c_nifti 0.0.1

data/ext/nifticlib/nifticlib-2.0.0/Makefile.cross_mingw32

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+#!/usr/bin/make -f
+# -*- Makefile -*-
+# 
+# This makefile was initially created by Michael Hanke
+# <michael.hanke@gmail.com> to cross compile the nifticlibs for win32 on a
+# Debian system -- although it should work on most Linux systems with possibly
+# minor modifications. The whole process should become a lot easier once
+# CMake 2.6 with cross-compiler toolchain support is released.
+#
+# Like the other parts of this package, this code is placed into the public
+# domain.
+#
+# The 'devpak' target generates a DevPak suiteable for Dev-Cpp, see:
+# http://www.bloodshed.net/devcpp.html
+#
+# Requirements:
+#  - cross-compiler environment (on Debian simply: apt-get install mingw32)
+#  - recent CMake (tested with 2.4)
+#  - cross-compiled zlib installed below $mingw_root_path. The easiest way to
+#    achieve this is using the zlib package provided by the gnuwin32 project:
+#    http://gnuwin32.sourceforge.net/
+#
+# Usage:
+#  Enter the root of the nifticlibs package and execute
+#
+#      make -f Makefile.cross_mingw32
+#
+#  now the generated DevPak should be located in the toplevel directory. This
+#  can be installed using the Package manager of Dev-Cpp under Windows.
+#
+
+
+# default settings
+build_dir = mingw32_cross
+devpak_dir = mingw32_devpak
+
+# where all the cross-compiled libs and binaries are installed
+mingw_root_path = /usr/local/mingw32
+# where the cross-compiler itself is installed
+mingw_bin_path = /usr/bin
+# the common filename prefix of all cross-compiler binaries
+mingw_bin_prefix = i586-mingw32msvc
+# don't touch this one, unless you know what you are doing
+mingw_bin = $(mingw_bin_path)/$(mingw_bin_prefix)
+
+# extract the most recent version from the README file
+nifti_version = $$(grep Version README | head -n1 | awk '{ print $$2 }')
+
+# compile CMake flags.
+cmake_flags = -DCMAKE_SYSTEM_NAME=Windows \
+			  -DCMAKE_AR=$(mingw_bin)-ar \
+			  -DCMAKE_RANLIB=$(mingw_bin)-ranlib \
+			  -DCMAKE_C_COMPILER=$(mingw_bin)-gcc \
+			  -DCMAKE_CXX_COMPILER=$(mingw_bin)-g++ \
+			  -DCMAKE_C_FLAGS="-I$(mingw_root_path)/include -L$(mingw_root_path)/lib -DWIN32"
+
+
+all: devpak
+
+
+clean:
+	-rm -rf $(build_dir)
+	-rm build-devpak configure-devpak
+
+distclean: clean
+	-rm -rf $(devpak_dir)
+
+configure-devpak:
+	if [ ! -d $(build_dir) ]; then mkdir $(build_dir); fi
+	cd $(build_dir) && cmake .. $(cmake_flags) -DCMAKE_INSTALL_PREFIX=/$(devpak_dir)
+	touch $@
+
+build-devpak: configure-devpak
+	cd $(build_dir) && make VERBOSE=1
+	touch $@
+
+install-devpak: build-devpak
+	if [ ! -d $(devpak_dir) ]; then mkdir $(devpak_dir); fi
+	cd $(build_dir) && make install DESTDIR=../
+
+devpak: install-devpak
+	# nifti_tool header is unecessary
+	rm $(devpak_dir)/include/nifti/nifti_tool.h
+	
+	# generate devpak info file
+	sed -e s/__full_version__/$(nifti_version)/g \
+	    -e s/__major_version__/$(nifti_version)/g \
+		< packaging/DevPackage.template > $(devpak_dir)/nifticlib.DevPackage
+	
+	# include license and readme
+	cp LICENSE README $(devpak_dir)
+	
+	# compress
+	cd $(devpak_dir) && tar cvjf ../nifticlib-$(nifti_version).DevPak *

data/ext/nifticlib/nifticlib-2.0.0/README

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+
+Nifti-1 C libraries
+-------------------
+
+Version 2.0.0 beta release Jul  2010
+Version 1.1.0 beta release Aug  2008
+Version 1.0.0 beta release Dec  2007
+Version 0.6 beta release Aug  2007
+Version 0.5 beta release May  2007
+Version 0.4 beta release Sept. 2006
+Version 0.3 beta release April 2006
+Version 0.2 beta release August 12, 2005
+Version 0.1 beta release March 11, 2005
+
+niftilib code is released into the public domain.
+
+
+Library directories
+-------------------
+znzlib   -- low level library for handling read/write of compressed files.
+
+niftilib -- core i/o routines for reading and writing nifti-1 format files.
+	    Primarily routines to read/write and manipulate the header field
+	    information, including orientation matrices.  Volume-wise,
+            timecourse-wise, access to image data.  
+
+nifticdf -- functions to compute cumulative distributions and their inverses
+
+fsliolib -- i/o routines for reading and writing nifti-1 format files, higher
+            level than niftilib, includes routines for reading the data blob by
+            volume, timecourse, etc., and, addresses image orientation issues.
+            *** work in progress, subject to significant revision.....
+
+utils    -- directory containing library utility programs (nifti_tool)
+
+
+
+
+Destination directories
+-----------------------
+bin      -- destination directory for installed programs
+include  -- destination directory for library header files
+lib      -- destination directory for compiled libraries
+docs     -- destination directory Doxygen html (created via "make doc")
+
+
+
+Example directories
+-------------------
+examples  -- directory containing sample code using nifti reference library
+real_easy -- code snippets to read nifti-1 files, not using nifti ref. lib.
+
+
+Other directories
+-----------------
+Testing   -- directory containing code to test the libraries
+packaging -- spec file for building RPMs, and template package
+             description for Dev-Cpp (http://www.bloodshed.net/devcpp.html)
+
+
+
+Instructions to build
+---------------------
+
+command  -- "make all" 
+
+            results will be left in the directories: bin/ include/ lib/
+
+command  -- "make help"
+
+	    will show more build options
+
+
+For more information
+--------------------
+
+See the niftilib webpage at http://niftilib.sourceforge.net/
+See the NIFTI webpage at http://nifti.nimh.nih.gov/
+

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

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+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(TESTING)
+
+SUBDIRS(niftilib)
+SUBDIRS(nifti_regress_test)
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/Makefile

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+
+TAR     ?= /bin/tar
+RM      ?= /bin/rm
+
+# get the regression testing data tree
+regress_data: nifti_regress_test/nifti_regress_data
+
+# remove any result directories
+regress_clean:
+	$(RM) -fr nifti_regress_test/results*
+
+# remove any result directories, and remove the data tree
+regress_clean_all: regress_clean
+	$(RM) -fr nifti_regress_test/nifti_regress_data
+
+# download and unpack the regression data tree
+nifti_regress_test/nifti_regress_data:
+	wget http://nifti.nimh.nih.gov/pub/dist/data/nifti_regress_data.tgz
+	( cd nifti_regress_test; $(TAR) -xzf ../nifti_regress_data.tgz; )
+	$(RM) nifti_regress_data.tgz
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/README_regress

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+Background:
+
+This is to perform regression testing, which is to say, make sure the
+software works the same way that it used to.  This is not to test new
+features (see "modify an existing tree" for that).
+
+When code has been changed for a certain program that is involved in a
+regression testing tree, go to that tree, run the test, and make sure
+that the results have not changed (in any bad way).  This is meant to
+be fast and easy.
+
+The test consists of command scripts that were written before.  The
+scripts are executed, and the output is compared with the output of
+an older execution.  The should ususally be identical.
+
+---------------------------------------------------------------------------
+
+To perform regression testing, one needs the data (via 'make regress_data').
+Given that, only the @test and @show_diffs are needed (sample commands are
+shown with a preceeding prompt, '> ').
+
+    1. Run the regression testing script.  It goes through the steps:
+
+       a. Create a "results" directory, including a timestamp.
+       b. Copy all "data" files into it.
+       c. 'cd' into the "results" directory.
+       d. For each command script in the commands directory, execute it,
+          storing all output text into a file called e."command name".
+
+        > ./@test
+
+
+    2. To compare against an older execution, run the @show_diffs script.
+       It goes through the steps:
+
+       a. Make a list of the "results" directories.
+       b. Create a new "diffs" directory.
+       c. Compare files between the newest and oldest "results" dirs:
+            - cd into newest "results" directory
+            - foreach file (*)
+                diff $file ../other.result/$file >& ../diffs/d.$file
+
+        > ./@show_diffs
+
+
+    3. Look at the sizes of the diff files, or the contents (only
+       expected differences should exist).
+
+        > ls -l diffs
+        > cat diffs/*

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@show.diffs

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+#! /usr/bin/env tcsh
+
+set ddir = diffs
+set rdirs = ( results_* )
+
+# verify that there are differences to view
+if ( $#rdirs < 2 ) then
+    echo cannot proceed, we need at least 2 result directories
+    exit
+endif
+
+# make sure the output directory exists
+if ( -d $ddir ) then
+    echo removing old diffs
+    \rm -f $ddir/* >& /dev/null
+else
+    mkdir $ddir
+    if ( ! -d $ddir ) then
+        echo failed to make output directory, $ddir
+        exit
+    endif
+endif
+
+set r1 = $rdirs[1]
+set r2 = $rdirs[$#rdirs]
+
+cd $r2
+
+foreach file (*)
+    echo $file...
+    diff ../$r1/$file $file >& ../$ddir/d.$file
+end
+

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/@test

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+#! /usr/bin/env tcsh
+
+set ddir = nifti_regress_data
+set prog = nifti_tool   # might allow this to change
+
+set grind = 0           # do we run with valgrind?
+
+if ( $#argv > 0 ) then
+    if ( "$argv[1]" == "-grind" ) then
+        set grind = 1
+    else
+        echo "usage: `basename $0` [-grind]"
+        exit
+    endif
+endif
+
+# make sure $prog at least exists
+# $prog -ver >& /dev/null
+# if ( $status ) then
+#     echo "missing program '$prog' (needs to be in PATH)"
+#     exit
+# endif
+
+# set date and output dir (based on grind)
+set date = `date +%Y_%m_%d_%H%M`
+if ( $grind ) then
+    set odir = vg_results_${prog}_${date}
+else
+    set odir = results_${prog}_${date}
+endif
+
+# note command files (in commands dir)
+if ( ! -d commands ) then
+    echo "** failure: missing commands directory"
+    exit
+endif
+
+cd commands ; set cfiles = ( c* ) ; cd ..
+
+if ( $#cfiles < 1 ) then
+    echo "** failure: no command files found in 'commands'"
+    exit
+endif
+
+# create the output directory
+if ( -e $odir ) then
+    echo "** failure: output directory '$odir' already exists"
+    exit
+endif
+
+mkdir $odir
+
+if ( $status ) then
+    echo "** failure: output directory '$odir' already exists"
+    exit
+endif
+
+# copy data files into output dir
+cp $ddir/* $odir
+
+cd $odir
+
+# now begin the work
+
+echo "++ using `which $prog` ..."
+
+if ( $grind ) then
+    alias $prog "valgrind --leak-resolution=high --leak-check=full $prog"
+endif
+
+foreach cfile ( $cfiles )
+    echo -n $cfile ...
+    echo "--------------------------------------------------------" > e.$cfile
+    cat ../commands/$cfile >> e.$cfile
+    echo "" >> e.$cfile
+    echo "--------------------------" >> e.$cfile
+    echo "" >> e.$cfile
+    source ../commands/$cfile >>& e.$cfile   # to keep alias
+    echo done
+end

data/ext/nifticlib/nifticlib-2.0.0/Testing/nifti_regress_test/CMakeLists.txt

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+# Do all regression tests
+PROJECT(REGRESSION_TEST)
+
+SET(NT ${NIFTI_BINARY_DIR}/utils/nifti_tool )
+SET(DATA ${REGRESSION_TEST_BINARY_DIR}/nifti_regress_data)
+SET(TESTS ${REGRESSION_TEST_SOURCE_DIR}/cmake_testscripts)
+
+ADD_TEST(fetch_data
+sh ${TESTS}/fetch_data_test.sh ${REGRESSION_TEST_BINARY_DIR} 
+)
+
+ADD_TEST(nifti_ver ${NT} -nifti_ver)
+ADD_TEST(nifti_tool_ver ${NT} -ver)
+ADD_TEST(nifti_help ${NT} -help)
+ADD_TEST(nifti_nifti_hist ${NT} -nifti_hist)
+ADD_TEST(nifti_hist ${NT} -hist)
+
+ADD_TEST(nifti_disp_hdr ${NT} -disp_hdr -infiles ${DATA}/anat0.nii )
+
+ADD_TEST(nifti_disp_nim ${NT} -disp_nim -infiles ${DATA}/anat0.nii )
+
+ADD_TEST(nifti_disp_ext ${NT} -disp_ext -infiles ${DATA}/anat0.nii )
+
+ADD_TEST(nifti_modhdr_exts
+sh ${TESTS}/mod_header_test.sh ${NT} ${DATA} )
+
+ADD_TEST(nifti_bricks_test
+sh ${TESTS}/bricks_test.sh ${NT} ${DATA} )
+
+ADD_TEST(nifti_dts_test
+sh ${TESTS}/dts_test.sh ${NT} ${DATA} )
+
+ADD_TEST(nifti_dci_test
+sh ${TESTS}/dci_test.sh ${NT} ${DATA} )
+
+ADD_TEST(nifti_comment_test
+sh ${TESTS}/comment_test.sh ${NT} ${DATA} )
+  
+ADD_TEST(nifti_header_check ${NT} -check_hdr -infiles ${DATA}/anat0.nii )
+
+ADD_TEST(nifti_nim_check ${NT} -check_nim -infiles ${DATA}/anat0.nii )
+
+ADD_TEST(nifti_dsets_test
+sh ${TESTS}/dsets_test.sh ${NT} ${DATA} )
+
+ADD_TEST(nifti_newfiles_test
+sh ${TESTS}/newfiles_test.sh ${NT} ${DATA} )

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

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+
+# - copy some of the sub-bricks of the default stat file,
+#   storing the history (command), and writing to a new 'f4.nii'
+# - compare these nifti_image structs
+
+if [ $# -lt 2 ]
+then
+echo Missing nifti tool and Binary directory name
+exit 1
+fi
+
+NT=$1
+DATA=$2
+
+rm -fr ${DATA}/f4*
+
+if ${NT} -keep_hist -cbl -infiles ${DATA}/stat0.nii'[178..$,0,1]' -prefix ${DATA}/f4
+then
+echo ""
+else
+echo "copy sub-bricks failed"
+fi
+
+if ${NT} -diff_nim -infiles ${DATA}/stat0.nii ${DATA}/f4.nii
+then
+echo diff failed '(no diffs found'
+exit 1
+else
+echo diff succeeded
+fi
+
+exit 0