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test: ngff v0.4 coordinate transform parsing
see #17
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17 files changed

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‎src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/NgffSingleScaleMetadataParser.java

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import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataWriter;
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import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.CoordinateTransformation;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.ScaleCoordinateTransformation;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.TranslationCoordinateTransformation;
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import com.google.gson.Gson;
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import com.google.gson.JsonArray;

‎src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMetadataParser.java

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import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataWriter;
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import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDataset;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.CoordinateTransformation;
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import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.CoordinateTransformationAdapter;
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import org.janelia.saalfeldlab.n5.zarr.ZarrDatasetAttributes;

‎src/test/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/CoordinateTransformParsingTest.java

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package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04;
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import static org.junit.Assert.assertArrayEquals;
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import static org.junit.Assert.assertTrue;
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import java.net.URI;
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import java.nio.file.Paths;
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import java.util.Optional;
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import org.janelia.saalfeldlab.n5.DataType;
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import org.janelia.saalfeldlab.n5.DatasetAttributes;
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import org.janelia.saalfeldlab.n5.N5Reader;
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import org.janelia.saalfeldlab.n5.RawCompression;
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import org.janelia.saalfeldlab.n5.universe.N5Factory;
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import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
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import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
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import org.junit.Test;
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import net.imglib2.realtransform.AffineGet;
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import net.imglib2.realtransform.AffineTransform3D;
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import net.imglib2.realtransform.ScaleAndTranslation;
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public class CoordinateTransformParsingTest {
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private static final double EPS = 1E-6;
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@Test
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public void testCoordinateTransformParsing() {
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URI rootF = Paths.get("src", "test", "resources", "metadata.zarr").toUri();
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final N5Reader zarr = new N5Factory().openReader(rootF.toString());
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final OmeNgffMetadataParser grpParser = new OmeNgffMetadataParser();
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test(grpParser.parseMetadata(zarr, setupNode("coordTforms/ss", "s0")),
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new double[]{4, 4},
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new double[]{0, 0});
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test(grpParser.parseMetadata(zarr, setupNode("coordTforms/st", "s0")),
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new double[]{2, 2},
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new double[]{10, 10});
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test(grpParser.parseMetadata(zarr, setupNode("coordTforms/ts", "s0")),
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new double[]{2, 2},
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new double[]{20, 20});
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test(grpParser.parseMetadata(zarr, setupNode("coordTforms/tt", "s0")),
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new double[]{1, 1},
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new double[]{20, 20});
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}
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private void test(final Optional<OmeNgffMetadata> metaOpt, final double[] expectedScale, final double[] expectedTranslation) {
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assertTrue("ss not parsable", metaOpt.isPresent());
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final OmeNgffMetadata meta = metaOpt.get();
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final AffineGet[] tforms = meta.spatialTransforms();
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assertTrue("ss has one transform", tforms.length == 1);
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final ScaleAndTranslation tform = (ScaleAndTranslation)tforms[0];
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assertArrayEquals(expectedScale, tform.getScaleCopy(), EPS);
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assertArrayEquals(expectedTranslation, tform.getTranslationCopy(), EPS);
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}
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private N5TreeNode setupNode(final String path, final String childPath) {
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final N5TreeNode node = new N5TreeNode(path);
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final N5TreeNode child = new N5TreeNode(path + "/" + childPath);
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final DatasetAttributes attrs = new DatasetAttributes(new long[]{4, 4}, new int[]{4, 4}, DataType.UINT8, new RawCompression());
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child.setMetadata(new N5SingleScaleMetadata(path + "/" + childPath, new AffineTransform3D(),
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new double[]{1, 1}, new double[]{1, 1}, new double[]{0, 0}, "", attrs, false));
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node.add(child);
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return node;
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}
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}

‎src/test/resources/metadata.zarr/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/ss/.zattrs

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{
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"multiscales": [
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{
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"name": "boats",
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"type": "Average",
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"version": "0.4",
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"axes": [
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{
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"type": "space",
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"name": "y",
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"unit": "pixel"
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},
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{
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"type": "space",
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"name": "x",
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"unit": "pixel"
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}
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],
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"scale": [
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2,
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2
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],
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"type": "scale"
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},
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{
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"scale": [
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2,
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2
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],
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"type": "scale"
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}
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]
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}
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],
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"coordinateTransformations": []
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}
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]
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}

‎src/test/resources/metadata.zarr/coordTforms/ss/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/ss/s0/.zarray

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{"zarr_format":2,"shape":[576,720],"chunks":[16,16],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":"0","filters":[],"order":"C","dimension_separator":"/"}

‎src/test/resources/metadata.zarr/coordTforms/st/.zattrs

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{
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"multiscales": [
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{
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"name": "boats",
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"type": "Average",
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"version": "0.4",
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"axes": [
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{
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"type": "space",
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"name": "y",
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"unit": "pixel"
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},
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{
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"type": "space",
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"name": "x",
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"unit": "pixel"
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}
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],
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"scale": [
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2,
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2
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],
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"type": "scale"
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},
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{
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"translation": [
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10
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],
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"type": "translation"
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}
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]
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}
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],
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"coordinateTransformations": []
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}
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]
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}

‎src/test/resources/metadata.zarr/coordTforms/st/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/st/s0/.zarray

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{"zarr_format":2,"shape":[576,720],"chunks":[16,16],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":"0","filters":[],"order":"C","dimension_separator":"/"}

‎src/test/resources/metadata.zarr/coordTforms/ts/.zattrs

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{
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"multiscales": [
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{
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"name": "boats",
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"type": "Average",
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"version": "0.4",
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"axes": [
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{
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"type": "space",
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"name": "y",
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"unit": "pixel"
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},
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{
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"type": "space",
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"name": "x",
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"unit": "pixel"
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}
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],
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"translation": [
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],
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"type": "translation"
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},
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{
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"scale": [
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2
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],
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"type": "scale"
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}
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]
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}
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],
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"coordinateTransformations": []
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}
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]
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}

‎src/test/resources/metadata.zarr/coordTforms/ts/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/ts/s0/.zarray

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{"zarr_format":2,"shape":[576,720],"chunks":[16,16],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":"0","filters":[],"order":"C","dimension_separator":"/"}

‎src/test/resources/metadata.zarr/coordTforms/tt/.zattrs

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{
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"multiscales": [
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{
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"name": "boats",
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"type": "Average",
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"version": "0.4",
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"axes": [
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{
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"type": "space",
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"name": "y",
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"unit": "pixel"
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},
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{
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"type": "space",
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"name": "x",
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"unit": "pixel"
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}
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],
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"translation": [
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10,
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10
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],
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"type": "translation"
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},
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{
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"translation": [
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10,
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10
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],
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"type": "translation"
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}
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]
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}
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],
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"coordinateTransformations": []
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}
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]
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}

‎src/test/resources/metadata.zarr/coordTforms/tt/.zgroup

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{"zarr_format":2}

‎src/test/resources/metadata.zarr/coordTforms/tt/s0/.zarray

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{"zarr_format":2,"shape":[576,720],"chunks":[16,16],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":"0","filters":[],"order":"C","dimension_separator":"/"}

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