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ngff spec 0.2: default to nested storage #94

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Apr 7, 2021
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ngff spec 0.2: default to nested storage #94

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ This option is not present in 0.3.0 and later, as only Zarr output is supported.

Versions 0.2.6 and prior used the input file's dimension order to determine the output
dimension order, unless `--dimension-order` was specified.
Version 0.3.0 uses the `TCZYX` order by default, for compatibility with https://ngff.openmicroscopy.org/0.1/#image-layout.
Version 0.3.0 uses the `TCZYX` order by default, for compatibility with https://ngff.openmicroscopy.org/0.2/#image-layout.
The `--dimension-order` option can still be used to set a specific output dimension order, e.g.:

bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --dimension-order XYCZT
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4 changes: 2 additions & 2 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Expand Up @@ -221,7 +221,7 @@ public class Converter implements Callable<Void> {
description = "Whether to use '/' as the chunk path seprator " +
"(false by default)"
)
private volatile boolean nested = false;
private volatile boolean nested = true;

@Option(
names = "--pyramid-name",
Expand Down Expand Up @@ -1308,7 +1308,7 @@ private void setSeriesLevelMetadata(int series, int resolutions)
multiscale.put("type", downsampling.getName());
}
multiscale.put("metadata", metadata);
multiscale.put("version", "0.1");
multiscale.put("version", nested ? "0.2" : "0.1");
multiscales.add(multiscale);
List<Map<String, String>> datasets = new ArrayList<Map<String, String>>();
for (int r = 0; r < resolutions; r++) {
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4 changes: 2 additions & 2 deletions src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Expand Up @@ -235,7 +235,7 @@ public void testMultiscalesMetadata() throws Exception {
z.getAttributes().get("multiscales");
assertEquals(1, multiscales.size());
Map<String, Object> multiscale = multiscales.get(0);
assertEquals("0.1", multiscale.get("version"));
assertEquals("0.2", multiscale.get("version"));
List<Map<String, Object>> datasets =
(List<Map<String, Object>>) multiscale.get("datasets");
assertTrue(datasets.size() > 0);
Expand Down Expand Up @@ -725,7 +725,7 @@ public void testDownsampleTypes(Downsampling type) throws IOException {
(List<Map<String, Object>>) z.getAttributes().get("multiscales");
assertEquals(1, multiscales.size());
Map<String, Object> multiscale = multiscales.get(0);
assertEquals("0.1", multiscale.get("version"));
assertEquals("0.2", multiscale.get("version"));

Map<String, String> metadata =
(Map<String, String>) multiscale.get("metadata");
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