Makefile

# Personal Makefile variables
#
# $Id$

.PHONY: clean install zip docs update cp_binaries archive check_pipeline release standalone tests

OLDVERSION="CAT26.0.rc3"
NEWVERSION="CAT26.0.rc4"
REVISION=`git rev-list --count HEAD`
DATE=`git log --date short |grep "Date:"|head -1|cut -f2 -d':'|sed -e s'/ //g'`
VERSION=`echo ${NEWVERSION} | sed -e 's/CAT//g'`

TARGET=/Users/gaser/spm/spm12/toolbox/CAT
TARGET2=/Volumes/UltraMax/spm12/toolbox/CAT
TARGET4=/Users/gaser/spm/spm-octave/toolbox/CAT

PRECOMPILED=/Users/gaser/matlab/Matlab_standalone

# matlab binary and SPM path used by the "tests" target (override on the command line)
MATLAB ?= matlab
SPMDIR ?= /Users/gaser/spm/spm12

STARGET3_HOST=paris.biomag.uni-jena.de
STARGET3_FOLDER=/home/gaser/spm12/toolbox/CAT
STARGET3=${STARGET3_HOST}:${STARGET3_FOLDER}

MATLAB_FILES=Contents.* cat_*.m spm_select.m spm_CAT.m spm_cat12.m tbx_cfg_cat.m sliderPanel.m slice_overlay.m cat_run* compile.m
C_FILES=Amap.[ch] ornlm_float.c sanlm_float.c MrfPrior.c Pve.c Kmeans.c cat_*.c* cat_*.mex* vollib.c genus0.[ch] tricases.h cat_glibc_compat.h spm_diffeo.* tfceMex_pthread.*
MISC_FILES=README.md CHANGES.txt INSTALL.txt doc standalone templates_MNI152NLin2009cAsym templates_surfaces templates_surfaces_32k atlases_surfaces atlases_surfaces_32k cat12.* CAT.* cat_*.sh  cat_long_main*txt glass_brain.mat clang*xml

FILES=${MATLAB_FILES} ${C_FILES} ${MISC_FILES}

ZIPFILE=cat${VERSION}.zip

BIN ?= CAT*

# remove .DS_Store files and correct file permissions
clean:
	-@find . -type f -name .DS_Store -exec rm {} \;
	-@chmod -R a+r,g+w,o-w .
	-@find . -type f \( -name "*.sh" -o -name "*.mex*" \) -exec chmod a+x {} \;
	-@find . -type f \( -name "*.c" -o -name "*.c??" -o -name "*.m" -o -name "*.gii" -o -name "*.nii" -o -name "*.txt" -o -name "*.html" -o -name "*.annot" \) -exec chmod a-x {} \;

# prepare txt file for deployed versions
copy_longmode:
	-@cp -R cat_long_main.m cat_long_main.txt

# install
install: copy_longmode
	-@echo install
	-@test ! -d ${TARGET} || rm -rf ${TARGET}/*
	-@mkdir -p ${TARGET}
	-@cp -R ${FILES} ${TARGET}/
	-@gzip -df ${TARGET}/*/*.nii.gz

#install on UltraMax
install2: copy_longmode
	-@echo install on ${TARGET2}
	-@test ! -d ${TARGET2} || rm -rf ${TARGET2}/*
	-@mkdir -p ${TARGET2}
	-@cp -R ${FILES} ${TARGET2}/
	-@gzip -d ${TARGET2}/*/*.nii.gz

#install on paris
install3: copy_longmode
	-@echo install on ${STARGET3}
	-@bash -c "ssh ${STARGET3_HOST} 'test ! -d ${STARGET3_FOLDER} || rm -rf ${STARGET3_FOLDER}/*'"
	-@bash -c "ssh ${STARGET3_HOST} 'test -d ${STARGET3_FOLDER} || mkdir ${STARGET3_FOLDER}'"
	-@scp -r ${FILES} ${STARGET3}/
	-@bash -c "ssh ${STARGET3_HOST} 'gzip -d ${STARGET3_FOLDER}/*/*.nii.gz'"

# install for octave
install4: copy_longmode
	-@echo install
	-@test ! -d ${TARGET4} || rm -rf ${TARGET4}/*
	-@mkdir -p ${TARGET4}
	-@cp -R ${FILES} ${TARGET4}/
	-@gzip -d ${TARGET4}/*/*.nii.gz

# print available commands
help:
	-@echo Available commands:
	-@echo clean install zip docs update cp_binaries archive check_pipeline release standalone tests
	-@echo "cp_binaries usage: make cp_binaries [BIN=CAT_MyBinary]"

#make html documentation
docs:
	-@cat doc/cat.txt | sed -e 's/VERSION/'${NEWVERSION}'/g' -e 's/RELNUMBER/r'${REVISION}'/g' -e 's/DATE/'${DATE}'/g' > doc/cat.html
	-@test ! -d ../cat12-help || cp -R doc/* ../cat12-help/

# update version numbers
update: docs copy_longmode
	-@git fetch
	-@echo '% Computational Anatomy Toolbox' > Contents.m
	-@echo '% Version' ${REVISION}' ('${NEWVERSION}')' ${DATE} >> Contents.m
	-@cat Contents_info.txt >> Contents.m
	-@cp Contents.m Contents.txt
	-@echo '% Computational Anatomy Toolbox' > INSTALL.txt
	-@echo '% Version ' ${REVISION} ${NEWVERSION} ${DATE} >> INSTALL.txt
	-@cat INSTALL_info.txt >> INSTALL.txt
	-@test ! -d ../tfce/ || cp cat_spm_results_ui.m ../tfce/
	-@perl -p -i -e "s/${OLDVERSION}/${NEWVERSION}/g" spm_CAT.m
	-@perl -p -i -e "s/${OLDVERSION}/${NEWVERSION}/g" cat_batch_bids.sh
	-@cp cat12.m CAT.m
	-@chmod a+x CAT.*/*

# zip release
zip: update clean
	-@echo zip
	-@test ! -d CAT || rm -r CAT
	-@mkdir CAT
	-@cp -rp ${FILES} CAT
	-@gzip -df CAT/templates_MNI152NLin2009cAsym/*.nii.gz
	-@bash update_revision.sh
	-@zip ${ZIPFILE} -rm CAT

# copy binaries after cross-compiling
cp_binaries: 
	-@echo copy binaries matching $(BIN)
	-@for file in ~/GitHub/CAT-Surface/build-*/Progs/*.o; do \
			[ -f "$$file" ] && rm "$$file"; \
	done
	-@for i in CAT.glnx86/$(BIN); do cp ~/GitHub/CAT-Surface/build-x86_64-pc-linux/Progs/`basename $${i}` CAT.glnx86/ ; done
	-@for i in CAT.w32/$(BIN); do cp ~/GitHub/CAT-Surface/build-x86_64-w64-mingw32/Progs/`basename $${i}` CAT.w32/ ; done
	-@for i in CAT.maci64/$(BIN); do cp ~/GitHub/CAT-Surface/build-native/Progs/`basename $${i}` CAT.maci64/ ; done
	-@for i in CAT.maca64/$(BIN); do cp ~/GitHub/CAT-Surface/build-native-arm64/Progs/`basename $${i}` CAT.maca64/ ; done

# print check list for releasing
release: checklist
checklist:
	@printf '%s\n' \
	'' \
	'Checklist for testing CAT12 in order to release' \
	'-----------------------------------------------' \
	'1. Make unittests' \
	'   make tests' \
	'' \
	21. Check Pipeline' \
	'   make check_pipeline' \
	'   check_pipeline.sh -p pid' \
	'   check_all_matrix.sh' \
	'   check_pipeline_ROIs -> check render views check_r*matrix.png and histograms' \
	'   check_pipeline_homogeneity -> check sample homogeneity' \
	'' \
	'3. Check Batches and Dependencies' \
	'   cd check_pipeline' \
	'   batch_volume_pipeline' \
	'   batch_surface_pipeline' \
	'' \
	'4. Check Expert Mode' \
	'   cat12('\''expert'\'')' \
	'   CAT12 GUI Segment' \
	'' \
	'5. Check Simple Preprocessing' \
	'   SPM->Tools->CAT12->CAT12 Simple Preprocessing' \
	'' \
	'6. Create and Check Standalone Versions' \
	'   https://github.com/ChristianGaser/cat12/actions/workflows/install_test_standalone.yml' \
	'' \
	'7. Build CAT-Surface binaries and apply make cp_binaries to copy them' \
	'   https://github.com/ChristianGaser/CAT-Surface/actions/workflows/binaries.yml' \
	'' \
	'8. Optionally check Skull-Stripping if Pipeline Changed' \
	'   cat12_all.m in /Volumes/UltraMax/validate_skullstripping_withT12' \
	'   calc_kappa_c0_SPM12_T12.m' \
	'' \
	'8. Check thickness phantom' \
	'' \
	'9. Make fork from new version!'

# print help for standalone
standalone:
	@printf '%s\n' \
	'' \
	'Use CAT action to compile and test standalone versions' \
	'https://github.com/ChristianGaser/cat12/actions/workflows/install_test_standalone.yml'

# rescue from archives
archive:
	-@echo available archives to install
	-@ls cat12_r*zip
	-@test ! -d cat12 || rm -rf cat12
	-@test ! -d ${TARGET} || rm -rf ${TARGET}
	-@read -p "Type release number (3 or 4 digits), followed by [ENTER]:" ver; unzip cat12_r$${ver}.zip; cp -R cat12 ${TARGET}

# run fast unit and compiled-function tests on the working copy
# (no image data required; needs SPM at ${SPMDIR})
tests:
	-@echo Running CAT12 unit and mex tests
	@${MATLAB} -nodisplay -nosplash -batch "addpath('${SPMDIR}'); cd('${CURDIR}'); ok1 = compile(0,1,2); [ok2,~] = cat_tst_unittests(1); if ~(ok1 && ok2), error('CAT12 tests failed'); end; disp('All CAT12 tests passed.')"

# run check pipeline
check_pipeline: update install
	-@echo Check pipeline
	-@cd /Volumes/UltraMax/check_pipeline/
	-@/Users/gaser/GitHub/cat12/check_pipeline.sh -d /Volumes/UltraMax/check_pipeline/ -s ~/spm/spm12 -bg 8 -f /Volumes/UltraMax/check_pipeline/check_pipeline_files.txt -l /Volumes/UltraMax/check_pipeline/check_pipeline_files_long.txt
	-@echo 1. cd /Volumes/UltraMax/check_pipeline/ 2. Call post-processing with the resp. pid: check_pipeline.sh -p pid