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test: ngff v0.4 coordinate transform parsing
see #17
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76 changes: 76 additions & 0 deletions
76
...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; | ||
| import static org.junit.Assert.assertTrue; | ||
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| import java.net.URI; | ||
| import java.nio.file.Paths; | ||
| import java.util.Optional; | ||
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| import org.janelia.saalfeldlab.n5.DataType; | ||
| import org.janelia.saalfeldlab.n5.DatasetAttributes; | ||
| import org.janelia.saalfeldlab.n5.N5Reader; | ||
| import org.janelia.saalfeldlab.n5.RawCompression; | ||
| import org.janelia.saalfeldlab.n5.universe.N5Factory; | ||
| import org.janelia.saalfeldlab.n5.universe.N5TreeNode; | ||
| import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata; | ||
| import org.junit.Test; | ||
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| import net.imglib2.realtransform.AffineGet; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| 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 | ||
| public void testCoordinateTransformParsing() { | ||
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| URI rootF = Paths.get("src", "test", "resources", "metadata.zarr").toUri(); | ||
| final N5Reader zarr = new N5Factory().openReader(rootF.toString()); | ||
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| final OmeNgffMetadataParser grpParser = new OmeNgffMetadataParser(); | ||
| test(grpParser.parseMetadata(zarr, setupNode("coordTforms/ss", "s0")), | ||
| new double[]{4, 4}, | ||
| new double[]{0, 0}); | ||
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| test(grpParser.parseMetadata(zarr, setupNode("coordTforms/st", "s0")), | ||
| new double[]{2, 2}, | ||
| new double[]{10, 10}); | ||
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| test(grpParser.parseMetadata(zarr, setupNode("coordTforms/ts", "s0")), | ||
| new double[]{2, 2}, | ||
| new double[]{20, 20}); | ||
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| test(grpParser.parseMetadata(zarr, setupNode("coordTforms/tt", "s0")), | ||
| new double[]{1, 1}, | ||
| new double[]{20, 20}); | ||
| } | ||
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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(); | ||
| final AffineGet[] tforms = meta.spatialTransforms(); | ||
| assertTrue("ss has one transform", tforms.length == 1); | ||
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| final ScaleAndTranslation tform = (ScaleAndTranslation)tforms[0]; | ||
| assertArrayEquals(expectedScale, tform.getScaleCopy(), EPS); | ||
| assertArrayEquals(expectedTranslation, tform.getTranslationCopy(), EPS); | ||
| } | ||
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| private N5TreeNode setupNode(final String path, final String childPath) { | ||
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| final N5TreeNode node = new N5TreeNode(path); | ||
| final N5TreeNode child = new N5TreeNode(path + "/" + childPath); | ||
| final DatasetAttributes attrs = new DatasetAttributes(new long[]{4, 4}, new int[]{4, 4}, DataType.UINT8, new RawCompression()); | ||
| child.setMetadata(new N5SingleScaleMetadata(path + "/" + childPath, new AffineTransform3D(), | ||
| new double[]{1, 1}, new double[]{1, 1}, new double[]{0, 0}, "", attrs, false)); | ||
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| node.add(child); | ||
| return node; | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
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| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "name": "boats", | ||
| "type": "Average", | ||
| "version": "0.4", | ||
| "axes": [ | ||
| { | ||
| "type": "space", | ||
| "name": "y", | ||
| "unit": "pixel" | ||
| }, | ||
| { | ||
| "type": "space", | ||
| "name": "x", | ||
| "unit": "pixel" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "s0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 2, | ||
| 2 | ||
| ], | ||
| "type": "scale" | ||
| }, | ||
| { | ||
| "scale": [ | ||
| 2, | ||
| 2 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| {"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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "name": "boats", | ||
| "type": "Average", | ||
| "version": "0.4", | ||
| "axes": [ | ||
| { | ||
| "type": "space", | ||
| "name": "y", | ||
| "unit": "pixel" | ||
| }, | ||
| { | ||
| "type": "space", | ||
| "name": "x", | ||
| "unit": "pixel" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "s0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 2, | ||
| 2 | ||
| ], | ||
| "type": "scale" | ||
| }, | ||
| { | ||
| "translation": [ | ||
| 10, | ||
| 10 | ||
| ], | ||
| "type": "translation" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "name": "boats", | ||
| "type": "Average", | ||
| "version": "0.4", | ||
| "axes": [ | ||
| { | ||
| "type": "space", | ||
| "name": "y", | ||
| "unit": "pixel" | ||
| }, | ||
| { | ||
| "type": "space", | ||
| "name": "x", | ||
| "unit": "pixel" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "s0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "translation": [ | ||
| 10, | ||
| 10 | ||
| ], | ||
| "type": "translation" | ||
| }, | ||
| { | ||
| "scale": [ | ||
| 2, | ||
| 2 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "name": "boats", | ||
| "type": "Average", | ||
| "version": "0.4", | ||
| "axes": [ | ||
| { | ||
| "type": "space", | ||
| "name": "y", | ||
| "unit": "pixel" | ||
| }, | ||
| { | ||
| "type": "space", | ||
| "name": "x", | ||
| "unit": "pixel" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "s0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "translation": [ | ||
| 10, | ||
| 10 | ||
| ], | ||
| "type": "translation" | ||
| }, | ||
| { | ||
| "translation": [ | ||
| 10, | ||
| 10 | ||
| ], | ||
| "type": "translation" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"zarr_format":2} |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| {"zarr_format":2,"shape":[576,720],"chunks":[16,16],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":"0","filters":[],"order":"C","dimension_separator":"/"} |