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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; | ||
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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; | ||
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import java.io.IOException; | ||
import java.util.Collections; | ||
import java.util.Iterator; | ||
import java.util.List; | ||
import java.util.function.Supplier; | ||
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import net.imglib2.util.Cast; | ||
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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; | ||
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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; | ||
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@BeforeEach | ||
public void setUp() | ||
{ | ||
try (Context context = new Context()) | ||
{ | ||
Model model = graph7.getModel(); | ||
FeatureModel featureModel = model.getFeatureModel(); | ||
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// 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 ); | ||
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// 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 ); | ||
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} | ||
} | ||
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@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 ) ); | ||
} | ||
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@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 ) ) ); | ||
} | ||
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@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
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.../java/org/mastodon/mamut/feature/spot/dimensionalityreduction/pca/SpotPcaFeatureTest.java
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Original file line number | Diff line number | Diff line change |
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@@ -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; | ||
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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; | ||
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import java.io.IOException; | ||
import java.util.Collections; | ||
import java.util.Iterator; | ||
import java.util.List; | ||
import java.util.function.Supplier; | ||
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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; | ||
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@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 ); | ||
} | ||
} | ||
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@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 ) ); | ||
} | ||
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@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 ) ) ); | ||
} | ||
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@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 ) ) ); | ||
} | ||
} |