Merge pull request #160 from melissalinkert/omero-metadata

Add optional OMERO rendering metadata

src/main/java/com/glencoesoftware/bioformats2raw/Colors.java

@@ -0,0 +1,180 @@
+/**
+ * Copyright (c) 2022 Glencoe Software, Inc. All rights reserved.
+ *
+ * This software is distributed under the terms described by the LICENSE.txt
+ * file you can find at the root of the distribution bundle.  If the file is
+ * missing please request a copy by contacting info@glencoesoftware.com
+ */
+package com.glencoesoftware.bioformats2raw;
+
+import java.util.List;
+
+import loci.formats.ome.OMEXMLMetadata;
+
+import ome.units.UNITS;
+import ome.units.quantity.Length;
+import ome.units.unit.Unit;
+import ome.xml.meta.OMEXMLMetadataRoot;
+import ome.xml.model.Channel;
+import ome.xml.model.Filter;
+import ome.xml.model.FilterSet;
+import ome.xml.model.Image;
+import ome.xml.model.LightPath;
+import ome.xml.model.TransmittanceRange;
+import ome.xml.model.primitives.Color;
+
+/**
+ * Helper methods for choosing channel colors.
+ */
+public class Colors {
+
+  private static final double BLUE_TO_GREEN = 500.0;
+  private static final double GREEN_TO_RED = 560.0;
+  private static final double RANGE = 15.0;
+
+  /**
+   * Determine which color to use for the given channel.
+   * If a channel color is already set, that will be returned.
+   * If a channel emission wavelength is set, that will be used
+   * to determine the color; red, green, or blue based on the
+   * wavelength in nm.
+   * If filter metadata is populated, the first filter with
+   * CutIn and/or CutOut wavelengths will be used to determine
+   * the color.
+   * Otherwise, the channel index is used to pick red, green, or blue.
+   *
+   * @param meta OME-XML object with acquisition metadata
+   * @param series Bio-Formats series/OME-XML Image index
+   * @param c channel index
+   * @return channel color
+   */
+  public static Color getColor(OMEXMLMetadata meta, int series, int c) {
+    Color color = meta.getChannelColor(series, c);
+    if (color != null) {
+      return color;
+    }
+
+    Length emWave = meta.getChannelEmissionWavelength(series, c);
+    if (emWave != null) {
+      return colorFromWavelength(emWave);
+    }
+
+    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
+    Image img = root.getImage(series);
+    Channel channel = img.getPixels().getChannel(c);
+    LightPath path = channel.getLightPath();
+    FilterSet filterSet = channel.getLinkedFilterSet();
+
+    Length valueFilter = null;
+
+    // look at LightPath.EmissionFilterRef
+
+    if (path != null) {
+      List<Filter> emFilters = path.copyLinkedEmissionFilterList();
+      valueFilter = handleFilters(emFilters, true);
+    }
+
+    // look at FilterSet.EmissionFilterRef
+
+    if (valueFilter == null && filterSet != null) {
+      List<Filter> emFilters = filterSet.copyLinkedEmissionFilterList();
+      valueFilter = handleFilters(emFilters, true);
+    }
+
+    // look at LightSourceSettings.Laser.Wavelength and return if present
+    // but EmissionFilterRef not present
+
+    Length exWave = meta.getChannelExcitationWavelength(series, c);
+    if (exWave != null) {
+      return colorFromWavelength(exWave);
+    }
+
+    // look at LightPath.ExcitationFilterRef
+
+    if (valueFilter == null && path != null) {
+      List<Filter> exFilters = path.copyLinkedExcitationFilterList();
+      valueFilter = handleFilters(exFilters, false);
+    }
+
+    // look at FilterSet.ExcitationFilterRef
+
+    if (valueFilter == null && filterSet != null) {
+      List<Filter> exFilters = filterSet.copyLinkedExcitationFilterList();
+      valueFilter = handleFilters(exFilters, false);
+    }
+
+    // if any filter ref has a valid value, return the first one found
+
+    if (valueFilter != null) {
+      return colorFromWavelength(valueFilter);
+    }
+
+    // return red, green, or blue depending on the channel index
+    int baseColor = 0xff;
+    int shift = (3 - (c % 3)) * 8;
+    baseColor = baseColor << shift;
+    return new Color(baseColor + 0xff);
+  }
+
+  private static Length handleFilters(List<Filter> filters, boolean emission) {
+    for (Filter f : filters) {
+      Length v = getValueFromFilter(f, emission);
+      if (v != null) {
+        return v;
+      }
+    }
+    return null;
+  }
+
+  private static Length getValueFromFilter(Filter filter, boolean emission) {
+    if (filter == null) {
+      return null;
+    }
+    TransmittanceRange transmittance = filter.getTransmittanceRange();
+    if (transmittance == null) {
+      return null;
+    }
+    Length cutIn = transmittance.getCutIn();
+
+    if (emission) {
+      if (cutIn == null) {
+        return null;
+      }
+      return new Length(cutIn.value().doubleValue() + RANGE, cutIn.unit());
+    }
+    Length cutOut = transmittance.getCutOut();
+    if (cutOut == null) {
+      return null;
+    }
+    double cutOutValue = cutOut.value().doubleValue();
+    if (cutIn == null || cutIn.value().doubleValue() == 0) {
+      cutIn = new Length(cutOutValue - 2 * RANGE, cutOut.unit());
+    }
+    Unit<Length> unit = cutOut.unit();
+    Length v =
+      new Length(cutIn.value(unit).doubleValue() + cutOutValue / 2, unit);
+    if (v.value().doubleValue() < 0) {
+      return new Length(0, unit);
+    }
+    return v;
+  }
+
+  private static Color colorFromWavelength(Length wave) {
+    if (wave == null) {
+      return null;
+    }
+
+    double nm = wave.value(UNITS.NM).doubleValue();
+
+    if (nm < BLUE_TO_GREEN) {
+      return new Color(0, 0, 255, 255);
+    }
+    else if (nm < GREEN_TO_RED) {
+      return new Color(0, 255, 0, 255);
+    }
+    return new Color(255, 0, 0, 255);
+  }
+
+
+
+}