131 lines
6.2 KiB
Makefile
131 lines
6.2 KiB
Makefile
SHELL:=/bin/bash
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FIJI_ROOT_PATH:=~/soft/Fiji.app
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FIJI_EXE_PATH=$(FIJI_ROOT_PATH)/ImageJ-linux64
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# RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images'
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RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images)
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TEMP_PATH:=$(shell echo ~/work/lipase/tmp)
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TESTS_OUTPUT_DATA_PATH:=$(TEMP_PATH)
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LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
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PLUGINS_SRC_FILES=$(shell find ./src/ij-plugins -name "*.py")
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LIPASE_VERSION=1.03
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BUILD_ROOT_PATH:=$(TEMP_PATH)/build
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PACKAGE_FILE_PATH=$(BUILD_ROOT_PATH)/lipase-$(LIPASE_VERSION).zip
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.PHONY: all
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all: test doc
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.PHONY: doc
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doc:
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cd doc; make
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.PHONY: clean_doc
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clean_doc:
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cd doc; make clean
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$(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar: $(LIB_SRC_FILES)
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pushd ./src; \
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mkdir -p $(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib ; \
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find ./lipase -name "*.py" > /tmp/files.txt ; \
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jar cvf $(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar @/tmp/files.txt ; \
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popd
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.PHONY: install_ij_opencv
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install_ij_opencv:
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# enable IJ-OpenCV-plugins site because it's disabled by default
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# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
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# <disabled-update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
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# graffy@graffy-ws2:~$ history | less
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# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
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# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
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# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
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# Done: Checksummer
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# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
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# <update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
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# $FIJI_ROOT_PATH/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
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# then apply an update to download and install IJ-OpenCV-plugins :
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# jars/IJ-OpenCV.jar
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# jars/javacv.far
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# jars/opencv-linux-x86.jar
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# jars/opencv-linux-x86_64.jar
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# jars/opencv-macosx-x86_64.jar
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# jars/opencv-windows-x86.jar
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# jars/opencv-windows-x86_64.jar
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# jars/opencv.jar
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# lib/haarcascade_frontalface_alt.xml
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# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update update
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# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
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# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
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# Done: Checksummer
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# Done: Downloading...
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# Done: Downloading...
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# $FIJI_ROOT_PATH/ImageJ-linux64 --update update
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ls $(FIJI_ROOT_PATH)/jars/IJ-OpenCV-*.jar ; \
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if [ $$? != 0 ] ; \
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then \
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$(FIJI_ROOT_PATH)/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/; \
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$(FIJI_ROOT_PATH)/ImageJ-linux64 --update update; \
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fi
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$(PACKAGE_FILE_PATH): $(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar $(PLUGINS_SRC_FILES)
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mkdir -p $(BUILD_ROOT_PATH)/ij_zip_source/plugins/Ipr ; \
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rsync -a ./src/ij-plugins/Ipr/ $(BUILD_ROOT_PATH)/ij_zip_source/plugins/Ipr/ ; \
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pushd $(BUILD_ROOT_PATH)/ij_zip_source ; \
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zip -r $(PACKAGE_FILE_PATH) * ; \
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popd
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.PHONY: package
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package: $(PACKAGE_FILE_PATH)
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.PHONY: install
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install: $(PACKAGE_FILE_PATH) install_ij_opencv
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pushd $(FIJI_ROOT_PATH); unzip -o $(PACKAGE_FILE_PATH); popd
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.PHONY: test0001
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test0001: install
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# on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py'
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# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './tests/test0001.py' "lipase_src_root_path='$(pwd)',raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images'"
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echo 2 > '/tmp/test_result.txt' ; \
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mkdir -p $(TESTS_OUTPUT_DATA_PATH)
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$(FIJI_EXE_PATH) --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$(RAW_IMAGES_ROOT_PATH)',tests_output_data_path='$(TESTS_OUTPUT_DATA_PATH)'" ; \
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ERROR_CODE=$$? ; \
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echo "Fiji 's return code : $$ERROR_CODE" ; \
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ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \
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echo "test's return code : $$ERROR_CODE" ; \
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exit $$ERROR_CODE
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.PHONY: test0001
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imgproc_tests: install
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echo 2 > '/tmp/test_result.txt' ; \
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$(FIJI_EXE_PATH) --ij2 --headless --run './tests/improc_tests.py' "tests_output_data_path='$(TESTS_OUTPUT_DATA_PATH)'" ; \
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ERROR_CODE=$$? ; \
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echo "Fiji 's return code : $$ERROR_CODE" ; \
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ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \
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echo "test's return code : $$ERROR_CODE" ; \
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exit $$ERROR_CODE
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.PHONY: test_globules_area
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test_globules_area: install
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# on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py'
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# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './tests/test0001.py' "lipase_src_root_path='$(pwd)',raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images'"
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echo 2 > '/tmp/test_result.txt' ; \
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$(FIJI_EXE_PATH) --ij2 --headless --run './src/ij-plugins/Ipr/Lipase/Compute_Globules_Area.py' "INPUT_STACK='$(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_nofilter_vis_000.tif', INPUT_BACKGROUND='$(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_nofilter_vis_000.tif', PARTICLE_THRESHOLD='2000'" ; \
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ERROR_CODE=$$? ; \
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echo "Fiji 's return code : $$ERROR_CODE" ; \
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ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \
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echo "test's return code : $$ERROR_CODE" ; \
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exit $$ERROR_CODE
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.PHONY: test
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test: test0001 imgproc_tests
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.PHONY: clean
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clean: clean_doc
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rm -Rf $(BUILD_ROOT_PATH)
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