c_nifti 0.0.1
Sign up to get free protection for your applications and to get access to all the features.
- 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
data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/comment_test.sh
ADDED
@@ -0,0 +1,65 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
|
13
|
+
# add some comment and afni extensions, then display them
|
14
|
+
if \
|
15
|
+
${NT} -keep_hist -prefix ${DATA}/f4.comment -infiles ${DATA}/anat0.nii \
|
16
|
+
-add_comment '4 slice time series' \
|
17
|
+
-add_afni_ext 'and an AFNI extension' \
|
18
|
+
-add_comment 'how about a question AND a comment?'
|
19
|
+
then
|
20
|
+
echo ""
|
21
|
+
else
|
22
|
+
echo "add comment failed"
|
23
|
+
exit 1
|
24
|
+
fi
|
25
|
+
|
26
|
+
if ${NT} -disp_ext -infiles ${DATA}/f4.comment.nii
|
27
|
+
then
|
28
|
+
echo ""
|
29
|
+
else
|
30
|
+
echo "failed"
|
31
|
+
exit 1
|
32
|
+
fi
|
33
|
+
|
34
|
+
if ${NT} -cbl -infiles ${DATA}/f4.comment.nii -prefix ${DATA}/f4.to.clear.nii
|
35
|
+
then
|
36
|
+
echo ""
|
37
|
+
else
|
38
|
+
echo "failed"
|
39
|
+
exit 1
|
40
|
+
fi
|
41
|
+
|
42
|
+
if ${NT} -overwrite -strip -infiles ${DATA}/f4.to.clear.nii
|
43
|
+
then
|
44
|
+
echo ""
|
45
|
+
else
|
46
|
+
echo "failed"
|
47
|
+
exit 1
|
48
|
+
fi
|
49
|
+
|
50
|
+
if ${NT} -disp_ext -infiles ${DATA}/f4.to.clear.nii
|
51
|
+
then
|
52
|
+
echo ""
|
53
|
+
else
|
54
|
+
echo "failed"
|
55
|
+
exit 1
|
56
|
+
fi
|
57
|
+
|
58
|
+
if ${NT} -diff_nim -infiles ${DATA}/f4.comment.nii ${DATA}/f4.to.clear.nii
|
59
|
+
then
|
60
|
+
echo "failed -- no changes found"
|
61
|
+
exit 1
|
62
|
+
else
|
63
|
+
echo "diff succeed -- found changes"
|
64
|
+
fi
|
65
|
+
|
@@ -0,0 +1,46 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
# get the time series for a slice, get the same sub-bricks,
|
13
|
+
# compare nifti_images, and display the time series again
|
14
|
+
#
|
15
|
+
# this should match the previous
|
16
|
+
|
17
|
+
${NT} -keep_hist -cci 3 3 3 -1 -1 -1 -1 -prefix ${DATA}/r.333 -infiles ${DATA}/run.210.nii
|
18
|
+
if [ $? -ne 0 ] ; then
|
19
|
+
echo cci failed
|
20
|
+
fi
|
21
|
+
|
22
|
+
${NT} -keep_hist -cci 3 3 3 -1 1 1 1 -prefix ${DATA}/r.333.111 -infiles ${DATA}/run.210.nii
|
23
|
+
if [ $? -ne 0 ] ; then
|
24
|
+
echo cci failed
|
25
|
+
fi
|
26
|
+
|
27
|
+
${NT} -disp_ci -1 -1 -1 -1 -1 -1 -1 -infiles ${DATA}/r.333.111.nii -quiet \
|
28
|
+
| tee o.10a.dci.1
|
29
|
+
if [ $? -ne 0 ] ; then
|
30
|
+
echo disp_ci failed
|
31
|
+
fi
|
32
|
+
|
33
|
+
${NT} -disp_ci 0 0 0 -1 1 1 1 -infiles ${DATA}/r.333.nii -quiet \
|
34
|
+
| tee o.10a.dci.2
|
35
|
+
if [ $? -ne 0 ] ; then
|
36
|
+
echo disp_ci failed
|
37
|
+
fi
|
38
|
+
|
39
|
+
if diff o.10a.dci.?
|
40
|
+
then
|
41
|
+
echo ""
|
42
|
+
rm -f o.10a.dci* ${DATA}/r.333*
|
43
|
+
else
|
44
|
+
echo '** failure, o.10a.dci timeseries files differ'
|
45
|
+
exit 1
|
46
|
+
fi
|
@@ -0,0 +1,61 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
|
13
|
+
# - create datasets out of nothing
|
14
|
+
#
|
15
|
+
# - modify some fields and compare against other datasets
|
16
|
+
rm -f ${DATA}/new_epi.nii
|
17
|
+
# just test a basic make im, mostly to capture the debug output
|
18
|
+
${NT} -make_im -debug 3 -new_dim 4 64 64 21 180 0 0 0 -prefix ${DATA}/new_epi.nii
|
19
|
+
if [ $? -ne 0 ] ; then
|
20
|
+
echo failed
|
21
|
+
exit 1
|
22
|
+
fi
|
23
|
+
|
24
|
+
# compare hdr and nim in a fresh image to the existing one
|
25
|
+
${NT} -diff_hdr -new_dim 4 64 64 21 180 0 0 0 \
|
26
|
+
-infiles MAKE_IM ${DATA}/stat0.nii
|
27
|
+
if [ $? = 0 ] ; then
|
28
|
+
echo unexpected 0 return code in diff
|
29
|
+
exit 1
|
30
|
+
fi
|
31
|
+
|
32
|
+
${NT} -diff_nim -new_dim 4 64 64 21 180 0 0 0 \
|
33
|
+
-infiles MAKE_IM ${DATA}/stat0.nii
|
34
|
+
if [ $? = 0 ] ; then
|
35
|
+
echo unexpected 0 return code in diff
|
36
|
+
exit 1
|
37
|
+
fi
|
38
|
+
|
39
|
+
|
40
|
+
rm -f ${DATA}/epi_180_pixdim.nii
|
41
|
+
|
42
|
+
# clean up the nim by adjusting pixdim (from empty MAKE_IM)
|
43
|
+
${NT} -mod_hdr -new_dim 4 64 64 21 180 0 0 0 \
|
44
|
+
-mod_field pixdim '0.0 4.0 4.0 6.0 3.0 1.0 1.0 1.0' \
|
45
|
+
-prefix ${DATA}/epi_180_pixdim.nii -infiles MAKE_IM
|
46
|
+
if [ $? -ne 0 ] ; then
|
47
|
+
echo mod_hdr failed
|
48
|
+
exit 1
|
49
|
+
fi
|
50
|
+
|
51
|
+
|
52
|
+
# and compare again
|
53
|
+
${NT} -diff_nim -infiles ${DATA}/stat0.nii ${DATA}/epi_180_pixdim.nii
|
54
|
+
if [ $? -ne 0 ] ; then
|
55
|
+
echo found changes -- success.
|
56
|
+
else
|
57
|
+
echo diff failed to find differences.
|
58
|
+
exit 1
|
59
|
+
fi
|
60
|
+
|
61
|
+
exit 0
|
@@ -0,0 +1,75 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii | tee o.08.ts.19.36.11
|
13
|
+
|
14
|
+
if [ $? -ne 0 ] ; then
|
15
|
+
echo disp_ts failed
|
16
|
+
exit 1
|
17
|
+
fi
|
18
|
+
rm -f o.08.ts.19.36.11
|
19
|
+
|
20
|
+
${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii \
|
21
|
+
| awk '{print $(NF-1), $NF, $1, $2}' | tee o.09.ts4.1.awk
|
22
|
+
|
23
|
+
if [ $? -ne 0 ] ; then
|
24
|
+
echo disp_ts failed
|
25
|
+
exit 1
|
26
|
+
fi
|
27
|
+
|
28
|
+
${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/f4.nii | tee o.09.ts4.2.awk
|
29
|
+
|
30
|
+
if diff o.09.ts4.1.awk o.09.ts4.2.awk
|
31
|
+
then
|
32
|
+
echo ""
|
33
|
+
else
|
34
|
+
echo '** failure, ts4 files differ'
|
35
|
+
exit 1
|
36
|
+
fi
|
37
|
+
rm -f 0.09.ts4.1.awk o.09.ts4.2.awk ${DATA}/f4.nii
|
38
|
+
exit 0
|
39
|
+
|
40
|
+
# get the time series for a slice, get the same sub-bricks,
|
41
|
+
# compare nifti_images, and display the time series again
|
42
|
+
#
|
43
|
+
# this should match the previous
|
44
|
+
|
45
|
+
if ${NT} -keep_hist -cci 19 36 -1 -1 0 0 0 -prefix ${DATA}f.19.36 \
|
46
|
+
-infiles ${DATA}/stat0.nii
|
47
|
+
then
|
48
|
+
echo ""
|
49
|
+
else
|
50
|
+
echo cci failed
|
51
|
+
exit 1
|
52
|
+
fi
|
53
|
+
|
54
|
+
if ${NT} -keep_hist -cbl -prefix ${DATA}/f.19.36.t4.nii \
|
55
|
+
-infiles ${DATA}/f.19.36.nii'[178..$,0,1]'
|
56
|
+
then
|
57
|
+
echo ""
|
58
|
+
else
|
59
|
+
echo cbi failed
|
60
|
+
exit 0
|
61
|
+
fi
|
62
|
+
|
63
|
+
${NT} -diff_nim -infiles ${DATA}/f.19.36.nii ${DATA}f.19.36.t4.nii | tee o.10.diff_nim
|
64
|
+
if [ $? -ne 0 ] ; then
|
65
|
+
echo f.19.36.nii and f.19.36.t4.nii differ
|
66
|
+
else
|
67
|
+
echo f.19.36.nii and f.19.36.t4.nii do not differ
|
68
|
+
fi
|
69
|
+
|
70
|
+
${NT} -quiet -disp_ci 0 0 11 -1 0 0 0 -infiles f.19.36.t4.nii \
|
71
|
+
| tee o.10.dci.4
|
72
|
+
#diff o.09.ts4.1.awk o.10.dci.4
|
73
|
+
#if( $status ) echo '** failure, o.09 and o.10 ts files differ'
|
74
|
+
|
75
|
+
exit 0
|
data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/fetch_data_test.sh
ADDED
@@ -0,0 +1,45 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
#
|
3
|
+
# arg[1] is TESTING_BINARY_DIR
|
4
|
+
if [ $# -lt 1 ]
|
5
|
+
then
|
6
|
+
echo Missing Binary directory name
|
7
|
+
exit 1
|
8
|
+
fi
|
9
|
+
|
10
|
+
|
11
|
+
if cd $1
|
12
|
+
then
|
13
|
+
echo working in `pwd`
|
14
|
+
else
|
15
|
+
echo can\'t cd to $1
|
16
|
+
exit 1
|
17
|
+
fi
|
18
|
+
|
19
|
+
|
20
|
+
if wget -nd http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz
|
21
|
+
then
|
22
|
+
echo wget succeeded
|
23
|
+
else
|
24
|
+
echo wget failed
|
25
|
+
exit 1
|
26
|
+
fi
|
27
|
+
|
28
|
+
if tar xzvf nifti_regress_data.tgz
|
29
|
+
then
|
30
|
+
echo ""
|
31
|
+
else
|
32
|
+
echo failed tar xzvf nifti_regress_data.tgz
|
33
|
+
exit 1
|
34
|
+
fi
|
35
|
+
|
36
|
+
if rm -f nifti_regress_data.tgz
|
37
|
+
then
|
38
|
+
echo ""
|
39
|
+
else
|
40
|
+
echo can\'t remove ../nifti_regress_data.tgz
|
41
|
+
exit 1
|
42
|
+
fi
|
43
|
+
|
44
|
+
exit 0
|
45
|
+
|
data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/mod_header_test.sh
ADDED
@@ -0,0 +1,60 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
rm -f ${DATA}/anat1*
|
13
|
+
|
14
|
+
if ${NT} -mod_hdr -prefix ${DATA}/anat1 \
|
15
|
+
-infiles ${DATA}/anat0.nii \
|
16
|
+
-mod_field qoffset_x -17.325 -mod_field slice_start 1 \
|
17
|
+
-mod_field descrip "beer, brats and cheese, mmmmm..."
|
18
|
+
then
|
19
|
+
echo ""
|
20
|
+
else
|
21
|
+
echo mod_field failed
|
22
|
+
exit 1
|
23
|
+
fi
|
24
|
+
|
25
|
+
if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
|
26
|
+
then
|
27
|
+
echo diff_hdr failed '(no difference seen)!'
|
28
|
+
exit 1
|
29
|
+
else
|
30
|
+
echo ""
|
31
|
+
fi
|
32
|
+
|
33
|
+
if ${NT} -add_afni_ext "wow, my first extension" \
|
34
|
+
-add_afni_ext "look, my second.." \
|
35
|
+
-overwrite -infiles ${DATA}/anat1.nii
|
36
|
+
then
|
37
|
+
echo ""
|
38
|
+
else
|
39
|
+
echo add_afni_ext failed
|
40
|
+
exit 1
|
41
|
+
fi
|
42
|
+
|
43
|
+
if ${NT} -disp_exts -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
|
44
|
+
then
|
45
|
+
echo ""
|
46
|
+
else
|
47
|
+
echo disp_exts failed
|
48
|
+
exit 1
|
49
|
+
fi
|
50
|
+
|
51
|
+
|
52
|
+
if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
|
53
|
+
then
|
54
|
+
echo diff_hdr failed '(no difference seen)!'
|
55
|
+
exit 1
|
56
|
+
else
|
57
|
+
echo ""
|
58
|
+
fi
|
59
|
+
|
60
|
+
exit 0
|
data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/newfiles_test.sh
ADDED
@@ -0,0 +1,36 @@
|
|
1
|
+
#!/bin/sh
|
2
|
+
|
3
|
+
if [ $# -lt 2 ]
|
4
|
+
then
|
5
|
+
echo Missing nifti tool and Binary directory name
|
6
|
+
exit 1
|
7
|
+
fi
|
8
|
+
|
9
|
+
NT=$1
|
10
|
+
DATA=$2
|
11
|
+
|
12
|
+
rm -f ${DATA}/new* ${DATA}/ncopy*
|
13
|
+
|
14
|
+
# test writing various output file types
|
15
|
+
${NT} -make_im -prefix ${DATA}/new1.hdr
|
16
|
+
${NT} -make_im -prefix ${DATA}/new2.hdr.gz
|
17
|
+
${NT} -make_im -prefix ${DATA}/new3.img.gz
|
18
|
+
${NT} -make_im -prefix ${DATA}/new4.nii.gz
|
19
|
+
${NT} -make_im -prefix ${DATA}/new5.nia
|
20
|
+
|
21
|
+
# test reading them
|
22
|
+
${NT} -copy_im -prefix ${DATA}/ncopy1.nii -infiles ${DATA}/new1.hdr
|
23
|
+
${NT} -copy_im -prefix ${DATA}/ncopy2.nii -infiles ${DATA}/new2.hdr.gz
|
24
|
+
${NT} -copy_im -prefix ${DATA}/ncopy3.nii -infiles ${DATA}/new3.img.gz
|
25
|
+
${NT} -copy_im -prefix ${DATA}/ncopy4.nii -infiles ${DATA}/new4.nii.gz
|
26
|
+
${NT} -copy_im -prefix ${DATA}/ncopy5.nii -infiles ${DATA}/new5.nia
|
27
|
+
|
28
|
+
# verify that they are all the same
|
29
|
+
set count = 0
|
30
|
+
for index in 2 3 4 5 ; do
|
31
|
+
diff ${DATA}/ncopy1.nii ${DATA}/ncopy$index.nii
|
32
|
+
if [ $? -ne 0 ] ; then
|
33
|
+
echo "-- failure on test index $index --"
|
34
|
+
exit 1
|
35
|
+
fi
|
36
|
+
done
|
@@ -0,0 +1,9 @@
|
|
1
|
+
|
2
|
+
# modify the header of default anat, creating a new anat
|
3
|
+
#
|
4
|
+
# then compare the resulting headers
|
5
|
+
|
6
|
+
nifti_tool -mod_hdr -prefix anat1 -infiles anat0.nii \
|
7
|
+
-mod_field qoffset_x -17.325 -mod_field slice_start 1 \
|
8
|
+
-mod_field descrip 'beer, brats and cheese, mmmmm...'
|
9
|
+
nifti_tool -diff_hdr -infiles anat0.nii anat1.nii
|
@@ -0,0 +1,22 @@
|
|
1
|
+
#!/bin/tcsh
|
2
|
+
|
3
|
+
# - add junk extensions to the new anat, overwriting it
|
4
|
+
# - display extensions for the two files
|
5
|
+
# - again, compare the headers
|
6
|
+
|
7
|
+
nifti_tool -add_afni_ext 'wow, my first extension :)' \
|
8
|
+
-add_afni_ext 'look, my second..' \
|
9
|
+
-overwrite -infiles anat1.nii
|
10
|
+
nifti_tool -disp_exts -infiles anat0.nii anat1.nii
|
11
|
+
nifti_tool -diff_hdr -infiles anat0.nii anat1.nii
|
12
|
+
|
13
|
+
# add one more, via a file
|
14
|
+
|
15
|
+
cat > my.extension << EOF
|
16
|
+
here is some formatted
|
17
|
+
extension, added via
|
18
|
+
a text file
|
19
|
+
EOF
|
20
|
+
|
21
|
+
nifti_tool -add_comment_ext 'file:my.extension' -overwrite -infiles anat1.nii
|
22
|
+
nifti_tool -disp_exts -infiles anat1.nii
|