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elevanselevans
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Split SACA framework test into two
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Lines changed: 60 additions & 38 deletions

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  • scijava-ops-image/src/test/java/org/scijava/ops/image/coloc/saca

‎scijava-ops-image/src/test/java/org/scijava/ops/image/coloc/saca/SACATest.java‎

Lines changed: 60 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -37,72 +37,94 @@
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import org.scijava.types.Nil;
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import org.scijava.ops.image.AbstractColocalisationTest;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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/**
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* Tests {@code coloc.saca} ops.
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*
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* @author Edward Evans
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*/
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public class SACATest extends AbstractColocalisationTest {
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@Test
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public void testSACAFramework() {
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final int[] xPositions = { 30, 79, 77, 104, 7, 52, 164, 88, 119, 65 };
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final int[] yPositions = { 30, 36, 80, 79, 139, 102, 77, 41, 142, 118 };
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final double[] zscoreExpected = { 0.0, 6.117364936585281, 0.0,
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-1.282447034877343, 0.0, 6.642396454955293, 0.0, -1.6567255788972388, 0.0,
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3.5385003044434877 };
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final double[] pvalueExpected = { 0.5, 0.9999999995243234, 0.5,
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0.09984293678613743, 0.5, 0.9999999999845688, 0.5, 0.04878748455758225,
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0.5, 0.9997987965912973 };
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final double[] sigExpected = { 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
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0.0 };
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// XY positions to sample
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private final static int[] xPositions = { 30, 79, 77, 104, 7, 52, 164, 88,
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119, 65 };
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private final static int[] yPositions = { 30, 36, 80, 79, 139, 102, 77, 41,
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142, 118 };
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// load sample colocalization data
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Img<UnsignedByteType> green = getPositiveCorrelationImageCh1();
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Img<UnsignedByteType> red = getPositiveCorrelationImageCh2();
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// green and red colocalization images
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private Img<UnsignedByteType> green;
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private Img<UnsignedByteType> red;
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// get slice 15 from the green/red images
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var gs = ops.op("transform.hyperSliceView").input(green, 2, 15).apply();
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var rs = ops.op("transform.hyperSliceView").input(red, 2, 15).apply();
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// green and red data slices
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private Img<UnsignedByteType> gs;
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private Img<UnsignedByteType> rs;
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// create image containers
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Img<DoubleType> zscore = ops.op("create.img").input(gs, new DoubleType())
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.outType(new Nil<Img<DoubleType>>()
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// SACA heatmap z score and sig mask image containers
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private Img<DoubleType> zscore;
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private Img<BitType> sigMask;
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@BeforeAll
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public void setUpTest() {
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// load colocalization data (3D)
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green = getPositiveCorrelationImageCh1();
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red = getPositiveCorrelationImageCh2();
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// get slice 15 from colocalization data
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gs = ops.op("transform.hyperSliceView").input(green, 2, 15).outType(
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new Nil<Img<UnsignedByteType>>()
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{}).apply();
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Img<DoubleType> pvalue = ops.op("create.img").input(gs, new DoubleType())
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.outType(new Nil<Img<DoubleType>>()
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rs = ops.op("transform.hyperSliceView").input(red, 2, 15).outType(
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new Nil<Img<UnsignedByteType>>()
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{}).apply();
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Img<BitType> sigMask = ops.op("create.img").input(gs, new BitType())
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.outType(new Nil<Img<BitType>>()
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// create image containers
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zscore = ops.op("create.img").input(gs, new DoubleType()).outType(
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new Nil<Img<DoubleType>>()
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{}).apply();
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sigMask = ops.op("create.img").input(gs, new BitType()).outType(
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new Nil<Img<BitType>>()
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{}).apply();
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}
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@Test
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public void testSACAHeatmapZScore() {
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final double[] zscoreExpected = { 0.0, 6.117364936585281, 0.0,
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-1.282447034877343, 0.0, 6.642396454955293, 0.0, -1.6567255788972388, 0.0,
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3.5385003044434877 };
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// run SACA heatmap Z score op
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ops.op("coloc.saca.heatmapZScore").input(gs, rs).output(zscore).compute();
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// run stats.pnorm op
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ops.op("stats.pnorm").input(zscore).output(pvalue).compute();
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// get random access and assert results are equal
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final RandomAccess<DoubleType> zRA = zscore.randomAccess();
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for (int i = 0; i < xPositions.length; i++) {
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zRA.setPosition(xPositions[i], 0);
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zRA.setPosition(yPositions[i], 1);
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assertEquals(zscoreExpected[i], zRA.get().getRealDouble());
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}
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}
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@Test
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public void testSACASigMask() {
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final double[] sigExpected = { 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
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0.0 };
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// run SACA significant pixel mask op
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ops.op("coloc.saca.sigMask").input(zscore).output(sigMask).compute();
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// get random access and compare pixels
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final RandomAccess<DoubleType> zRA = zscore.randomAccess();
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final RandomAccess<DoubleType> pRA = pvalue.randomAccess();
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// get random access and assert results are equal
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final RandomAccess<BitType> sRA = sigMask.randomAccess();
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// assert results are equal
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for (int i = 0; i < xPositions.length; i++) {
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zRA.setPosition(xPositions[i], 0);
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zRA.setPosition(yPositions[i], 1);
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pRA.setPosition(xPositions[i], 0);
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pRA.setPosition(yPositions[i], 1);
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sRA.setPosition(xPositions[i], 0);
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sRA.setPosition(yPositions[i], 1);
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assertEquals(zscoreExpected[i], zRA.get().getRealDouble());
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assertEquals(pvalueExpected[i], pRA.get().getRealDouble());
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assertEquals(sigExpected[i], sRA.get().getRealDouble());
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}
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}
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}

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