Merge pull request #155 from melissalinkert/ngff-version-report

Add NGFF spec version to `--version` output
glencoesoftware · May 19, 2022 · b1e6f7d · b1e6f7d
2 parents 6ee2587 + ba198b9
commit b1e6f7d
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -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",
@@ -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;
     }
 
@@ -1525,6 +1529,7 @@ 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);
@@ -1576,7 +1581,7 @@ 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;

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -962,6 +962,7 @@ 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");
@@ -1034,6 +1035,7 @@ 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");
@@ -1112,6 +1114,7 @@ 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");
@@ -1174,6 +1177,7 @@ 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");
@@ -1234,6 +1238,7 @@ 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");
@@ -1289,6 +1294,7 @@ 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");