Add support for per-series channel wavelength specification

sbesson · Feb 7, 2025 · e74143d · e74143d
1 parent 0f47e17
commit e74143d
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diff --git a/components/formats-bsd/src/loci/formats/in/FakeReader.java b/components/formats-bsd/src/loci/formats/in/FakeReader.java
@@ -1244,6 +1244,18 @@ private void parseSeriesTable(IniTable table, MetadataStore store, int newSeries
     for (int c=0; c<getEffectiveSizeC(); c++) {
       String channelName = table.get("ChannelName_" + c);
       store.setChannelName(channelName, newSeries, c);
+      String emissionWavelength = table.get("ChannelEmissionWavelength_" + c);
+      if (emissionWavelength != null) {
+        store.setChannelEmissionWavelength(
+          parseWavelength(emissionWavelength, getEmissionWavelengthUnitXsdDefault()),
+          newSeries, c);
+      }
+      String excitationWavelength = table.get("ChannelExcitationWavelength_" + c);
+      if (excitationWavelength != null) {
+        store.setChannelExcitationWavelength(
+          parseWavelength(excitationWavelength, getExcitationWavelengthUnitXsdDefault()),
+          newSeries, c);
+      }
     }
 
     for (int i=0; i<getImageCount(); i++) {

diff --git a/components/formats-bsd/test/loci/formats/utests/FakeReaderTest.java b/components/formats-bsd/test/loci/formats/utests/FakeReaderTest.java
@@ -762,6 +762,33 @@ public void testEmissionWavelengths() throws Exception {
     reader.close();
   }
 
+  @Test
+  public void testWavelengthSeries() throws Exception {
+    File fakeIni = mkIni("multiseries_wavelengths.fake.ini",
+      "series=2",
+      "sizeC=2",
+      "[series_0]",
+      "ChannelExcitationWavelength_0=340.0nm",
+      "ChannelEmissionWavelength_0=450.0nm",
+      "ChannelExcitationWavelength_1=470.0nm",
+      "ChannelEmissionWavelength_1=512.0nm",
+      "[series_1]",
+      "ChannelExcitationWavelength_0=350.0nm",
+      "ChannelEmissionWavelength_0=425.0nm",
+      "ChannelExcitationWavelength_1=500.0nm",
+      "ChannelEmissionWavelength_1=580.0nm");
+    reader.setId(fakeIni.getAbsolutePath());
+    m = service.asRetrieve(reader.getMetadataStore());
+    assertEquals(m.getChannelExcitationWavelength(0, 0), new Length(340.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelEmissionWavelength(0, 0), new Length(450.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelExcitationWavelength(0, 1), new Length(470.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelEmissionWavelength(0, 1), new Length(512.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelExcitationWavelength(1, 0), new Length(350.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelEmissionWavelength(1, 0), new Length(425.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelExcitationWavelength(1, 1), new Length(500.0, UNITS.NANOMETER));
+    assertEquals(m.getChannelEmissionWavelength(1, 1), new Length(580.0, UNITS.NANOMETER));
+  }
+
   @Test
   public void testInstrument() throws Exception {
     reader.setId("test&withInstrument=true.fake");