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Update jzarr to 0.3.5 #148

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May 6, 2022
Merged

Update jzarr to 0.3.5 #148

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2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ dependencies {
implementation 'ome:formats-gpl:6.9.1'
implementation 'info.picocli:picocli:4.6.1'
implementation 'com.univocity:univocity-parsers:2.8.4'
implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT'
implementation 'com.bc.zarr:jzarr:0.3.5'
// implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT'
// implementation 'io.nextflow:nxf-s3fs:1.1.0'
implementation 'org.lasersonlab:s3fs:2.2.3'
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7 changes: 6 additions & 1 deletion src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Expand Up @@ -69,6 +69,7 @@
import com.bc.zarr.ArrayParams;
import com.bc.zarr.CompressorFactory;
import com.bc.zarr.DataType;
import com.bc.zarr.DimensionSeparator;
import com.bc.zarr.ZarrArray;
import com.bc.zarr.ZarrGroup;
import com.glencoesoftware.bioformats2raw.MiraxReader.TilePointer;
Expand Down Expand Up @@ -1217,7 +1218,7 @@ public void saveResolutions(int series)
.chunks(new int[] {1, 1, activeChunkDepth, activeTileHeight,
activeTileWidth})
.dataType(dataType)
.nested(nested)
.dimensionSeparator(getDimensionSeparator())
.compressor(CompressorFactory.create(
compressionType.toString(), compressionProperties));
ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);
Expand Down Expand Up @@ -1853,6 +1854,10 @@ public static DataType getZarrType(int type) {
}
}

private DimensionSeparator getDimensionSeparator() {
return nested ? DimensionSeparator.SLASH : DimensionSeparator.DOT;
}

private void checkOutputPaths() {
if (pyramidName != null || !scaleFormatString.equals("%d/%d")) {
LOGGER.info("Output will be incompatible with raw2ometiff " +
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13 changes: 12 additions & 1 deletion src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Expand Up @@ -240,7 +240,12 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception {
Integer layout = (Integer)
z.getAttributes().get("bioformats2raw.layout");
ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
assertTrue(series0.getNested());

// no getter for DimensionSeparator in ZarrArray
// check that the correct separator was used by checking
// that the expected first chunk file exists
assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());

// Also ensure we're using the latest .zarray metadata
ObjectMapper objectMapper = new ObjectMapper();
JsonNode root = objectMapper.readTree(
Expand Down Expand Up @@ -878,6 +883,12 @@ public void testDownsampleTypes(Downsampling type) throws IOException {
public void testNestedStorage(boolean nested) throws IOException {
input = fake();
assertTool(nested ? "--nested" : "--no-nested");
if (nested) {
assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());
}
else {
assertTrue(output.resolve("0/0/0.0.0.0.0").toFile().exists());
}
}

/**
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