c_nifti 0.0.1

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/fslio.tcl

@@ -0,0 +1,83 @@
+#{{{ copyright and setup 
+
+#   FEAT TCL FSLIO wrappers
+#
+#   Stephen Smith, FMRIB Image Analysis Group
+#
+#
+#   
+#   The fslio.tcl file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   fslio.tcl has now been placed in the public domain.
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+#}}}
+
+proc imcp { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/imcp $args" ]
+}
+
+proc imglob { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/imglob $args" ]
+}
+
+proc imln { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/imln $args" ]
+}
+
+proc immv { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/immv $args" ]
+}
+
+proc imrm { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/imrm $args" ]
+}
+
+proc imtest { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/imtest $args" ]
+}
+
+proc remove_ext { args } {
+    global FSLDIR
+
+    regsub -all "\{" $args "" cleanedargs
+    regsub -all "\}" $cleanedargs "" cleanedargs
+
+    return [ exec sh -c "${FSLDIR}/bin/remove_ext $cleanedargs" ]
+}
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imcp

@@ -0,0 +1,65 @@
+#!/bin/sh
+
+#   imcp - copy image files
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The imcp file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   imcp has now been placed in the public domain.
+#   
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+if [ $# -lt 1 ] ; then
+  echo "Usage: $0 <file1> <file2>"
+  echo "Usage: $0 <file1> <file2> ... <fileN> <directory>"
+  echo "  Copies images from file1 to file2 (including all extensions)"
+  echo "  NB: filenames can be basenames or include an extension"
+  exit 1;
+fi
+
+if [ $# -eq 2 -a ! -d $2 ] ; then
+  f1=`${FSLDIR}/bin/remove_ext $1`;
+  f2=`${FSLDIR}/bin/remove_ext $2`;
+  # do the copies
+  if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${f2}.hdr ; fi
+  if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${f2}.hdr.gz ; fi 
+  if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${f2}.img ; fi 
+  if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${f2}.img.gz ; fi 
+  if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${f2}.nii ; fi 
+  if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${f2}.nii.gz ; fi 
+  if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${f2}.mnc ; fi 
+  if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${f2}.mnc.gz ; fi 
+fi
+
+if [ $# -gt 2 -o -d $2 ] ; then
+  for nm in $@ ; do
+      dir=$nm;
+  done
+  if [ ! -d $dir ] ; then
+      echo "When using multiple arguments, last name must be a directory"
+      exit 1;
+  fi
+  # remove directory from list of files
+  flist="echo $@ | sed s/$dir \*\$//";
+  for fn in $flist ; do
+      f1=`${FSLDIR}/bin/remove_ext $fn`;
+      # do the copies
+      if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${dir} ; fi
+      if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${dir} ; fi 
+      if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${dir} ; fi 
+      if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${dir} ; fi 
+      if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${dir} ; fi 
+      if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${dir} ; fi 
+      if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${dir} ; fi 
+      if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${dir} ; fi 
+  done
+fi
+
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imglob

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+#!/bin/sh
+
+#   imglob - expand list of image filenames
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The imglob file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   imglob has now been placed in the public domain.
+#   
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+if [ $# -lt 1 ] ; then
+  echo "Usage: $0 [-oneperimage] <list of names>"
+  exit 0;
+fi
+
+oneperimg=0;
+if [ X"$1"X = "X-oneperimageX" ] ; then
+  oneperimg=1;
+  shift;
+fi
+
+# process each argument, removing any possible extension and
+#  then expanding for valid extensions
+
+lst="";
+for aa in $@ ; do
+  # repeat remove_ext a few times to expand out all wildmasking
+  a=`${FSLDIR}/bin/remove_ext ${aa}`;
+  # at this point variable 'a' may have been expanded into a list
+  for b in $a ; do
+    if [ $oneperimg = 1 ] ; then
+      fn=`echo ${b}.hdr ${b}.hdr.gz ${b}.nii ${b}.nii.gz ${b}.mnc ${b}.mnc.gz`;
+    else
+      fn=`echo ${b}.hdr ${b}.hdr.gz ${b}.nii ${b}.nii.gz ${b}.mnc ${b}.mnc.gz ${b}.img ${b}.img.gz`;
+    fi
+    lst="$lst $fn";
+  done
+done
+
+# remove any instances of unmatched wildmasks (still with * in them)
+lst2="";
+for fn in $lst ; do
+  if [ -f $fn ] ; then
+     lst2="$lst2 $fn";
+  fi
+done
+
+# make list unique
+lst=`echo $lst2 | tr ' ' '\n' | sort -u`;
+echo $lst
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imln

@@ -0,0 +1,37 @@
+#!/bin/sh
+
+#   imln - make symbolic link(s) to image file(s)
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The imln file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   imln has now been placed in the public domain.
+#   
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+if [ $# -lt 2 ] ; then
+  echo "Usage: $0 <file1> <file2>"
+  echo "  Makes a link (called file2) to file1"
+  echo "  NB: filenames can be basenames or include an extension"
+  exit 1;
+fi
+
+f1=`${FSLDIR}/bin/remove_ext $1`;
+f2=`${FSLDIR}/bin/remove_ext $2`;
+
+if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi 
+if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi 
+if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi 
+if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi 
+if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi 
+if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi 
+if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi 
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/immv

@@ -0,0 +1,64 @@
+#!/bin/sh
+
+#   immv - rename/move image files
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The immv file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   immv has now been placed in the public domain.
+#   
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+if [ $# -lt 1 ] ; then
+  echo "Usage: $0 <file1> <file2>"
+  echo "  Moves images from file1 to file2 (including all extensions)"
+  echo "  NB: filenames can be basenames or include an extension"
+  exit 1;
+fi
+
+if [ $# -eq 2 -a ! -d $2 ] ; then
+  f1=`${FSLDIR}/bin/remove_ext $1`;
+  f2=`${FSLDIR}/bin/remove_ext $2`;
+  # do the moves
+  if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${f2}.hdr ; fi
+  if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${f2}.hdr.gz ; fi 
+  if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${f2}.img ; fi 
+  if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${f2}.img.gz ; fi 
+  if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${f2}.nii ; fi 
+  if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${f2}.nii.gz ; fi 
+  if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${f2}.mnc ; fi 
+  if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${f2}.mnc.gz ; fi 
+fi
+
+if [ $# -gt 2 -o -d $2 ] ; then
+  for nm in $@ ; do
+      dir=$nm;
+  done
+  if [ ! -d $dir ] ; then
+      echo "When using multiple arguments, last name must be a directory"
+      exit 1;
+  fi
+  # remove directory from list of files
+  flist="echo $@ | sed s/$dir \*\$//";
+  for fn in $flist ; do
+      f1=`${FSLDIR}/bin/remove_ext $fn`;
+      # do the copies
+      if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${dir} ; fi
+      if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${dir} ; fi 
+      if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${dir} ; fi 
+      if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${dir} ; fi 
+      if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${dir} ; fi 
+      if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${dir} ; fi 
+      if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${dir} ; fi 
+      if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${dir} ; fi 
+  done
+fi
+
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imrm

@@ -0,0 +1,29 @@
+#!/bin/sh
+
+#   imrm - remove image files
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The imrm file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   imrm has now been placed in the public domain.
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+if [ $# -lt 1 ] ; then
+  echo "Usage: $0 <list of image names to remove>"
+  echo "NB: filenames can be basenames or not"
+  exit 1;
+fi
+
+for f in $@ ; do
+  fn=`${FSLDIR}/bin/remove_ext $f`;
+  # do the rm silently
+  /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+done
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/imtest

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+#   imtest - test to see if a valid image file exists with this name (root)
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The fslio.c file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   imtest has now been placed in the public domain.
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+# return 0 if no image exists or 1 if the image exists
+
+if [ $# -lt 1 ] ; then
+ echo "0";
+ exit;
+fi
+
+filename=`${FSLDIR}/bin/remove_ext $1`;
+
+if [ -r ${filename}.nii -o -r ${filename}.nii.gz ] ; then
+  echo "1";
+  exit;
+fi
+
+if [ -r ${filename}.mnc -o -r ${filename}.mnc.gz ] ; then
+  echo "1";
+  exit;
+fi
+
+if [ ! -r ${filename}.hdr -a ! -r ${filename}.hdr.gz ] ; then
+  # return 0 here as no header exists and no single image means no image!
+  echo "0";
+  exit;
+fi
+
+if [ ! -r ${filename}.img -a ! -r ${filename}.img.gz ] ; then
+  # return 0 here as no img file exists and no single image means no image!
+  echo "0";
+  exit;
+fi
+
+# only gets to here if there was a hdr and an img file
+
+echo "1";
+exit;
+

data/ext/nifticlib/nifticlib-2.0.0/fsliolib/remove_ext

@@ -0,0 +1,33 @@
+#!/bin/sh
+
+#   remove_ext - remove extension from image filename
+#
+#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+#   The remove_ext file was originally part of FSL - FMRIB's Software Library
+#   http://www.fmrib.ox.ac.uk/fsl
+#   remove_ext has now been placed in the public domain.
+#   
+#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+#   Imaging of the Brain), Department of Clinical Neurology, Oxford
+#   University, Oxford, UK
+#   
+#   
+
+
+if [ $# -lt 1 ] ; then
+  exit 0
+fi
+
+lst="";
+for fn in $@ ; do
+    # for the ones at the end of the line
+  f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+    # for the ones in the middle of the line
+  f=`echo "$f" | sed 's/\.hdr\.gz[ 	]/ /g' | sed 's/\.img\.gz[ 	]/ /g' | sed 's/\.hdr[ 	]/ /g' | sed 's/\.img[ 	]/ /g' | sed 's/\.nii\.gz[ 	]/ /g' | sed 's/\.nii[ 	]/ /g' | sed 's/\.mnc\.gz[ 	]/ /g' | sed 's/\.mnc[ 	]/ /g' |sed 's/\.[ 	]/ /g'`;
+  lst="$lst $f";
+done
+echo $lst;
+
+

data/ext/nifticlib/nifticlib-2.0.0/nifticdf/CMakeLists.txt

@@ -0,0 +1,28 @@
+PROJECT(NIFTICDFLIB)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR})
+#INCLUDE_DIRECTORIES(/usr/include/nifti)
+SET(NIFTICDFLIB_SRC nifticdf.c)
+
+SET(NIFTI_CDFLIB_NAME ${PACKAGE_PREFIX}nifticdf)
+
+ADD_LIBRARY(${NIFTI_CDFLIB_NAME} ${NIFTICDFLIB_SRC} )
+
+IF (BUILD_SHARED_LIBS)
+  SET_TARGET_PROPERTIES(${NIFTI_CDFLIB_NAME} PROPERTIES ${NIFTI_LIBRARY_PROPERTIES})
+ENDIF (BUILD_SHARED_LIBS)
+
+
+IF(NOT NIFTI_INSTALL_NO_LIBRARIES)
+  INSTALL(TARGETS ${NIFTI_CDFLIB_NAME}
+    RUNTIME DESTINATION ${NIFTI_INSTALL_BIN_DIR} COMPONENT RuntimeLibraries
+    LIBRARY DESTINATION ${NIFTI_INSTALL_LIB_DIR} COMPONENT RuntimeLibraries
+    ARCHIVE DESTINATION ${NIFTI_INSTALL_LIB_DIR} COMPONENT Development)
+ENDIF(NOT NIFTI_INSTALL_NO_LIBRARIES)
+
+IF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)
+  FILE(GLOB __files "${CMAKE_CURRENT_SOURCE_DIR}/*.h")
+  INSTALL(FILES ${__files}
+    DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR}
+    COMPONENT Development)
+ENDIF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)