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fix: axis reversal for NGFF metadata parsing
1 parent 9f4bc9a commit fdf4886

1 file changed

Lines changed: 3 additions & 5 deletions

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

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,6 @@
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import java.util.Optional;
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import org.apache.commons.lang3.ArrayUtils;
7-
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.N5Writer;
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import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
@@ -38,6 +37,7 @@ public Optional<NgffSingleScaleAxesMetadata> parseMetadata(final N5Reader n5, fi
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final JsonArray axArr = n5.getAttribute(node.getPath(), NgffSingleScaleAxesMetadata.AXIS_KEY, JsonArray.class);
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final Axis[] axes = gson.fromJson(axArr, Axis[].class);
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40+
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final JsonArray ctArr = n5.getAttribute(node.getPath(), NgffSingleScaleAxesMetadata.COORDINATETRANSFORMATIONS_KEY, JsonArray.class);
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final CoordinateTransformation<?>[] cts = gson.fromJson(ctArr, CoordinateTransformation[].class);
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@@ -48,17 +48,15 @@ public Optional<NgffSingleScaleAxesMetadata> parseMetadata(final N5Reader n5, fi
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final double[] scale = scaleAndTranslation.getScaleCopy();
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final double[] translation = scaleAndTranslation.getTranslationCopy();
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final DatasetAttributes dsetAttrs = n5.getDatasetAttributes(node.getPath());
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if( OmeNgffMetadataParser.cOrder(dsetAttrs))
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ArrayUtils.reverse( axes );
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// TODO need to figure out if I even do not need to reverse axes
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ArrayUtils.reverse(axes);
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return Optional.of(new NgffSingleScaleAxesMetadata(node.getPath(), scale, translation, axes, null));
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}
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return Optional.empty();
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}
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61-
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@Override
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public void writeMetadata(final NgffSingleScaleAxesMetadata t, final N5Writer n5, final String path) throws Exception {
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