c_nifti 0.0.1

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/comment_test.sh

@@ -0,0 +1,65 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+
+# add some comment and afni extensions, then display them
+if \
+${NT} -keep_hist -prefix ${DATA}/f4.comment -infiles ${DATA}/anat0.nii   \
+           -add_comment '4 slice time series'                      \
+           -add_afni_ext 'and an AFNI extension'                   \
+           -add_comment 'how about a question AND a comment?'
+then
+echo ""
+else
+echo "add comment failed"
+exit 1
+fi
+
+if ${NT} -disp_ext -infiles ${DATA}/f4.comment.nii
+then
+echo ""
+else
+echo "failed"
+exit 1
+fi
+
+if ${NT} -cbl -infiles ${DATA}/f4.comment.nii -prefix ${DATA}/f4.to.clear.nii
+then
+echo ""
+else
+echo "failed"
+exit 1
+fi
+
+if ${NT} -overwrite -strip -infiles ${DATA}/f4.to.clear.nii
+then
+echo ""
+else
+echo "failed"
+exit 1
+fi
+
+if ${NT} -disp_ext -infiles ${DATA}/f4.to.clear.nii
+then
+echo ""
+else
+echo "failed"
+exit 1
+fi
+
+if ${NT} -diff_nim -infiles ${DATA}/f4.comment.nii ${DATA}/f4.to.clear.nii
+then
+echo "failed -- no changes found"
+exit 1
+else
+echo "diff succeed -- found changes"
+fi
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dci_test.sh

@@ -0,0 +1,46 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+# get the time series for a slice, get the same sub-bricks,
+# compare nifti_images, and display the time series again
+#
+# this should match the previous
+
+${NT} -keep_hist -cci 3 3 3 -1 -1 -1 -1 -prefix ${DATA}/r.333 -infiles ${DATA}/run.210.nii
+if [ $? -ne 0 ] ; then
+echo cci failed
+fi
+
+${NT} -keep_hist -cci 3 3 3 -1 1 1 1 -prefix ${DATA}/r.333.111 -infiles ${DATA}/run.210.nii
+if [ $? -ne 0 ] ; then
+echo cci failed
+fi
+
+${NT} -disp_ci -1 -1 -1 -1 -1 -1 -1 -infiles ${DATA}/r.333.111.nii -quiet \
+        | tee o.10a.dci.1
+if [ $? -ne 0 ] ; then
+echo disp_ci failed
+fi
+
+${NT} -disp_ci  0  0  0 -1  1  1  1 -infiles ${DATA}/r.333.nii -quiet \
+        | tee o.10a.dci.2
+if [ $? -ne 0 ] ; then
+echo disp_ci failed
+fi
+
+if diff o.10a.dci.?
+then
+echo ""
+rm -f o.10a.dci* ${DATA}/r.333*
+else
+echo '** failure, o.10a.dci timeseries files differ'
+exit 1
+fi

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dsets_test.sh

@@ -0,0 +1,61 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+
+# - create datasets out of nothing
+#
+# - modify some fields and compare against other datasets
+rm -f ${DATA}/new_epi.nii
+# just test a basic make im, mostly to capture the debug output
+${NT} -make_im -debug 3 -new_dim 4 64 64 21 180 0 0 0 -prefix ${DATA}/new_epi.nii
+if [ $? -ne 0 ] ; then
+echo failed
+exit 1
+fi
+
+# compare hdr and nim in a fresh image to the existing one
+${NT} -diff_hdr -new_dim 4 64 64 21 180 0 0 0      \
+           -infiles MAKE_IM ${DATA}/stat0.nii
+if [ $? = 0 ] ; then
+echo unexpected 0 return code in diff
+exit 1
+fi
+
+${NT} -diff_nim -new_dim 4 64 64 21 180 0 0 0      \
+           -infiles MAKE_IM ${DATA}/stat0.nii
+if [ $? = 0 ] ; then
+echo unexpected 0 return code in diff
+exit 1
+fi
+
+
+rm -f ${DATA}/epi_180_pixdim.nii
+
+# clean up the nim by adjusting pixdim (from empty MAKE_IM)
+${NT} -mod_hdr -new_dim 4 64 64 21 180 0 0 0               \
+           -mod_field pixdim '0.0 4.0 4.0 6.0 3.0 1.0 1.0 1.0'  \
+           -prefix ${DATA}/epi_180_pixdim.nii -infiles MAKE_IM
+if [ $? -ne 0 ] ; then
+echo mod_hdr failed
+exit 1
+fi
+
+
+# and compare again
+${NT} -diff_nim -infiles ${DATA}/stat0.nii ${DATA}/epi_180_pixdim.nii
+if [ $? -ne 0 ] ; then
+echo found changes -- success.
+else
+echo diff failed to find differences.
+exit 1
+fi
+
+exit 0

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/dts_test.sh

@@ -0,0 +1,75 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii | tee o.08.ts.19.36.11
+
+if [ $? -ne 0 ] ; then
+echo disp_ts failed
+exit 1
+fi
+rm -f o.08.ts.19.36.11
+
+${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/stat0.nii \
+        | awk '{print $(NF-1), $NF, $1, $2}' | tee o.09.ts4.1.awk
+
+if [ $? -ne 0 ] ; then
+echo disp_ts failed
+exit 1
+fi
+
+${NT} -quiet -disp_ts 19 36 11 -infiles ${DATA}/f4.nii | tee o.09.ts4.2.awk
+
+if diff o.09.ts4.1.awk o.09.ts4.2.awk
+then
+echo ""
+else
+echo '** failure, ts4 files differ'
+exit 1
+fi
+rm -f 0.09.ts4.1.awk o.09.ts4.2.awk ${DATA}/f4.nii
+exit 0
+
+# get the time series for a slice, get the same sub-bricks,
+# compare nifti_images, and display the time series again
+#
+# this should match the previous
+
+if ${NT} -keep_hist -cci 19 36 -1 -1 0 0 0 -prefix ${DATA}f.19.36 \
+-infiles ${DATA}/stat0.nii
+then
+echo ""
+else
+echo cci failed
+exit 1
+fi
+
+if ${NT} -keep_hist -cbl -prefix ${DATA}/f.19.36.t4.nii \
+           -infiles ${DATA}/f.19.36.nii'[178..$,0,1]'
+then
+echo ""
+else
+echo cbi failed
+exit 0
+fi
+
+${NT} -diff_nim -infiles ${DATA}/f.19.36.nii ${DATA}f.19.36.t4.nii | tee o.10.diff_nim
+if [ $? -ne 0 ] ; then
+echo f.19.36.nii and f.19.36.t4.nii differ
+else
+echo f.19.36.nii and f.19.36.t4.nii do not differ
+fi
+
+${NT} -quiet -disp_ci 0 0 11 -1 0 0 0 -infiles f.19.36.t4.nii \
+          | tee o.10.dci.4
+#diff o.09.ts4.1.awk o.10.dci.4
+#if( $status ) echo '** failure, o.09 and o.10 ts files differ'
+
+exit 0

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/fetch_data_test.sh

@@ -0,0 +1,45 @@
+#!/bin/sh
+#
+# arg[1] is TESTING_BINARY_DIR
+if [ $# -lt 1 ]
+then
+echo Missing Binary directory name
+exit 1
+fi
+
+
+if cd $1
+then
+echo working in `pwd`
+else
+echo can\'t cd to $1
+exit 1
+fi
+
+
+if wget -nd http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz
+then
+echo wget succeeded
+else
+echo wget failed
+exit 1
+fi
+
+if tar xzvf nifti_regress_data.tgz
+then
+echo ""
+else
+echo failed tar xzvf nifti_regress_data.tgz
+exit 1
+fi
+
+if rm -f nifti_regress_data.tgz
+then
+echo ""
+else
+echo can\'t remove ../nifti_regress_data.tgz
+exit 1
+fi
+
+exit 0
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/mod_header_test.sh

@@ -0,0 +1,60 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+rm -f ${DATA}/anat1*
+
+if ${NT} -mod_hdr -prefix ${DATA}/anat1 \
+-infiles ${DATA}/anat0.nii \
+-mod_field qoffset_x -17.325 -mod_field slice_start 1 \
+-mod_field descrip "beer, brats and cheese, mmmmm..."
+then
+echo ""
+else
+echo mod_field failed
+exit 1
+fi
+
+if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
+then
+echo diff_hdr failed '(no difference seen)!'
+exit 1
+else
+echo ""
+fi
+
+if ${NT} -add_afni_ext "wow, my first extension" \
+           -add_afni_ext "look, my second.." \
+           -overwrite -infiles ${DATA}/anat1.nii
+then
+echo ""
+else
+echo add_afni_ext failed
+exit 1
+fi
+
+if ${NT} -disp_exts -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
+then
+echo ""
+else
+echo disp_exts failed
+exit 1
+fi
+
+
+if ${NT} -diff_hdr -infiles ${DATA}/anat0.nii ${DATA}/anat1.nii
+then
+echo diff_hdr failed '(no difference seen)!'
+exit 1
+else
+echo ""
+fi
+
+exit 0

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/cmake_testscripts/newfiles_test.sh

@@ -0,0 +1,36 @@
+#!/bin/sh
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+rm -f ${DATA}/new* ${DATA}/ncopy*
+
+# test writing various output file types
+${NT} -make_im -prefix ${DATA}/new1.hdr
+${NT} -make_im -prefix ${DATA}/new2.hdr.gz
+${NT} -make_im -prefix ${DATA}/new3.img.gz
+${NT} -make_im -prefix ${DATA}/new4.nii.gz
+${NT} -make_im -prefix ${DATA}/new5.nia
+
+# test reading them
+${NT} -copy_im -prefix ${DATA}/ncopy1.nii -infiles ${DATA}/new1.hdr
+${NT} -copy_im -prefix ${DATA}/ncopy2.nii -infiles ${DATA}/new2.hdr.gz
+${NT} -copy_im -prefix ${DATA}/ncopy3.nii -infiles ${DATA}/new3.img.gz
+${NT} -copy_im -prefix ${DATA}/ncopy4.nii -infiles ${DATA}/new4.nii.gz
+${NT} -copy_im -prefix ${DATA}/ncopy5.nii -infiles ${DATA}/new5.nia
+
+# verify that they are all the same
+set count = 0
+for index in 2 3 4 5 ; do
+    diff ${DATA}/ncopy1.nii ${DATA}/ncopy$index.nii
+    if [ $? -ne 0 ] ; then 
+        echo "-- failure on test index $index --"
+        exit 1
+    fi
+done

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c01.versions

@@ -0,0 +1,10 @@
+
+# check the version numbers for the library and tool
+
+nifti_tool -nifti_ver
+nifti_tool -ver
+
+# also, check whether the library was compiled with zlib support
+
+nifti_tool -with_zlib
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c02.nt.help

@@ -0,0 +1,5 @@
+
+nifti_tool -help
+nifti_tool -help_datatypes
+nifti_tool -help_datatypes T
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c03.hist

@@ -0,0 +1,5 @@
+
+# library and tool history
+
+nifti_tool -nifti_hist
+nifti_tool -hist

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c04.disp.anat0.info

@@ -0,0 +1,7 @@
+
+# display header, nifti_image and extensions for default anat
+
+nifti_tool -disp_hdr -infiles anat0
+nifti_tool -disp_nim -infiles anat0
+nifti_tool -disp_ana -infiles anat0
+nifti_tool -disp_ext -infiles anat0

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c05.mod.hdr

@@ -0,0 +1,9 @@
+
+# modify the header of default anat, creating a new anat
+# 
+# then compare the resulting headers
+
+nifti_tool -mod_hdr -prefix anat1 -infiles anat0.nii     \
+           -mod_field qoffset_x -17.325 -mod_field slice_start 1  \
+           -mod_field descrip 'beer, brats and cheese, mmmmm...'
+nifti_tool -diff_hdr -infiles anat0.nii anat1.nii

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/commands/c06.add.ext

@@ -0,0 +1,22 @@
+#!/bin/tcsh
+
+#  - add junk extensions to the new anat, overwriting it
+#  - display extensions for the two files 
+#  - again, compare the headers
+
+nifti_tool -add_afni_ext 'wow, my first extension :)'    \
+           -add_afni_ext 'look, my second..'             \
+           -overwrite -infiles anat1.nii
+nifti_tool -disp_exts -infiles anat0.nii anat1.nii
+nifti_tool -diff_hdr -infiles anat0.nii anat1.nii
+
+# add one more, via a file
+
+cat > my.extension << EOF
+here is some formatted
+  extension, added via
+  a text file
+EOF
+
+nifti_tool -add_comment_ext 'file:my.extension' -overwrite -infiles anat1.nii
+nifti_tool -disp_exts -infiles anat1.nii