fix: don't use platform paths for groups

On windows, `\` is interpreted as an escape character when normalizing the group path, and it is removed.
saalfeldlab · Sep 1, 2023 · 606731c · 606731c
1 parent bc0da63
commit 606731c
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Showing 3 changed files with 13 additions and 17 deletions.
diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/n5/CommitCanvasN5.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/n5/CommitCanvasN5.java
@@ -37,12 +37,7 @@
 import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookupKey;
 import org.janelia.saalfeldlab.labels.blocks.n5.IsRelativeToContainer;
 import org.janelia.saalfeldlab.labels.downsample.WinnerTakesAll;
-import org.janelia.saalfeldlab.n5.ByteArrayDataBlock;
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.DatasetAttributes;
-import org.janelia.saalfeldlab.n5.LongArrayDataBlock;
-import org.janelia.saalfeldlab.n5.N5Reader;
-import org.janelia.saalfeldlab.n5.N5Writer;
+import org.janelia.saalfeldlab.n5.*;
 import org.janelia.saalfeldlab.n5.imglib2.N5LabelMultisets;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.paintera.data.mask.persist.PersistCanvas;
@@ -57,7 +52,6 @@
 
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -136,7 +130,8 @@ public void updateLabelBlockLookup(final List<TLongObjectMap<BlockDiff>> blockDi
 
 			LOG.debug("Found scale datasets {}", (Object)scaleUniqueLabels);
 			for (int level = 0; level < scaleUniqueLabels.length; ++level) {
-				final DatasetSpec datasetUniqueLabels = DatasetSpec.of(n5Writer, Paths.get(uniqueLabelsPath, scaleUniqueLabels[level]).toString());
+				final String uniqueLabelScalePath = N5URI.normalizeGroupPath(uniqueLabelsPath + n5Writer.getGroupSeparator() + scaleUniqueLabels[level]);
+				final DatasetSpec datasetUniqueLabels = DatasetSpec.of(n5Writer, uniqueLabelScalePath);
 				final TLongObjectMap<TLongHashSet> removedById = new TLongObjectHashMap<>();
 				final TLongObjectMap<TLongHashSet> addedById = new TLongObjectHashMap<>();
 				final TLongObjectMap<BlockDiff> blockDiffs = blockDiffsByLevel.get(level);
@@ -262,8 +257,8 @@ public List<TLongObjectMap<BlockDiff>> persistCanvas(final CachedCellImg<Unsigne
 
 					final TLongObjectHashMap<BlockDiff> blockDiffsAt = new TLongObjectHashMap<>();
 					blockDiffs.add(blockDiffsAt);
-					final DatasetSpec targetDataset = DatasetSpec.of(n5Writer, Paths.get(dataset, scaleDatasets[level]).toString());
-					final DatasetSpec previousDataset = DatasetSpec.of(n5Writer, Paths.get(dataset, scaleDatasets[level - 1]).toString());
+					final DatasetSpec targetDataset = DatasetSpec.of(n5Writer, N5URI.normalizeGroupPath(dataset + n5Writer.getGroupSeparator() + scaleDatasets[level]));
+					final DatasetSpec previousDataset = DatasetSpec.of(n5Writer, N5URI.normalizeGroupPath(dataset + n5Writer.getGroupSeparator() + scaleDatasets[level - 1]));
 
 					final double[] targetDownsamplingFactors = N5Helpers.getDownsamplingFactors(n5Writer, targetDataset.dataset);
 					final double[] previousDownsamplingFactors = N5Helpers.getDownsamplingFactors(n5Writer, previousDataset.dataset);

diff --git a/src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java b/src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java
@@ -380,7 +380,7 @@ ImagesWithTransform<T, V>[] openRawMultiscale(
 
 		final double[] initialDonwsamplingFactors = N5Helpers.getDownsamplingFactors(
 				reader,
-				Paths.get(dataset, scaleDatasets[0]).toString()
+				N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[0])
 		);
 		LOG.debug("Initial transform={}", transform);
 		final ExecutorService es = Executors.newFixedThreadPool(
@@ -393,7 +393,7 @@ ImagesWithTransform<T, V>[] openRawMultiscale(
 			final int fScale = scale;
 			futures.add(es.submit(ThrowingSupplier.unchecked(() -> {
 				LOG.debug("Populating scale level {}", fScale);
-				final String scaleDataset = Paths.get(dataset, scaleDatasets[fScale]).toString();
+				final String scaleDataset = N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[fScale]);
 				imagesWithInvalidate[fScale] = openRaw(reader, scaleDataset, transform.copy(), queue, priority);
 				final double[] downsamplingFactors = N5Helpers.getDownsamplingFactors(reader, scaleDataset);
 				LOG.debug("Read downsampling factors: {}", Arrays.toString(downsamplingFactors));
@@ -685,7 +685,7 @@ public static ImagesWithTransform<LabelMultisetType, VolatileLabelMultisetType>[
 
 		final double[] initialDonwsamplingFactors = N5Helpers.getDownsamplingFactors(
 				reader,
-				Paths.get(dataset, scaleDatasets[0]).toString());
+				N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[0]));
 		final ExecutorService es = Executors.newFixedThreadPool(
 				scaleDatasets.length,
 				new NamedThreadFactory("populate-mipmap-scales-%d", true));
@@ -695,7 +695,7 @@ public static ImagesWithTransform<LabelMultisetType, VolatileLabelMultisetType>[
 			final int fScale = scale;
 			futures.add(es.submit(ThrowingSupplier.unchecked(() -> {
 				LOG.debug("Populating scale level {}", fScale);
-				final String scaleDataset = Paths.get(dataset, scaleDatasets[fScale]).toString();
+				final String scaleDataset = N5URI.normalizeGroupPath(dataset + reader.getGroupSeparator() + scaleDatasets[fScale]);
 				imagesWithInvalidate[fScale] = openLabelMultiset(reader, scaleDataset, transform.copy(), queue, priority);
 				final double[] downsamplingFactors = N5Helpers.getDownsamplingFactors(reader, scaleDataset);
 				LOG.debug("Read downsampling factors: {}", Arrays.toString(downsamplingFactors));

diff --git a/src/test/java/org/janelia/saalfeldlab/paintera/data/n5/CommitCanvasN5Test.java b/src/test/java/org/janelia/saalfeldlab/paintera/data/n5/CommitCanvasN5Test.java
@@ -352,10 +352,11 @@ private static <T> void testPainteraData(
 		testCanvasPersistance(container, dataset, s0, canvas, openLabels, asserts);
 
 		// test highest level block lookups
-		final String uniqueBlock0 = String.join("/", dataset, "unique-labels", "s0");
+		final String groupSeparator = container.getReader().getGroupSeparator();
+		final String uniqueBlock0Group = N5URI.normalizeGroupPath(String.join(groupSeparator, dataset, "unique-labels","s0"));
 		final Path mappingPattern = Paths.get(container.getUri().getPath(), dataset, "label-to-block-mapping", "s%d", "%d");
 		final Path mapping0 = Paths.get(container.getUri().getPath(), dataset, "label-to-block-mapping", "s0");
-		final DatasetAttributes uniqueBlockAttributes = writer.getDatasetAttributes(uniqueBlock0);
+		final DatasetAttributes uniqueBlockAttributes = writer.getDatasetAttributes(uniqueBlock0Group);
 		final List<Interval> blocks = Grids.collectAllContainedIntervals(dims, blockSize);
 		final TLongObjectMap<TLongSet> labelToBLockMapping = new TLongObjectHashMap<>();
 		for (final Interval block : blocks) {
@@ -375,7 +376,7 @@ private static <T> void testPainteraData(
 				}
 			});
 
-			final DataBlock<?> uniqueBlock = writer.readBlock(uniqueBlock0, uniqueBlockAttributes, blockPos);
+			final DataBlock<?> uniqueBlock = writer.readBlock(uniqueBlock0Group, uniqueBlockAttributes, blockPos);
 			Assert.assertEquals(labels, new TLongHashSet((long[])uniqueBlock.getData()));
 		}