84 lines
4.1 KiB
Makefile
84 lines
4.1 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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LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
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.PHONY: all
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all: test0001
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$(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar: $(LIB_SRC_FILES)
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pushd ./src; \
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mkdir -p $(FIJI_ROOT_PATH)/jars/Lib ; \
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find ./lipase -name "*.py" > /tmp/files.txt ; \
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jar cvf $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt ; \
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popd
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.PHONY: install_ij_opencv
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install_ij_opencv:
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# enable IJ-OpenCV-plugins site because it's disabled by default
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# graffy@graffy-ws2:~$ 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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.PHONY: install_lipase_libs
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install_lipase_libs: $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar install_ij_opencv
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.PHONY: install_lipase_plugins
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install_lipase_plugins:
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mkdir -p $(FIJI_ROOT_PATH)/plugins/Ipr ; \
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rsync -a ./src/ij-plugins/Ipr/ $(FIJI_ROOT_PATH)/plugins/Ipr/
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.PHONY: install
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install: install_lipase_libs install_lipase_plugins
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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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$(FIJI_EXE_PATH) --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$(RAW_IMAGES_ROOT_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
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test: test0001
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