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Makefile
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.PHONY: clean test
clean:
rm -rf ExampleCometAssay/output
rm -rf ExampleFly/output
rm -rf ExampleHuman/output
rm -rf ExamplePercentPositive/output
rm -rf ExampleTumor/output
rm -rf ExampleYeastColonies/output
rm -rf ExampleYeastPatches/output
rm -rf ExampleColocalization/output
rm -rf ExampleIlluminationCorrection/output_all
rm -rf ExampleIlluminationCorrection/output_each
rm -rf ExampleIlluminationCorrection/output2
rm -rf ExampleIlluminationCorrection/output3
rm -rf ExampleNeighbors/output
rm -rf ExampleSpeckles/output
rm -rf ExampleTrackObjects/output
rm -rf ExampleWoundHealing/output
rm -rf ExampleImagingFlowCytometryObjectsInGrid/output
rm -rf ExampleVitraImages/output
test:
cellprofiler -c -r -p ExampleCometAssay/ExampleCometAssay.cppipe \
-i ExampleCometAssay/images \
-o ExampleCometAssay/output \
-d ExampleCometAssay/output/done
cellprofiler -c -r -p ExampleFly/ExampleFly.cppipe \
-i ExampleFly/images \
-o ExampleFly/output \
-d ExampleFly/output/done
cellprofiler -c -r -p ExampleHuman/ExampleHuman.cppipe \
-i ExampleHuman/images \
-o ExampleHuman/output \
-d ExampleHuman/output/done
cellprofiler -c -r -p ExamplePercentPositive/ExamplePercentPositive.cppipe \
-i ExamplePercentPositive/images \
-o ExamplePercentPositive/output \
-d ExamplePercentPositive/output/done
cellprofiler -c -r -p ExampleTumor/ExampleTumor.cppipe \
-i ExampleTumor/images \
-o ExampleTumor/output \
-d ExampleTumor/output/done
cellprofiler -c -r -p ExampleYeastColonies/ExampleYeastColonies.cppipe \
-i ExampleYeastColonies/images \
-o ExampleYeastColonies/output \
-d ExampleYeastColonies/output/done
cellprofiler -c -r -p ExampleYeastPatches/ExampleYeastPatches.cppipe \
-i ExampleYeastPatches/images \
-o ExampleYeastPatches/output \
-d ExampleYeastPatches/output/done
cellprofiler -c -r -p ExampleColocalization/ExampleColocalization.cppipe \
-i ExampleColocalization/images \
-o ExampleColocalization/output \
-d ExampleColocalization/output/done
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_AllMethod.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output_all \
-d ExampleIlluminationCorrection/output_all/done
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_EachMethod.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output_each \
-d ExampleIlluminationCorrection/output_each/done
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example2.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output2 \
-d ExampleIlluminationCorrection/output2/done
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example3.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output3 \
-d ExampleIlluminationCorrection/output3/done
cellprofiler -c -r -p ExampleNeighbors/ExampleNeighbors.cppipe \
-i ExampleNeighbors/images \
-o ExampleNeighbors/output \
-d ExampleNeighbors/output/done
cellprofiler -c -r -p ExampleSpeckles/ExampleSpeckles.cppipe \
-i ExampleSpeckles/images \
-o ExampleSpeckles/output \
-d ExampleSpeckles/output/done
cellprofiler -c -r -p ExampleTrackObjects/ExampleTrackObjects.cppipe \
-i ExampleTrackObjects/images \
-o ExampleTrackObjects/output \
-d ExampleTrackObjects/output/done
cellprofiler -c -r -p ExampleWoundHealing/ExampleWoundHealing.cppipe \
-i ExampleWoundHealing/images \
-o ExampleWoundHealing/output \
-d ExampleWoundHealing/output/done
cellprofiler -c -r -p ExampleImagingFlowCytometryObjectsInGrid/ExampleImagingFlowCytometryObjectsInGrid.cppipe \
-i ExampleImagingFlowCytometryObjectsInGrid/images \
-o ExampleImagingFlowCytometryObjectsInGrid/output \
-d ExampleImagingFlowCytometryObjectsInGrid/output/done
cellprofiler -c -r -p ExampleUntangleWorms/ExampleUntangleWorms.cppipe \
-i ExampleUntangleWorms/images \
-o ExampleUntangleWorms/output \
-d ExampleUntangleWorms/output/done
cellprofiler -c -r -p ExampleStraightenWorms/ExampleUntangleAndStraightenWorms.cppipe \
-i ExampleStraightenWorms/images \
-o ExampleStraightenWorms/output \
-d ExampleStraightenWorms/output/done
cellprofiler -c -r -p ExampleUntangleWormsBrightField/ExampleUntangleWormsBrightField.cppipe \
-i ExampleUntangleWormsBrightField/images \
-o ExampleUntangleWormsBrightField/output \
-d ExampleUntangleWormsBrightField/output/done
cellprofiler -c -r -p ExampleVitraImages/ExampleVitra.cppipe \
-i ExampleVitraImages/images \
-o ExampleVitraImages/output \
-d ExampleVitraImages/output/done
@if [ $$(cat ExampleCometAssay/output/done) = Failure ] || \
[ $$(cat ExampleFly/output/done) = Failure ] || \
[ $$(cat ExampleHuman/output/done) = Failure ] || \
[ $$(cat ExamplePercentPositive/output/done) = Failure ] || \
[ $$(cat ExampleTumor/output/done) = Failure ] || \
[ $$(cat ExampleYeastColonies/output/done) = Failure ] || \
[ $$(cat ExampleYeastPatches/output/done) = Failure ] || \
[ $$(cat ExampleColocalization/output/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output_all/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output_each/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output2/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output3/done) = Failure ] || \
[ $$(cat ExampleNeighbors/output/done) = Failure ] || \
[ $$(cat ExampleSpeckles/output/done) = Failure ] || \
[ $$(cat ExampleTrackObjects/output/done) = Failure ] || \
[ $$(cat ExampleWoundHealing/output/done) = Failure ] || \
[ $$(cat ExampleUntangleWorms/output/done) = Failure ] || \
[ $$(cat ExampleStraightenWorms/output/done) = Failure ] || \
[ $$(cat ExampleUntangleWormsBrightField/output/done) = Failure ] || \
[ $$(cat ExampleImagingFlowCytometryObjectsInGrid/output/done) = Failure ] || \
[ $$(cat ExampleVitraImages/output/done) = Failure ]; then \
false; \
else true; fi