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Add NGFF spec version to --version output #155

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merged 2 commits into from
May 19, 2022
Merged

Add NGFF spec version to --version output #155

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33d461b
Add NGFF spec version to `--version` output
melissalinkert May 16, 2022
ba198b9
Also store NGFF_VERSION in plate metadata
sbesson May 17, 2022
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7 changes: 6 additions & 1 deletion src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,9 @@ public class Converter implements Callable<Void> {
/** Version of the bioformats2raw layout. */
public static final Integer LAYOUT = 3;

/** NGFF specification version.*/
public static final String NGFF_VERSION = "0.4";

@Parameters(
index = "0",
arity = "1",
Expand Down Expand Up @@ -426,6 +429,7 @@ public Void call() throws Exception {
).orElse("development");
System.out.println("Version = " + version);
System.out.println("Bio-Formats version = " + FormatTools.VERSION);
System.out.println("NGFF specification version = " + NGFF_VERSION);
return null;
}

Expand Down Expand Up @@ -1519,6 +1523,7 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
plateMap.put("rows", rows);

plateMap.put("field_count", maxField + 1);
plateMap.put("version", NGFF_VERSION);

Map<String, Object> attributes = root.getAttributes();
attributes.put("plate", plateMap);
Expand Down Expand Up @@ -1570,7 +1575,7 @@ private void setSeriesLevelMetadata(int series, int resolutions)
multiscale.put("type", downsampling.getName());
}
multiscale.put("metadata", metadata);
multiscale.put("version", nested ? "0.4" : "0.1");
multiscale.put("version", nested ? NGFF_VERSION : "0.1");
multiscales.add(multiscale);

IFormatReader v = null;
Expand Down
6 changes: 6 additions & 0 deletions src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -956,6 +956,7 @@ public void testHCSMetadata() throws Exception {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> acquisitions =
(List<Map<String, Object>>) plate.get("acquisitions");
Expand Down Expand Up @@ -1028,6 +1029,7 @@ public void testHCSMetadataNoAcquisitions() throws Exception {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> rows =
(List<Map<String, Object>>) plate.get("rows");
Expand Down Expand Up @@ -1106,6 +1108,7 @@ public void testSingleWell() throws IOException {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> acquisitions =
(List<Map<String, Object>>) plate.get("acquisitions");
Expand Down Expand Up @@ -1168,6 +1171,7 @@ public void testTwoWells(String resourceName) throws IOException {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> acquisitions =
(List<Map<String, Object>>) plate.get("acquisitions");
Expand Down Expand Up @@ -1228,6 +1232,7 @@ public void testOnePlateRow() throws IOException {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> acquisitions =
(List<Map<String, Object>>) plate.get("acquisitions");
Expand Down Expand Up @@ -1283,6 +1288,7 @@ public void testSingleWellTwoAcquisitions() throws IOException {
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
assertEquals("0.4", plate.get("version"));

List<Map<String, Object>> acquisitions =
(List<Map<String, Object>>) plate.get("acquisitions");
Expand Down