Merge branch 'master' of github.com:glencoesoftware/bioformats2raw in…

…to jna-bump

README.md

@@ -65,7 +65,7 @@ If the input file has multiple series, a subset of the series can be converted b
 
     bioformats2raw /path/to/file.scn /path/to/zarr-pyramid --series 0,2,3,4
 
-By default, three additional readers (MiraxReader, PyramidTiffReader, and BioTekReader) are added to the beginning of Bio-Formats' list of reader classes.
+By default, four additional readers (MiraxReader, PyramidTiffReader, BioTekReader, and ND2PlateReader) are added to the beginning of Bio-Formats' list of reader classes.
 These readers are considered to be experimental and as a result only a limited range of input data is supported.
 
 Any of these readers can be excluded with the `--extra-readers` option:

build.gradle

@@ -31,7 +31,11 @@ repositories {
         url 'https://artifacts.glencoesoftware.com/artifactory/scijava-thirdparty'
     }
     maven {
-        url 'https://nexus.senbox.net/nexus/content/groups/public'
+        url 'https://artifacts.glencoesoftware.com/artifactory/jzarr-releases'
+    }
+    maven {
+        name 'Unidata'
+        url 'https://artifacts.glencoesoftware.com/artifactory/unidata-releases'
     }
 }
 
@@ -42,7 +46,7 @@ configurations.all {
 
 dependencies {
     implementation 'net.java.dev.jna:jna:5.10.0'
-    implementation 'ome:formats-gpl:6.8.0'
+    implementation 'ome:formats-gpl:6.9.1'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.univocity:univocity-parsers:2.8.4'
     implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT'

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

@@ -19,7 +19,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
@@ -56,6 +55,7 @@
 import loci.formats.ome.OMEXMLMetadata;
 import loci.formats.services.OMEXMLService;
 import loci.formats.services.OMEXMLServiceImpl;
+import ome.units.quantity.Quantity;
 import ome.xml.meta.OMEXMLMetadataRoot;
 import ome.xml.model.enums.DimensionOrder;
 import ome.xml.model.enums.EnumerationException;
@@ -239,7 +239,8 @@ public class Converter implements Callable<Void> {
                   "(default: ${DEFAULT-VALUE})"
   )
   private volatile Class<?>[] extraReaders = new Class[] {
-    PyramidTiffReader.class, MiraxReader.class, BioTekReader.class
+    PyramidTiffReader.class, MiraxReader.class,
+    BioTekReader.class, ND2PlateReader.class
   };
 
   @Option(
@@ -562,6 +563,12 @@ public void convert()
 
         if (!noHCS) {
           noHCS = !hasValidPlate(meta);
+          int plateCount = meta.getPlateCount();
+          if (!noHCS && plateCount > 1) {
+            throw new IllegalArgumentException(
+              "Found " + plateCount + " plates; only one can be converted. " +
+              "Use --no-hcs to as a work-around.");
+          }
         }
         else {
           ((OMEXMLMetadata) meta).resolveReferences();
@@ -1522,35 +1529,84 @@ private void setSeriesLevelMetadata(int series, int resolutions)
       multiscale.put("type", downsampling.getName());
     }
     multiscale.put("metadata", metadata);
-    multiscale.put("version", nested ? "0.2" : "0.1");
+    multiscale.put("version", nested ? "0.4" : "0.1");
     multiscales.add(multiscale);
-    List<Map<String, String>> datasets = new ArrayList<Map<String, String>>();
+
+    IFormatReader v = null;
+    IMetadata meta = null;
+    String axisOrder = null;
+    try {
+      v = readers.take();
+      meta = (IMetadata) v.getMetadataStore();
+
+      if (dimensionOrder != null) {
+        axisOrder = dimensionOrder.toString();
+      }
+      else {
+        axisOrder = v.getDimensionOrder();
+      }
+    }
+    finally {
+      readers.put(v);
+    }
+
+    List<Map<String, Object>> datasets = new ArrayList<Map<String, Object>>();
     for (int r = 0; r < resolutions; r++) {
       resolutionString = String.format(
               scaleFormatString, getScaleFormatStringArgs(series, r));
       String lastPath = resolutionString.substring(
               resolutionString.lastIndexOf('/') + 1);
-      datasets.add(Collections.singletonMap("path", lastPath));
-    }
-    multiscale.put("datasets", datasets);
 
-    String axisOrder = null;
-    if (dimensionOrder != null) {
-      axisOrder = dimensionOrder.toString();
-    }
-    else {
-      IFormatReader reader = readers.take();
-      try {
-        axisOrder = reader.getDimensionOrder();
-      }
-      finally {
-        readers.put(reader);
+      List<Map<String, Object>> transforms =
+        new ArrayList<Map<String, Object>>();
+      Map<String, Object> scale = new HashMap<String, Object>();
+      scale.put("type", "scale");
+      List<Double> axisValues = new ArrayList<Double>();
+      double resolutionScale = Math.pow(PYRAMID_SCALE, r);
+      for (int i=axisOrder.length()-1; i>=0; i--) {
+        Quantity axisScale = getScale(meta, series, axisOrder, i);
+        String axisChar = axisOrder.substring(i, i + 1).toLowerCase();
+
+        if (axisScale != null) {
+          // if physical dimension information is defined,
+          // use it directly for dimensions that aren't scaled (Z and T)
+          // increase it according to the resolution number for dimensions that
+          // are scaled (X and Y)
+          if (axisChar.equals("x") || axisChar.equals("y")) {
+            axisValues.add(axisScale.value().doubleValue() * resolutionScale);
+          }
+          else {
+            axisValues.add(axisScale.value().doubleValue());
+          }
+        }
+        else {
+          // if physical dimension information is not defined,
+          // store the scale factor for the dimension in the current resolution,
+          // i.e. 1.0 for everything other than X and Y
+          if (axisChar.equals("x") || axisChar.equals("y")) {
+            axisValues.add(resolutionScale);
+          }
+          else {
+            axisValues.add(1.0);
+          }
+        }
       }
+      scale.put("scale", axisValues);
+
+      transforms.add(scale);
+
+      Map<String, Object> dataset = new HashMap<String, Object>();
+      dataset.put("path", lastPath);
+      dataset.put("coordinateTransformations", transforms);
+      datasets.add(dataset);
     }
+    multiscale.put("datasets", datasets);
+
     List<Map<String, String>> axes = new ArrayList<Map<String, String>>();
     for (int i=axisOrder.length()-1; i>=0; i--) {
       String axis = axisOrder.substring(i, i + 1).toLowerCase();
       String type = "space";
+      Quantity scale = getScale(meta, series, axisOrder, i);
       if (axis.equals("t")) {
         type = "time";
       }
@@ -1560,6 +1616,9 @@ else if (axis.equals("c")) {
       Map<String, String> thisAxis = new HashMap<String, String>();
       thisAxis.put("name", axis);
       thisAxis.put("type", type);
+      if (scale != null) {
+        thisAxis.put("unit", scale.unit().getSymbol());
+      }
       axes.add(thisAxis);
     }
     multiscale.put("axes", axes);
@@ -1573,6 +1632,33 @@ else if (axis.equals("c")) {
     LOGGER.debug("    finished writing subgroup attributes");
   }
 
+  private Quantity getScale(
+    IMetadata meta, int series, String axisOrder, int axis)
+  {
+    if (meta == null) {
+      return null;
+    }
+    int seriesIndex = seriesList.indexOf(series);
+
+    if (seriesIndex < 0 || seriesIndex >= meta.getImageCount()) {
+      return null;
+    }
+
+    String axisChar = axisOrder.substring(axis, axis + 1).toLowerCase();
+    switch (axisChar.charAt(0)) {
+      case 'x':
+        return meta.getPixelsPhysicalSizeX(seriesIndex);
+      case 'y':
+        return meta.getPixelsPhysicalSizeY(seriesIndex);
+      case 'z':
+        return meta.getPixelsPhysicalSizeZ(seriesIndex);
+      case 't':
+        return meta.getPixelsTimeIncrement(seriesIndex);
+      default:
+        return null;
+    }
+  }
+
   /**
    * Takes exception from asynchronous execution and re-throw known exception
    * types. If the end is reached with no known exception detected, either the

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

@@ -273,7 +273,11 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
         TilePointer thisOffset = lookupTile(index, col, row, no / MAX_CHANNELS);
         if (thisOffset != null) {
           int channel = no % MAX_CHANNELS;
-          if (fluorescence && getSizeC() != 2) {
+          // 2 channel JPEG data needs to have the channel index inverted
+          // 2 channel JPEG-2000 data should not have the channel index inverted
+          if (fluorescence &&
+            (getSizeC() != 2 || format.get(index).equals("JPEG")))
+          {
             channel = MAX_CHANNELS - channel - 1;
           }