From 6693198dbcfd784fa96a74acb6d2ec918175fe19 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Mon, 29 Aug 2022 16:01:40 -0500
Subject: [PATCH] Fix a few small issues with OMERO rendering metadata

...and add more tests.
---
 .../bioformats2raw/Colors.java                |  2 +-
 .../bioformats2raw/Converter.java             | 11 +++---
 .../bioformats2raw/test/ZarrTest.java         | 35 +++++++++++++++++++
 .../test/multichannel-colors.ome.xml          | 20 +++++++++++
 4 files changed, 62 insertions(+), 6 deletions(-)
 create mode 100644 src/test/resources/com/glencoesoftware/bioformats2raw/test/multichannel-colors.ome.xml

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Colors.java b/src/main/java/com/glencoesoftware/bioformats2raw/Colors.java
index e643d2b..020943d 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Colors.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Colors.java
@@ -111,7 +111,7 @@ public static Color getColor(OMEXMLMetadata meta, int series, int c) {
 
     // return red, green, or blue depending on the channel index
     int baseColor = 0xff;
-    int shift = (2 - (c % 3)) * 8;
+    int shift = (3 - (c % 3)) * 8;
     baseColor = baseColor << shift;
     return new Color(baseColor + 0xff);
   }
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index 7498a2a..42c0502 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -1714,18 +1714,19 @@ else if (scale instanceof Time) {
       int seriesIndex = seriesList.indexOf(series);
 
       Map<String, Object> omero = new HashMap<String, Object>();
-      omero.put("id", 0);
       String name = meta.getImageName(seriesIndex);
       if (name == null) {
         name = "Series " + seriesIndex;
       }
       omero.put("name", name);
-      omero.put("version", NGFF_VERSION);
+
+      int channelCount = meta.getChannelCount(seriesIndex);
+      boolean colorRender = channelCount > 1 && channelCount < 8;
 
       Map<String, Object> rdefs = new HashMap<String, Object>();
       rdefs.put("defaultT", 0);
       rdefs.put("defaultZ", meta.getPixelsSizeZ(seriesIndex).getValue() / 2);
-      rdefs.put("model", "greyscale");
+      rdefs.put("model", colorRender ? "color" : "greyscale");
       omero.put("rdefs", rdefs);
 
       double[] defaultMinMax =
@@ -1733,9 +1734,9 @@ else if (scale instanceof Time) {
           meta.getPixelsType(seriesIndex).toString()));
 
       List<Map<String, Object>> channels = new ArrayList<Map<String, Object>>();
-      for (int c=0; c<meta.getChannelCount(seriesIndex); c++) {
+      for (int c=0; c<channelCount; c++) {
         Map<String, Object> channel = new HashMap<String, Object>();
-        channel.put("active", true);
+        channel.put("active", c < 3);
         channel.put("coefficient", 1);
 
         // set an RGB color (alpha removed)
diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
index e4a7559..7970a29 100644
--- a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
+++ b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -1026,6 +1026,10 @@ public void testOMERO() throws Exception {
         ZarrGroup.open(output.resolve(String.valueOf(i)).toString());
       Map<String, Object> omero =
             (Map<String, Object>) z.getAttributes().get("omero");
+
+      Map<String, Object> rdefs = (Map<String, Object>) omero.get("rdefs");
+      assertEquals("greyscale", rdefs.get("model"));
+
       List<Map<String, Object>> channels =
             (List<Map<String, Object>>) omero.get("channels");
       assertEquals(1, channels.size());
@@ -1033,6 +1037,37 @@ public void testOMERO() throws Exception {
       Map<String, Object> channel = channels.get(0);
       assertEquals(names[i], channel.get("label"));
       assertEquals(colors[i], channel.get("color"));
+      assertEquals(true, channel.get("active"));
+    }
+  }
+
+  /**
+   * Check for OMERO rendering metadata on a 4 channel image.
+   */
+  @Test
+  public void testOMEROMultiC() throws Exception {
+    input = getTestFile("multichannel-colors.ome.xml");
+    assertTool();
+
+    String[] names = {"orange", "green", "blue", "red"};
+    String[] colors = {"FF7F00", "00FF00", "0000FF", "FF0000"};
+
+    ZarrGroup z = ZarrGroup.open(output.resolve("0").toString());
+    Map<String, Object> omero =
+          (Map<String, Object>) z.getAttributes().get("omero");
+
+    Map<String, Object> rdefs = (Map<String, Object>) omero.get("rdefs");
+    assertEquals("color", rdefs.get("model"));
+
+    List<Map<String, Object>> channels =
+          (List<Map<String, Object>>) omero.get("channels");
+    assertEquals(names.length, channels.size());
+
+    for (int c=0; c<channels.size(); c++) {
+      Map<String, Object> channel = channels.get(c);
+      assertEquals(names[c], channel.get("label"));
+      assertEquals(colors[c], channel.get("color"));
+      assertEquals(c < 3, channel.get("active"));
     }
   }
 
diff --git a/src/test/resources/com/glencoesoftware/bioformats2raw/test/multichannel-colors.ome.xml b/src/test/resources/com/glencoesoftware/bioformats2raw/test/multichannel-colors.ome.xml
new file mode 100644
index 0000000..32042a0
--- /dev/null
+++ b/src/test/resources/com/glencoesoftware/bioformats2raw/test/multichannel-colors.ome.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 6.6.1-SNAPSHOT" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+<Instrument ID="Instrument:0">
+  <Filter ID="Filter:0:0">
+    <TransmittanceRange CutIn="350" CutOut="450"/>
+  </Filter>
+</Instrument>
+<Image ID="Image:0" Name="test">
+<Description>Image Description 0</Description>
+<Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SignificantBits="8" SizeC="4" SizeT="1" SizeX="1" SizeY="1" SizeZ="1" Type="uint8">
+<Channel AcquisitionMode="FluorescenceLifetime" Color="-8453889" ContrastMethod="Brightfield" EmissionWavelength="300.3" EmissionWavelengthUnit="nm" ExcitationWavelength="400.3" ExcitationWavelengthUnit="nm" Fluor="Fluor" ID="Channel:0:0" IlluminationType="Oblique" NDFilter="1.0" Name="orange" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1"/>
+<Channel AcquisitionMode="FluorescenceLifetime" ContrastMethod="Brightfield" EmissionWavelength="520.0" EmissionWavelengthUnit="nm" ExcitationWavelength="600.0" ExcitationWavelengthUnit="nm" Fluor="Fluor" ID="Channel:0:1" IlluminationType="Oblique" NDFilter="1.0" Name="green" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1"/>
+<Channel AcquisitionMode="FluorescenceLifetime" ContrastMethod="Brightfield" Fluor="Fluor" ID="Channel:0:2" IlluminationType="Oblique" NDFilter="1.0" Name="blue" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1">
+  <LightPath>
+    <EmissionFilterRef ID="Filter:0:0"/>
+  </LightPath>
+</Channel>
+<Channel AcquisitionMode="FluorescenceLifetime" ContrastMethod="Brightfield" Fluor="Fluor" ID="Channel:0:3" IlluminationType="Oblique" NDFilter="1.0" Name="red" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1"/>
+<Plane DeltaT="0.1" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1.0" PositionXUnit="reference frame" PositionY="1.0" PositionYUnit="reference frame" PositionZ="1.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
+<BinData xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" Length="4" BigEndian="false">AAAAAA==</BinData></Pixels></Image></OME>