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Makefile.paczuszka
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Makefile.paczuszka
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#------------------------------------------------------------------------------
# Author: Piotr Majka, M.Sc.
# E-mail: [email protected]
# Affiliation: Laboratory of Neuroinformatics
# Nencki Institute of Experimental Biology
# 3 Pasteur St, 02-093 Warsaw, Poland
#
# Licencing: GNU General Public License
# http://www.gnu.org/licenses/gpl.html
#
#------------------------------------------------------------------------------
PARSERS_DIR = bin/parsers/
ATLASES_DIR = atlases/
SBA_PARSERS = sba_DB08 sba_PHT00 sba_WHS09 sba_WHS10 sba_LPBA40_on_SRI24 sba_RM_on_F99
FAST_PARSERS = ${SBA_PARSERS}
WHS = whs_0.5 whs_0.51 whs_0.5_symm
PARSERS = aba ${FAST_PARSERS} ${WHS}
all: clean ${PARSERS} doc
echo "Done"
doc_clean:
rm -rfv doc/api doc/gui/
doc: doc_api doc_gui
echo "Done doc"
doc_api:
mkdir -p doc/api/html
epydoc lib/pymodules/python2.6/bar -v --graph all --no-sourcecode --output doc/api/html
cd doc/sphinx/; make html
doc_gui:
mkdir -p doc/gui/html
epydoc bin/reconstructor -v --graph all --output doc/gui/html
parsers: ${PARSERS}
parsers_fast: ${FAST_PARSERS}
echo "Done"
whs_0.5:
mkdir -p ${ATLASES_DIR}whs_0.5/src
mkdir -p ${ATLASES_DIR}whs_0.5/caf
wget --keep-session-cookies --save-cookies ${ATLASES_DIR}whs_0.5/src/cookies.txt --post-data 'username=civmpub&password=civmpub' http://civmvoxport.duhs.duke.edu/voxbase/login.php -O /dev/null
wget --load-cookies ${ATLASES_DIR}whs_0.5/src/cookies.txt http://civmvoxport.duhs.duke.edu/voxbase/downloaddataset.php?stackID=18746 -O ${ATLASES_DIR}whs_0.5/src/canon_labels_r.nii.gz
rm ${ATLASES_DIR}whs_0.5/src/cookies.txt
gunzip -f -d ${ATLASES_DIR}whs_0.5/src/canon_labels_r.nii.gz
python ${PARSERS_DIR}whs_0.5/__init__.py
if [ -e ${ATLASES_DIR}whs_0.5/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.5/caf ${ATLASES_DIR}whs_0.5/caf-reference > diff_whs_0.5.txt; fi
whs_0.5_symm:
mkdir -p ${ATLASES_DIR}whs_0.5_symm/src
mkdir -p ${ATLASES_DIR}whs_0.5_symm/caf
wget --keep-session-cookies --save-cookies ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt --post-data 'username=civmpub&password=civmpub' http://civmvoxport.duhs.duke.edu/voxbase/login.php -O /dev/null
wget --load-cookies ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt http://civmvoxport.duhs.duke.edu/voxbase/downloaddataset.php?stackID=20494 -O ${ATLASES_DIR}whs_0.5_symm/src/SYMCLabel.nii.gz
rm ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt
gunzip -f -d ${ATLASES_DIR}whs_0.5_symm/src/SYMCLabel.nii.gz
python ${PARSERS_DIR}whs_0.5_symm/__init__.py
if [ -e ${ATLASES_DIR}whs_0.5_symm/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.5_symm/caf ${ATLASES_DIR}whs_0.5_symm/caf-reference > diff_whs_0.5_symm.txt; fi
whs_0.51:
mkdir -p ${ATLASES_DIR}whs_0.51/src
mkdir -p ${ATLASES_DIR}whs_0.51/caf
wget -O ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip "http://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=file"
unzip -o ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip -d ${ATLASES_DIR}whs_0.51/src/
rm ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip
python ${PARSERS_DIR}whs_0.51/__init__.py
if [ -e ${ATLASES_DIR}whs_0.51/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.51/caf ${ATLASES_DIR}whs_0.51/caf-reference > diff_whs_0.51.txt; fi
sba_DB08:
mkdir -p ${ATLASES_DIR}sba_DB08/src
mkdir -p ${ATLASES_DIR}sba_DB08/caf
python ${PARSERS_DIR}sba_DB08/__init__.py
if [ -e ${ATLASES_DIR}sba_DB08/caf-reference ]; then diff -r ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/caf-reference > diff_sba_DB08.txt; fi
sba_PHT00:
mkdir -p ${ATLASES_DIR}sba_PHT00/src
mkdir -p ${ATLASES_DIR}sba_PHT00/caf
python ${PARSERS_DIR}sba_PHT00/__init__.py
if [ -e ${ATLASES_DIR}sba_PHT00/caf-reference ]; then diff -r ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/caf-reference > diff_sba_PHT00.txt; fi
sba_WHS09:
mkdir -p ${ATLASES_DIR}sba_WHS09/src
mkdir -p ${ATLASES_DIR}sba_WHS09/caf
python ${PARSERS_DIR}sba_WHS09/__init__.py
if [ -e ${ATLASES_DIR}sba_WHS09/caf-reference ]; then diff -r ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf-reference > diff_sba_WHS09.txt; fi
sba_WHS10:
mkdir -p ${ATLASES_DIR}sba_WHS10/src
mkdir -p ${ATLASES_DIR}sba_WHS10/caf
python ${PARSERS_DIR}sba_WHS10/__init__.py
if [ -e ${ATLASES_DIR}sba_WHS10/caf-reference ]; then diff -r ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/caf-reference > diff_sba_WHS10.txt; fi
sba_LPBA40_on_SRI24:
mkdir -p ${ATLASES_DIR}sba_LPBA40_on_SRI24/src
mkdir -p ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf
python ${PARSERS_DIR}sba_LPBA40_on_SRI24/__init__.py
if [ -e ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference ]; then diff -r ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference > diff_sba_LPBA40_on_SRI24.txt; fi
sba_RM_on_F99:
mkdir -p ${ATLASES_DIR}sba_RM_on_F99/src
mkdir -p ${ATLASES_DIR}sba_RM_on_F99/caf
python ${PARSERS_DIR}sba_RM_on_F99/__init__.py
if [ -e ${ATLASES_DIR}sba_RM_on_F99/caf-reference ]; then diff -r ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/caf-reference > diff_sba_RM_on_F99.txt; fi
aba:
mkdir -p ${ATLASES_DIR}aba/src
mkdir -p ${ATLASES_DIR}aba/caf
python ${PARSERS_DIR}aba/preprocess_volume.py
python ${PARSERS_DIR}aba/__init__.py
if [ -e ${ATLASES_DIR}aba/caf-reference ]; then diff -r ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/caf-reference > diff_aba.txt; fi
clean: clean_diff doc_clean
rm -rfv ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/src
rm -rfv ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/src
rm -rfv ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf/src
rm -rfv ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/src
rm -rfv ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/src
rm -rfv ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/src
rm -rfv ${ATLASES_DIR}whs_0.51/caf
rm -rfv ${ATLASES_DIR}whs_0.5/caf
rm -rfv ${ATLASES_DIR}whs_0.5_symm/caf
rm -rfv ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/src
reference_datasets:
rm -rf ${ATLASES_DIR}whs_0.5/caf-reference; cp -r ${ATLASES_DIR}whs_0.5/caf ${ATLASES_DIR}whs_0.5/caf-reference
rm -rf ${ATLASES_DIR}whs_0.5_symm/caf-reference; cp -r ${ATLASES_DIR}whs_0.5_symm/caf ${ATLASES_DIR}whs_0.5_symm/caf-reference
rm -rf ${ATLASES_DIR}whs_0.51/caf-reference; cp -r ${ATLASES_DIR}whs_0.51/caf ${ATLASES_DIR}whs_0.51/caf-reference
rm -rf ${ATLASES_DIR}sba_DB08/caf-reference; cp -r ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/caf-reference
rm -rf ${ATLASES_DIR}sba_PHT00/caf-reference; cp -r ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/caf-reference
rm -rf ${ATLASES_DIR}sba_WHS09/caf-reference; cp -r ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf-reference
rm -rf ${ATLASES_DIR}sba_WHS10/caf-reference; cp -r ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/caf-reference
rm -rf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference; cp -r ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference
rm -rf ${ATLASES_DIR}sba_RM_on_F99/caf-reference; cp -r ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/caf-reference
rm -rf ${ATLASES_DIR}aba/caf-reference; cp -r ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/caf-reference
clean_diff:
rm -rfv diff_whs_0.51.txt diff_whs_0.5.txt diff_sba_PHT00.txt diff_sba_DB08.txt\
diff_sba_WHS09.txt diff_sba_WHS10.txt diff_sba_LPBA40_on_SRI24.txt\
diff_sba_RM_on_F99.txt diff_aba.txt