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lipase
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allows the user to choose the location of the tests output data 

This prevents pollution of git repository with temporary files and is done via a makefile variable TESTS_OUTPUT_DATA_PATH.
This commit is contained in:
Guillaume Raffy 2020-04-10 13:26:05 +02:00
parent 2505d69692
commit 13eb92c76e
4 changed files with 13 additions and 6 deletions
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2
Jenkinsfile vendored
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@ -17,7 +17,7 @@ pipeline {
} }
stage('Testing the package...') { stage('Testing the package...') {
steps { steps {
sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images test' sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images TESTS_OUTPUT_DATA_PATH=$TMP/$(whoami)/$JOB_NAME test'
} }
} }
stage('Building documentation...') { stage('Building documentation...') {

6
Makefile
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@ -3,6 +3,7 @@ FIJI_ROOT_PATH:=~/soft/Fiji.app
FIJI_EXE_PATH=$(FIJI_ROOT_PATH)/ImageJ-linux64 FIJI_EXE_PATH=$(FIJI_ROOT_PATH)/ImageJ-linux64
# RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images' # RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images'
RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images) RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images)
TESTS_OUTPUT_DATA_PATH:=$(shell echo ~/work/lipase/tmp)
LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py") LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
PLUGINS_SRC_FILES=$(shell find ./src/ij-plugins -name "*.py") PLUGINS_SRC_FILES=$(shell find ./src/ij-plugins -name "*.py")
LIPASE_VERSION=1.01 LIPASE_VERSION=1.01
@ -89,7 +90,8 @@ test0001: install
# on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py' # on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py'
# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './tests/test0001.py' "lipase_src_root_path='$(pwd)',raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images'" # /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'"
echo 2 > '/tmp/test_result.txt' ; \ echo 2 > '/tmp/test_result.txt' ; \
$(FIJI_EXE_PATH) --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$(RAW_IMAGES_ROOT_PATH)'" ; \ mkdir -p $(TESTS_OUTPUT_DATA_PATH)
$(FIJI_EXE_PATH) --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$(RAW_IMAGES_ROOT_PATH)',tests_output_data_path='$(TESTS_OUTPUT_DATA_PATH)'" ; \
ERROR_CODE=$$? ; \ ERROR_CODE=$$? ; \
echo "Fiji 's return code : $$ERROR_CODE" ; \ echo "Fiji 's return code : $$ERROR_CODE" ; \
ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \ ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \
@ -99,7 +101,7 @@ test0001: install
.PHONY: test0001 .PHONY: test0001
imgproc_tests: install imgproc_tests: install
echo 2 > '/tmp/test_result.txt' ; \ echo 2 > '/tmp/test_result.txt' ; \
$(FIJI_EXE_PATH) --ij2 --headless --run './tests/improc_tests.py' ; \ $(FIJI_EXE_PATH) --ij2 --headless --run './tests/improc_tests.py' "tests_output_data_path='$(TESTS_OUTPUT_DATA_PATH)'" ; \
ERROR_CODE=$$? ; \ ERROR_CODE=$$? ; \
echo "Fiji 's return code : $$ERROR_CODE" ; \ echo "Fiji 's return code : $$ERROR_CODE" ; \
ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \ ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \

4
tests/improc_tests.py
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@ -3,6 +3,7 @@
# # note: fiji's jython doesn't support encoding keyword # # note: fiji's jython doesn't support encoding keyword
# https://imagej.net/Scripting_Headless # https://imagej.net/Scripting_Headless
#@ String tests_output_data_path
import unittest # unittest2 doesn't exist in fiji import unittest # unittest2 doesn't exist in fiji
import sys import sys
@ -14,10 +15,11 @@ class ImProcTester(unittest.TestCase):
# we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method # we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method
# CURRENT_RESULT = None # holds last result object passed to run method # CURRENT_RESULT = None # holds last result object passed to run method
TESTS_OUTPUT_DATA_PATH = tests_output_data_path # eg '/tmp/lipase/tests-output-data' pylint: disable=undefined-variable
def setUp(self): def setUp(self):
print("initializing ImProcTester instance") print("initializing ImProcTester instance")
IImageEngine.set_instance(IJImageEngine(debugger=FileBasedDebugger('./debug-images'))) IImageEngine.set_instance(IJImageEngine(debugger=FileBasedDebugger('%s/debug-images' % self.TESTS_OUTPUT_DATA_PATH)))
def tearDown(self): def tearDown(self):
print("uninitializing ImProcTester instance") print("uninitializing ImProcTester instance")

7
tests/test0001.py
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@ -4,6 +4,8 @@
# https://imagej.net/Scripting_Headless # https://imagej.net/Scripting_Headless
#@ String raw_images_root_path #@ String raw_images_root_path
#@ String tests_output_data_path
import unittest # unittest2 doesn't exist in fiji import unittest # unittest2 doesn't exist in fiji
import sys import sys
@ -23,13 +25,14 @@ from lipase.imagej.hdf5serializer import save_hdf5_file
class TestLipase(unittest.TestCase): class TestLipase(unittest.TestCase):
RAW_IMAGES_ROOT_PATH = raw_images_root_path # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images' pylint: disable=undefined-variable RAW_IMAGES_ROOT_PATH = raw_images_root_path # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images' pylint: disable=undefined-variable
TESTS_OUTPUT_DATA_PATH = tests_output_data_path # eg '/tmp/lipase/tests-output-data' pylint: disable=undefined-variable
# we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method # we need to know if the test succeeded or not https://stackoverflow.com/questions/4414234/getting-pythons-unittest-results-in-a-teardown-method
# CURRENT_RESULT = None # holds last result object passed to run method # CURRENT_RESULT = None # holds last result object passed to run method
def setUp(self): def setUp(self):
print("initializing TestLipase instance") print("initializing TestLipase instance")
IImageEngine.set_instance(IJImageEngine(debugger=FileBasedDebugger('./debug-images'))) IImageEngine.set_instance(IJImageEngine(debugger=FileBasedDebugger('%s/debug-images' % self.TESTS_OUTPUT_DATA_PATH)))
self.catalog = ImageCatalog(self.RAW_IMAGES_ROOT_PATH) self.catalog = ImageCatalog(self.RAW_IMAGES_ROOT_PATH)
def tearDown(self): def tearDown(self):
@ -102,7 +105,7 @@ class TestLipase(unittest.TestCase):
background_estimator = EmptyFrameBackgroundEstimator(empty_frame_index=39) background_estimator = EmptyFrameBackgroundEstimator(empty_frame_index=39)
processor = GlobulesAreaEstimator(background_estimator=background_estimator, particle_threshold=2000.0) processor = GlobulesAreaEstimator(background_estimator=background_estimator, particle_threshold=2000.0)
results = processor.detect_particles(visible_traps_sequence) results = processor.detect_particles(visible_traps_sequence)
save_hdf5_file('results.h5', results) save_hdf5_file('%s/results.h5' % self.TESTS_OUTPUT_DATA_PATH, results)
# results file could be checked with "h5dump --xml ./lipase.git/results.h5" # results file could be checked with "h5dump --xml ./lipase.git/results.h5"
first_frame_measured_ratio = results['globules_area_ratio'][(0,)] first_frame_measured_ratio = results['globules_area_ratio'][(0,)]
first_frame_expected_ratio = 0.008 first_frame_expected_ratio = 0.008