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test: BdvMetadataIoTests improvements #46

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test: BdvMetadataIoTests improvements #46

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677aa02
test: BdvMetadataIoTests improvements
bogovicj Oct 4, 2024
2bd2533
wip/test: BdvMetadataIoTests temporarily don't clean up
bogovicj Oct 4, 2024
989ec72
test/wip: BdvMetadataIoTests clearer assertions
bogovicj Oct 4, 2024
cfe8e36
wip/tests: omg add sleeps!?
bogovicj Oct 4, 2024
7f474d8
test: BdvMetadataIoTests use tryWaitRepeat
bogovicj Oct 8, 2024
aa5ccd7
Merge branch 'master' into random-test-failures-oct2024
bogovicj Oct 8, 2024
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9 changes: 8 additions & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@
<n5.version>3.3.0</n5.version>
<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
<n5-google-cloud.version>4.1.1</n5-google-cloud.version>
<n5-ij.version>4.2.5</n5-ij.version>
<n5-ij.version>4.2.6-SNAPSHOT</n5-ij.version>
<n5-imglib2.version>7.0.2</n5-imglib2.version>
<n5-universe.version>1.6.0</n5-universe.version>
</properties>
Expand Down Expand Up @@ -216,6 +216,13 @@
<classifier>tests</classifier>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-ij</artifactId>
<version>${n5-ij.version}</version>
<classifier>tests</classifier>
<scope>test</scope>
</dependency>
</dependencies>

<repositories>
Expand Down
168 changes: 106 additions & 62 deletions src/test/java/org/janelia/saalfeldlab/n5/bdv/BdvMetadataIoTests.java
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
package org.janelia.saalfeldlab.n5.bdv;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
Expand All @@ -15,8 +16,8 @@
import java.util.concurrent.Executors;
import java.util.stream.Collectors;

import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.TestRunners;
import org.janelia.saalfeldlab.n5.ij.N5Importer;
import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
import org.janelia.saalfeldlab.n5.metadata.imagej.ImagePlusLegacyMetadataParser;
Expand All @@ -26,7 +27,9 @@
import org.janelia.saalfeldlab.n5.universe.N5Factory;
import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;

Expand All @@ -46,17 +49,28 @@
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.util.ValuePair;
import net.imglib2.view.Views;

public class BdvMetadataIoTests {

private File baseDir;
private static File baseDir;

@Before
public void before() {
@BeforeClass
public static void before() {

final URL configUrl = BdvMetadataIoTests.class.getResource("/plugins.config");
baseDir = new File(configUrl.getFile()).getParentFile();
try {
baseDir = Files.createTempDirectory("n5-ij-tests-").toFile();
baseDir.deleteOnExit();
} catch (IOException e) {
e.printStackTrace();
}
}

@AfterClass
public static void after() {

baseDir.delete();
}

public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & NumericType<V>> void readWriteParseTest(
Expand All @@ -76,66 +90,91 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
writer.setOverwrite(true); // overwrite on for this test
writer.run(); // run() closes the n5 writer

try {
Thread.sleep(20);
} catch (InterruptedException e) {}

final String readerDataset = dataset;

final N5Reader n5 = new N5Factory().openReader(outputPath);
final N5DatasetDiscoverer datasetDiscoverer = new N5DatasetDiscoverer(n5, Executors.newSingleThreadExecutor(), (x) -> true,
Arrays.asList(N5ViewerCreator.n5vParsers),
Arrays.asList(N5ViewerCreator.n5vGroupParsers));

final N5TreeNode root = datasetDiscoverer.discoverAndParseRecursive("");
final Optional<N5TreeNode> metaOpt = root.getDescendant(readerDataset);
if (!metaOpt.isPresent())
fail("could not find metadata at: " + readerDataset);

final List<ConverterSetup> converterSetups = new ArrayList<>();
final List<SourceAndConverter<T>> sourcesAndConverters = new ArrayList<>();

final SharedQueue sharedQueue = new SharedQueue(1);
final BdvOptions options = BdvOptions.options().frameTitle("N5 Viewer");

final int numTimepoints = N5Viewer.buildN5Sources(
n5,
new DataSelection(n5, Collections.singletonList(metaOpt.get().getMetadata())),
sharedQueue,
converterSetups,
sourcesAndConverters,
options);

assertEquals(String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size());
assertEquals(String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints);

final Source<T> src0 = sourcesAndConverters.get(0).getSpimSource();
assertEquals(String.format("slices for %s", dataset), imp.getNSlices(),
src0.getSource(0, 0).dimension(2));

final AffineTransform3D tform = new AffineTransform3D();
src0.getSourceTransform(0, 0, tform);
final double rx = tform.get(0, 0);
final double ry = tform.get(1, 1);
final double rz = tform.get(2, 2);
final String unit = src0.getVoxelDimensions().unit();

if (testMeta) {
final boolean resEqual = rx == imp.getCalibration().pixelWidth &&
ry == imp.getCalibration().pixelHeight &&
rz == imp.getCalibration().pixelDepth;

assertTrue(String.format("%s resolutions ", dataset), resEqual);
assertTrue(String.format("%s units ", dataset),
unit.equals(imp.getCalibration().getUnit()));
try( final N5Writer n5 = new N5Factory().openWriter(outputPath) ) {

}
final N5DatasetDiscoverer datasetDiscoverer = new N5DatasetDiscoverer(
n5,
Executors.newSingleThreadExecutor(),
(x) -> true,
Arrays.asList(N5ViewerCreator.n5vParsers),
Arrays.asList(N5ViewerCreator.n5vGroupParsers));

if (testData) {
final List<Source<T>> srcList = sourcesAndConverters.stream().map(sac -> sac.getSpimSource()).collect(Collectors.toList());
assertTrue(String.format("%s data ", dataset), sourceDataIdentical(imp, srcList));
}
n5.close();
TestRunners.tryWaitRepeat(() -> {

N5TreeNode root;
try {
root = datasetDiscoverer.discoverAndParseRecursive("");
} catch (IOException e) {
return null; // to trigger retry
}

final Optional<N5TreeNode> metaOpt = root.getDescendant(readerDataset);
final List<ConverterSetup> converterSetups = new ArrayList<>();
final List<SourceAndConverter<T>> sourcesAndConverters = new ArrayList<>();

final SharedQueue sharedQueue = new SharedQueue(1);
final BdvOptions options = BdvOptions.options().frameTitle("N5 Viewer");

int numTimepoints;
try {
numTimepoints = N5Viewer.buildN5Sources(
n5,
new DataSelection(n5, Collections.singletonList(metaOpt.get().getMetadata())),
sharedQueue,
converterSetups,
sourcesAndConverters,
options);
} catch (IOException e) {
return null; // to trigger retry
}

return new ValuePair<List<SourceAndConverter<T>>, Integer>(sourcesAndConverters, numTimepoints);

}).ifPresent(sacAndNtime -> {

// remove
final N5Writer n5w = new N5Factory().openWriter(outputPath);
n5w.remove();
final List<SourceAndConverter<T>> sourcesAndConverters = sacAndNtime.getA();
final int numTimepoints = sacAndNtime.getB();

assertEquals(String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size());
assertEquals(String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints);

final Source<T> src0 = sourcesAndConverters.get(0).getSpimSource();
assertEquals(String.format("slices for %s", dataset), imp.getNSlices(),
src0.getSource(0, 0).dimension(2));

final AffineTransform3D tform = new AffineTransform3D();
src0.getSourceTransform(0, 0, tform);
final double rx = tform.get(0, 0);
final double ry = tform.get(1, 1);
final double rz = tform.get(2, 2);
final String unit = src0.getVoxelDimensions().unit();

if (testMeta) {
final boolean resEqual = rx == imp.getCalibration().pixelWidth &&
ry == imp.getCalibration().pixelHeight &&
rz == imp.getCalibration().pixelDepth;

assertTrue(String.format("%s resolutions ", dataset), resEqual);
assertTrue(String.format("%s units ", dataset),
unit.equals(imp.getCalibration().getUnit()));

}

if (testData) {
final List<Source<T>> srcList = sourcesAndConverters.stream().map(sac -> sac.getSpimSource()).collect(Collectors.toList());
assertTrue(String.format("%s data ", dataset), sourceDataIdentical(imp, srcList));
}

});

n5.close();
}
}

/*
Expand Down Expand Up @@ -186,6 +225,11 @@ public void testMultiChannelHelper(final String metatype, final String suffix) t

final String dataset = String.format("/c%dz%dt%d", nc, nz, nt);
readWriteParseTest(imp, n5RootPath, dataset, blockSizeString, metatype, compressionString, true, true);

try {
Thread.sleep(20);
} catch (InterruptedException e) {}

}
}
}
Expand Down
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