fix: number of downsampling levels

see #98
saalfeldlab · Dec 4, 2024 · 51671ce · 51671ce
1 parent 976766a
commit 51671ce
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Showing 2 changed files with 31 additions and 8 deletions.
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java b/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java
@@ -571,7 +571,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
 				Arrays.fill(relativeFactors, 1);
 
 				if (s > 0) {
-					relativeFactors = getRelativeDownsampleFactors(currentMetadata, currentChannelImg.numDimensions(), s, currentAbsoluteDownsampling);
+					relativeFactors = getRelativeDownsampleFactors(currentMetadata, currentChannelImg, s, currentAbsoluteDownsampling);
 
 					// update absolute downsampling factors
 					for (int i = 0; i < nd; i++)
@@ -610,7 +610,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
 				anyScalesWritten = true;
 
 				// chunkSize variable is updated by the write method
-				if (lastScale(chunkSize, currentChannelImg))
+				if (lastScale(chunkSize, currentChannelImg, currentMetadata))
 					break;
 			}
 
@@ -720,13 +720,15 @@ protected <N extends SpatialMetadataGroup<?>> N finalizeMultiscaleMetadata(final
 		return multiscaleMetadata;
 	}
 
-	protected boolean lastScale(final int[] chunkSize, final Interval imageDimensions) {
+	protected <M extends N5Metadata> boolean lastScale(final int[] chunkSize, final Interval imageDimensions, final M metadata) {
+
+		final Axis[] axes = getAxes(metadata, imageDimensions.numDimensions());
 
 		for (int i = 0; i < imageDimensions.numDimensions(); i++) {
-			if (imageDimensions.dimension(i) <= chunkSize[i])
-				return true;
+			if (axes[i].getType().equals(Axis.SPACE) && imageDimensions.dimension(i) > chunkSize[i])
+				return false;
 		}
-		return false;
+		return true;
 	}
 
 	protected <M extends N5DatasetMetadata> void fillResolution(final M baseMetadata, final double[] resolution) {
@@ -861,17 +863,18 @@ protected <M extends N5Metadata> long[] getDownsampleFactors(final M metadata, f
 		return factors;
 	}
 
-	protected <M extends N5Metadata> long[] getRelativeDownsampleFactors(final M metadata, final int nd, final int scale,
+	protected <M extends N5Metadata> long[] getRelativeDownsampleFactors(final M metadata, final Interval img, final int scale,
 			final long[] downsampleFactors) {
 
+		int nd = img.numDimensions();
 		final Axis[] axes = getAxes(metadata, nd);
 
 		// under what condisions is nd != axes.length
 		final long[] factors = new long[axes.length];
 		for (int i = 0; i < nd; i++) {
 
 			// only downsample spatial dimensions
-			if (axes[i].getType().equals(Axis.SPACE))
+			if (axes[i].getType().equals(Axis.SPACE) && img.dimension(i) > 1)
 				factors[i] = 2;
 			else
 				factors[i] = 1;

diff --git a/src/test/java/org/janelia/saalfeldlab/n5/TestExportImports.java b/src/test/java/org/janelia/saalfeldlab/n5/TestExportImports.java
@@ -617,6 +617,26 @@ public void testReadWriteParsePyramid()
 		}
 	}
 
+	@Test
+	public void testNumDownsamplingLevels() {
+
+		final int bitDepth = 8;
+		final String dset = "scaleLevelsTest";
+
+		// the size of mitosis.tif sample image
+		final ImagePlus imp = NewImage.createImage("test", 171, 196, 2 * 5 * 51, bitDepth, NewImage.FILL_BLACK);
+		imp.setDimensions(2, 5, 51);
+
+		final N5ScalePyramidExporter exp = new N5ScalePyramidExporter();
+		exp.setOptions(imp, baseDir.getAbsolutePath(), dset, "16", true, N5ScalePyramidExporter.DOWN_AVERAGE,
+				N5Importer.MetadataOmeZarrKey, N5ScalePyramidExporter.RAW_COMPRESSION);
+		exp.run();
+
+		try (final N5Reader n5 = new N5FSReader(baseDir.getAbsolutePath())) {
+			assertEquals("5 scale levels", 5, n5.list(dset).length);
+		}
+	}
+
 	public void pyramidReadWriteParseTest(
 			final ImagePlus imp,
 			final String outputPath,