdr\n"
|
1596
|
+
"\n");
|
1597
|
+
printf(
|
1598
|
+
" -mod_field NAME 'VALUE_LIST' : provide new values for a field\n"
|
1599
|
+
"\n"
|
1600
|
+
" This parameter is required for any the modification actions.\n"
|
1601
|
+
" If the user wants to modify any fields of a dataset, this is\n"
|
1602
|
+
" where the fields and values are specified.\n"
|
1603
|
+
"\n");
|
1604
|
+
printf(
|
1605
|
+
" NAME is a field name (in either the nifti_1_header structure or\n"
|
1606
|
+
" the nifti_image structure). If the action option is '-mod_hdr',\n"
|
1607
|
+
" then NAME must be the name of a nifti_1_header field. If the\n"
|
1608
|
+
" action is '-mod_nim', NAME must be from a nifti_image structure.\n"
|
1609
|
+
"\n");
|
1610
|
+
printf(
|
1611
|
+
" VALUE_LIST must be one or more values, as many as are required\n"
|
1612
|
+
" for the field, contained in quotes if more than one is provided.\n"
|
1613
|
+
"\n"
|
1614
|
+
" Use 'nifti_tool -help_hdr' to get a list of nifti_1_header fields\n"
|
1615
|
+
" Use 'nifti_tool -help_nim' to get a list of nifti_image fields\n"
|
1616
|
+
"\n"
|
1617
|
+
" See '-mod_hdr', above, for complete examples.\n"
|
1618
|
+
"\n");
|
1619
|
+
printf(
|
1620
|
+
" e.g. modifying nifti_1_header fields:\n"
|
1621
|
+
" -mod_field descrip 'toga, toga, toga'\n"
|
1622
|
+
" -mod_field qoffset_x 19.4 -mod_field qoffset_z -11\n"
|
1623
|
+
" -mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'\n"
|
1624
|
+
"\n");
|
1625
|
+
printf(
|
1626
|
+
" -keep_hist : add the command as COMMENT (to the 'history')\n"
|
1627
|
+
"\n"
|
1628
|
+
" When this option is used, the current command will be added\n"
|
1629
|
+
" as a NIFTI_ECODE_COMMENT type extension. This provides the\n"
|
1630
|
+
" ability to keep a history of commands affecting a dataset.\n"
|
1631
|
+
"\n"
|
1632
|
+
" e.g. -keep_hist\n"
|
1633
|
+
"\n");
|
1634
|
+
printf(
|
1635
|
+
" -overwrite : any modifications will be made to input files\n"
|
1636
|
+
"\n"
|
1637
|
+
" This option is used so that all field modifications, including\n"
|
1638
|
+
" extension additions or deletions, will be made to the files that\n"
|
1639
|
+
" are input.\n"
|
1640
|
+
"\n");
|
1641
|
+
printf(
|
1642
|
+
" In general, the user is recommended to use the '-prefix' option\n"
|
1643
|
+
" to create new files. But if overwriting the contents of the\n"
|
1644
|
+
" input files is prefered, this is how to do it.\n"
|
1645
|
+
"\n"
|
1646
|
+
" See '-mod_hdr' or '-add_afni_ext', above, for complete examples.\n"
|
1647
|
+
"\n"
|
1648
|
+
" e.g. -overwrite\n"
|
1649
|
+
"\n");
|
1650
|
+
printf(
|
1651
|
+
" -prefix : specify an output file to write change into\n"
|
1652
|
+
"\n"
|
1653
|
+
" This option is used to specify an output file to write, after\n"
|
1654
|
+
" modifications have been made. If modifications are being made,\n"
|
1655
|
+
" then either '-prefix' or '-overwrite' is required.\n"
|
1656
|
+
"\n"
|
1657
|
+
" If no extension is given, the output extension will be '.nii'.\n"
|
1658
|
+
"\n");
|
1659
|
+
printf(
|
1660
|
+
" e.g. -prefix new_dset\n"
|
1661
|
+
" e.g. -prefix new_dset.nii\n"
|
1662
|
+
" e.g. -prefix new_dset.hdr\n"
|
1663
|
+
"\n"
|
1664
|
+
" -quiet : report only errors or requested information\n"
|
1665
|
+
"\n"
|
1666
|
+
" This option is equivalent to '-debug 0'.\n"
|
1667
|
+
"\n"
|
1668
|
+
" ------------------------------\n");
|
1669
|
+
|
1670
|
+
printf(
|
1671
|
+
"\n"
|
1672
|
+
" basic help options:\n"
|
1673
|
+
"\n"
|
1674
|
+
" -help : show this help\n"
|
1675
|
+
"\n"
|
1676
|
+
" e.g. nifti_tool -help\n"
|
1677
|
+
"\n"
|
1678
|
+
" -help_hdr : show nifti_1_header field info\n"
|
1679
|
+
"\n"
|
1680
|
+
" e.g. nifti_tool -help_hdr\n"
|
1681
|
+
"\n"
|
1682
|
+
" -help_nim : show nifti_image field info\n"
|
1683
|
+
"\n"
|
1684
|
+
" e.g. nifti_tool -help_nim\n"
|
1685
|
+
"\n"
|
1686
|
+
" -help_ana : show nifti_analyze75 field info\n"
|
1687
|
+
"\n"
|
1688
|
+
" e.g. nifti_tool -help_ana\n"
|
1689
|
+
);
|
1690
|
+
|
1691
|
+
printf(
|
1692
|
+
"\n"
|
1693
|
+
" -help_datatypes [TYPE] : display datatype table\n"
|
1694
|
+
"\n"
|
1695
|
+
" e.g. nifti_tool -help_datatypes\n"
|
1696
|
+
" e.g. nifti_tool -help_datatypes N\n"
|
1697
|
+
"\n"
|
1698
|
+
" This displays the contents of the nifti_type_list table.\n"
|
1699
|
+
" An additional 'D' or 'N' parameter will restrict the type\n"
|
1700
|
+
" name to 'DT_' or 'NIFTI_TYPE_' names, 'T' will test.\n");
|
1701
|
+
|
1702
|
+
printf(
|
1703
|
+
"\n"
|
1704
|
+
" -ver : show the program version number\n"
|
1705
|
+
"\n"
|
1706
|
+
" e.g. nifti_tool -ver\n"
|
1707
|
+
"\n"
|
1708
|
+
" -hist : show the program modification history\n"
|
1709
|
+
"\n"
|
1710
|
+
" e.g. nifti_tool -hist\n"
|
1711
|
+
"\n");
|
1712
|
+
printf(
|
1713
|
+
" -nifti_ver : show the nifti library version number\n"
|
1714
|
+
"\n"
|
1715
|
+
" e.g. nifti_tool -nifti_ver\n"
|
1716
|
+
"\n"
|
1717
|
+
" -nifti_hist : show the nifti library modification history\n"
|
1718
|
+
"\n"
|
1719
|
+
" e.g. nifti_tool -nifti_hist\n"
|
1720
|
+
"\n"
|
1721
|
+
" -with_zlib : print whether library was compiled with zlib\n"
|
1722
|
+
"\n"
|
1723
|
+
" e.g. nifti_tool -with_zlib\n"
|
1724
|
+
"\n"
|
1725
|
+
" ------------------------------\n"
|
1726
|
+
"\n"
|
1727
|
+
" R. Reynolds\n"
|
1728
|
+
" compiled: %s\n"
|
1729
|
+
" %s\n\n",
|
1730
|
+
__DATE__, g_version );
|
1731
|
+
|
1732
|
+
return 1;
|
1733
|
+
}
|
1734
|
+
|
1735
|
+
|
1736
|
+
/*----------------------------------------------------------------------
|
1737
|
+
* display the contents of the struct and all lists
|
1738
|
+
*----------------------------------------------------------------------*/
|
1739
|
+
int disp_nt_opts(char * mesg, nt_opts * opts)
|
1740
|
+
{
|
1741
|
+
int c;
|
1742
|
+
|
1743
|
+
if( mesg ) fputs(mesg, stderr);
|
1744
|
+
if( ! opts )
|
1745
|
+
{
|
1746
|
+
fprintf(stderr,"** disp_nt_opts: missing opts\n");
|
1747
|
+
return -1;
|
1748
|
+
}
|
1749
|
+
|
1750
|
+
fprintf(stderr,"nt_opts @ %p\n"
|
1751
|
+
" check_hdr, check_nim = %d, %d\n"
|
1752
|
+
" diff_hdr, diff_nim = %d, %d\n"
|
1753
|
+
" disp_hdr, disp_nim = %d, %d\n"
|
1754
|
+
" disp_ana, disp_exts = %d, %d\n"
|
1755
|
+
" add_exts, rm_exts = %d, %d\n"
|
1756
|
+
" mod_hdr, mod_nim = %d, %d\n"
|
1757
|
+
" swap_hdr, swap_ana = %d, %d\n"
|
1758
|
+
" swap_old = %d\n"
|
1759
|
+
" cbl, cci = %d, %d\n"
|
1760
|
+
" dts, dci_lines = %d, %d\n"
|
1761
|
+
" make_im = %d\n",
|
1762
|
+
(void *)opts,
|
1763
|
+
opts->check_hdr, opts->check_nim,
|
1764
|
+
opts->diff_hdr, opts->diff_nim, opts->disp_hdr, opts->disp_nim,
|
1765
|
+
opts->disp_ana, opts->disp_exts, opts->add_exts, opts->rm_exts,
|
1766
|
+
opts->mod_hdr, opts->mod_nim,
|
1767
|
+
opts->swap_hdr, opts->swap_ana, opts->swap_old,
|
1768
|
+
opts->cbl, opts->cci,
|
1769
|
+
opts->dts, opts->dci_lines, opts->make_im );
|
1770
|
+
|
1771
|
+
fprintf(stderr," ci_dims[8] = ");
|
1772
|
+
disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1);
|
1773
|
+
fprintf(stderr," new_dim[8] = ");
|
1774
|
+
disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1);
|
1775
|
+
|
1776
|
+
fprintf(stderr,"\n"
|
1777
|
+
" new_datatype = %d\n"
|
1778
|
+
" debug, keep_hist = %d, %d\n"
|
1779
|
+
" overwrite = %d\n"
|
1780
|
+
" prefix = '%s'\n",
|
1781
|
+
opts->new_datatype, opts->debug, opts->keep_hist, opts->overwrite,
|
1782
|
+
opts->prefix ? opts->prefix : "(NULL)" );
|
1783
|
+
|
1784
|
+
fprintf(stderr," elist (length %d) :\n", opts->elist.len);
|
1785
|
+
for( c = 0; c < opts->elist.len; c++ )
|
1786
|
+
fprintf(stderr," %d : %s\n", c, opts->elist.list[c]);
|
1787
|
+
|
1788
|
+
fprintf(stderr," etypes (length %d) : ", opts->etypes.len);
|
1789
|
+
disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 0);
|
1790
|
+
fputc('\n',stderr);
|
1791
|
+
|
1792
|
+
fprintf(stderr," flist (length %d) :\n", opts->flist.len);
|
1793
|
+
for( c = 0; c < opts->flist.len; c++ )
|
1794
|
+
fprintf(stderr," %d : %s\n", c, opts->flist.list[c]);
|
1795
|
+
|
1796
|
+
fprintf(stderr," vlist (length %d) :\n", opts->vlist.len);
|
1797
|
+
for( c = 0; c < opts->vlist.len; c++ )
|
1798
|
+
fprintf(stderr," %d : %s\n", c, opts->vlist.list[c]);
|
1799
|
+
|
1800
|
+
fprintf(stderr," infiles (length %d) :\n", opts->infiles.len);
|
1801
|
+
for( c = 0; c < opts->infiles.len; c++ )
|
1802
|
+
fprintf(stderr," %d : %s\n", c, opts->infiles.list[c]);
|
1803
|
+
|
1804
|
+
fprintf(stderr," command len : %d\n",(int)strlen(opts->command));
|
1805
|
+
|
1806
|
+
return 0;
|
1807
|
+
}
|
1808
|
+
|
1809
|
+
|
1810
|
+
/*----------------------------------------------------------------------
|
1811
|
+
* For each file, add all extensions with type NIFTI_ECODE_AFNI.
|
1812
|
+
* Though it should not matter, copy the trailing null characters.
|
1813
|
+
*----------------------------------------------------------------------*/
|
1814
|
+
int act_add_exts( nt_opts * opts )
|
1815
|
+
{
|
1816
|
+
nifti_image * nim;
|
1817
|
+
char * ext, * edata = NULL;
|
1818
|
+
int fc, ec, elen;
|
1819
|
+
|
1820
|
+
if( g_debug > 2 ){
|
1821
|
+
fprintf(stderr,"+d adding %d extensions to %d files...\n"
|
1822
|
+
" extension types are: ",
|
1823
|
+
opts->elist.len, opts->infiles.len);
|
1824
|
+
disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 1);
|
1825
|
+
}
|
1826
|
+
|
1827
|
+
if( opts->prefix && opts->infiles.len != 1 ){
|
1828
|
+
fprintf(stderr,"** error: we have a prefix but %d files\n",
|
1829
|
+
opts->infiles.len);
|
1830
|
+
return 1;
|
1831
|
+
}
|
1832
|
+
|
1833
|
+
if( opts->elist.len <= 0 ) return 0;
|
1834
|
+
|
1835
|
+
for( fc = 0; fc < opts->infiles.len; fc++ )
|
1836
|
+
{
|
1837
|
+
nim = nt_image_read( opts, opts->infiles.list[fc], 1 );
|
1838
|
+
if( !nim ) return 1; /* errors come from the library */
|
1839
|
+
|
1840
|
+
for( ec = 0; ec < opts->elist.len; ec++ ){
|
1841
|
+
ext = opts->elist.list[ec];
|
1842
|
+
elen = strlen(ext);
|
1843
|
+
if( !strncmp(ext,"file:",5) ){
|
1844
|
+
edata = read_file_text(ext+5, &elen);
|
1845
|
+
if( !edata || elen <= 0 ) {
|
1846
|
+
fprintf(stderr,"** failed to read extension data from '%s'\n",
|
1847
|
+
ext+5);
|
1848
|
+
continue;
|
1849
|
+
}
|
1850
|
+
ext = edata;
|
1851
|
+
}
|
1852
|
+
|
1853
|
+
if( nifti_add_extension(nim, ext, elen, opts->etypes.list[ec]) ){
|
1854
|
+
nifti_image_free(nim);
|
1855
|
+
return 1;
|
1856
|
+
}
|
1857
|
+
|
1858
|
+
/* if extension came from file, free the data */
|
1859
|
+
if( edata ){ free(edata); edata = NULL; }
|
1860
|
+
}
|
1861
|
+
|
1862
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
1863
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
1864
|
+
fprintf(stderr,"** failed to add command to image as extension\n");
|
1865
|
+
|
1866
|
+
if( opts->prefix &&
|
1867
|
+
nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) )
|
1868
|
+
{
|
1869
|
+
nifti_image_free(nim);
|
1870
|
+
return 1;
|
1871
|
+
}
|
1872
|
+
|
1873
|
+
if( g_debug > 1 )
|
1874
|
+
fprintf(stderr,"+d writing %s with %d new extension(s)\n",
|
1875
|
+
opts->infiles.list[fc], opts->elist.len);
|
1876
|
+
|
1877
|
+
nifti_image_write(nim);
|
1878
|
+
nifti_image_free(nim);
|
1879
|
+
}
|
1880
|
+
|
1881
|
+
if( g_debug > 0 )
|
1882
|
+
fprintf(stderr,"+d added %d extension(s) to %d files\n",
|
1883
|
+
opts->elist.len, opts->infiles.len);
|
1884
|
+
|
1885
|
+
return 0;
|
1886
|
+
}
|
1887
|
+
|
1888
|
+
/*----------------------------------------------------------------------
|
1889
|
+
* Return the allocated file contents.
|
1890
|
+
*----------------------------------------------------------------------*/
|
1891
|
+
static char * read_file_text(char * filename, int * length)
|
1892
|
+
{
|
1893
|
+
FILE * fp;
|
1894
|
+
char * text;
|
1895
|
+
int len, bytes;
|
1896
|
+
|
1897
|
+
if( !filename || !length ) {
|
1898
|
+
fprintf(stderr,"** bad params to read_file_text\n");
|
1899
|
+
return NULL;
|
1900
|
+
}
|
1901
|
+
|
1902
|
+
len = nifti_get_filesize(filename);
|
1903
|
+
if( len <= 0 ) {
|
1904
|
+
fprintf(stderr,"** RFT: file '%s' appears empty\n", filename);
|
1905
|
+
return NULL;
|
1906
|
+
}
|
1907
|
+
|
1908
|
+
fp = fopen(filename, "r");
|
1909
|
+
if( !fp ) {
|
1910
|
+
fprintf(stderr,"** RFT: failed to open '%s' for reading\n", filename);
|
1911
|
+
return NULL;
|
1912
|
+
}
|
1913
|
+
|
1914
|
+
/* allocate the bytes, and fill them with the file contents */
|
1915
|
+
|
1916
|
+
text = (char *)malloc(len * sizeof(char));
|
1917
|
+
if( !text ) {
|
1918
|
+
fprintf(stderr,"** RFT: failed to allocate %d bytes\n", len);
|
1919
|
+
fclose(fp);
|
1920
|
+
return NULL;
|
1921
|
+
}
|
1922
|
+
|
1923
|
+
bytes = fread(text, sizeof(char), len, fp);
|
1924
|
+
fclose(fp); /* in any case */
|
1925
|
+
|
1926
|
+
if( bytes != len ) {
|
1927
|
+
fprintf(stderr,"** RFT: read only %d of %d bytes from %s\n",
|
1928
|
+
bytes, len, filename);
|
1929
|
+
free(text);
|
1930
|
+
return NULL;
|
1931
|
+
}
|
1932
|
+
|
1933
|
+
/* success */
|
1934
|
+
|
1935
|
+
if( g_debug > 1 ) {
|
1936
|
+
fprintf(stderr,"++ found extension of length %d in file %s\n",
|
1937
|
+
len, filename);
|
1938
|
+
if( g_debug > 2 )
|
1939
|
+
fprintf(stderr,"++ text is:\n%s\n", text);
|
1940
|
+
}
|
1941
|
+
|
1942
|
+
*length = len;
|
1943
|
+
|
1944
|
+
return text;
|
1945
|
+
}
|
1946
|
+
|
1947
|
+
/*----------------------------------------------------------------------
|
1948
|
+
* For each file, strip the extra fields.
|
1949
|
+
*
|
1950
|
+
* Clear extensions and descrip field. No other generic strings will get
|
1951
|
+
* passed to nifti_1_header struct.
|
1952
|
+
*
|
1953
|
+
* - this may make the datasets more anonymous
|
1954
|
+
* - no history is appended here
|
1955
|
+
*----------------------------------------------------------------------*/
|
1956
|
+
int act_strip( nt_opts * opts )
|
1957
|
+
{
|
1958
|
+
nifti_image * nim;
|
1959
|
+
int fc;
|
1960
|
+
|
1961
|
+
if( g_debug > 2 )
|
1962
|
+
fprintf(stderr,"+d stripping extras from %d files\n", opts->infiles.len);
|
1963
|
+
|
1964
|
+
if( opts->prefix && opts->infiles.len != 1 ){
|
1965
|
+
fprintf(stderr,"** error: we have a prefix but %d files\n",
|
1966
|
+
opts->infiles.len);
|
1967
|
+
return 1;
|
1968
|
+
}
|
1969
|
+
|
1970
|
+
for( fc = 0; fc < opts->infiles.len; fc++ )
|
1971
|
+
{
|
1972
|
+
nim = nt_image_read( opts, opts->infiles.list[fc], 1 );
|
1973
|
+
if( !nim ) return 1; /* errors come from the library */
|
1974
|
+
|
1975
|
+
/* now remove the extensions */
|
1976
|
+
nifti_free_extensions(nim);
|
1977
|
+
memset(nim->descrip, 0, 80);
|
1978
|
+
|
1979
|
+
if( opts->prefix &&
|
1980
|
+
nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){
|
1981
|
+
nifti_image_free(nim);
|
1982
|
+
return 1;
|
1983
|
+
}
|
1984
|
+
|
1985
|
+
if( g_debug > 1 )
|
1986
|
+
fprintf(stderr,"+d writing %s without extensions or 'descrip'\n",
|
1987
|
+
nim->fname);
|
1988
|
+
|
1989
|
+
nifti_image_write(nim);
|
1990
|
+
|
1991
|
+
if( g_debug > 3 ) nifti_image_infodump(nim);
|
1992
|
+
nifti_image_free(nim);
|
1993
|
+
}
|
1994
|
+
|
1995
|
+
if( g_debug > 0 )
|
1996
|
+
fprintf(stderr,"+d stripped extras from %d files\n", opts->infiles.len);
|
1997
|
+
|
1998
|
+
return 0;
|
1999
|
+
}
|
2000
|
+
|
2001
|
+
|
2002
|
+
/*----------------------------------------------------------------------
|
2003
|
+
* For each file, remove the given extension for the given indices.
|
2004
|
+
*
|
2005
|
+
* Note that index = -1 means to remove them all.
|
2006
|
+
*----------------------------------------------------------------------*/
|
2007
|
+
int act_rm_ext( nt_opts * opts )
|
2008
|
+
{
|
2009
|
+
nifti_image * nim;
|
2010
|
+
int fc, ext_ind, num_ext;
|
2011
|
+
|
2012
|
+
if( g_debug > 2 )
|
2013
|
+
fprintf(stderr,"+d removing %d extensions from %d files...\n",
|
2014
|
+
opts->elist.len, opts->infiles.len);
|
2015
|
+
|
2016
|
+
if( opts->elist.len <= 0 ) return 0;
|
2017
|
+
|
2018
|
+
if( opts->prefix && opts->infiles.len != 1 ){
|
2019
|
+
fprintf(stderr,"** error: we have a prefix but %d files\n",
|
2020
|
+
opts->infiles.len);
|
2021
|
+
return 1;
|
2022
|
+
}
|
2023
|
+
else if( opts->overwrite && opts->infiles.len != 1 &&
|
2024
|
+
strcmp(opts->elist.list[0], "-1") ) {
|
2025
|
+
fprintf(stderr,"** error: for multiple files, can only delete ALL\n");
|
2026
|
+
return 1;
|
2027
|
+
}
|
2028
|
+
|
2029
|
+
ext_ind = atoi(opts->elist.list[0]);
|
2030
|
+
if( ext_ind < -1 ){
|
2031
|
+
fprintf(stderr,"** bad extension index to remove: %d\n", ext_ind);
|
2032
|
+
return 1;
|
2033
|
+
}
|
2034
|
+
|
2035
|
+
if( g_debug > 1 ) fprintf(stderr,"+d removing extension index %d\n",ext_ind);
|
2036
|
+
|
2037
|
+
for( fc = 0; fc < opts->infiles.len; fc++ )
|
2038
|
+
{
|
2039
|
+
nim = nt_image_read( opts, opts->infiles.list[fc], 1 );
|
2040
|
+
if( !nim ) return 1; /* errors come from the library */
|
2041
|
+
|
2042
|
+
/* note the number of extensions for later */
|
2043
|
+
num_ext = nim->num_ext;
|
2044
|
+
|
2045
|
+
/* now remove the extensions */
|
2046
|
+
if( remove_ext_list(nim, opts->elist.list, opts->elist.len) )
|
2047
|
+
return 1;
|
2048
|
+
|
2049
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
2050
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
2051
|
+
fprintf(stderr,"** failed to add command to image as extension\n");
|
2052
|
+
|
2053
|
+
if( opts->prefix &&
|
2054
|
+
nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){
|
2055
|
+
nifti_image_free(nim);
|
2056
|
+
return 1;
|
2057
|
+
}
|
2058
|
+
|
2059
|
+
if( g_debug > 1 )
|
2060
|
+
fprintf(stderr,"+d writing %s with %d fewer extension(s)\n",
|
2061
|
+
nim->fname, ext_ind == -1 ? num_ext : opts->elist.len);
|
2062
|
+
|
2063
|
+
nifti_image_write(nim);
|
2064
|
+
nifti_image_free(nim);
|
2065
|
+
}
|
2066
|
+
|
2067
|
+
if( g_debug > 0 )
|
2068
|
+
fprintf(stderr,"+d removed %s extension(s) from %d files\n",
|
2069
|
+
ext_ind == -1 ? "ALL" : "1", opts->infiles.len);
|
2070
|
+
|
2071
|
+
return 0;
|
2072
|
+
}
|
2073
|
+
|
2074
|
+
|
2075
|
+
/*----------------------------------------------------------------------
|
2076
|
+
* remove extensions by index
|
2077
|
+
*
|
2078
|
+
* return: 0 on success, -1 on failure
|
2079
|
+
*----------------------------------------------------------------------*/
|
2080
|
+
int remove_ext_list( nifti_image * nim, char ** elist, int len )
|
2081
|
+
{
|
2082
|
+
int * marks;
|
2083
|
+
int c, ec, extval;
|
2084
|
+
|
2085
|
+
if( len > nim->num_ext ){
|
2086
|
+
fprintf(stderr, "** cannot remove %d exts from image '%s' with only %d\n",
|
2087
|
+
len, nim->fname, nim->num_ext);
|
2088
|
+
return -1;
|
2089
|
+
}
|
2090
|
+
|
2091
|
+
if( len <= 0 ){
|
2092
|
+
fprintf(stderr,"** REL: (%d) no extensions to remove?\n",len);
|
2093
|
+
return -1;
|
2094
|
+
}
|
2095
|
+
|
2096
|
+
extval = atoi(elist[0]); /* check the first value */
|
2097
|
+
|
2098
|
+
/* first special case, elist[0] == -1 */
|
2099
|
+
if( extval == -1 )
|
2100
|
+
{
|
2101
|
+
if( g_debug > 1 )
|
2102
|
+
fprintf(stderr,"+d removing ALL (%d) extensions from '%s'\n",
|
2103
|
+
nim->num_ext, nim->fname );
|
2104
|
+
nifti_free_extensions(nim);
|
2105
|
+
return 0;
|
2106
|
+
}
|
2107
|
+
|
2108
|
+
if( g_debug > 2 )
|
2109
|
+
fprintf(stderr,"+d removing %d exts from '%s'\n", len, nim->fname );
|
2110
|
+
|
2111
|
+
if( ! (marks = (int *)calloc(nim->num_ext, sizeof(int))) ) {
|
2112
|
+
fprintf(stderr,"** failed to alloc %d marks\n",nim->num_ext);
|
2113
|
+
return -1;
|
2114
|
+
}
|
2115
|
+
|
2116
|
+
/* mark all extensions for removal */
|
2117
|
+
for( ec = 0; ec < len; ec++ )
|
2118
|
+
{
|
2119
|
+
extval = atoi(elist[ec]);
|
2120
|
+
|
2121
|
+
if( extval < 0 || extval >= nim->num_ext ){
|
2122
|
+
fprintf(stderr,"** ext #%d (= %d) is out of range [0,%d] for %s\n",
|
2123
|
+
ec, extval, nim->num_ext-1, nim->fname);
|
2124
|
+
free(marks); return -1;
|
2125
|
+
}
|
2126
|
+
|
2127
|
+
if( marks[extval] ){
|
2128
|
+
fprintf(stderr,"** ext #%d (= %d) is a duplicate", ec, extval);
|
2129
|
+
free(marks); return -1;
|
2130
|
+
}
|
2131
|
+
|
2132
|
+
marks[extval]++;
|
2133
|
+
}
|
2134
|
+
|
2135
|
+
/* now remove them - count from top down to do lazy programming */
|
2136
|
+
for( ec = nim->num_ext-1; ec >= 0; ec-- )
|
2137
|
+
{
|
2138
|
+
if( !marks[ec] ) continue; /* do not delete this one */
|
2139
|
+
|
2140
|
+
if( g_debug > 2 )
|
2141
|
+
disp_nifti1_extension("+d removing ext: ",nim->ext_list+ec,-1);
|
2142
|
+
|
2143
|
+
/* delete this data, and shift the list down (yeah, inefficient) */
|
2144
|
+
if( nim->ext_list[ec].edata ) free( nim->ext_list[ec].edata );
|
2145
|
+
|
2146
|
+
/* move anything above down one */
|
2147
|
+
for( c = ec+1; c < nim->num_ext; c++ )
|
2148
|
+
nim->ext_list[c-1] = nim->ext_list[c];
|
2149
|
+
|
2150
|
+
nim->num_ext--;
|
2151
|
+
}
|
2152
|
+
|
2153
|
+
if( g_debug > 3 ) fprintf(stderr,"-d done removing extensions\n");
|
2154
|
+
|
2155
|
+
if( nim->num_ext == 0 ){ /* did we trash the only extension? */
|
2156
|
+
if( g_debug > 1 )
|
2157
|
+
fprintf(stderr,"-d removed ALL extensions from %s\n",nim->fname);
|
2158
|
+
free(nim->ext_list);
|
2159
|
+
nim->ext_list = NULL;
|
2160
|
+
}
|
2161
|
+
|
2162
|
+
return 0;
|
2163
|
+
}
|
2164
|
+
|
2165
|
+
|
2166
|
+
/*----------------------------------------------------------------------
|
2167
|
+
* check for diffs between all fields in opts->flist, or in the
|
2168
|
+
* entire nifti_1_header
|
2169
|
+
*
|
2170
|
+
* if quiet mode (debug == 0) return on first diff
|
2171
|
+
*
|
2172
|
+
* return: 1 if diffs exist, 0 otherwise
|
2173
|
+
*----------------------------------------------------------------------*/
|
2174
|
+
int act_diff_hdrs( nt_opts * opts )
|
2175
|
+
{
|
2176
|
+
nifti_1_header * nhdr0, * nhdr1;
|
2177
|
+
int diffs = 0;
|
2178
|
+
|
2179
|
+
if( opts->infiles.len != 2 ){
|
2180
|
+
fprintf(stderr,"** -diff_hdr requires 2 -infiles, have %d\n",
|
2181
|
+
opts->infiles.len);
|
2182
|
+
return 1;
|
2183
|
+
}
|
2184
|
+
|
2185
|
+
if( g_debug > 2 )
|
2186
|
+
fprintf(stderr,"-d nifti_1_header diff between %s and %s...\n",
|
2187
|
+
opts->infiles.list[0], opts->infiles.list[1]);
|
2188
|
+
|
2189
|
+
/* get the nifiti headers (but do not validate them) */
|
2190
|
+
|
2191
|
+
nhdr0 = nt_read_header(opts, opts->infiles.list[0], NULL, 0);
|
2192
|
+
if( ! nhdr0 ) return 1; /* errors have been printed */
|
2193
|
+
|
2194
|
+
nhdr1 = nt_read_header(opts, opts->infiles.list[1], NULL, 0);
|
2195
|
+
if( ! nhdr1 ){ free(nhdr0); return 1; }
|
2196
|
+
|
2197
|
+
if( g_debug > 1 )
|
2198
|
+
fprintf(stderr,"\n-d nifti_1_header diffs between '%s' and '%s'...\n",
|
2199
|
+
opts->infiles.list[0], opts->infiles.list[1]);
|
2200
|
+
|
2201
|
+
if( opts->flist.len <= 0 )
|
2202
|
+
diffs = diff_hdrs(nhdr0, nhdr1, g_debug > 0);
|
2203
|
+
else
|
2204
|
+
diffs = diff_hdrs_list(nhdr0, nhdr1, &opts->flist, g_debug > 0);
|
2205
|
+
|
2206
|
+
if( diffs == 0 && g_debug > 1 )
|
2207
|
+
fprintf(stderr,"+d no differences found\n");
|
2208
|
+
else if ( g_debug > 2 )
|
2209
|
+
fprintf(stderr,"+d %d differences found\n", diffs);
|
2210
|
+
|
2211
|
+
free(nhdr0);
|
2212
|
+
free(nhdr1);
|
2213
|
+
|
2214
|
+
return (diffs > 0);
|
2215
|
+
}
|
2216
|
+
|
2217
|
+
|
2218
|
+
/*----------------------------------------------------------------------
|
2219
|
+
* check for diffs between all fields in opts->flist, or in the
|
2220
|
+
* entire nifti_image
|
2221
|
+
*
|
2222
|
+
* if quiet mode (debug == 0) return on first diff
|
2223
|
+
*
|
2224
|
+
* return: 1 if diffs exist, 0 otherwise
|
2225
|
+
*----------------------------------------------------------------------*/
|
2226
|
+
int act_diff_nims( nt_opts * opts )
|
2227
|
+
{
|
2228
|
+
nifti_image * nim0, * nim1;
|
2229
|
+
int diffs = 0;
|
2230
|
+
|
2231
|
+
if( opts->infiles.len != 2 ){
|
2232
|
+
fprintf(stderr,"** -diff_nim requires 2 -infiles, have %d\n",
|
2233
|
+
opts->infiles.len);
|
2234
|
+
return 1;
|
2235
|
+
}
|
2236
|
+
|
2237
|
+
if( g_debug > 2 )
|
2238
|
+
fprintf(stderr,"-d nifti_image diff between %s and %s...\n",
|
2239
|
+
opts->infiles.list[0], opts->infiles.list[1]);
|
2240
|
+
|
2241
|
+
/* get the nifiti images */
|
2242
|
+
|
2243
|
+
nim0 = nt_image_read(opts, opts->infiles.list[0], 0);
|
2244
|
+
if( ! nim0 ) return 1; /* errors have been printed */
|
2245
|
+
|
2246
|
+
nim1 = nt_image_read(opts, opts->infiles.list[1], 0);
|
2247
|
+
if( ! nim1 ){ free(nim0); return 1; }
|
2248
|
+
|
2249
|
+
if( g_debug > 1 )
|
2250
|
+
fprintf(stderr,"\n-d nifti_image diffs between '%s' and '%s'...\n",
|
2251
|
+
opts->infiles.list[0], opts->infiles.list[1]);
|
2252
|
+
|
2253
|
+
if( opts->flist.len <= 0 )
|
2254
|
+
diffs = diff_nims(nim0, nim1, g_debug > 0);
|
2255
|
+
else
|
2256
|
+
diffs = diff_nims_list(nim0, nim1, &opts->flist, g_debug > 0);
|
2257
|
+
|
2258
|
+
if( diffs == 0 && g_debug > 1 )
|
2259
|
+
fprintf(stderr,"+d no differences found\n");
|
2260
|
+
else if ( g_debug > 2 )
|
2261
|
+
fprintf(stderr,"+d %d differences found\n", diffs);
|
2262
|
+
|
2263
|
+
nifti_image_free(nim0);
|
2264
|
+
nifti_image_free(nim1);
|
2265
|
+
|
2266
|
+
return (diffs > 0);
|
2267
|
+
}
|
2268
|
+
|
2269
|
+
|
2270
|
+
/*----------------------------------------------------------------------
|
2271
|
+
* for each file, read nifti1_header
|
2272
|
+
* if checking header, check it
|
2273
|
+
* if checking nifti_image, convert and check it
|
2274
|
+
*----------------------------------------------------------------------*/
|
2275
|
+
int act_check_hdrs( nt_opts * opts )
|
2276
|
+
{
|
2277
|
+
nifti_1_header * nhdr;
|
2278
|
+
nifti_image * nim;
|
2279
|
+
int filenum, rv;
|
2280
|
+
|
2281
|
+
if( g_debug > 2 )
|
2282
|
+
fprintf(stderr,"-d checking hdrs/nims for %d nifti datasets...\n",
|
2283
|
+
opts->infiles.len);
|
2284
|
+
|
2285
|
+
for( filenum = 0; filenum < opts->infiles.len; filenum++ )
|
2286
|
+
{
|
2287
|
+
/* do not validate the header structure */
|
2288
|
+
nhdr = nt_read_header(opts, opts->infiles.list[filenum], NULL, 0);
|
2289
|
+
if( !nhdr ) continue; /* errors are printed from library */
|
2290
|
+
|
2291
|
+
if( opts->check_hdr )
|
2292
|
+
{
|
2293
|
+
if( g_debug > 1 )
|
2294
|
+
fprintf(stdout,"\nchecking nifti_1_header for file '%s'\n",
|
2295
|
+
opts->infiles.list[filenum]);
|
2296
|
+
|
2297
|
+
rv = nifti_hdr_looks_good(nhdr);
|
2298
|
+
|
2299
|
+
if( rv && g_debug > 0 ) /* if quiet, no GOOD response */
|
2300
|
+
printf("header IS GOOD for file %s\n",opts->infiles.list[filenum]);
|
2301
|
+
else if( ! rv )
|
2302
|
+
printf("header FAILURE for file %s\n",opts->infiles.list[filenum]);
|
2303
|
+
}
|
2304
|
+
|
2305
|
+
if( opts->check_nim )
|
2306
|
+
{
|
2307
|
+
nim = nifti_convert_nhdr2nim(*nhdr, opts->infiles.list[filenum]);
|
2308
|
+
if( !nim ) continue; /* errors are printed from library */
|
2309
|
+
|
2310
|
+
if( g_debug > 1 )
|
2311
|
+
fprintf(stdout,"\nchecking nifti_image for file '%s'\n",
|
2312
|
+
opts->infiles.list[filenum]);
|
2313
|
+
|
2314
|
+
rv = nifti_nim_is_valid(nim, 1); /* complain about errors */
|
2315
|
+
|
2316
|
+
if( rv && g_debug > 0 ) /* if quiet, no GOOD response */
|
2317
|
+
printf("nifti_image IS GOOD for file %s\n",
|
2318
|
+
opts->infiles.list[filenum]);
|
2319
|
+
else if( ! rv )
|
2320
|
+
printf("nifti_image FAILURE for file %s\n",
|
2321
|
+
opts->infiles.list[filenum]);
|
2322
|
+
|
2323
|
+
nifti_image_free(nim);
|
2324
|
+
}
|
2325
|
+
|
2326
|
+
free(nhdr);
|
2327
|
+
}
|
2328
|
+
|
2329
|
+
return 0;
|
2330
|
+
}
|
2331
|
+
|
2332
|
+
|
2333
|
+
/*----------------------------------------------------------------------
|
2334
|
+
* display all extensions for each dataset
|
2335
|
+
*----------------------------------------------------------------------*/
|
2336
|
+
int act_disp_exts( nt_opts * opts )
|
2337
|
+
{
|
2338
|
+
nifti_image * nim;
|
2339
|
+
char mesg[32];
|
2340
|
+
int ec, fc;
|
2341
|
+
|
2342
|
+
if( g_debug > 2 )
|
2343
|
+
fprintf(stderr,"-d displaying all extensions for %d files...\n",
|
2344
|
+
opts->infiles.len);
|
2345
|
+
|
2346
|
+
for( fc = 0; fc < opts->infiles.len; fc++ )
|
2347
|
+
{
|
2348
|
+
nim = nt_image_read(opts, opts->infiles.list[fc], 0);
|
2349
|
+
if( !nim ) return 1; /* errors are printed from library */
|
2350
|
+
|
2351
|
+
if( g_debug > 0 )
|
2352
|
+
fprintf(stdout,"header file '%s', num_ext = %d\n",
|
2353
|
+
nim->fname, nim->num_ext);
|
2354
|
+
for( ec = 0; ec < nim->num_ext; ec++ )
|
2355
|
+
{
|
2356
|
+
sprintf(mesg, " ext #%d : ", ec);
|
2357
|
+
disp_nifti1_extension(mesg, nim->ext_list + ec, -1);
|
2358
|
+
}
|
2359
|
+
|
2360
|
+
nifti_image_free(nim);
|
2361
|
+
}
|
2362
|
+
|
2363
|
+
return 0;
|
2364
|
+
}
|
2365
|
+
|
2366
|
+
|
2367
|
+
/*----------------------------------------------------------------------
|
2368
|
+
* for each file, read nifti1_header and display all fields
|
2369
|
+
*----------------------------------------------------------------------*/
|
2370
|
+
int act_disp_hdrs( nt_opts * opts )
|
2371
|
+
{
|
2372
|
+
nifti_1_header * nhdr;
|
2373
|
+
field_s * fnhdr;
|
2374
|
+
char ** sptr;
|
2375
|
+
int nfields, filenum, fc;
|
2376
|
+
|
2377
|
+
/* set the number of fields to display */
|
2378
|
+
nfields = opts->flist.len > 0 ? opts->flist.len : NT_HDR_NUM_FIELDS;
|
2379
|
+
|
2380
|
+
if( g_debug > 2 )
|
2381
|
+
fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n",
|
2382
|
+
nfields, opts->infiles.len);
|
2383
|
+
|
2384
|
+
for( filenum = 0; filenum < opts->infiles.len; filenum++ )
|
2385
|
+
{
|
2386
|
+
/* do not validate the header structure */
|
2387
|
+
nhdr = nt_read_header(opts, opts->infiles.list[filenum], NULL, 0);
|
2388
|
+
if( !nhdr ) return 1; /* errors are printed from library */
|
2389
|
+
|
2390
|
+
if( g_debug > 0 )
|
2391
|
+
fprintf(stdout,"\nheader file '%s', num_fields = %d\n",
|
2392
|
+
opts->infiles.list[filenum], nfields);
|
2393
|
+
if( g_debug > 1 )
|
2394
|
+
fprintf(stderr,"-d header is: %s\n",
|
2395
|
+
nifti_hdr_looks_good(nhdr) ? "valid" : "invalid");
|
2396
|
+
|
2397
|
+
if( opts->flist.len <= 0 ) /* then display all fields */
|
2398
|
+
disp_field("\nall fields:\n", g_hdr_fields, nhdr, nfields, g_debug>0);
|
2399
|
+
else /* print only the requested fields... */
|
2400
|
+
{
|
2401
|
+
/* must locate each field before printing it */
|
2402
|
+
sptr = opts->flist.list;
|
2403
|
+
for( fc = 0; fc < opts->flist.len; fc++ )
|
2404
|
+
{
|
2405
|
+
fnhdr = get_hdr_field(*sptr, filenum == 0);
|
2406
|
+
if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0);
|
2407
|
+
sptr++;
|
2408
|
+
}
|
2409
|
+
}
|
2410
|
+
|
2411
|
+
free(nhdr);
|
2412
|
+
}
|
2413
|
+
|
2414
|
+
return 0;
|
2415
|
+
}
|
2416
|
+
|
2417
|
+
|
2418
|
+
/*----------------------------------------------------------------------
|
2419
|
+
* for each file, read nifti_analyze75 and display all fields
|
2420
|
+
*----------------------------------------------------------------------*/
|
2421
|
+
int act_disp_anas( nt_opts * opts )
|
2422
|
+
{
|
2423
|
+
nifti_analyze75 * nhdr;
|
2424
|
+
field_s * fnhdr;
|
2425
|
+
char ** sptr;
|
2426
|
+
int nfields, filenum, fc;
|
2427
|
+
|
2428
|
+
/* set the number of fields to display */
|
2429
|
+
nfields = opts->flist.len > 0 ? opts->flist.len : NT_ANA_NUM_FIELDS;
|
2430
|
+
|
2431
|
+
if( g_debug > 2 )
|
2432
|
+
fprintf(stderr,"-d displaying %d fields for %d ANALYZE datasets...\n",
|
2433
|
+
nfields, opts->infiles.len);
|
2434
|
+
|
2435
|
+
for( filenum = 0; filenum < opts->infiles.len; filenum++ )
|
2436
|
+
{
|
2437
|
+
/* do not validate the header structure */
|
2438
|
+
nhdr = (nifti_analyze75 *)nt_read_header(opts,
|
2439
|
+
opts->infiles.list[filenum], NULL, 0);
|
2440
|
+
if( !nhdr ) return 1; /* errors are printed from library */
|
2441
|
+
|
2442
|
+
if( g_debug > 0 )
|
2443
|
+
fprintf(stdout,"\nanalyze header file '%s', num_fields = %d\n",
|
2444
|
+
opts->infiles.list[filenum], nfields);
|
2445
|
+
if( g_debug > 1 )
|
2446
|
+
fprintf(stderr,"-d analyze header is: %s\n",
|
2447
|
+
nifti_hdr_looks_good((nifti_1_header *)nhdr) ?
|
2448
|
+
"valid" : "invalid");
|
2449
|
+
|
2450
|
+
if( opts->flist.len <= 0 ) /* then display all fields */
|
2451
|
+
disp_field("\nall fields:\n", g_ana_fields, nhdr, nfields, g_debug>0);
|
2452
|
+
else /* print only the requested fields... */
|
2453
|
+
{
|
2454
|
+
/* must locate each field before printing it */
|
2455
|
+
sptr = opts->flist.list;
|
2456
|
+
for( fc = 0; fc < opts->flist.len; fc++ )
|
2457
|
+
{
|
2458
|
+
fnhdr = get_hdr_field(*sptr, filenum == 0);
|
2459
|
+
if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0);
|
2460
|
+
sptr++;
|
2461
|
+
}
|
2462
|
+
}
|
2463
|
+
|
2464
|
+
free(nhdr);
|
2465
|
+
}
|
2466
|
+
|
2467
|
+
return 0;
|
2468
|
+
}
|
2469
|
+
|
2470
|
+
|
2471
|
+
/*----------------------------------------------------------------------
|
2472
|
+
* for each file, get nifti_image and display all fields
|
2473
|
+
*----------------------------------------------------------------------*/
|
2474
|
+
int act_disp_nims( nt_opts * opts )
|
2475
|
+
{
|
2476
|
+
nifti_image * nim;
|
2477
|
+
field_s * fnim;
|
2478
|
+
char ** sptr;
|
2479
|
+
int nfields, filenum, fc;
|
2480
|
+
|
2481
|
+
/* set the number of fields to display */
|
2482
|
+
nfields = opts->flist.len > 0 ? opts->flist.len : NT_NIM_NUM_FIELDS;
|
2483
|
+
|
2484
|
+
if( g_debug > 2 )
|
2485
|
+
fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n",
|
2486
|
+
nfields, opts->infiles.len);
|
2487
|
+
|
2488
|
+
for( filenum = 0; filenum < opts->infiles.len; filenum++ )
|
2489
|
+
{
|
2490
|
+
nim = nt_image_read(opts, opts->infiles.list[filenum], 0);
|
2491
|
+
if( !nim ) return 1; /* errors are printed from library */
|
2492
|
+
|
2493
|
+
if( g_debug > 0 )
|
2494
|
+
fprintf(stdout,"\nheader file '%s', num_fields = %d, fields:\n\n",
|
2495
|
+
nim->fname, nfields);
|
2496
|
+
|
2497
|
+
if( opts->flist.len <= 0 ) /* then display all fields */
|
2498
|
+
disp_field("all fields:\n", g_nim_fields, nim, nfields, g_debug > 0);
|
2499
|
+
else /* print only the requested fields... */
|
2500
|
+
{
|
2501
|
+
/* must locate each field before printing it */
|
2502
|
+
sptr = opts->flist.list;
|
2503
|
+
for( fc = 0; fc < opts->flist.len; fc++ )
|
2504
|
+
{
|
2505
|
+
fnim = get_nim_field(*sptr, filenum == 0);
|
2506
|
+
if( fnim ) disp_field(NULL, fnim, nim, 1, g_debug > 0 && fc == 0);
|
2507
|
+
sptr++;
|
2508
|
+
}
|
2509
|
+
}
|
2510
|
+
|
2511
|
+
nifti_image_free(nim);
|
2512
|
+
}
|
2513
|
+
|
2514
|
+
return 0;
|
2515
|
+
}
|
2516
|
+
|
2517
|
+
|
2518
|
+
/*----------------------------------------------------------------------
|
2519
|
+
* - read header
|
2520
|
+
* - modify header
|
2521
|
+
* - if -prefix duplicate file
|
2522
|
+
* - else if swapped, swap back
|
2523
|
+
* - overwrite file header (allows (danger-of) no evaluation of data)
|
2524
|
+
*----------------------------------------------------------------------*/
|
2525
|
+
int act_mod_hdrs( nt_opts * opts )
|
2526
|
+
{
|
2527
|
+
nifti_1_header * nhdr;
|
2528
|
+
nifti_image * nim; /* for reading/writing entire datasets */
|
2529
|
+
int filec, swap;
|
2530
|
+
char * fname, * dupname;
|
2531
|
+
char func[] = { "act_mod_hdrs" };
|
2532
|
+
|
2533
|
+
if( g_debug > 2 )
|
2534
|
+
fprintf(stderr,"-d modifying %d fields for %d nifti headers...\n",
|
2535
|
+
opts->flist.len, opts->infiles.len);
|
2536
|
+
if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0;
|
2537
|
+
|
2538
|
+
for( filec = 0; filec < opts->infiles.len; filec++ )
|
2539
|
+
{
|
2540
|
+
fname = opts->infiles.list[filec]; /* for convenience and mod file */
|
2541
|
+
|
2542
|
+
if( nifti_is_gzfile(fname) ){
|
2543
|
+
fprintf(stderr,"** sorry, cannot modify a gzipped file: %s\n", fname);
|
2544
|
+
continue;
|
2545
|
+
}
|
2546
|
+
|
2547
|
+
/* do not validate the header structure */
|
2548
|
+
nhdr = nt_read_header(opts, fname, &swap, 0);
|
2549
|
+
if( !nhdr ) return 1;
|
2550
|
+
|
2551
|
+
if( g_debug > 1 )
|
2552
|
+
{
|
2553
|
+
fprintf(stderr,"-d modifying %d fields of '%s' header\n",
|
2554
|
+
opts->flist.len, fname);
|
2555
|
+
fprintf(stderr,"-d header is: %s\n",
|
2556
|
+
nifti_hdr_looks_good(nhdr) ? "valid" : "invalid");
|
2557
|
+
}
|
2558
|
+
|
2559
|
+
/* okay, let's actually trash the data fields */
|
2560
|
+
if( modify_all_fields(nhdr, opts, g_hdr_fields, NT_HDR_NUM_FIELDS) )
|
2561
|
+
{
|
2562
|
+
free(nhdr);
|
2563
|
+
return 1;
|
2564
|
+
}
|
2565
|
+
|
2566
|
+
dupname = NULL; /* unless we duplicate file */
|
2567
|
+
|
2568
|
+
/* possibly duplicate the current dataset before writing new header */
|
2569
|
+
if( opts->prefix )
|
2570
|
+
{
|
2571
|
+
nim = nt_image_read(opts, fname, 1); /* get data */
|
2572
|
+
if( !nim ) {
|
2573
|
+
fprintf(stderr,"** failed to dup file '%s' before modifying\n",
|
2574
|
+
fname);
|
2575
|
+
return 1;
|
2576
|
+
}
|
2577
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
2578
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
2579
|
+
fprintf(stderr,"** failed to add command to image as exten\n");
|
2580
|
+
if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
|
2581
|
+
{
|
2582
|
+
NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix);
|
2583
|
+
nifti_image_free(nim);
|
2584
|
+
return 1;
|
2585
|
+
}
|
2586
|
+
dupname = nifti_strdup(nim->fname); /* so we know to free it */
|
2587
|
+
fname = dupname;
|
2588
|
+
nifti_image_write(nim); /* create the duplicate file */
|
2589
|
+
/* if we added a history note, get the new offset into the header */
|
2590
|
+
/* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */
|
2591
|
+
if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset;
|
2592
|
+
nifti_image_free(nim);
|
2593
|
+
}
|
2594
|
+
else if ( swap )
|
2595
|
+
swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr));
|
2596
|
+
|
2597
|
+
/* if all is well, overwrite header in fname dataset */
|
2598
|
+
(void)write_hdr_to_file(nhdr, fname); /* errors printed in function */
|
2599
|
+
|
2600
|
+
if( dupname ) free(dupname);
|
2601
|
+
free(nhdr);
|
2602
|
+
}
|
2603
|
+
|
2604
|
+
return 0;
|
2605
|
+
}
|
2606
|
+
|
2607
|
+
|
2608
|
+
/*----------------------------------------------------------------------
|
2609
|
+
* - read header
|
2610
|
+
* - swap header
|
2611
|
+
* - if -prefix duplicate file
|
2612
|
+
* - overwrite file header (allows (danger-of) no evaluation of data)
|
2613
|
+
*----------------------------------------------------------------------*/
|
2614
|
+
int act_swap_hdrs( nt_opts * opts )
|
2615
|
+
{
|
2616
|
+
nifti_1_header * nhdr;
|
2617
|
+
nifti_image * nim; /* for reading/writing entire datasets */
|
2618
|
+
int filec, swap;
|
2619
|
+
char * fname, * dupname;
|
2620
|
+
char func[] = { "act_mod_hdrs" };
|
2621
|
+
|
2622
|
+
/* count requested operations: "there can be only one", and not Sean */
|
2623
|
+
swap = opts->swap_hdr + opts->swap_ana + opts->swap_old;
|
2624
|
+
if( swap > 1 ) {
|
2625
|
+
fprintf(stderr,"** can perform only one swap method\n");
|
2626
|
+
return 1;
|
2627
|
+
} else if( ! swap )
|
2628
|
+
return 0; /* probably shouldn't be here */
|
2629
|
+
|
2630
|
+
if( g_debug > 2 )
|
2631
|
+
fprintf(stderr,"-d swapping headers of %d files...\n",opts->infiles.len);
|
2632
|
+
|
2633
|
+
for( filec = 0; filec < opts->infiles.len; filec++ )
|
2634
|
+
{
|
2635
|
+
fname = opts->infiles.list[filec]; /* for convenience and mod file */
|
2636
|
+
|
2637
|
+
if( nifti_is_gzfile(fname) ){
|
2638
|
+
fprintf(stderr,"** sorry, cannot swap a gzipped header: %s\n", fname);
|
2639
|
+
continue;
|
2640
|
+
}
|
2641
|
+
|
2642
|
+
/* do not validate the header structure */
|
2643
|
+
nhdr = nt_read_header(opts, fname, &swap, 0);
|
2644
|
+
if( !nhdr ) return 1;
|
2645
|
+
|
2646
|
+
if( g_debug > 1 ) {
|
2647
|
+
char * str = "NIfTI";
|
2648
|
+
if( opts->swap_ana || (opts->swap_old && !NIFTI_VERSION(*nhdr)) )
|
2649
|
+
str = "ANALYZE";
|
2650
|
+
fprintf(stderr,"-d %sswapping %s header of file %s\n",
|
2651
|
+
opts->swap_old ? "OLD " : "", str, fname);
|
2652
|
+
}
|
2653
|
+
|
2654
|
+
if( ! swap ) { /* if not yet swapped, do as the user requested */
|
2655
|
+
|
2656
|
+
if( opts->swap_old ) old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr));
|
2657
|
+
else swap_nifti_header(nhdr, opts->swap_ana ? 0 : 1);
|
2658
|
+
|
2659
|
+
} else { /* swapped already: if not correct, need to undo */
|
2660
|
+
|
2661
|
+
/* if swapped the wrong way, undo and swap as the user requested */
|
2662
|
+
if ( opts->swap_ana && NIFTI_VERSION(*nhdr) ) {
|
2663
|
+
/* want swapped as ANALYZE, but was swapped as NIFTI */
|
2664
|
+
swap_nifti_header(nhdr, 1); /* undo NIFTI */
|
2665
|
+
swap_nifti_header(nhdr, 0); /* swap ANALYZE */
|
2666
|
+
} else if( opts->swap_hdr && !NIFTI_VERSION(*nhdr) ) {
|
2667
|
+
/* want swapped as NIFTI, but was swapped as ANALYZE */
|
2668
|
+
swap_nifti_header(nhdr, 0); /* undo ANALYZE */
|
2669
|
+
swap_nifti_header(nhdr, 1); /* swap NIFTI */
|
2670
|
+
} else if ( opts->swap_old ) {
|
2671
|
+
/* undo whichever was done and apply the old way */
|
2672
|
+
swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr));
|
2673
|
+
old_swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr));
|
2674
|
+
}
|
2675
|
+
|
2676
|
+
/* else it was swapped the right way to begin with */
|
2677
|
+
|
2678
|
+
}
|
2679
|
+
|
2680
|
+
dupname = NULL; /* unless we duplicate file */
|
2681
|
+
|
2682
|
+
/* possibly duplicate the current dataset before writing new header */
|
2683
|
+
if( opts->prefix )
|
2684
|
+
{
|
2685
|
+
nim = nt_image_read(opts, fname, 1); /* get data */
|
2686
|
+
if( !nim ) {
|
2687
|
+
fprintf(stderr,"** failed to dup file '%s' before modifying\n",
|
2688
|
+
fname);
|
2689
|
+
return 1;
|
2690
|
+
}
|
2691
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
2692
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
2693
|
+
fprintf(stderr,"** failed to add command to image as exten\n");
|
2694
|
+
if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
|
2695
|
+
{
|
2696
|
+
NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix);
|
2697
|
+
nifti_image_free(nim);
|
2698
|
+
return 1;
|
2699
|
+
}
|
2700
|
+
dupname = nifti_strdup(nim->fname); /* so we know to free it */
|
2701
|
+
fname = dupname;
|
2702
|
+
nifti_image_write(nim); /* create the duplicate file */
|
2703
|
+
/* if we added a history note, get the new offset into the header */
|
2704
|
+
/* mod: if the new offset is valid, use it 31 Jan 2006 [rickr] */
|
2705
|
+
if( nim->iname_offset >= 348 ) nhdr->vox_offset = nim->iname_offset;
|
2706
|
+
nifti_image_free(nim);
|
2707
|
+
}
|
2708
|
+
|
2709
|
+
/* if all is well, overwrite header in fname dataset */
|
2710
|
+
(void)write_hdr_to_file(nhdr, fname); /* errors printed in function */
|
2711
|
+
|
2712
|
+
if( dupname ) free(dupname);
|
2713
|
+
free(nhdr);
|
2714
|
+
}
|
2715
|
+
|
2716
|
+
return 0;
|
2717
|
+
}
|
2718
|
+
|
2719
|
+
|
2720
|
+
/*----------------------------------------------------------------------
|
2721
|
+
* - read image w/data, modify and write
|
2722
|
+
*----------------------------------------------------------------------*/
|
2723
|
+
int act_mod_nims( nt_opts * opts )
|
2724
|
+
{
|
2725
|
+
nifti_image * nim; /* for reading/writing entire datasets */
|
2726
|
+
int filec;
|
2727
|
+
char func[] = { "act_mod_nims" };
|
2728
|
+
|
2729
|
+
if( g_debug > 2 )
|
2730
|
+
fprintf(stderr,"-d modifying %d fields for %d nifti images...\n",
|
2731
|
+
opts->flist.len, opts->infiles.len);
|
2732
|
+
if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0;
|
2733
|
+
|
2734
|
+
for( filec = 0; filec < opts->infiles.len; filec++ )
|
2735
|
+
{
|
2736
|
+
nim = nt_image_read(opts, opts->infiles.list[filec], 1); /* with data */
|
2737
|
+
|
2738
|
+
if( g_debug > 1 )
|
2739
|
+
fprintf(stderr,"-d modifying %d fields from '%s' image\n",
|
2740
|
+
opts->flist.len, opts->infiles.list[filec]);
|
2741
|
+
|
2742
|
+
/* okay, let's actually trash the data fields */
|
2743
|
+
if( modify_all_fields(nim, opts, g_nim_fields, NT_NIM_NUM_FIELDS) )
|
2744
|
+
{
|
2745
|
+
nifti_image_free(nim);
|
2746
|
+
return 1;
|
2747
|
+
}
|
2748
|
+
|
2749
|
+
/* add command as COMMENT extension */
|
2750
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
2751
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
2752
|
+
fprintf(stderr,"** failed to add command to image as extension\n");
|
2753
|
+
|
2754
|
+
/* possibly duplicate the current dataset before writing new header */
|
2755
|
+
if( opts->prefix )
|
2756
|
+
if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
|
2757
|
+
{
|
2758
|
+
NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix);
|
2759
|
+
nifti_image_free(nim);
|
2760
|
+
return 1;
|
2761
|
+
}
|
2762
|
+
|
2763
|
+
nifti_image_write(nim); /* and write it out, piece of cake :) */
|
2764
|
+
nifti_image_free(nim);
|
2765
|
+
}
|
2766
|
+
|
2767
|
+
return 0;
|
2768
|
+
}
|
2769
|
+
|
2770
|
+
|
2771
|
+
/*----------------------------------------------------------------------
|
2772
|
+
* overwrite nifti_1_header in the given file
|
2773
|
+
*----------------------------------------------------------------------*/
|
2774
|
+
int write_hdr_to_file( nifti_1_header * nhdr, char * fname )
|
2775
|
+
{
|
2776
|
+
znzFile fp;
|
2777
|
+
size_t bytes;
|
2778
|
+
char func[] = { "write_hdr_to_file" };
|
2779
|
+
int rv = 0;
|
2780
|
+
|
2781
|
+
fp = znzopen(fname,"r+b",nifti_is_gzfile(fname));
|
2782
|
+
if( znz_isnull(fp) ){
|
2783
|
+
NTL_FERR(func, "failed to re-open mod file", fname);
|
2784
|
+
return 1;
|
2785
|
+
}
|
2786
|
+
|
2787
|
+
bytes = znzwrite(nhdr, 1, sizeof(nifti_1_header), fp);
|
2788
|
+
if( bytes != sizeof(nifti_1_header)){
|
2789
|
+
NTL_FERR(func, "failed to write header to file",fname);
|
2790
|
+
fprintf(stderr," - wrote %d of %d bytes\n",
|
2791
|
+
(int)bytes,(int)sizeof(nifti_1_header));
|
2792
|
+
rv = 1;
|
2793
|
+
}
|
2794
|
+
|
2795
|
+
if( g_debug > 3 )
|
2796
|
+
disp_nifti_1_header("+d writing new header to file : ", nhdr);
|
2797
|
+
|
2798
|
+
znzclose(fp);
|
2799
|
+
|
2800
|
+
return rv;
|
2801
|
+
}
|
2802
|
+
|
2803
|
+
|
2804
|
+
/*----------------------------------------------------------------------
|
2805
|
+
* modify all fields in the list
|
2806
|
+
*----------------------------------------------------------------------*/
|
2807
|
+
int modify_all_fields( void * basep, nt_opts * opts, field_s * fields, int flen)
|
2808
|
+
{
|
2809
|
+
field_s * fp;
|
2810
|
+
int fc, lc; /* field and list counters */
|
2811
|
+
|
2812
|
+
if( opts->flist.len <= 0 ) return 0;
|
2813
|
+
if( opts->flist.len != opts->vlist.len ){
|
2814
|
+
fprintf(stderr,"** have %d fields but %d new values\n",
|
2815
|
+
opts->flist.len, opts->vlist.len);
|
2816
|
+
return 1;
|
2817
|
+
}
|
2818
|
+
|
2819
|
+
for( lc = 0; lc < opts->flist.len; lc++ )
|
2820
|
+
{
|
2821
|
+
/* is it in the list? */
|
2822
|
+
fp = fields;
|
2823
|
+
for( fc = 0; fc < flen; fc++, fp++ )
|
2824
|
+
if( strcmp(opts->flist.list[lc], fp->name) == 0 ) break;
|
2825
|
+
|
2826
|
+
if( fc == flen ) /* do no modifications on failure */
|
2827
|
+
{
|
2828
|
+
fprintf(stderr,"** field '%s' not found in structure\n",
|
2829
|
+
opts->flist.list[lc]);
|
2830
|
+
return 1;
|
2831
|
+
}
|
2832
|
+
|
2833
|
+
if( modify_field( basep, fp, opts->vlist.list[lc]) )
|
2834
|
+
return 1;
|
2835
|
+
}
|
2836
|
+
|
2837
|
+
return 0;
|
2838
|
+
}
|
2839
|
+
|
2840
|
+
|
2841
|
+
/*----------------------------------------------------------------------
|
2842
|
+
* modify a single field with the given value field
|
2843
|
+
*
|
2844
|
+
* pointer fields are not allowed here
|
2845
|
+
*----------------------------------------------------------------------*/
|
2846
|
+
int modify_field(void * basep, field_s * field, char * data)
|
2847
|
+
{
|
2848
|
+
float fval;
|
2849
|
+
char * posn = data;
|
2850
|
+
int val, max, fc, nchars;
|
2851
|
+
|
2852
|
+
if( g_debug > 1 )
|
2853
|
+
fprintf(stderr,"+d modifying field '%s' with '%s'\n", field->name, data);
|
2854
|
+
|
2855
|
+
if( !data || strlen(data) == 0 )
|
2856
|
+
{
|
2857
|
+
fprintf(stderr,"** no data for '%s' field modification\n",field->name);
|
2858
|
+
return 1;
|
2859
|
+
}
|
2860
|
+
|
2861
|
+
switch( field->type )
|
2862
|
+
{
|
2863
|
+
case DT_UNKNOWN:
|
2864
|
+
case NT_DT_POINTER:
|
2865
|
+
case NT_DT_CHAR_PTR:
|
2866
|
+
case NT_DT_EXT_PTR:
|
2867
|
+
default:
|
2868
|
+
fprintf(stderr,"** refusing to modify a pointer field, '%s'\n",
|
2869
|
+
field->name);
|
2870
|
+
return 1;
|
2871
|
+
|
2872
|
+
case DT_INT8:
|
2873
|
+
{
|
2874
|
+
max = 127;
|
2875
|
+
for( fc = 0; fc < field->len; fc++ )
|
2876
|
+
{
|
2877
|
+
if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
|
2878
|
+
{
|
2879
|
+
fprintf(stderr,"** found %d of %d modify values\n",
|
2880
|
+
fc,field->len);
|
2881
|
+
return 1;
|
2882
|
+
}
|
2883
|
+
if( val > max || val < -(max+1) )
|
2884
|
+
{
|
2885
|
+
fprintf(stderr,
|
2886
|
+
"** mod val #%d (= %d) outside byte range [-%d,%d]\n",
|
2887
|
+
fc, val, max+1, max);
|
2888
|
+
return 1;
|
2889
|
+
}
|
2890
|
+
/* otherwise, we're good */
|
2891
|
+
(((char *)basep + field->offset))[fc] = (char)val;
|
2892
|
+
if( g_debug > 1 )
|
2893
|
+
fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
|
2894
|
+
fc, field->name, val);
|
2895
|
+
posn += nchars;
|
2896
|
+
}
|
2897
|
+
}
|
2898
|
+
break;
|
2899
|
+
|
2900
|
+
case DT_INT16:
|
2901
|
+
{
|
2902
|
+
max = 32767;
|
2903
|
+
for( fc = 0; fc < field->len; fc++ )
|
2904
|
+
{
|
2905
|
+
if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
|
2906
|
+
{
|
2907
|
+
fprintf(stderr,"** found %d of %d modify values\n",
|
2908
|
+
fc,field->len);
|
2909
|
+
return 1;
|
2910
|
+
}
|
2911
|
+
if( val > max || val < -(max+1) )
|
2912
|
+
{
|
2913
|
+
fprintf(stderr,
|
2914
|
+
"** mod val #%d (= %d) outside byte range [-%d,%d]\n",
|
2915
|
+
fc, val, max+1, max);
|
2916
|
+
return 1;
|
2917
|
+
}
|
2918
|
+
/* otherwise, we're good */
|
2919
|
+
((short *)((char *)basep + field->offset))[fc] = (short)val;
|
2920
|
+
if( g_debug > 1 )
|
2921
|
+
fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
|
2922
|
+
fc, field->name, val);
|
2923
|
+
posn += nchars;
|
2924
|
+
}
|
2925
|
+
}
|
2926
|
+
break;
|
2927
|
+
|
2928
|
+
case DT_INT32:
|
2929
|
+
{
|
2930
|
+
for( fc = 0; fc < field->len; fc++ )
|
2931
|
+
{
|
2932
|
+
if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
|
2933
|
+
{
|
2934
|
+
fprintf(stderr,"** found %d of %d modify values\n",
|
2935
|
+
fc,field->len);
|
2936
|
+
return 1;
|
2937
|
+
}
|
2938
|
+
((int *)((char *)basep + field->offset))[fc] = val;
|
2939
|
+
if( g_debug > 1 )
|
2940
|
+
fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
|
2941
|
+
fc, field->name, val);
|
2942
|
+
posn += nchars;
|
2943
|
+
}
|
2944
|
+
}
|
2945
|
+
break;
|
2946
|
+
|
2947
|
+
case DT_FLOAT32:
|
2948
|
+
{
|
2949
|
+
for( fc = 0; fc < field->len; fc++ )
|
2950
|
+
{
|
2951
|
+
if( sscanf(posn, " %f%n", &fval, &nchars) != 1 )
|
2952
|
+
{
|
2953
|
+
fprintf(stderr,"** found %d of %d modify values\n",
|
2954
|
+
fc,field->len);
|
2955
|
+
return 1;
|
2956
|
+
}
|
2957
|
+
/* otherwise, we're good */
|
2958
|
+
((float *)((char *)basep + field->offset))[fc] = fval;
|
2959
|
+
if( g_debug > 1 )
|
2960
|
+
fprintf(stderr,"+d setting posn %d of '%s' to %f\n",
|
2961
|
+
fc, field->name, fval);
|
2962
|
+
posn += nchars;
|
2963
|
+
}
|
2964
|
+
}
|
2965
|
+
break;
|
2966
|
+
|
2967
|
+
case NT_DT_STRING:
|
2968
|
+
{
|
2969
|
+
char * dest = (char *)basep + field->offset;
|
2970
|
+
nchars = strlen(data);
|
2971
|
+
strncpy(dest, data, field->len);
|
2972
|
+
if( nchars < field->len ) /* clear the rest */
|
2973
|
+
memset(dest+nchars, '\0', field->len-nchars);
|
2974
|
+
}
|
2975
|
+
break;
|
2976
|
+
}
|
2977
|
+
|
2978
|
+
return 0;
|
2979
|
+
}
|
2980
|
+
|
2981
|
+
|
2982
|
+
/*----------------------------------------------------------------------
|
2983
|
+
* fill the nifti_1_header field list
|
2984
|
+
*----------------------------------------------------------------------*/
|
2985
|
+
int fill_hdr_field_array( field_s * nh_fields )
|
2986
|
+
{
|
2987
|
+
nifti_1_header nhdr;
|
2988
|
+
field_s * nhf = nh_fields;
|
2989
|
+
int rv, errs;
|
2990
|
+
|
2991
|
+
memset(nhf, 0, NT_HDR_NUM_FIELDS*sizeof(field_s));
|
2992
|
+
|
2993
|
+
/* this macro takes (TYPE, NAME, NUM) and does:
|
2994
|
+
fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME");
|
2995
|
+
nhf++;
|
2996
|
+
*/
|
2997
|
+
errs = 0;
|
2998
|
+
NT_SFILL(nhdr, nhf, DT_INT32, sizeof_hdr, 1, rv); errs += rv;
|
2999
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, data_type, 10, rv); errs += rv;
|
3000
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, db_name, 18, rv); errs += rv;
|
3001
|
+
NT_SFILL(nhdr, nhf, DT_INT32, extents, 1, rv); errs += rv;
|
3002
|
+
NT_SFILL(nhdr, nhf, DT_INT16, session_error, 1, rv); errs += rv;
|
3003
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, regular, 1, rv); errs += rv;
|
3004
|
+
NT_SFILL(nhdr, nhf, DT_INT8, dim_info, 1, rv); errs += rv;
|
3005
|
+
|
3006
|
+
NT_SFILL(nhdr, nhf, DT_INT16, dim, 8, rv); errs += rv;
|
3007
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p1, 1, rv); errs += rv;
|
3008
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p2, 1, rv); errs += rv;
|
3009
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p3, 1, rv); errs += rv;
|
3010
|
+
NT_SFILL(nhdr, nhf, DT_INT16, intent_code, 1, rv); errs += rv;
|
3011
|
+
|
3012
|
+
NT_SFILL(nhdr, nhf, DT_INT16, datatype, 1, rv); errs += rv;
|
3013
|
+
NT_SFILL(nhdr, nhf, DT_INT16, bitpix, 1, rv); errs += rv;
|
3014
|
+
NT_SFILL(nhdr, nhf, DT_INT16, slice_start, 1, rv); errs += rv;
|
3015
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, pixdim, 8, rv); errs += rv;
|
3016
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, vox_offset, 1, rv); errs += rv;
|
3017
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_slope, 1, rv); errs += rv;
|
3018
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_inter, 1, rv); errs += rv;
|
3019
|
+
NT_SFILL(nhdr, nhf, DT_INT16, slice_end, 1, rv); errs += rv;
|
3020
|
+
|
3021
|
+
NT_SFILL(nhdr, nhf, DT_INT8, slice_code, 1, rv); errs += rv;
|
3022
|
+
NT_SFILL(nhdr, nhf, DT_INT8, xyzt_units, 1, rv); errs += rv;
|
3023
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_max, 1, rv); errs += rv;
|
3024
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_min, 1, rv); errs += rv;
|
3025
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, slice_duration, 1, rv); errs += rv;
|
3026
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, toffset, 1, rv); errs += rv;
|
3027
|
+
NT_SFILL(nhdr, nhf, DT_INT32, glmax, 1, rv); errs += rv;
|
3028
|
+
NT_SFILL(nhdr, nhf, DT_INT32, glmin, 1, rv); errs += rv;
|
3029
|
+
|
3030
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, descrip, 80, rv); errs += rv;
|
3031
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, aux_file, 24, rv); errs += rv;
|
3032
|
+
NT_SFILL(nhdr, nhf, DT_INT16, qform_code, 1, rv); errs += rv;
|
3033
|
+
NT_SFILL(nhdr, nhf, DT_INT16, sform_code, 1, rv); errs += rv;
|
3034
|
+
|
3035
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_b, 1, rv); errs += rv;
|
3036
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_c, 1, rv); errs += rv;
|
3037
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_d, 1, rv); errs += rv;
|
3038
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_x, 1, rv); errs += rv;
|
3039
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_y, 1, rv); errs += rv;
|
3040
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_z, 1, rv); errs += rv;
|
3041
|
+
|
3042
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_x, 4, rv); errs += rv;
|
3043
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_y, 4, rv); errs += rv;
|
3044
|
+
NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_z, 4, rv); errs += rv;
|
3045
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, intent_name, 16, rv); errs += rv;
|
3046
|
+
NT_SFILL(nhdr, nhf, NT_DT_STRING, magic, 4, rv); errs += rv;
|
3047
|
+
|
3048
|
+
if( errs > 0 ){
|
3049
|
+
fprintf(stderr, "** %d fill_fields errors!\n", errs);
|
3050
|
+
return 1;
|
3051
|
+
}
|
3052
|
+
|
3053
|
+
/* failure here is a serious problem */
|
3054
|
+
if( check_total_size("nifti_1_header test: ", nh_fields,
|
3055
|
+
NT_HDR_NUM_FIELDS, sizeof(nhdr)) )
|
3056
|
+
return 1;
|
3057
|
+
|
3058
|
+
if( g_debug > 3 )
|
3059
|
+
disp_field_s_list("nh_fields: ", nh_fields, NT_HDR_NUM_FIELDS);
|
3060
|
+
|
3061
|
+
return 0;
|
3062
|
+
}
|
3063
|
+
|
3064
|
+
|
3065
|
+
/*----------------------------------------------------------------------
|
3066
|
+
* fill the nifti_image field list
|
3067
|
+
*----------------------------------------------------------------------*/
|
3068
|
+
int fill_nim_field_array( field_s * nim_fields )
|
3069
|
+
{
|
3070
|
+
nifti_image nim;
|
3071
|
+
field_s * nif = nim_fields;
|
3072
|
+
int rv, errs;
|
3073
|
+
|
3074
|
+
memset(nif, 0, NT_NIM_NUM_FIELDS*sizeof(field_s));
|
3075
|
+
|
3076
|
+
errs = 0;
|
3077
|
+
|
3078
|
+
NT_SFILL(nim, nif, DT_INT32, ndim, 1, rv); errs += rv;
|
3079
|
+
NT_SFILL(nim, nif, DT_INT32, nx, 1, rv); errs += rv;
|
3080
|
+
NT_SFILL(nim, nif, DT_INT32, ny, 1, rv); errs += rv;
|
3081
|
+
NT_SFILL(nim, nif, DT_INT32, nz, 1, rv); errs += rv;
|
3082
|
+
NT_SFILL(nim, nif, DT_INT32, nt, 1, rv); errs += rv;
|
3083
|
+
NT_SFILL(nim, nif, DT_INT32, nu, 1, rv); errs += rv;
|
3084
|
+
NT_SFILL(nim, nif, DT_INT32, nv, 1, rv); errs += rv;
|
3085
|
+
NT_SFILL(nim, nif, DT_INT32, nw, 1, rv); errs += rv;
|
3086
|
+
NT_SFILL(nim, nif, DT_INT32, dim, 8, rv); errs += rv;
|
3087
|
+
NT_SFILL(nim, nif, DT_INT32, nvox, 1, rv); errs += rv;
|
3088
|
+
NT_SFILL(nim, nif, DT_INT32, nbyper, 1, rv); errs += rv;
|
3089
|
+
NT_SFILL(nim, nif, DT_INT32, datatype, 1, rv); errs += rv;
|
3090
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dx, 1, rv); errs += rv;
|
3091
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dy, 1, rv); errs += rv;
|
3092
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dz, 1, rv); errs += rv;
|
3093
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dt, 1, rv); errs += rv;
|
3094
|
+
NT_SFILL(nim, nif, DT_FLOAT32, du, 1, rv); errs += rv;
|
3095
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dv, 1, rv); errs += rv;
|
3096
|
+
NT_SFILL(nim, nif, DT_FLOAT32, dw, 1, rv); errs += rv;
|
3097
|
+
NT_SFILL(nim, nif, DT_FLOAT32, pixdim, 8, rv); errs += rv;
|
3098
|
+
NT_SFILL(nim, nif, DT_FLOAT32, scl_slope, 1, rv); errs += rv;
|
3099
|
+
NT_SFILL(nim, nif, DT_FLOAT32, scl_inter, 1, rv); errs += rv;
|
3100
|
+
NT_SFILL(nim, nif, DT_FLOAT32, cal_min, 1, rv); errs += rv;
|
3101
|
+
NT_SFILL(nim, nif, DT_FLOAT32, cal_max, 1, rv); errs += rv;
|
3102
|
+
NT_SFILL(nim, nif, DT_INT32, qform_code, 1, rv); errs += rv;
|
3103
|
+
NT_SFILL(nim, nif, DT_INT32, sform_code, 1, rv); errs += rv;
|
3104
|
+
NT_SFILL(nim, nif, DT_INT32, freq_dim, 1, rv); errs += rv;
|
3105
|
+
NT_SFILL(nim, nif, DT_INT32, phase_dim, 1, rv); errs += rv;
|
3106
|
+
NT_SFILL(nim, nif, DT_INT32, slice_dim, 1, rv); errs += rv;
|
3107
|
+
NT_SFILL(nim, nif, DT_INT32, slice_code, 1, rv); errs += rv;
|
3108
|
+
NT_SFILL(nim, nif, DT_INT32, slice_start, 1, rv); errs += rv;
|
3109
|
+
NT_SFILL(nim, nif, DT_INT32, slice_end, 1, rv); errs += rv;
|
3110
|
+
NT_SFILL(nim, nif, DT_FLOAT32, slice_duration, 1, rv); errs += rv;
|
3111
|
+
NT_SFILL(nim, nif, DT_FLOAT32, quatern_b, 1, rv); errs += rv;
|
3112
|
+
NT_SFILL(nim, nif, DT_FLOAT32, quatern_c, 1, rv); errs += rv;
|
3113
|
+
NT_SFILL(nim, nif, DT_FLOAT32, quatern_d, 1, rv); errs += rv;
|
3114
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qoffset_x, 1, rv); errs += rv;
|
3115
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qoffset_y, 1, rv); errs += rv;
|
3116
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qoffset_z, 1, rv); errs += rv;
|
3117
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qfac, 1, rv); errs += rv;
|
3118
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qto_xyz, 16, rv); errs += rv;
|
3119
|
+
NT_SFILL(nim, nif, DT_FLOAT32, qto_ijk, 16, rv); errs += rv;
|
3120
|
+
NT_SFILL(nim, nif, DT_FLOAT32, sto_xyz, 16, rv); errs += rv;
|
3121
|
+
NT_SFILL(nim, nif, DT_FLOAT32, sto_ijk, 16, rv); errs += rv;
|
3122
|
+
NT_SFILL(nim, nif, DT_FLOAT32, toffset, 1, rv); errs += rv;
|
3123
|
+
NT_SFILL(nim, nif, DT_INT32, xyz_units, 1, rv); errs += rv;
|
3124
|
+
NT_SFILL(nim, nif, DT_INT32, time_units, 1, rv); errs += rv;
|
3125
|
+
NT_SFILL(nim, nif, DT_INT32, nifti_type, 1, rv); errs += rv;
|
3126
|
+
NT_SFILL(nim, nif, DT_INT32, intent_code, 1, rv); errs += rv;
|
3127
|
+
NT_SFILL(nim, nif, DT_FLOAT32, intent_p1, 1, rv); errs += rv;
|
3128
|
+
NT_SFILL(nim, nif, DT_FLOAT32, intent_p2, 1, rv); errs += rv;
|
3129
|
+
NT_SFILL(nim, nif, DT_FLOAT32, intent_p3, 1, rv); errs += rv;
|
3130
|
+
NT_SFILL(nim, nif, NT_DT_STRING, intent_name, 16, rv); errs += rv;
|
3131
|
+
NT_SFILL(nim, nif, NT_DT_STRING, descrip, 80, rv); errs += rv;
|
3132
|
+
NT_SFILL(nim, nif, NT_DT_STRING, aux_file, 24, rv); errs += rv;
|
3133
|
+
NT_SFILL(nim, nif, NT_DT_CHAR_PTR, fname, 1, rv); errs += rv;
|
3134
|
+
NT_SFILL(nim, nif, NT_DT_CHAR_PTR, iname, 1, rv); errs += rv;
|
3135
|
+
NT_SFILL(nim, nif, DT_INT32, iname_offset, 1, rv); errs += rv;
|
3136
|
+
NT_SFILL(nim, nif, DT_INT32, swapsize, 1, rv); errs += rv;
|
3137
|
+
NT_SFILL(nim, nif, DT_INT32, byteorder, 1, rv); errs += rv;
|
3138
|
+
NT_SFILL(nim, nif, NT_DT_POINTER, data, 1, rv); errs += rv;
|
3139
|
+
NT_SFILL(nim, nif, DT_INT32, num_ext, 1, rv); errs += rv;
|
3140
|
+
NT_SFILL(nim, nif, NT_DT_EXT_PTR, ext_list, 1, rv); errs += rv;
|
3141
|
+
|
3142
|
+
if( errs > 0 ){
|
3143
|
+
fprintf(stderr, "** %d fill_fields errors "
|
3144
|
+
"(note that pointers get aligned)\n", errs);
|
3145
|
+
return 1;
|
3146
|
+
}
|
3147
|
+
|
3148
|
+
if( g_debug > 3 ) /* failure here is not an error condition */
|
3149
|
+
check_total_size("nifti_image test: ", nim_fields,
|
3150
|
+
NT_NIM_NUM_FIELDS, sizeof(nim));
|
3151
|
+
|
3152
|
+
if( g_debug > 3 )
|
3153
|
+
disp_field_s_list("nim_fields: ", nim_fields, NT_NIM_NUM_FIELDS);
|
3154
|
+
|
3155
|
+
return 0;
|
3156
|
+
}
|
3157
|
+
|
3158
|
+
|
3159
|
+
/*----------------------------------------------------------------------
|
3160
|
+
* fill the nifti_analyze75 field list
|
3161
|
+
*----------------------------------------------------------------------*/
|
3162
|
+
int fill_ana_field_array( field_s * ah_fields )
|
3163
|
+
{
|
3164
|
+
nifti_analyze75 nhdr;
|
3165
|
+
field_s * ahf = ah_fields;
|
3166
|
+
int rv, errs;
|
3167
|
+
|
3168
|
+
memset(ahf, 0, NT_ANA_NUM_FIELDS*sizeof(field_s));
|
3169
|
+
|
3170
|
+
/* this macro takes (TYPE, NAME, NUM) and does:
|
3171
|
+
fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME");
|
3172
|
+
nhf++;
|
3173
|
+
*/
|
3174
|
+
errs = 0;
|
3175
|
+
NT_SFILL(nhdr, ahf, DT_INT32, sizeof_hdr, 1, rv); errs += rv;
|
3176
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, data_type, 10, rv); errs += rv;
|
3177
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, db_name, 18, rv); errs += rv;
|
3178
|
+
NT_SFILL(nhdr, ahf, DT_INT32, extents, 1, rv); errs += rv;
|
3179
|
+
NT_SFILL(nhdr, ahf, DT_INT16, session_error, 1, rv); errs += rv;
|
3180
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, regular, 1, rv); errs += rv;
|
3181
|
+
NT_SFILL(nhdr, ahf, DT_INT8, hkey_un0, 1, rv); errs += rv;
|
3182
|
+
|
3183
|
+
NT_SFILL(nhdr, ahf, DT_INT16, dim, 8, rv); errs += rv;
|
3184
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused8, 1, rv); errs += rv;
|
3185
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused9, 1, rv); errs += rv;
|
3186
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused10, 1, rv); errs += rv;
|
3187
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused11, 1, rv); errs += rv;
|
3188
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused12, 1, rv); errs += rv;
|
3189
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused13, 1, rv); errs += rv;
|
3190
|
+
NT_SFILL(nhdr, ahf, DT_INT16, unused14, 1, rv); errs += rv;
|
3191
|
+
|
3192
|
+
NT_SFILL(nhdr, ahf, DT_INT16, datatype, 1, rv); errs += rv;
|
3193
|
+
NT_SFILL(nhdr, ahf, DT_INT16, bitpix, 1, rv); errs += rv;
|
3194
|
+
NT_SFILL(nhdr, ahf, DT_INT16, dim_un0, 1, rv); errs += rv;
|
3195
|
+
|
3196
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, pixdim, 8, rv); errs += rv;
|
3197
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, vox_offset, 1, rv); errs += rv;
|
3198
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, funused1, 1, rv); errs += rv;
|
3199
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, funused2, 1, rv); errs += rv;
|
3200
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, funused3, 1, rv); errs += rv;
|
3201
|
+
|
3202
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_max, 1, rv); errs += rv;
|
3203
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, cal_min, 1, rv); errs += rv;
|
3204
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, compressed, 1, rv); errs += rv;
|
3205
|
+
NT_SFILL(nhdr, ahf, DT_FLOAT32, verified, 1, rv); errs += rv;
|
3206
|
+
NT_SFILL(nhdr, ahf, DT_INT32, glmax, 1, rv); errs += rv;
|
3207
|
+
NT_SFILL(nhdr, ahf, DT_INT32, glmin, 1, rv); errs += rv;
|
3208
|
+
|
3209
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, descrip, 80, rv); errs += rv;
|
3210
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, aux_file, 24, rv); errs += rv;
|
3211
|
+
|
3212
|
+
NT_SFILL(nhdr, ahf, DT_INT8, orient, 1, rv); errs += rv;
|
3213
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, originator, 10, rv); errs += rv;
|
3214
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, generated, 10, rv); errs += rv;
|
3215
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, scannum, 10, rv); errs += rv;
|
3216
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, patient_id, 10, rv); errs += rv;
|
3217
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_date, 10, rv); errs += rv;
|
3218
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, exp_time, 10, rv); errs += rv;
|
3219
|
+
NT_SFILL(nhdr, ahf, NT_DT_STRING, hist_un0, 3, rv); errs += rv;
|
3220
|
+
|
3221
|
+
NT_SFILL(nhdr, ahf, DT_INT32, views , 1, rv); errs += rv;
|
3222
|
+
NT_SFILL(nhdr, ahf, DT_INT32, vols_added, 1, rv); errs += rv;
|
3223
|
+
NT_SFILL(nhdr, ahf, DT_INT32, start_field, 1, rv); errs += rv;
|
3224
|
+
NT_SFILL(nhdr, ahf, DT_INT32, field_skip, 1, rv); errs += rv;
|
3225
|
+
|
3226
|
+
NT_SFILL(nhdr, ahf, DT_INT32, omax, 1, rv); errs += rv;
|
3227
|
+
NT_SFILL(nhdr, ahf, DT_INT32, omin, 1, rv); errs += rv;
|
3228
|
+
NT_SFILL(nhdr, ahf, DT_INT32, smax, 1, rv); errs += rv;
|
3229
|
+
NT_SFILL(nhdr, ahf, DT_INT32, smin, 1, rv); errs += rv;
|
3230
|
+
|
3231
|
+
if( errs > 0 ){
|
3232
|
+
fprintf(stderr, "** %d ana fill_fields errors!\n", errs);
|
3233
|
+
return 1;
|
3234
|
+
}
|
3235
|
+
|
3236
|
+
/* failure here is a serious problem */
|
3237
|
+
if( check_total_size("nifti_analyze75 test: ", ah_fields, NT_ANA_NUM_FIELDS,
|
3238
|
+
sizeof(nhdr)) )
|
3239
|
+
return 1;
|
3240
|
+
|
3241
|
+
if( g_debug > 3 )
|
3242
|
+
disp_field_s_list("ah_fields: ", ah_fields, NT_ANA_NUM_FIELDS);
|
3243
|
+
|
3244
|
+
return 0;
|
3245
|
+
}
|
3246
|
+
|
3247
|
+
|
3248
|
+
/*----------------------------------------------------------------------
|
3249
|
+
* compare sizes to offset, including total
|
3250
|
+
*----------------------------------------------------------------------*/
|
3251
|
+
int check_total_size( char * mesg, field_s * fields, int nfields, int tot_size )
|
3252
|
+
{
|
3253
|
+
field_s * fp;
|
3254
|
+
int c, total;
|
3255
|
+
int bad_offs;
|
3256
|
+
|
3257
|
+
total = 0;
|
3258
|
+
bad_offs = 0;
|
3259
|
+
for( c = 0, fp = fields; c < nfields; c++, fp++ ){
|
3260
|
+
if( fp->offset != total ){
|
3261
|
+
if( g_debug > 2 )
|
3262
|
+
fprintf(stderr,"** bad offset for field '%s'\n"
|
3263
|
+
" offset = %d, total = %d\n",
|
3264
|
+
fp->name, fp->offset, total);
|
3265
|
+
bad_offs++;
|
3266
|
+
}
|
3267
|
+
|
3268
|
+
total += fp->size * fp->len;
|
3269
|
+
}
|
3270
|
+
|
3271
|
+
if( g_debug > 1 || (g_debug > 0 && bad_offs > 0) ){
|
3272
|
+
fputs(mesg, stderr); c = 0;
|
3273
|
+
if( bad_offs > 0 ){
|
3274
|
+
fprintf(stderr,"** found %d bad offsets\n", bad_offs); c++; }
|
3275
|
+
if( total != tot_size ){
|
3276
|
+
fprintf(stderr,"** computed total %d not equal to struct size %d\n",
|
3277
|
+
total, tot_size); c++; }
|
3278
|
+
if( c == 0 ) fputs("... okay\n", stderr);
|
3279
|
+
}
|
3280
|
+
|
3281
|
+
if( bad_offs > 0 ) return 1;
|
3282
|
+
|
3283
|
+
return 0;
|
3284
|
+
}
|
3285
|
+
|
3286
|
+
|
3287
|
+
/*----------------------------------------------------------------------
|
3288
|
+
* fill the field structure with the given data
|
3289
|
+
*----------------------------------------------------------------------*/
|
3290
|
+
int fill_field( field_s * fp, int type, int offset, int num, char * name )
|
3291
|
+
{
|
3292
|
+
fp->type = type;
|
3293
|
+
fp->offset = offset;
|
3294
|
+
fp->size = 1; /* init before check */
|
3295
|
+
fp->len = num;
|
3296
|
+
|
3297
|
+
strncpy(fp->name, name, NT_FIELD_NAME_LEN-1);
|
3298
|
+
|
3299
|
+
switch( type ){
|
3300
|
+
case DT_UNKNOWN:
|
3301
|
+
case DT_INT8:
|
3302
|
+
case NT_DT_STRING:
|
3303
|
+
fp->size = 1;
|
3304
|
+
break;
|
3305
|
+
|
3306
|
+
case DT_INT16:
|
3307
|
+
fp->size = 2;
|
3308
|
+
break;
|
3309
|
+
|
3310
|
+
case DT_INT32:
|
3311
|
+
case DT_FLOAT32:
|
3312
|
+
fp->size = 4;
|
3313
|
+
break;
|
3314
|
+
|
3315
|
+
case NT_DT_POINTER:
|
3316
|
+
case NT_DT_CHAR_PTR:
|
3317
|
+
case NT_DT_EXT_PTR:
|
3318
|
+
fp->size = (int)sizeof(void *);
|
3319
|
+
break;
|
3320
|
+
|
3321
|
+
default:
|
3322
|
+
fprintf(stderr,"** fill_field: invalid type %d\n", type );
|
3323
|
+
return 1;
|
3324
|
+
}
|
3325
|
+
|
3326
|
+
return 0;
|
3327
|
+
}
|
3328
|
+
|
3329
|
+
|
3330
|
+
/*----------------------------------------------------------------------
|
3331
|
+
* display the contents of all of the field structures
|
3332
|
+
*----------------------------------------------------------------------*/
|
3333
|
+
char * field_type_str( int type )
|
3334
|
+
{
|
3335
|
+
if( type == DT_INT8 ) return "DT_INT8";
|
3336
|
+
if( type == DT_INT16 ) return "DT_INT16";
|
3337
|
+
if( type == DT_INT32 ) return "DT_INT32";
|
3338
|
+
if( type == DT_FLOAT32 ) return "DT_FLOAT32";
|
3339
|
+
if( type == NT_DT_STRING ) return "NT_DT_STRING";
|
3340
|
+
if( type == NT_DT_POINTER ) return "NT_DT_POINTER";
|
3341
|
+
if( type == NT_DT_CHAR_PTR ) return "NT_DT_CHAR_PTR"; /* longest: 14 */
|
3342
|
+
if( type == NT_DT_EXT_PTR ) return "NT_DT_EXT_PTR";
|
3343
|
+
|
3344
|
+
return "DT_UNKNOWN"; /* for DT_UNKNOWN, or as an else */
|
3345
|
+
}
|
3346
|
+
|
3347
|
+
#define NT_MAX_DT_STR_LEN 14
|
3348
|
+
|
3349
|
+
/*----------------------------------------------------------------------
|
3350
|
+
* display the contents of all of the field structures
|
3351
|
+
*----------------------------------------------------------------------*/
|
3352
|
+
int disp_field_s_list( char * mesg, field_s * fp, int nfields )
|
3353
|
+
{
|
3354
|
+
int c;
|
3355
|
+
|
3356
|
+
if( mesg ) fputs(mesg, stdout);
|
3357
|
+
|
3358
|
+
fprintf(stdout," %d fields:\n"
|
3359
|
+
" name size len offset type\n"
|
3360
|
+
" ------------------- ---- --- ------ --------------\n",
|
3361
|
+
nfields);
|
3362
|
+
|
3363
|
+
for( c = 0; c < nfields; c++, fp++ )
|
3364
|
+
fprintf(stdout," %-*s %4d %3d %4d %-14s\n",
|
3365
|
+
NT_FIELD_NAME_LEN-1, fp->name, fp->size, fp->len,
|
3366
|
+
fp->offset, field_type_str(fp->type));
|
3367
|
+
|
3368
|
+
return 0;
|
3369
|
+
}
|
3370
|
+
|
3371
|
+
|
3372
|
+
/*----------------------------------------------------------------------
|
3373
|
+
* display the contents of all of the field structures
|
3374
|
+
*----------------------------------------------------------------------*/
|
3375
|
+
int disp_field(char *mesg, field_s *fieldp, void * str, int nfields, int header)
|
3376
|
+
{
|
3377
|
+
field_s * fp;
|
3378
|
+
int c;
|
3379
|
+
|
3380
|
+
if( mesg ) fputs(mesg, stdout);
|
3381
|
+
|
3382
|
+
if( header && g_debug > 0 ){
|
3383
|
+
fprintf(stdout, " name offset nvals values\n");
|
3384
|
+
fprintf(stdout, " ------------------- ------ ----- ------\n");
|
3385
|
+
}
|
3386
|
+
|
3387
|
+
fp = fieldp;
|
3388
|
+
for( c = 0; c < nfields; c++, fp++ )
|
3389
|
+
{
|
3390
|
+
/* start by displaying the field information */
|
3391
|
+
if( g_debug > 0 )
|
3392
|
+
fprintf(stdout, " %-*.*s %4d %3d ",
|
3393
|
+
NT_FIELD_NAME_LEN-1, NT_FIELD_NAME_LEN-1, fp->name,
|
3394
|
+
fp->offset, fp->len);
|
3395
|
+
|
3396
|
+
/* now, print the value(s), depending on the type */
|
3397
|
+
switch( fp->type ){
|
3398
|
+
case DT_UNKNOWN:
|
3399
|
+
default:
|
3400
|
+
fprintf(stdout,"(unknown data type)\n");
|
3401
|
+
break;
|
3402
|
+
|
3403
|
+
case DT_INT8: case DT_UINT8:
|
3404
|
+
case DT_INT16: case DT_UINT16:
|
3405
|
+
case DT_INT32: case DT_UINT32:
|
3406
|
+
case DT_FLOAT32: case DT_FLOAT64:
|
3407
|
+
disp_raw_data((char *)str+fp->offset, fp->type, fp->len, ' ', 1);
|
3408
|
+
break;
|
3409
|
+
|
3410
|
+
case NT_DT_POINTER:
|
3411
|
+
fprintf(stdout,"(raw data of unknown type)\n");
|
3412
|
+
break;
|
3413
|
+
|
3414
|
+
case NT_DT_CHAR_PTR: /* look for string of length <= 40 */
|
3415
|
+
{
|
3416
|
+
char * sp;
|
3417
|
+
int len;
|
3418
|
+
|
3419
|
+
/* start by sucking the pointer stored here */
|
3420
|
+
sp = *(char **)((char *)str + fp->offset);
|
3421
|
+
|
3422
|
+
if( ! sp ){ fprintf(stdout,"(NULL)\n"); break; } /* anything? */
|
3423
|
+
|
3424
|
+
/* see if we have a printable string here */
|
3425
|
+
for(len = 0; len <= 40 && *sp && isprint(*sp); len++, sp++ )
|
3426
|
+
;
|
3427
|
+
if( len > 40 )
|
3428
|
+
fprintf(stdout,"(apparent long string)\n");
|
3429
|
+
else if ( len == 0 )
|
3430
|
+
fprintf(stdout,"(empty string)\n");
|
3431
|
+
else if( *sp && !isprint(*sp) ) /* if no termination, it's bad */
|
3432
|
+
fprintf(stdout,"(non-printable string)\n");
|
3433
|
+
else /* woohoo! a good string */
|
3434
|
+
fprintf(stdout,"'%.40s'\n",*(char **)((char *)str + fp->offset));
|
3435
|
+
break;
|
3436
|
+
}
|
3437
|
+
|
3438
|
+
case NT_DT_EXT_PTR:
|
3439
|
+
{
|
3440
|
+
nifti1_extension * extp;
|
3441
|
+
|
3442
|
+
/* yank the address sitting there into extp */
|
3443
|
+
extp = *(nifti1_extension **)((char *)str + fp->offset);
|
3444
|
+
|
3445
|
+
/* the user may use -disp_exts to display all of them */
|
3446
|
+
if( extp ) disp_nifti1_extension(NULL, extp, 6);
|
3447
|
+
else fprintf(stdout,"(NULL)\n");
|
3448
|
+
break;
|
3449
|
+
}
|
3450
|
+
|
3451
|
+
case NT_DT_STRING:
|
3452
|
+
{
|
3453
|
+
char * charp = (char *)str + fp->offset;
|
3454
|
+
fprintf(stdout,"%.*s\n", fp->len, charp);
|
3455
|
+
break;
|
3456
|
+
}
|
3457
|
+
}
|
3458
|
+
}
|
3459
|
+
|
3460
|
+
return 0;
|
3461
|
+
}
|
3462
|
+
|
3463
|
+
|
3464
|
+
/*----------------------------------------------------------------------
|
3465
|
+
* no display, just return whether any fields differ
|
3466
|
+
*----------------------------------------------------------------------*/
|
3467
|
+
int diff_field(field_s *fieldp, void * str0, void * str1, int nfields)
|
3468
|
+
{
|
3469
|
+
field_s * fp;
|
3470
|
+
char * cp0, * cp1;
|
3471
|
+
int fnum, c, size;
|
3472
|
+
|
3473
|
+
fp = fieldp;
|
3474
|
+
for( fnum = 0; fnum < nfields; fnum++, fp++ )
|
3475
|
+
{
|
3476
|
+
switch( fp->type ){
|
3477
|
+
case DT_UNKNOWN: /* all basic types are easy */
|
3478
|
+
case DT_INT8:
|
3479
|
+
case DT_INT16:
|
3480
|
+
case DT_INT32:
|
3481
|
+
case DT_FLOAT32:
|
3482
|
+
case NT_DT_STRING:
|
3483
|
+
size = fp->size * fp->len; /* total field size */
|
3484
|
+
cp0 = (char *)str0 + fp->offset;
|
3485
|
+
cp1 = (char *)str1 + fp->offset;
|
3486
|
+
for( c = 0; c < size; c++, cp0++, cp1++ )
|
3487
|
+
if( *cp0 != *cp1 ) break;
|
3488
|
+
|
3489
|
+
if(c < size) return 1; /* found a diff */
|
3490
|
+
|
3491
|
+
break;
|
3492
|
+
|
3493
|
+
case NT_DT_POINTER: /* let's pass on these - no diff */
|
3494
|
+
case NT_DT_CHAR_PTR:
|
3495
|
+
|
3496
|
+
break;
|
3497
|
+
|
3498
|
+
case NT_DT_EXT_PTR:
|
3499
|
+
{
|
3500
|
+
nifti1_extension * ext0, * ext1;
|
3501
|
+
|
3502
|
+
ext0 = *(nifti1_extension **)((char *)str0 + fp->offset);
|
3503
|
+
ext1 = *(nifti1_extension **)((char *)str1 + fp->offset);
|
3504
|
+
|
3505
|
+
if( ! ext0 && ! ext1 ) break; /* continue on */
|
3506
|
+
|
3507
|
+
if( ext0 && ! ext1 ) return 1; /* pointer diff is diff */
|
3508
|
+
if( ! ext0 && ext1 ) return 1;
|
3509
|
+
|
3510
|
+
/* just check size and type for a single extension */
|
3511
|
+
if( ext0->esize != ext1->esize ) return 1;
|
3512
|
+
if( ext0->ecode != ext1->ecode ) return 1;
|
3513
|
+
|
3514
|
+
break;
|
3515
|
+
}
|
3516
|
+
}
|
3517
|
+
}
|
3518
|
+
|
3519
|
+
return 0; /* no diffs found */
|
3520
|
+
}
|
3521
|
+
|
3522
|
+
|
3523
|
+
/*----------------------------------------------------------------------
|
3524
|
+
* display a single extension
|
3525
|
+
*----------------------------------------------------------------------*/
|
3526
|
+
int disp_nifti1_extension(char *mesg, nifti1_extension * ext, int maxlen)
|
3527
|
+
{
|
3528
|
+
int len;
|
3529
|
+
if( mesg ) fputs(mesg, stdout);
|
3530
|
+
|
3531
|
+
if( !ext )
|
3532
|
+
{
|
3533
|
+
fprintf(stderr,"** no extension to display\n");
|
3534
|
+
return 1;
|
3535
|
+
}
|
3536
|
+
|
3537
|
+
fprintf(stdout,"ecode = %d, esize = %d, edata = ",
|
3538
|
+
ext->ecode, ext->esize);
|
3539
|
+
|
3540
|
+
if( !ext->edata )
|
3541
|
+
fprintf(stdout,"(NULL)\n");
|
3542
|
+
else if ( ext->ecode == NIFTI_ECODE_AFNI ||
|
3543
|
+
ext->ecode == NIFTI_ECODE_COMMENT )
|
3544
|
+
{
|
3545
|
+
len = ext->esize-8;
|
3546
|
+
if( maxlen >= 0 && len > maxlen ) len = maxlen;
|
3547
|
+
fprintf(stdout,"%.*s\n", len, (char *)ext->edata);
|
3548
|
+
}
|
3549
|
+
else
|
3550
|
+
fprintf(stdout,"(unknown data type)\n");
|
3551
|
+
|
3552
|
+
fflush(stdout);
|
3553
|
+
|
3554
|
+
return 0;
|
3555
|
+
}
|
3556
|
+
|
3557
|
+
|
3558
|
+
/*----------------------------------------------------------------------
|
3559
|
+
* return the appropritate pointer into the g_hdr_fields struct
|
3560
|
+
*----------------------------------------------------------------------*/
|
3561
|
+
field_s * get_hdr_field( char * fname, int show_fail )
|
3562
|
+
{
|
3563
|
+
field_s * fp;
|
3564
|
+
int c;
|
3565
|
+
|
3566
|
+
if( ! fname || *fname == '\0' ) return NULL;
|
3567
|
+
|
3568
|
+
fp = g_hdr_fields;
|
3569
|
+
for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ )
|
3570
|
+
if( strcmp(fname, fp->name) == 0 ) break;
|
3571
|
+
|
3572
|
+
if( c == NT_HDR_NUM_FIELDS )
|
3573
|
+
{
|
3574
|
+
if( show_fail > 0 )
|
3575
|
+
fprintf(stderr,"** get_hdr_field: field not found in hdr: %s\n",fname);
|
3576
|
+
return NULL;
|
3577
|
+
}
|
3578
|
+
|
3579
|
+
return fp;
|
3580
|
+
}
|
3581
|
+
|
3582
|
+
|
3583
|
+
/*----------------------------------------------------------------------
|
3584
|
+
* return the appropritate pointer into the g_hdr_fields struct
|
3585
|
+
*----------------------------------------------------------------------*/
|
3586
|
+
field_s * get_nim_field( char * fname, int show_fail )
|
3587
|
+
{
|
3588
|
+
field_s * fp;
|
3589
|
+
int c;
|
3590
|
+
|
3591
|
+
if( ! fname || *fname == '\0' ) return NULL;
|
3592
|
+
|
3593
|
+
fp = g_nim_fields;
|
3594
|
+
for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ )
|
3595
|
+
if( strcmp(fname, fp->name) == 0 ) break;
|
3596
|
+
|
3597
|
+
if( c == NT_NIM_NUM_FIELDS )
|
3598
|
+
{
|
3599
|
+
if( show_fail > 0 )
|
3600
|
+
fprintf(stderr,"** get_nim_field: field not found in hdr: %s\n",fname);
|
3601
|
+
return NULL;
|
3602
|
+
}
|
3603
|
+
|
3604
|
+
return fp;
|
3605
|
+
}
|
3606
|
+
|
3607
|
+
|
3608
|
+
/*----------------------------------------------------------------------
|
3609
|
+
* return the number of fields that differ
|
3610
|
+
*----------------------------------------------------------------------*/
|
3611
|
+
int diff_hdrs( nifti_1_header * s0, nifti_1_header * s1, int display )
|
3612
|
+
{
|
3613
|
+
field_s * fp = g_hdr_fields;
|
3614
|
+
int c, ndiff = 0;
|
3615
|
+
|
3616
|
+
for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ )
|
3617
|
+
if( diff_field(fp, s0, s1, 1) )
|
3618
|
+
{
|
3619
|
+
if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
|
3620
|
+
if( display ) disp_field(NULL, fp, s1, 1, 0);
|
3621
|
+
ndiff++;
|
3622
|
+
}
|
3623
|
+
|
3624
|
+
return ndiff;
|
3625
|
+
}
|
3626
|
+
|
3627
|
+
|
3628
|
+
/*----------------------------------------------------------------------
|
3629
|
+
* return the number of fields that differ
|
3630
|
+
*----------------------------------------------------------------------*/
|
3631
|
+
int diff_nims( nifti_image * s0, nifti_image * s1, int display )
|
3632
|
+
{
|
3633
|
+
field_s * fp = g_nim_fields;
|
3634
|
+
int c, ndiff = 0;
|
3635
|
+
|
3636
|
+
for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ )
|
3637
|
+
if( diff_field(fp, s0, s1, 1) )
|
3638
|
+
{
|
3639
|
+
if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
|
3640
|
+
if( display ) disp_field(NULL, fp, s1, 1, 0);
|
3641
|
+
ndiff++;
|
3642
|
+
}
|
3643
|
+
|
3644
|
+
return ndiff;
|
3645
|
+
}
|
3646
|
+
|
3647
|
+
|
3648
|
+
/*----------------------------------------------------------------------
|
3649
|
+
* return the number of fields that differ
|
3650
|
+
*----------------------------------------------------------------------*/
|
3651
|
+
int diff_hdrs_list( nifti_1_header * s0, nifti_1_header * s1, str_list * slist,
|
3652
|
+
int display )
|
3653
|
+
{
|
3654
|
+
field_s * fp;
|
3655
|
+
char ** sptr;
|
3656
|
+
int c, ndiff = 0;
|
3657
|
+
|
3658
|
+
sptr = slist->list;
|
3659
|
+
for( c = 0; c < slist->len; c++ )
|
3660
|
+
{
|
3661
|
+
fp = get_hdr_field(*sptr, 1); /* "not found" displayed in func */
|
3662
|
+
if( fp && diff_field(fp, s0, s1, 1) )
|
3663
|
+
{
|
3664
|
+
if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
|
3665
|
+
if( display ) disp_field(NULL, fp, s1, 1, 0);
|
3666
|
+
ndiff++;
|
3667
|
+
}
|
3668
|
+
sptr++;
|
3669
|
+
}
|
3670
|
+
|
3671
|
+
return ndiff;
|
3672
|
+
}
|
3673
|
+
|
3674
|
+
|
3675
|
+
/*----------------------------------------------------------------------
|
3676
|
+
* return the number of fields that differ
|
3677
|
+
*----------------------------------------------------------------------*/
|
3678
|
+
int diff_nims_list( nifti_image * s0, nifti_image * s1, str_list * slist,
|
3679
|
+
int display )
|
3680
|
+
{
|
3681
|
+
field_s * fp;
|
3682
|
+
char ** sptr;
|
3683
|
+
int c, ndiff = 0;
|
3684
|
+
|
3685
|
+
sptr = slist->list;
|
3686
|
+
for( c = 0; c < slist->len; c++ )
|
3687
|
+
{
|
3688
|
+
fp = get_nim_field(*sptr, 1); /* "not found" displayed in func */
|
3689
|
+
if( fp && diff_field(fp, s0, s1, 1) )
|
3690
|
+
{
|
3691
|
+
if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
|
3692
|
+
if( display ) disp_field(NULL, fp, s1, 1, 0);
|
3693
|
+
ndiff++;
|
3694
|
+
}
|
3695
|
+
sptr++;
|
3696
|
+
}
|
3697
|
+
|
3698
|
+
return ndiff;
|
3699
|
+
}
|
3700
|
+
|
3701
|
+
|
3702
|
+
/*----------------------------------------------------------------------
|
3703
|
+
* display data from collapsed_image
|
3704
|
+
*----------------------------------------------------------------------*/
|
3705
|
+
int act_disp_ci( nt_opts * opts )
|
3706
|
+
{
|
3707
|
+
nifti_image * nim;
|
3708
|
+
void * data = NULL;
|
3709
|
+
char space = ' '; /* use space or newline */
|
3710
|
+
int filenum, len, err;
|
3711
|
+
|
3712
|
+
if( opts->dci_lines ) space = '\n'; /* then use newlines as separators */
|
3713
|
+
|
3714
|
+
if( g_debug > 2 && opts->dts )
|
3715
|
+
{
|
3716
|
+
fprintf(stderr,"-d displaying time series at (i,j,k) = (%d,%d,%d)\n"
|
3717
|
+
" for %d nifti datasets...\n\n", opts->ci_dims[1],
|
3718
|
+
opts->ci_dims[2], opts->ci_dims[3], opts->infiles.len);
|
3719
|
+
}
|
3720
|
+
else if ( g_debug > 2 ) /* the general collapsed image form */
|
3721
|
+
{
|
3722
|
+
fprintf(stderr,"-d displaying collapsed image for %d datasets...\n\n"
|
3723
|
+
" dims = ", opts->infiles.len);
|
3724
|
+
disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1);
|
3725
|
+
}
|
3726
|
+
|
3727
|
+
for( filenum = 0; filenum < opts->infiles.len; filenum++ )
|
3728
|
+
{
|
3729
|
+
err = 0;
|
3730
|
+
nim = nt_image_read(opts, opts->infiles.list[filenum], 0);
|
3731
|
+
if( !nim ) continue; /* errors are printed from library */
|
3732
|
+
if( opts->dts && nim->ndim != 4 )
|
3733
|
+
{
|
3734
|
+
fprintf(stderr,"** error: dataset '%s' is not 4-dimensional\n",
|
3735
|
+
nim->fname);
|
3736
|
+
err++;
|
3737
|
+
}
|
3738
|
+
|
3739
|
+
switch( nim->datatype )
|
3740
|
+
{
|
3741
|
+
case DT_INT8: case DT_INT16: case DT_INT32:
|
3742
|
+
case DT_UINT8: case DT_UINT16: case DT_UINT32:
|
3743
|
+
case DT_FLOAT32: case DT_FLOAT64:
|
3744
|
+
if( g_debug > 1 )
|
3745
|
+
fprintf(stderr,"-d datatype %d of size %d\n",
|
3746
|
+
nim->datatype, nim->nbyper);
|
3747
|
+
break;
|
3748
|
+
default:
|
3749
|
+
fprintf(stderr,"** dataset '%s' has unknown type %d\n",
|
3750
|
+
nim->fname, nim->datatype);
|
3751
|
+
err++;
|
3752
|
+
break;
|
3753
|
+
}
|
3754
|
+
|
3755
|
+
if( err ) { nifti_image_free(nim); continue; }
|
3756
|
+
|
3757
|
+
len = nifti_read_collapsed_image(nim, opts->ci_dims, &data);
|
3758
|
+
if( len < 0 || !data )
|
3759
|
+
{
|
3760
|
+
fprintf(stderr,"** FAILURE for dataset '%s'\n", nim->fname);
|
3761
|
+
if( data ) free(data);
|
3762
|
+
err++;
|
3763
|
+
}
|
3764
|
+
|
3765
|
+
/* remove check for length of time series 24 Apr 2006 */
|
3766
|
+
|
3767
|
+
if( err ){ nifti_image_free(nim); continue; }
|
3768
|
+
|
3769
|
+
/* now just print the results */
|
3770
|
+
if( g_debug > 0 )
|
3771
|
+
{
|
3772
|
+
fprintf(stdout,"\ndataset '%s' @ (", nim->fname);
|
3773
|
+
if( opts->dts ) disp_raw_data(opts->ci_dims+1, DT_INT32, 3, ' ', 0);
|
3774
|
+
else disp_raw_data(opts->ci_dims+1, DT_INT32, 7, ' ', 0);
|
3775
|
+
fprintf(stdout,")\n");
|
3776
|
+
}
|
3777
|
+
|
3778
|
+
disp_raw_data(data, nim->datatype, len / nim->nbyper, space, 1);
|
3779
|
+
|
3780
|
+
nifti_image_free(nim);
|
3781
|
+
}
|
3782
|
+
|
3783
|
+
if( data ) free(data);
|
3784
|
+
|
3785
|
+
return 0;
|
3786
|
+
}
|
3787
|
+
|
3788
|
+
|
3789
|
+
int disp_raw_data( void * data, int type, int nvals, char space, int newline )
|
3790
|
+
{
|
3791
|
+
char * dp, fbuf[32];
|
3792
|
+
int c, size;
|
3793
|
+
|
3794
|
+
nifti_datatype_sizes( type, &size, NULL ); /* get nbyper */
|
3795
|
+
|
3796
|
+
for( c = 0, dp = (char *)data; c < nvals; c++, dp += size )
|
3797
|
+
{
|
3798
|
+
switch( type )
|
3799
|
+
{
|
3800
|
+
case DT_INT8:
|
3801
|
+
printf("%d", *(char *)dp);
|
3802
|
+
break;
|
3803
|
+
case DT_INT16:
|
3804
|
+
printf("%d", *(short *)dp);
|
3805
|
+
break;
|
3806
|
+
case DT_INT32:
|
3807
|
+
printf("%d", *(int *)dp);
|
3808
|
+
break;
|
3809
|
+
case DT_UINT8:
|
3810
|
+
printf("%u", *(unsigned char *)dp);
|
3811
|
+
break;
|
3812
|
+
case DT_UINT16:
|
3813
|
+
printf("%u", *(unsigned short *)dp);
|
3814
|
+
break;
|
3815
|
+
case DT_UINT32:
|
3816
|
+
printf("%u", *(unsigned int *)dp);
|
3817
|
+
break;
|
3818
|
+
case DT_FLOAT32:
|
3819
|
+
{
|
3820
|
+
sprintf(fbuf,"%f", *(float *)dp);
|
3821
|
+
clear_float_zeros(fbuf);
|
3822
|
+
printf("%s", fbuf);
|
3823
|
+
break;
|
3824
|
+
}
|
3825
|
+
case DT_FLOAT64:
|
3826
|
+
{
|
3827
|
+
sprintf(fbuf,"%f", *(double *)dp);
|
3828
|
+
clear_float_zeros(fbuf);
|
3829
|
+
printf("%s", fbuf);
|
3830
|
+
break;
|
3831
|
+
}
|
3832
|
+
default:
|
3833
|
+
fprintf(stderr,"** disp_raw_data: unknown type %d\n", type);
|
3834
|
+
return 1;
|
3835
|
+
}
|
3836
|
+
if( c < nvals - 1 ) fputc(space,stdout);
|
3837
|
+
}
|
3838
|
+
|
3839
|
+
if ( newline ) fputc('\n',stdout);
|
3840
|
+
|
3841
|
+
return 0;
|
3842
|
+
}
|
3843
|
+
|
3844
|
+
/*----------------------------------------------------------------------
|
3845
|
+
* remove trailing zeros from string of printed float
|
3846
|
+
* return 1 if something was cleared
|
3847
|
+
* 0 if not
|
3848
|
+
*----------------------------------------------------------------------*/
|
3849
|
+
int clear_float_zeros( char * str )
|
3850
|
+
{
|
3851
|
+
char * dp = strchr(str, '.'), * valp;
|
3852
|
+
int len;
|
3853
|
+
|
3854
|
+
if( !dp ) return 0; /* nothing to clear */
|
3855
|
+
|
3856
|
+
len = strlen(dp);
|
3857
|
+
|
3858
|
+
/* never clear what is just to the right of '.' */
|
3859
|
+
for( valp = dp+len-1; (valp > dp+1) && (*valp==' ' || *valp=='0'); valp-- )
|
3860
|
+
*valp = '\0'; /* clear, so we don't worry about break conditions */
|
3861
|
+
|
3862
|
+
if( valp < dp + len - 1 ) return 1;
|
3863
|
+
return 0;
|
3864
|
+
}
|
3865
|
+
|
3866
|
+
/* return the number of volumes in the nifti_image */
|
3867
|
+
static int num_volumes(nifti_image * nim)
|
3868
|
+
{
|
3869
|
+
int ind, nvols = 1;
|
3870
|
+
|
3871
|
+
if( nim->dim[0] < 1 ) return 0;
|
3872
|
+
|
3873
|
+
for( ind = 4; ind <= nim->dim[0]; ind++ )
|
3874
|
+
nvols *= nim->dim[ind];
|
3875
|
+
|
3876
|
+
return nvols;
|
3877
|
+
}
|
3878
|
+
|
3879
|
+
|
3880
|
+
/*----------------------------------------------------------------------
|
3881
|
+
* create a new dataset using sub-brick selection
|
3882
|
+
*----------------------------------------------------------------------*/
|
3883
|
+
int act_cbl( nt_opts * opts )
|
3884
|
+
{
|
3885
|
+
nifti_brick_list NBL;
|
3886
|
+
nifti_image * nim;
|
3887
|
+
char * fname, * selstr, * cp;
|
3888
|
+
int * blist;
|
3889
|
+
int err = 0;
|
3890
|
+
|
3891
|
+
if( g_debug > 2 )
|
3892
|
+
fprintf(stderr,"-d copying file info from '%s' to '%s'\n",
|
3893
|
+
opts->infiles.list[0], opts->prefix);
|
3894
|
+
|
3895
|
+
/* sanity checks */
|
3896
|
+
if( ! opts->prefix ) {
|
3897
|
+
fprintf(stderr,"** error: -prefix is required with -cbl function\n");
|
3898
|
+
return 1;
|
3899
|
+
} else if( opts->infiles.len > 1 ) {
|
3900
|
+
fprintf(stderr,"** sorry, at the moment -cbl allows only 1 input\n");
|
3901
|
+
return 1;
|
3902
|
+
}
|
3903
|
+
|
3904
|
+
/* remove selector from fname, and copy selector string */
|
3905
|
+
fname = nifti_strdup(opts->infiles.list[0]);
|
3906
|
+
cp = strchr(fname,'['); if( !cp ) cp = strchr(fname,'{');
|
3907
|
+
|
3908
|
+
if( !cp ) {
|
3909
|
+
if( g_debug > 1 )
|
3910
|
+
fprintf(stderr,"-d using -cbl without brick list in '%s'\n",fname);
|
3911
|
+
selstr = nifti_strdup("[0..$]");
|
3912
|
+
} else {
|
3913
|
+
selstr = nifti_strdup(cp);
|
3914
|
+
*cp = '\0'; /* remove selection string from fname */
|
3915
|
+
}
|
3916
|
+
|
3917
|
+
if( g_debug > 1 )
|
3918
|
+
fprintf(stderr,"+d -cbl: using '%s' for selection string\n", selstr);
|
3919
|
+
|
3920
|
+
nim = nt_image_read(opts, fname, 0); /* get image */
|
3921
|
+
if( !nim ) return 1;
|
3922
|
+
|
3923
|
+
/* since nt can be zero now (sigh), check for it 02 Mar 2006 [rickr] */
|
3924
|
+
blist = nifti_get_intlist(nim->nt > 0 ? num_volumes(nim) : 1, selstr);
|
3925
|
+
nifti_image_free(nim); /* throw away, will re-load */
|
3926
|
+
if( !blist ){
|
3927
|
+
fprintf(stderr,"** failed sub-brick selection using '%s'\n",selstr);
|
3928
|
+
free(fname); free(selstr); return 1;
|
3929
|
+
}
|
3930
|
+
|
3931
|
+
nim = nt_read_bricks(opts, fname, blist[0], blist+1, &NBL);
|
3932
|
+
free(blist); /* with this */
|
3933
|
+
if( !nim ){ free(fname); free(selstr); return 1; }
|
3934
|
+
|
3935
|
+
if( g_debug > 1 ) fprintf(stderr,"+d sub-bricks loaded\n");
|
3936
|
+
|
3937
|
+
/* add command as COMMENT extension */
|
3938
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
3939
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
3940
|
+
fprintf(stderr,"** failed to add command to image as extension\n");
|
3941
|
+
|
3942
|
+
/* replace filenames using prefix */
|
3943
|
+
if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
|
3944
|
+
{
|
3945
|
+
fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix);
|
3946
|
+
err++;
|
3947
|
+
}
|
3948
|
+
|
3949
|
+
if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1);
|
3950
|
+
|
3951
|
+
/* and finally, write out results */
|
3952
|
+
if( err == 0 && nifti_nim_is_valid(nim, g_debug) )
|
3953
|
+
nifti_image_write_bricks(nim, &NBL);
|
3954
|
+
|
3955
|
+
nifti_image_free(nim);
|
3956
|
+
nifti_free_NBL(&NBL);
|
3957
|
+
free(fname);
|
3958
|
+
free(selstr);
|
3959
|
+
|
3960
|
+
return 0;
|
3961
|
+
}
|
3962
|
+
|
3963
|
+
|
3964
|
+
/*----------------------------------------------------------------------
|
3965
|
+
* create a new dataset using read_collapsed_image
|
3966
|
+
*----------------------------------------------------------------------*/
|
3967
|
+
int act_cci( nt_opts * opts )
|
3968
|
+
{
|
3969
|
+
nifti_image * nim;
|
3970
|
+
int c;
|
3971
|
+
|
3972
|
+
if( g_debug > 2 )
|
3973
|
+
fprintf(stderr,"-d collapsing file info from '%s' to '%s'\n",
|
3974
|
+
opts->infiles.list[0], opts->prefix);
|
3975
|
+
|
3976
|
+
/* sanity checks */
|
3977
|
+
if( ! opts->prefix ) {
|
3978
|
+
fprintf(stderr,"** error: -prefix is required with -cci function\n");
|
3979
|
+
return 1;
|
3980
|
+
} else if( opts->infiles.len > 1 ) {
|
3981
|
+
fprintf(stderr,"** sorry, at the moment -cci allows only 1 input\n");
|
3982
|
+
return 1;
|
3983
|
+
}
|
3984
|
+
|
3985
|
+
nim = nt_image_read(opts, opts->infiles.list[0], 0);
|
3986
|
+
if( !nim ) return 1;
|
3987
|
+
nim->data = NULL; /* just to be sure */
|
3988
|
+
|
3989
|
+
if( nifti_read_collapsed_image(nim, opts->ci_dims, &nim->data) < 0 )
|
3990
|
+
{
|
3991
|
+
nifti_image_free(nim);
|
3992
|
+
return 1;
|
3993
|
+
}
|
3994
|
+
|
3995
|
+
/* add command as COMMENT extension */
|
3996
|
+
if( opts->keep_hist && nifti_add_extension(nim, opts->command,
|
3997
|
+
strlen(opts->command), NIFTI_ECODE_COMMENT) )
|
3998
|
+
fprintf(stderr,"** failed to add command to image as extension\n");
|
3999
|
+
|
4000
|
+
/* replace filenames using prefix */
|
4001
|
+
if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
|
4002
|
+
{
|
4003
|
+
fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix);
|
4004
|
+
nifti_image_free(nim);
|
4005
|
+
return 1;
|
4006
|
+
}
|
4007
|
+
|
4008
|
+
for( c = 1; c < 8; c++ ) /* nuke any collapsed dimension */
|
4009
|
+
if( opts->ci_dims[c] >= 0 ) nim->dim[c] = 1;
|
4010
|
+
|
4011
|
+
nifti_update_dims_from_array(nim);
|
4012
|
+
|
4013
|
+
if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1);
|
4014
|
+
|
4015
|
+
/* and finally, write out results */
|
4016
|
+
if( nifti_nim_is_valid(nim, g_debug) ) nifti_image_write(nim);
|
4017
|
+
|
4018
|
+
nifti_image_free(nim);
|
4019
|
+
|
4020
|
+
return 0;
|
4021
|
+
}
|
4022
|
+
|
4023
|
+
|
4024
|
+
/*----------------------------------------------------------------------
|
4025
|
+
* free all of the lists in the struct
|
4026
|
+
* note: strings were not allocated
|
4027
|
+
*----------------------------------------------------------------------*/
|
4028
|
+
static int free_opts_mem( nt_opts * nopt )
|
4029
|
+
{
|
4030
|
+
if( !nopt ) return 1;
|
4031
|
+
|
4032
|
+
if( nopt->elist.list ) free(nopt->elist.list);
|
4033
|
+
if( nopt->etypes.list ) free(nopt->etypes.list);
|
4034
|
+
if( nopt->flist.list ) free(nopt->flist.list);
|
4035
|
+
if( nopt->vlist.list ) free(nopt->vlist.list);
|
4036
|
+
if( nopt->infiles.list ) free(nopt->infiles.list);
|
4037
|
+
|
4038
|
+
return 0;
|
4039
|
+
}
|
4040
|
+
|
4041
|
+
|
4042
|
+
/*----------------------------------------------------------------------
|
4043
|
+
* wrapper for nifti_image_read
|
4044
|
+
*
|
4045
|
+
* this adds the option to generage an empty image, if the
|
4046
|
+
* filename starts with "MAKE_IM"
|
4047
|
+
*----------------------------------------------------------------------*/
|
4048
|
+
nifti_image * nt_image_read( nt_opts * opts, char * fname, int doread )
|
4049
|
+
{
|
4050
|
+
if( !opts || !fname ) {
|
4051
|
+
fprintf(stderr,"** nt_image_read: bad params (%p,%p)\n",
|
4052
|
+
(void *)opts, (void *)fname);
|
4053
|
+
return NULL;
|
4054
|
+
}
|
4055
|
+
|
4056
|
+
/* if the user does not want an empty image, do normal image_read */
|
4057
|
+
if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) {
|
4058
|
+
if(g_debug > 1)
|
4059
|
+
fprintf(stderr,"-d calling nifti_image_read(%s,%d)\n",fname,doread);
|
4060
|
+
return nifti_image_read(fname, doread);
|
4061
|
+
}
|
4062
|
+
|
4063
|
+
/* so generate an emtpy image */
|
4064
|
+
if(g_debug > 1) {
|
4065
|
+
fprintf(stderr,"+d NT_IR: generating EMPTY IMAGE from %s...\n",fname);
|
4066
|
+
if(g_debug > 2) {
|
4067
|
+
printf(" new_dim[8] = ");
|
4068
|
+
disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1);
|
4069
|
+
printf(" new_datatype = %d\n", opts->new_datatype);
|
4070
|
+
fflush(stdout);
|
4071
|
+
}
|
4072
|
+
}
|
4073
|
+
|
4074
|
+
/* create a new nifti_image, with data depending on doread */
|
4075
|
+
return nifti_make_new_nim(opts->new_dim, opts->new_datatype, doread);
|
4076
|
+
}
|
4077
|
+
|
4078
|
+
|
4079
|
+
/*----------------------------------------------------------------------
|
4080
|
+
* wrapper for nifti_read_header
|
4081
|
+
*
|
4082
|
+
* this adds the option to generage an empty image, if the
|
4083
|
+
* filename starts with "MAKE_IM"
|
4084
|
+
*----------------------------------------------------------------------*/
|
4085
|
+
nifti_1_header * nt_read_header(nt_opts * opts, char * fname, int * swapped,
|
4086
|
+
int check)
|
4087
|
+
{
|
4088
|
+
/* swapped is not necessary */
|
4089
|
+
if( !opts || !fname ) {
|
4090
|
+
fprintf(stderr,"** nt_read_header: bad params (%p,%p)\n",
|
4091
|
+
(void *)opts,(void *)fname);
|
4092
|
+
return NULL;
|
4093
|
+
}
|
4094
|
+
|
4095
|
+
/* if the user does not want an empty image, do normal image_read */
|
4096
|
+
if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) {
|
4097
|
+
if(g_debug > 1)
|
4098
|
+
fprintf(stderr,"-d calling nifti_read_header(%s,...)\n", fname);
|
4099
|
+
return nifti_read_header(fname, swapped, check);
|
4100
|
+
}
|
4101
|
+
|
4102
|
+
/* so generate an emtpy image */
|
4103
|
+
if(g_debug > 1) {
|
4104
|
+
fprintf(stderr,"+d NT_RH: generating EMPTY IMAGE from %s...\n",fname);
|
4105
|
+
if(g_debug > 2) {
|
4106
|
+
printf(" new_dim[8] = ");
|
4107
|
+
disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1);
|
4108
|
+
printf(" new_datatype = %d\n", opts->new_datatype);
|
4109
|
+
fflush(stdout);
|
4110
|
+
}
|
4111
|
+
}
|
4112
|
+
|
4113
|
+
/* return creation of new header */
|
4114
|
+
return nifti_make_new_header(opts->new_dim, opts->new_datatype);
|
4115
|
+
}
|
4116
|
+
|
4117
|
+
|
4118
|
+
|
4119
|
+
/*----------------------------------------------------------------------
|
4120
|
+
* wrapper for nifti_read_header
|
4121
|
+
*
|
4122
|
+
* this adds the option to generage an empty image, if the
|
4123
|
+
* filename starts with "MAKE_IM"
|
4124
|
+
*----------------------------------------------------------------------*/
|
4125
|
+
nifti_image * nt_read_bricks(nt_opts * opts, char * fname, int len, int * list,
|
4126
|
+
nifti_brick_list * NBL)
|
4127
|
+
{
|
4128
|
+
nifti_image * nim;
|
4129
|
+
int c;
|
4130
|
+
|
4131
|
+
/* swapped is not necessary */
|
4132
|
+
if( !opts || !fname || !NBL ) {
|
4133
|
+
fprintf(stderr,"** nt_read_bricks: bad params (%p,%p,%p)\n",
|
4134
|
+
(void *)opts, (void *)fname, (void *)NBL);
|
4135
|
+
return NULL;
|
4136
|
+
}
|
4137
|
+
|
4138
|
+
/* if the user does not want an empty image, do normal read_bricks */
|
4139
|
+
if( strncmp(fname,NT_MAKE_IM_NAME,strlen(NT_MAKE_IM_NAME)) ) {
|
4140
|
+
if(g_debug > 1)
|
4141
|
+
fprintf(stderr,"-d calling nifti_image_read_bricks(%s,...)\n",fname);
|
4142
|
+
return nifti_image_read_bricks(fname, len, list, NBL);
|
4143
|
+
}
|
4144
|
+
|
4145
|
+
/* so generate an emtpy image */
|
4146
|
+
if(g_debug > 1) {
|
4147
|
+
fprintf(stderr,"+d NT_RB: generating EMPTY IMAGE from %s...\n",fname);
|
4148
|
+
if(g_debug > 2) {
|
4149
|
+
printf(" new_dim[8] = ");
|
4150
|
+
disp_raw_data(opts->new_dim, DT_INT32, 8, ' ', 1);
|
4151
|
+
printf(" new_datatype = %d\n", opts->new_datatype);
|
4152
|
+
if( list && len > 0 ) {
|
4153
|
+
printf(" brick_list[%d] = ", len);
|
4154
|
+
disp_raw_data(list, DT_INT32, len, ' ', 1);
|
4155
|
+
}
|
4156
|
+
fflush(stdout); /* disp_raw_data uses stdout */
|
4157
|
+
}
|
4158
|
+
}
|
4159
|
+
|
4160
|
+
/* first, get nim struct without data */
|
4161
|
+
nim = nifti_make_new_nim(opts->new_dim, opts->new_datatype, 0);
|
4162
|
+
if( !nim ) {
|
4163
|
+
fprintf(stderr,"** nt_read_bricks, nifti_make_new_nim failure\n");
|
4164
|
+
return NULL;
|
4165
|
+
}
|
4166
|
+
|
4167
|
+
/* now populate NBL (can be based only on len and nim) */
|
4168
|
+
NBL->nbricks = len;
|
4169
|
+
NBL->bsize = (size_t)nim->nbyper * nim->nx * nim->ny * nim->nz;
|
4170
|
+
NBL->bricks = (void **)calloc(NBL->nbricks, sizeof(void *));
|
4171
|
+
if( !NBL->bricks ){
|
4172
|
+
fprintf(stderr,"** NRB: failed to alloc %d pointers\n",NBL->nbricks);
|
4173
|
+
nifti_image_free(nim);
|
4174
|
+
return NULL;
|
4175
|
+
}
|
4176
|
+
|
4177
|
+
if(g_debug > 1)
|
4178
|
+
fprintf(stderr,"+d NRB, allocating %d bricks of %u bytes...\n",
|
4179
|
+
NBL->nbricks, (unsigned)NBL->bsize);
|
4180
|
+
|
4181
|
+
/* now allocate the data pointers */
|
4182
|
+
for( c = 0; c < len; c++ ) {
|
4183
|
+
NBL->bricks[c] = calloc(1, NBL->bsize);
|
4184
|
+
if( !NBL->bricks[c] ){
|
4185
|
+
fprintf(stderr,"** NRB: failed to alloc brick %d of %u bytes\n",
|
4186
|
+
c, (unsigned)NBL->bsize);
|
4187
|
+
nifti_free_NBL(NBL); nifti_image_free(nim); return NULL;
|
4188
|
+
}
|
4189
|
+
}
|
4190
|
+
|
4191
|
+
return nim;
|
4192
|
+
}
|
4193
|
+
|