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Diffusion BIOP Run Macro d9f3613f194e

Merge branch 'results-api'
d9f3613f194e
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Authored by Curtis Rueden <ctrueden@wisc.edu> on May 3 2017, 20:22.

Description

Merge branch 'results-api'

This branch does several things:

  • Moves the classes into a common sc.fiji.coloc package prefix.
  • Makes Coloc_2 usable from a script, and usable headless.
  • Adds a script template illustrating usage from a script.
  • Fixes a couple of serious memory leaks, and quitting-related problems.
  • Adds support for registering additional ResultHandlers.

This commit is dedicated to Stephan Grein.

Details

Committed
Curtis Rueden <ctrueden@wisc.edu>May 3 2017, 20:22
Pushed
oburriMar 8 2018, 18:06
Parents
R6269:db38c26db03a: Use sc.fiji.coloc as package prefix
R6269:a80151fb704e: Bump to next development cycle
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Event Timeline

Curtis Rueden <ctrueden@wisc.edu> committed R6269:d9f3613f194e: Merge branch 'results-api' (authored by Curtis Rueden <ctrueden@wisc.edu>).May 3 2017, 20:22

Merged Changes

CommitAuthorDetailsCommitted
db38c26db03aCurtis Rueden
Use sc.fiji.coloc as package prefix 
May 3 2017
7479ef73dd90Curtis Rueden
Organize imports 
May 3 2017
b7f84a775050Curtis Rueden
Fix a memory leak 
May 3 2017
acfe92317c3aCurtis Rueden
Coloc_2: remove old main method 
May 3 2017
5230beb0482fCurtis Rueden
Make SpearmanRankCorrelation not static 
May 3 2017
125146324f1aCurtis Rueden
Dispose the SingleWindowDisplay window on close 
May 3 2017
ad56fd31ad91Curtis Rueden
SingleWindowDisplay: do not keep list of displays 
May 3 2017
d9e552927c2fCurtis Rueden
Add a Groovy script to test programmatic execution 
May 3 2017
ca1c74598c2aEllen T Arena/Curtis Rueden
Coloc_2: split settings logic out of showDialog 
May 3 2017
9b46bccd3a2cCurtis Rueden
Coloc_2: fix Eclipse warnings 
May 3 2017
9962b762390aCurtis Rueden
Coloc_2: add support for headless operation 
May 3 2017
2db10aeef83aCurtis Rueden
Coloc_2: return analysis results data structure 
May 3 2017
312b100b876aCurtis Rueden
Coloc_2: add support for passing additional handlers 
May 3 2017
8a9515166dbbCurtis Rueden
Coloc_2: clean up style 
May 3 2017

Changes (118)
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Path
Mpom.xml
Vsrc/main/java/{ → sc/fiji/coloc}/ColocImgLibGadgets.java
Dsrc/main/java/Coloc_2.java
Vsrc/main/java/{ → sc/fiji/coloc}/Colocalisation_Test.java
Vsrc/main/java/{ → sc/fiji/coloc}/Colocalisation_Threshold.java
Dsrc/main/java/algorithms
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/Accumulator.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/Algorithm.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/AutoThresholdRegression.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/BisectionStepper.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/ChannelMapper.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/CostesSignificanceTest.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/Histogram2D.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/InputCheck.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/IntArraySorter.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/IntComparator.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/KendallTauRankCorrelation.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/LiHistogram2D.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/LiICQ.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/MandersColocalization.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/MissingPreconditionException.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/PearsonsCorrelation.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/SimpleStepper.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/SpearmanRankCorrelation.java
Vsrc/main/java/{ → sc/fiji/coloc}/algorithms/Stepper.java
Dsrc/main/java/gadgets
Vsrc/main/java/{ → sc/fiji/coloc}/gadgets/DataContainer.java
Vsrc/main/java/{ → sc/fiji/coloc}/gadgets/MaskFactory.java
Vsrc/main/java/{ → sc/fiji/coloc}/gadgets/Statistics.java
Vsrc/main/java/{ → sc/fiji/coloc}/gadgets/ThresholdMode.java
Dsrc/main/java/results
Vsrc/main/java/{ → sc/fiji/coloc}/results/EasyDisplay.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/NamedContainer.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/PDFWriter.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/ResultHandler.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/SingleWindowDisplay.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/ValueResult.java
Vsrc/main/java/{ → sc/fiji/coloc}/results/Warning.java
A(dir)src/main/java/sc/
A(dir)src/main/java/sc/fiji/
A(dir)src/main/java/sc/fiji/coloc/
Vsrc/main/java/{sc/fiji/coloc ← }/ColocImgLibGadgets.java
Asrc/main/java/sc/fiji/coloc/Coloc_2.java
Vsrc/main/java/{sc/fiji/coloc ← }/Colocalisation_Test.java
Vsrc/main/java/{sc/fiji/coloc ← }/Colocalisation_Threshold.java
A(dir)src/main/java/sc/fiji/coloc/algorithms/
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/Accumulator.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/Algorithm.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/AutoThresholdRegression.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/BisectionStepper.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/ChannelMapper.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/CostesSignificanceTest.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/Histogram2D.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/InputCheck.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/IntArraySorter.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/IntComparator.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/KendallTauRankCorrelation.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/LiHistogram2D.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/LiICQ.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/MandersColocalization.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/MissingPreconditionException.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/PearsonsCorrelation.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/SimpleStepper.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/SpearmanRankCorrelation.java
Vsrc/main/java/{sc/fiji/coloc ← }/algorithms/Stepper.java
A(dir)src/main/java/sc/fiji/coloc/gadgets/
Vsrc/main/java/{sc/fiji/coloc ← }/gadgets/DataContainer.java
Vsrc/main/java/{sc/fiji/coloc ← }/gadgets/MaskFactory.java
Vsrc/main/java/{sc/fiji/coloc ← }/gadgets/Statistics.java
Vsrc/main/java/{sc/fiji/coloc ← }/gadgets/ThresholdMode.java
A(dir)src/main/java/sc/fiji/coloc/results/
Asrc/main/java/sc/fiji/coloc/results/AnalysisResults.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/EasyDisplay.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/NamedContainer.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/PDFWriter.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/ResultHandler.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/SingleWindowDisplay.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/ValueResult.java
Vsrc/main/java/{sc/fiji/coloc ← }/results/Warning.java
Msrc/main/resources/plugins.config
A(dir)src/main/resources/script_templates/
A(dir)src/main/resources/script_templates/Examples/
Asrc/main/resources/script_templates/Examples/Colocalisation.groovy
Vsrc/test/java/{ → sc/fiji/coloc}/Main.java
A(dir)src/test/java/sc/
A(dir)src/test/java/sc/fiji/
A(dir)src/test/java/sc/fiji/coloc/
Vsrc/test/java/{sc/fiji/coloc ← }/Main.java
A(dir)src/test/java/sc/fiji/coloc/tests/
Vsrc/test/java/{sc/fiji/coloc ← }/tests/AutoThresholdRegressionTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/ColocalisationTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/CommutativityTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/CostesSignificanceTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/ImprovedNoise.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/KendallTauTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/LiICQTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/MandersColocalizationTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/MaskAndRoiTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/PearsonsCorrelationTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/SpearmanRankTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/StatisticsTest.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/TestImageAccessor.java
Vsrc/test/java/{sc/fiji/coloc ← }/tests/TestInteractively.java
Dsrc/test/java/tests
Vsrc/test/java/{ → sc/fiji/coloc}/tests/AutoThresholdRegressionTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/ColocalisationTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/CommutativityTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/CostesSignificanceTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/ImprovedNoise.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/KendallTauTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/LiICQTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/MandersColocalizationTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/MaskAndRoiTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/PearsonsCorrelationTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/SpearmanRankTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/StatisticsTest.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/TestImageAccessor.java
Vsrc/test/java/{ → sc/fiji/coloc}/tests/TestInteractively.java

R6269:d9f3613f194e

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src/main/java/ColocImgLibGadgets.java

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src/main/java/Coloc_2.java

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src/main/java/Colocalisation_Test.java

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src/main/java/Colocalisation_Threshold.java

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src/main/java/algorithms

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src/main/java/algorithms/Accumulator.java

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src/main/java/algorithms/Algorithm.java

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src/main/java/algorithms/AutoThresholdRegression.java

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src/main/java/algorithms/BisectionStepper.java

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src/main/java/algorithms/ChannelMapper.java

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src/main/java/algorithms/CostesSignificanceTest.java

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src/main/java/algorithms/Histogram2D.java

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src/main/java/algorithms/InputCheck.java

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src/main/java/algorithms/IntArraySorter.java

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src/main/java/algorithms/IntComparator.java

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src/main/java/algorithms/KendallTauRankCorrelation.java

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src/main/java/algorithms/LiHistogram2D.java

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src/main/java/algorithms/LiICQ.java

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src/main/java/algorithms/MandersColocalization.java

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src/main/java/algorithms/MissingPreconditionException.java

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src/main/java/algorithms/PearsonsCorrelation.java

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src/main/java/algorithms/SimpleStepper.java

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src/main/java/algorithms/SpearmanRankCorrelation.java

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src/main/java/algorithms/Stepper.java

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src/main/java/gadgets

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src/main/java/gadgets/DataContainer.java

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src/main/java/gadgets/MaskFactory.java

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src/main/java/gadgets/Statistics.java

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src/main/java/gadgets/ThresholdMode.java

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src/main/java/results

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src/main/java/results/EasyDisplay.java

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src/main/java/results/NamedContainer.java

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src/main/java/results/PDFWriter.java

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src/main/java/results/ResultHandler.java

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src/main/java/results/SingleWindowDisplay.java

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src/main/java/results/ValueResult.java

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src/main/java/results/Warning.java

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src/main/java/sc/fiji/coloc/ColocImgLibGadgets.java

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src/main/java/sc/fiji/coloc/Coloc_2.java

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src/main/java/sc/fiji/coloc/Colocalisation_Test.java

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src/main/java/sc/fiji/coloc/Colocalisation_Threshold.java

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src/main/java/sc/fiji/coloc/algorithms/Accumulator.java

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src/main/java/sc/fiji/coloc/algorithms/Algorithm.java

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src/main/java/sc/fiji/coloc/algorithms/AutoThresholdRegression.java

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src/main/java/sc/fiji/coloc/algorithms/BisectionStepper.java

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src/main/java/sc/fiji/coloc/algorithms/ChannelMapper.java

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src/main/java/sc/fiji/coloc/algorithms/CostesSignificanceTest.java

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src/main/java/sc/fiji/coloc/algorithms/Histogram2D.java

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src/main/java/sc/fiji/coloc/algorithms/InputCheck.java

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src/main/java/sc/fiji/coloc/algorithms/IntArraySorter.java

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src/main/java/sc/fiji/coloc/algorithms/IntComparator.java

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src/main/java/sc/fiji/coloc/algorithms/KendallTauRankCorrelation.java

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src/main/java/sc/fiji/coloc/algorithms/LiHistogram2D.java

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src/main/java/sc/fiji/coloc/algorithms/LiICQ.java

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src/main/java/sc/fiji/coloc/algorithms/MandersColocalization.java

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src/main/java/sc/fiji/coloc/algorithms/MissingPreconditionException.java

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src/main/java/sc/fiji/coloc/algorithms/PearsonsCorrelation.java

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src/main/java/sc/fiji/coloc/algorithms/SimpleStepper.java

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src/main/java/sc/fiji/coloc/algorithms/SpearmanRankCorrelation.java

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src/main/java/sc/fiji/coloc/algorithms/Stepper.java

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src/main/java/sc/fiji/coloc/gadgets/DataContainer.java

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src/main/java/sc/fiji/coloc/gadgets/MaskFactory.java

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src/main/java/sc/fiji/coloc/gadgets/Statistics.java

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src/main/java/sc/fiji/coloc/gadgets/ThresholdMode.java

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src/main/java/sc/fiji/coloc/results/AnalysisResults.java

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src/main/java/sc/fiji/coloc/results/EasyDisplay.java

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src/main/java/sc/fiji/coloc/results/NamedContainer.java

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src/main/java/sc/fiji/coloc/results/PDFWriter.java

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src/main/java/sc/fiji/coloc/results/ResultHandler.java

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src/main/java/sc/fiji/coloc/results/SingleWindowDisplay.java

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src/main/java/sc/fiji/coloc/results/ValueResult.java

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src/main/java/sc/fiji/coloc/results/Warning.java

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src/main/resources/plugins.config

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src/main/resources/script_templates/Examples/Colocalisation.groovy

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src/test/java/Main.java

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src/test/java/sc/fiji/coloc/Main.java

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src/test/java/sc/fiji/coloc/tests/AutoThresholdRegressionTest.java

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src/test/java/sc/fiji/coloc/tests/ColocalisationTest.java

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src/test/java/sc/fiji/coloc/tests/CommutativityTest.java

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src/test/java/sc/fiji/coloc/tests/CostesSignificanceTest.java

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src/test/java/sc/fiji/coloc/tests/ImprovedNoise.java

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src/test/java/sc/fiji/coloc/tests/KendallTauTest.java

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src/test/java/sc/fiji/coloc/tests/LiICQTest.java

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src/test/java/sc/fiji/coloc/tests/MandersColocalizationTest.java

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src/test/java/sc/fiji/coloc/tests/MaskAndRoiTest.java

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src/test/java/sc/fiji/coloc/tests/PearsonsCorrelationTest.java

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src/test/java/sc/fiji/coloc/tests/SpearmanRankTest.java

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src/test/java/sc/fiji/coloc/tests/StatisticsTest.java

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src/test/java/sc/fiji/coloc/tests/TestImageAccessor.java

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src/test/java/sc/fiji/coloc/tests/TestInteractively.java

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src/test/java/tests

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src/test/java/tests/AutoThresholdRegressionTest.java

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src/test/java/tests/ColocalisationTest.java

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src/test/java/tests/CommutativityTest.java

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src/test/java/tests/CostesSignificanceTest.java

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src/test/java/tests/ImprovedNoise.java

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src/test/java/tests/KendallTauTest.java

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src/test/java/tests/LiICQTest.java

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src/test/java/tests/MandersColocalizationTest.java

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src/test/java/tests/MaskAndRoiTest.java

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src/test/java/tests/PearsonsCorrelationTest.java

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src/test/java/tests/SpearmanRankTest.java

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src/test/java/tests/StatisticsTest.java

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src/test/java/tests/TestImageAccessor.java

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src/test/java/tests/TestInteractively.java

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