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Add unit tests for BranchPcaFeature and SpotPcaFeature
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...a/org/mastodon/mamut/feature/branch/dimensionalityreduction/pca/BranchPcaFeatureTest.java
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| /*- | ||
| * #%L | ||
| * mastodon-deep-lineage | ||
| * %% | ||
| * Copyright (C) 2022 - 2024 Stefan Hahmann | ||
| * %% | ||
| * Redistribution and use in source and binary forms, with or without | ||
| * modification, are permitted provided that the following conditions are met: | ||
| * | ||
| * 1. Redistributions of source code must retain the above copyright notice, | ||
| * this list of conditions and the following disclaimer. | ||
| * 2. Redistributions in binary form must reproduce the above copyright notice, | ||
| * this list of conditions and the following disclaimer in the documentation | ||
| * and/or other materials provided with the distribution. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE | ||
| * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | ||
| * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | ||
| * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | ||
| * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| * POSSIBILITY OF SUCH DAMAGE. | ||
| * #L% | ||
| */ | ||
| package org.mastodon.mamut.feature.branch.dimensionalityreduction.pca; | ||
|
|
||
| import static org.junit.jupiter.api.Assertions.assertFalse; | ||
| import static org.junit.jupiter.api.Assertions.assertNotEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.Collections; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
| import java.util.function.Supplier; | ||
|
|
||
| import net.imglib2.util.Cast; | ||
|
|
||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.mastodon.feature.Dimension; | ||
| import org.mastodon.feature.FeatureModel; | ||
| import org.mastodon.feature.FeatureProjection; | ||
| import org.mastodon.feature.FeatureProjectionSpec; | ||
| import org.mastodon.mamut.feature.AbstractFeatureTest; | ||
| import org.mastodon.mamut.feature.FeatureComputerTestUtils; | ||
| import org.mastodon.mamut.feature.FeatureSerializerTestUtils; | ||
| import org.mastodon.mamut.feature.FeatureUtils; | ||
| import org.mastodon.mamut.feature.branch.BranchDisplacementDurationFeature; | ||
| import org.mastodon.mamut.feature.branch.exampleGraph.ExampleGraph7; | ||
| import org.mastodon.mamut.feature.branch.sinuosity.BranchSinuosityFeature; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.DimensionalityReductionAlgorithm; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.DimensionalityReductionController; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.util.InputDimension; | ||
| import org.mastodon.mamut.model.Model; | ||
| import org.mastodon.mamut.model.branch.BranchLink; | ||
| import org.mastodon.mamut.model.branch.BranchSpot; | ||
| import org.scijava.Context; | ||
|
|
||
| public class BranchPcaFeatureTest extends AbstractFeatureTest< BranchSpot > | ||
| { | ||
| private BranchPcaFeature pcaFeature; | ||
|
|
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| private final ExampleGraph7 graph7 = new ExampleGraph7(); | ||
|
|
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| private FeatureProjectionSpec spec0; | ||
|
|
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| private FeatureProjectionSpec spec1; | ||
|
|
||
| @BeforeEach | ||
| public void setUp() | ||
| { | ||
| try (Context context = new Context()) | ||
| { | ||
| Model model = graph7.getModel(); | ||
| FeatureModel featureModel = model.getFeatureModel(); | ||
|
|
||
| // declare some features as input dimensions | ||
| BranchDisplacementDurationFeature branchDisplacementDurationFeature = Cast.unchecked( | ||
| FeatureComputerTestUtils.getFeature( context, model, BranchDisplacementDurationFeature.SPEC ) ); | ||
| featureModel.declareFeature( branchDisplacementDurationFeature ); | ||
| BranchSinuosityFeature branchSinuosityFeature = Cast.unchecked( | ||
| FeatureComputerTestUtils.getFeature( context, model, BranchSinuosityFeature.BRANCH_SINUOSITY_FEATURE_SPEC ) ); | ||
| featureModel.declareFeature( branchSinuosityFeature ); | ||
| List< InputDimension< BranchSpot > > inputDimensions = | ||
| InputDimension.getListFromFeatureModel( featureModel, BranchSpot.class, BranchLink.class ); | ||
|
|
||
| // set up the controller and compute the feature | ||
| Supplier< List< InputDimension< BranchSpot > > > inputDimensionsSupplier = () -> inputDimensions; | ||
| DimensionalityReductionController controller = new DimensionalityReductionController( graph7.getModel(), context ); | ||
| controller.setModelGraph( false ); | ||
| controller.setAlgorithm( DimensionalityReductionAlgorithm.PCA ); | ||
| controller.computeFeature( inputDimensionsSupplier ); | ||
| pcaFeature = FeatureUtils.getFeature( graph7.getModel(), BranchPcaFeature.BranchSpotPcaFeatureSpec.class ); | ||
| assertNotNull( pcaFeature ); | ||
| spec0 = new FeatureProjectionSpec( pcaFeature.getProjectionName( 0 ), Dimension.NONE ); | ||
| spec1 = new FeatureProjectionSpec( pcaFeature.getProjectionName( 1 ), Dimension.NONE ); | ||
|
|
||
| } | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureComputation() | ||
| { | ||
| assertNotNull( pcaFeature ); | ||
| FeatureProjection< BranchSpot > projection0 = getProjection( pcaFeature, spec0 ); | ||
| FeatureProjection< BranchSpot > projection1 = getProjection( pcaFeature, spec1 ); | ||
| Iterator< BranchSpot > branchSpotIterator = graph7.getModel().getBranchGraph().vertices().iterator(); | ||
| BranchSpot branchSpot = branchSpotIterator.next(); | ||
| assertFalse( Double.isNaN( projection0.value( branchSpot ) ) ); | ||
| assertNotEquals( 0, projection0.value( branchSpot ) ); | ||
| assertFalse( Double.isNaN( projection1.value( branchSpot ) ) ); | ||
| assertNotEquals( 0, projection1.value( branchSpot ) ); | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureSerialization() throws IOException | ||
| { | ||
| BranchPcaFeature pcaFeatureReloaded; | ||
| try (Context context = new Context()) | ||
| { | ||
| pcaFeatureReloaded = | ||
| ( BranchPcaFeature ) FeatureSerializerTestUtils.saveAndReload( context, graph7.getModel(), this.pcaFeature ); | ||
| } | ||
| assertNotNull( pcaFeatureReloaded ); | ||
| Iterator< BranchSpot > branchSpotIterator = graph7.getModel().getBranchGraph().vertices().iterator(); | ||
| BranchSpot branchSpot = branchSpotIterator.next(); | ||
| // check that the feature has correct values after saving and reloading | ||
| assertTrue( FeatureSerializerTestUtils.checkFeatureProjectionEquality( this.pcaFeature, pcaFeatureReloaded, | ||
| Collections.singleton( branchSpot ) ) ); | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureInvalidate() | ||
| { | ||
| Iterator< BranchSpot > branchSpotIterator = graph7.getModel().getBranchGraph().vertices().iterator(); | ||
| BranchSpot branchSpot = branchSpotIterator.next(); | ||
|
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| // test, if features are not NaN before invalidation | ||
| assertFalse( Double.isNaN( getProjection( pcaFeature, spec0 ).value( branchSpot ) ) ); | ||
| assertFalse( Double.isNaN( getProjection( pcaFeature, spec1 ).value( branchSpot ) ) ); | ||
|
|
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| // invalidate feature | ||
| pcaFeature.invalidate( branchSpot ); | ||
|
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| // test, if features are NaN after invalidation | ||
| assertTrue( Double.isNaN( getProjection( pcaFeature, spec0 ).value( branchSpot ) ) ); | ||
| assertTrue( Double.isNaN( getProjection( pcaFeature, spec1 ).value( branchSpot ) ) ); | ||
| } | ||
| } |
143 changes: 143 additions & 0 deletions
143
.../java/org/mastodon/mamut/feature/spot/dimensionalityreduction/pca/SpotPcaFeatureTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,143 @@ | ||
| /*- | ||
| * #%L | ||
| * mastodon-deep-lineage | ||
| * %% | ||
| * Copyright (C) 2022 - 2024 Stefan Hahmann | ||
| * %% | ||
| * Redistribution and use in source and binary forms, with or without | ||
| * modification, are permitted provided that the following conditions are met: | ||
| * | ||
| * 1. Redistributions of source code must retain the above copyright notice, | ||
| * this list of conditions and the following disclaimer. | ||
| * 2. Redistributions in binary form must reproduce the above copyright notice, | ||
| * this list of conditions and the following disclaimer in the documentation | ||
| * and/or other materials provided with the distribution. | ||
| * | ||
| * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE | ||
| * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | ||
| * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | ||
| * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | ||
| * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| * POSSIBILITY OF SUCH DAMAGE. | ||
| * #L% | ||
| */ | ||
| package org.mastodon.mamut.feature.spot.dimensionalityreduction.pca; | ||
|
|
||
| import static org.junit.jupiter.api.Assertions.assertFalse; | ||
| import static org.junit.jupiter.api.Assertions.assertNotEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.Collections; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
| import java.util.function.Supplier; | ||
|
|
||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.mastodon.feature.Dimension; | ||
| import org.mastodon.feature.FeatureModel; | ||
| import org.mastodon.feature.FeatureProjection; | ||
| import org.mastodon.feature.FeatureProjectionSpec; | ||
| import org.mastodon.mamut.feature.AbstractFeatureTest; | ||
| import org.mastodon.mamut.feature.FeatureSerializerTestUtils; | ||
| import org.mastodon.mamut.feature.FeatureUtils; | ||
| import org.mastodon.mamut.feature.branch.exampleGraph.ExampleGraph7; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.DimensionalityReductionAlgorithm; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.DimensionalityReductionController; | ||
| import org.mastodon.mamut.feature.dimensionalityreduction.util.InputDimension; | ||
| import org.mastodon.mamut.model.Link; | ||
| import org.mastodon.mamut.model.Spot; | ||
| import org.scijava.Context; | ||
|
|
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| public class SpotPcaFeatureTest extends AbstractFeatureTest< Spot > | ||
| { | ||
| private SpotPcaFeature spotPcaFeature; | ||
|
|
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| private final ExampleGraph7 graph7 = new ExampleGraph7(); | ||
|
|
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| private FeatureProjectionSpec spec0; | ||
|
|
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| private FeatureProjectionSpec spec1; | ||
|
|
||
| @BeforeEach | ||
| public void setUp() | ||
| { | ||
| try (Context context = new Context()) | ||
| { | ||
| FeatureModel featureModel = graph7.getModel().getFeatureModel(); | ||
| DimensionalityReductionController controller = new DimensionalityReductionController( graph7.getModel(), context ); | ||
| controller.setAlgorithm( DimensionalityReductionAlgorithm.PCA ); | ||
| Supplier< List< InputDimension< Spot > > > inputDimensionsSupplier = | ||
| () -> InputDimension.getListFromFeatureModel( featureModel, Spot.class, Link.class ); | ||
| controller.computeFeature( inputDimensionsSupplier ); | ||
| spotPcaFeature = FeatureUtils.getFeature( graph7.getModel(), SpotPcaFeature.SpotPcaFeatureSpec.class ); | ||
| assertNotNull( spotPcaFeature ); | ||
| spec0 = new FeatureProjectionSpec( spotPcaFeature.getProjectionName( 0 ), Dimension.NONE ); | ||
| spec1 = new FeatureProjectionSpec( spotPcaFeature.getProjectionName( 1 ), Dimension.NONE ); | ||
| } | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureComputation() | ||
| { | ||
| assertNotNull( spotPcaFeature ); | ||
| FeatureProjection< Spot > projection0 = getProjection( spotPcaFeature, spec0 ); | ||
| FeatureProjection< Spot > projection1 = getProjection( spotPcaFeature, spec1 ); | ||
| Iterator< Spot > spotIterator = graph7.getModel().getGraph().vertices().iterator(); | ||
| Spot spot0 = spotIterator.next(); | ||
| assertTrue( Double.isNaN( projection0.value( spot0 ) ) ); | ||
| assertTrue( Double.isNaN( projection1.value( spot0 ) ) ); | ||
| Spot spot1 = spotIterator.next(); | ||
| assertFalse( Double.isNaN( projection0.value( spot1 ) ) ); | ||
| assertFalse( Double.isNaN( projection1.value( spot1 ) ) ); | ||
| assertNotEquals( 0, projection0.value( spot1 ) ); | ||
| assertNotEquals( 0, projection1.value( spot1 ) ); | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureSerialization() throws IOException | ||
| { | ||
| SpotPcaFeature spotPcaFeatureReloaded; | ||
| try (Context context = new Context()) | ||
| { | ||
| spotPcaFeatureReloaded = | ||
| ( SpotPcaFeature ) FeatureSerializerTestUtils.saveAndReload( context, graph7.getModel(), spotPcaFeature ); | ||
| } | ||
| assertNotNull( spotPcaFeatureReloaded ); | ||
| // check that the feature has correct values after saving and reloading | ||
| Iterator< Spot > spotIterator = graph7.getModel().getGraph().vertices().iterator(); | ||
| spotIterator.next(); | ||
| Spot spot1 = spotIterator.next(); | ||
| assertTrue( FeatureSerializerTestUtils.checkFeatureProjectionEquality( | ||
| spotPcaFeature, spotPcaFeatureReloaded, | ||
| Collections.singleton( spot1 ) ) ); | ||
| } | ||
|
|
||
| @Test | ||
| @Override | ||
| public void testFeatureInvalidate() | ||
| { | ||
| // test, if features are not NaN before invalidation | ||
| Iterator< Spot > spotIterator = graph7.getModel().getGraph().vertices().iterator(); | ||
| spotIterator.next(); | ||
| Spot spot1 = spotIterator.next(); | ||
| assertFalse( Double.isNaN( getProjection( spotPcaFeature, spec0 ).value( spot1 ) ) ); | ||
| assertFalse( Double.isNaN( getProjection( spotPcaFeature, spec1 ).value( spot1 ) ) ); | ||
|
|
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| // invalidate feature | ||
| spotPcaFeature.invalidate( spot1 ); | ||
|
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| // test, if features are NaN after invalidation | ||
| assertTrue( Double.isNaN( getProjection( spotPcaFeature, spec0 ).value( spot1 ) ) ); | ||
| assertTrue( Double.isNaN( getProjection( spotPcaFeature, spec1 ).value( spot1 ) ) ); | ||
| } | ||
| } |