diff --git a/src/test/java/tests/ColocalisationTest.java b/src/test/java/tests/ColocalisationTest.java index de4008d..7bcec0f 100644 --- a/src/test/java/tests/ColocalisationTest.java +++ b/src/test/java/tests/ColocalisationTest.java @@ -1,126 +1,126 @@ package tests; import gadgets.MaskFactory; import net.imglib2.RandomAccessibleInterval; import net.imglib2.algorithm.math.ImageStatistics; import net.imglib2.type.logic.BitType; import net.imglib2.type.numeric.RealType; import net.imglib2.type.numeric.integer.UnsignedByteType; import org.junit.After; import org.junit.Before; public abstract class ColocalisationTest { // images and meta data for zero correlation RandomAccessibleInterval zeroCorrelationImageCh1; RandomAccessibleInterval zeroCorrelationImageCh2; RandomAccessibleInterval zeroCorrelationAlwaysTrueMask; double zeroCorrelationImageCh1Mean; double zeroCorrelationImageCh2Mean; // images and meta data for positive correlation RandomAccessibleInterval positiveCorrelationImageCh1; RandomAccessibleInterval positiveCorrelationImageCh2; RandomAccessibleInterval positiveCorrelationAlwaysTrueMask; double positiveCorrelationImageCh1Mean; double positiveCorrelationImageCh2Mean; // images and meta data for a synthetic negative correlation dataset RandomAccessibleInterval syntheticNegativeCorrelationImageCh1; RandomAccessibleInterval syntheticNegativeCorrelationImageCh2; RandomAccessibleInterval syntheticNegativeCorrelationAlwaysTrueMask; double syntheticNegativeCorrelationImageCh1Mean; double syntheticNegativeCorrelationImageCh2Mean; // images like in the manders paper RandomAccessibleInterval mandersA, mandersB, mandersC, mandersD, mandersE, mandersF, mandersG, mandersH, mandersI; RandomAccessibleInterval mandersAlwaysTrueMask; /** * This method is run before every single test is run and is meant to set up * the images and meta data needed for testing image colocalisation. */ @Before public void setup() { - zeroCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("Data/greenZstack.tif"); + zeroCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("/greenZstack.tif"); zeroCorrelationImageCh1Mean = ImageStatistics.getImageMean(zeroCorrelationImageCh1); - zeroCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("Data/redZstack.tif"); + zeroCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("/redZstack.tif"); zeroCorrelationImageCh2Mean = ImageStatistics.getImageMean(zeroCorrelationImageCh2); final long[] dimZeroCorrCh1 = new long[ zeroCorrelationImageCh1.numDimensions() ]; zeroCorrelationImageCh1.dimensions(dimZeroCorrCh1); zeroCorrelationAlwaysTrueMask = MaskFactory.createMask(dimZeroCorrCh1, true); - positiveCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("Data/colocsample1b-green.tif"); + positiveCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("/colocsample1b-green.tif"); positiveCorrelationImageCh1Mean = ImageStatistics.getImageMean(positiveCorrelationImageCh1); - positiveCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("Data/colocsample1b-red.tif"); + positiveCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("/colocsample1b-red.tif"); positiveCorrelationImageCh2Mean = ImageStatistics.getImageMean(positiveCorrelationImageCh2); final long[] dimPosCorrCh1 = new long[ positiveCorrelationImageCh1.numDimensions() ]; positiveCorrelationImageCh1.dimensions(dimPosCorrCh1); positiveCorrelationAlwaysTrueMask = MaskFactory.createMask(dimPosCorrCh1, true); - syntheticNegativeCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("Data/syntheticNegCh1.tif"); + syntheticNegativeCorrelationImageCh1 = TestImageAccessor.loadTiffFromJar("/syntheticNegCh1.tif"); syntheticNegativeCorrelationImageCh1Mean = ImageStatistics.getImageMean(syntheticNegativeCorrelationImageCh1); - syntheticNegativeCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("Data/syntheticNegCh2.tif"); + syntheticNegativeCorrelationImageCh2 = TestImageAccessor.loadTiffFromJar("/syntheticNegCh2.tif"); syntheticNegativeCorrelationImageCh2Mean = ImageStatistics.getImageMean(syntheticNegativeCorrelationImageCh2); final long[] dimSynthNegCorrCh1 = new long[ syntheticNegativeCorrelationImageCh1.numDimensions() ]; syntheticNegativeCorrelationImageCh1.dimensions(dimSynthNegCorrCh1); syntheticNegativeCorrelationAlwaysTrueMask = MaskFactory.createMask(dimSynthNegCorrCh1, true); - mandersA = TestImageAccessor.loadTiffFromJar("Data/mandersA.tiff"); - mandersB = TestImageAccessor.loadTiffFromJar("Data/mandersB.tiff"); - mandersC = TestImageAccessor.loadTiffFromJar("Data/mandersC.tiff"); - mandersD = TestImageAccessor.loadTiffFromJar("Data/mandersD.tiff"); - mandersE = TestImageAccessor.loadTiffFromJar("Data/mandersE.tiff"); - mandersF = TestImageAccessor.loadTiffFromJar("Data/mandersF.tiff"); - mandersG = TestImageAccessor.loadTiffFromJar("Data/mandersG.tiff"); - mandersH = TestImageAccessor.loadTiffFromJar("Data/mandersH.tiff"); - mandersI = TestImageAccessor.loadTiffFromJar("Data/mandersI.tiff"); + mandersA = TestImageAccessor.loadTiffFromJar("/mandersA.tiff"); + mandersB = TestImageAccessor.loadTiffFromJar("/mandersB.tiff"); + mandersC = TestImageAccessor.loadTiffFromJar("/mandersC.tiff"); + mandersD = TestImageAccessor.loadTiffFromJar("/mandersD.tiff"); + mandersE = TestImageAccessor.loadTiffFromJar("/mandersE.tiff"); + mandersF = TestImageAccessor.loadTiffFromJar("/mandersF.tiff"); + mandersG = TestImageAccessor.loadTiffFromJar("/mandersG.tiff"); + mandersH = TestImageAccessor.loadTiffFromJar("/mandersH.tiff"); + mandersI = TestImageAccessor.loadTiffFromJar("/mandersI.tiff"); final long[] dimMandersA = new long[ mandersA.numDimensions() ]; mandersA.dimensions(dimMandersA); mandersAlwaysTrueMask = MaskFactory.createMask(dimMandersA, true); } /** * This method is run after every single test and is meant to clean up. */ @After public void cleanup() { // nothing to do } /** * Creates a ROI offset array with a distance of 1/4 to the origin * in each dimension. */ protected > long[] createRoiOffset(RandomAccessibleInterval img) { final long[] offset = new long[ img.numDimensions() ]; img.dimensions(offset); for (int i=0; i> long[] createRoiSize(RandomAccessibleInterval img) { final long[] size = new long[ img.numDimensions() ]; img.dimensions(size); for (int i=0; i " + "li_histogram_channel_1 " + "li_histogram_channel_2 " + "li_icq " + "spearman's_rank_correlation " + "manders'_correlation " + "kendall's_tau_rank_correlation " + "2d_instensity_histogram " + "costes'_significance_test " + "psf=3 " + "costes_randomisations=10" ); } } diff --git a/tests/Data/SineXCosY.ijm b/src/test/resources/SineXCosY.ijm similarity index 100% rename from tests/Data/SineXCosY.ijm rename to src/test/resources/SineXCosY.ijm diff --git a/tests/Data/colocsample1b-green.tif b/src/test/resources/colocsample1b-green.tif similarity index 100% rename from tests/Data/colocsample1b-green.tif rename to src/test/resources/colocsample1b-green.tif diff --git a/tests/Data/colocsample1b-red.tif b/src/test/resources/colocsample1b-red.tif similarity index 100% rename from tests/Data/colocsample1b-red.tif rename to src/test/resources/colocsample1b-red.tif diff --git a/tests/Data/greenZstack.tif b/src/test/resources/greenZstack.tif similarity index 100% rename from tests/Data/greenZstack.tif rename to src/test/resources/greenZstack.tif diff --git a/tests/Data/high_random_overlap1.tif b/src/test/resources/high_random_overlap1.tif similarity index 100% rename from tests/Data/high_random_overlap1.tif rename to src/test/resources/high_random_overlap1.tif diff --git a/tests/Data/high_random_overlap2.tif b/src/test/resources/high_random_overlap2.tif similarity index 100% rename from tests/Data/high_random_overlap2.tif rename to src/test/resources/high_random_overlap2.tif diff --git a/tests/Data/mandersA.tiff b/src/test/resources/mandersA.tiff similarity index 100% rename from tests/Data/mandersA.tiff rename to src/test/resources/mandersA.tiff diff --git a/tests/Data/mandersB.tiff b/src/test/resources/mandersB.tiff similarity index 100% rename from tests/Data/mandersB.tiff rename to src/test/resources/mandersB.tiff diff --git a/tests/Data/mandersC.tiff b/src/test/resources/mandersC.tiff similarity index 100% rename from tests/Data/mandersC.tiff rename to src/test/resources/mandersC.tiff diff --git a/tests/Data/mandersD.tiff b/src/test/resources/mandersD.tiff similarity index 100% rename from tests/Data/mandersD.tiff rename to src/test/resources/mandersD.tiff diff --git a/tests/Data/mandersE.tiff b/src/test/resources/mandersE.tiff similarity index 100% rename from tests/Data/mandersE.tiff rename to src/test/resources/mandersE.tiff diff --git a/tests/Data/mandersF.tiff b/src/test/resources/mandersF.tiff similarity index 100% rename from tests/Data/mandersF.tiff rename to src/test/resources/mandersF.tiff diff --git a/tests/Data/mandersG.tiff b/src/test/resources/mandersG.tiff similarity index 100% rename from tests/Data/mandersG.tiff rename to src/test/resources/mandersG.tiff diff --git a/tests/Data/mandersH.tiff b/src/test/resources/mandersH.tiff similarity index 100% rename from tests/Data/mandersH.tiff rename to src/test/resources/mandersH.tiff diff --git a/tests/Data/mandersI.tiff b/src/test/resources/mandersI.tiff similarity index 100% rename from tests/Data/mandersI.tiff rename to src/test/resources/mandersI.tiff diff --git a/tests/Data/random-dots-smoothed.ijm b/src/test/resources/random-dots-smoothed.ijm similarity index 100% rename from tests/Data/random-dots-smoothed.ijm rename to src/test/resources/random-dots-smoothed.ijm diff --git a/tests/Data/redZstack.tif b/src/test/resources/redZstack.tif similarity index 100% rename from tests/Data/redZstack.tif rename to src/test/resources/redZstack.tif diff --git a/tests/Data/syntheticNegCh1.tif b/src/test/resources/syntheticNegCh1.tif similarity index 100% rename from tests/Data/syntheticNegCh1.tif rename to src/test/resources/syntheticNegCh1.tif diff --git a/tests/Data/syntheticNegCh2.tif b/src/test/resources/syntheticNegCh2.tif similarity index 100% rename from tests/Data/syntheticNegCh2.tif rename to src/test/resources/syntheticNegCh2.tif