Pyramid TIFF: support multiple planes and OME-XML comments

components/formats-api/src/loci/formats/readers.txt

@@ -146,8 +146,8 @@ loci.formats.in.NDPIReader            # ndpi
 loci.formats.in.PCORAWReader          # pcoraw
 
 # TIFF-based readers with slow isThisType
-loci.formats.in.OMETiffReader         # tif
 loci.formats.in.PyramidTiffReader     # tif, tiff
+loci.formats.in.OMETiffReader         # tif
 loci.formats.in.MIASReader            # tif
 loci.formats.in.TCSReader             # xml, tif
 loci.formats.in.LeicaReader           # lei, tif

components/formats-gpl/src/loci/formats/in/PyramidTiffReader.java

@@ -26,19 +26,33 @@
 package loci.formats.in;
 
 import java.io.IOException;
+import java.util.List;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import loci.common.RandomAccessInputStream;
+import loci.common.services.DependencyException;
+import loci.common.services.ServiceException;
+import loci.common.services.ServiceFactory;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
+import loci.formats.MissingLibraryException;
+import loci.formats.meta.IMetadata;
+import loci.formats.meta.MetadataConverter;
 import loci.formats.meta.MetadataStore;
+import loci.formats.services.OMEXMLService;
+import loci.formats.services.OMEXMLServiceImpl;
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.PhotoInterp;
 import loci.formats.tiff.TiffParser;
 
+import ome.xml.meta.OMEXMLMetadataRoot;
+import ome.xml.model.Image;
+import ome.xml.model.Pixels;
+import ome.xml.model.TiffData;
+
 /**
  * PyramidTiffReader is the file format reader for pyramid TIFFs.
  */
@@ -52,6 +66,8 @@ public class PyramidTiffReader extends BaseTiffReader {
 
   // -- Fields --
 
+  private IMetadata omexml = null;
+
   // -- Constructor --
 
   /** Constructs a new pyramid TIFF reader. */
@@ -77,6 +93,17 @@ public boolean isThisType(RandomAccessInputStream stream) throws IOException {
     return software.indexOf("Faas") >= 0;
   }
 
+  /**
+   * @see loci.formats.IFormatReader#close(boolean)
+   */
+  @Override
+  public void close(boolean fileOnly) throws IOException {
+    super.close(fileOnly);
+    if (!fileOnly) {
+      omexml = null;
+    }
+  }
+
   /**
    * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
    */
@@ -85,7 +112,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     throws FormatException, IOException
   {
     FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
-    int index = getCoreIndex();
+    int index = getCoreIndex() * getImageCount() + no;
     tiffParser.setAssumeEqualStrips(equalStrips);
     tiffParser.getSamples(ifds.get(index), buf, x, y, w, h);
     return buf;
@@ -96,7 +123,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
   public int getOptimalTileWidth() {
     FormatTools.assertId(currentId, true, 1);
     try {
-      return (int) ifds.get(getCoreIndex()).getTileWidth();
+      return (int) ifds.get(getCoreIndex() * getImageCount()).getTileWidth();
     }
     catch (FormatException e) {
       LOGGER.debug("", e);
@@ -109,7 +136,7 @@ public int getOptimalTileWidth() {
   public int getOptimalTileHeight() {
     FormatTools.assertId(currentId, true, 1);
     try {
-      return (int) ifds.get(getCoreIndex()).getTileLength();
+      return (int) ifds.get(getCoreIndex() * getImageCount()).getTileLength();
     }
     catch (FormatException e) {
       LOGGER.debug("", e);
@@ -122,7 +149,38 @@ public int getOptimalTileHeight() {
   /* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
   @Override
   protected void initStandardMetadata() throws FormatException, IOException {
-    int seriesCount = ifds.size();
+    // count number of consecutive planes with the same XY dimensions
+
+    int nPlanes = 1;
+    long baseWidth = ifds.get(0).getImageWidth();
+    long baseHeight = ifds.get(0).getImageLength();
+    for (int i=1; i<ifds.size(); i++) {
+      long width = ifds.get(i).getImageWidth();
+      long height = ifds.get(i).getImageLength();
+      if (width == baseWidth && height == baseHeight) {
+        nPlanes++;
+      }
+      else {
+        break;
+      }
+    }
+
+    int seriesCount = ifds.size() / nPlanes;
+
+    String comment = ifds.get(0).getComment();
+    if (comment != null && comment.length() > 0 && comment.trim().startsWith("<")) {
+      try {
+        ServiceFactory factory = new ServiceFactory();
+        OMEXMLService service = factory.getInstance(OMEXMLService.class);
+        omexml = service.createOMEXMLMetadata(comment);
+      }
+      catch (DependencyException de) {
+       throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
+      }
+      catch (ServiceException e) {
+        LOGGER.debug("Could not parse comment as OME-XML", e);
+      }
+    }
 
     // repopulate core metadata
     core.clear();
@@ -134,7 +192,7 @@ protected void initStandardMetadata() throws FormatException, IOException {
         ms.resolutionCount = seriesCount;
       }
 
-      IFD ifd = ifds.get(s);
+      IFD ifd = ifds.get(s * nPlanes);
 
       PhotoInterp p = ifd.getPhotometricInterpretation();
       int samples = ifd.getSamplesPerPixel();
@@ -145,31 +203,68 @@ protected void initStandardMetadata() throws FormatException, IOException {
 
       ms.sizeX = (int) ifd.getImageWidth();
       ms.sizeY = (int) ifd.getImageLength();
-      ms.sizeZ = 1;
-      ms.sizeT = 1;
-      ms.sizeC = ms.rgb ? samples : 1;
+      if (omexml != null) {
+        ms.sizeZ = omexml.getPixelsSizeZ(0).getValue();
+        ms.sizeT = omexml.getPixelsSizeT(0).getValue();
+        ms.sizeC = omexml.getPixelsSizeC(0).getValue();
+        ms.dimensionOrder = omexml.getPixelsDimensionOrder(0).getValue();
+      }
+      else {
+        ms.sizeZ = 1;
+        ms.sizeT = 1;
+        ms.sizeC = ms.rgb ? samples : 1;
+        // assuming all planes are channels
+        ms.sizeC *= nPlanes;
+        ms.dimensionOrder = "XYCZT";
+      }
       ms.littleEndian = ifd.isLittleEndian();
       ms.indexed = p == PhotoInterp.RGB_PALETTE &&
         (get8BitLookupTable() != null || get16BitLookupTable() != null);
-      ms.imageCount = 1;
+      ms.imageCount = nPlanes;
       ms.pixelType = ifd.getPixelType();
       ms.metadataComplete = true;
       ms.interleaved = false;
       ms.falseColor = false;
-      ms.dimensionOrder = "XYCZT";
       ms.thumbnail = s > 0;
     }
   }
 
   /* @see loci.formats.BaseTiffReader#initMetadataStore() */
   @Override
   protected void initMetadataStore() throws FormatException {
-    super.initMetadataStore();
+    boolean setImageNames = true;
+    if (omexml == null) {
+      super.initMetadataStore();
+    }
+    else {
+      OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
+      List<Image> images = root.copyImageList();
+      for (int i=0; i<images.size(); i++) {
+        Image img = images.get(i);
+        if (i > 0 && !hasFlattenedResolutions()) {
+          root.removeImage(img);
+          continue;
+        }
+        Pixels pix = img.getPixels();
+        List<TiffData> tiffData = pix.copyTiffDataList();
+        for (TiffData t : tiffData) {
+          pix.removeTiffData(t);
+        }
+        if (img.getName() != null) {
+          setImageNames = false;
+        }
+      }
+      omexml.setRoot(root);
 
-    MetadataStore store = makeFilterMetadata();
+      MetadataConverter.convertMetadata(omexml, makeFilterMetadata());
+    }
+
+    if (setImageNames) {
+     MetadataStore store = makeFilterMetadata();
 
-    for (int i=0; i<getSeriesCount(); i++) {
-      store.setImageName("Series " + (i + 1), i);
+      for (int i=0; i<getSeriesCount(); i++) {
+        store.setImageName("Series " + (i + 1), i);
+      }
     }
   }
 

components/test-suite/src/loci/tests/testng/FormatReaderTest.java

@@ -2251,6 +2251,13 @@ else if (r instanceof FileStitcher) {
               continue;
             }
 
+            // Pyramid TIFF files may include an OME-XML comment
+            if (result && r instanceof PyramidTiffReader &&
+              readers[j] instanceof OMETiffReader)
+            {
+              continue;
+            }
+
             if (result && r instanceof TrestleReader &&
               (readers[j] instanceof JPEGReader ||
               readers[j] instanceof PGMReader ||