Merge pull request #3471 from melissalinkert/qptiff-metadata

QPTIFF: metadata fixes

Author: dgault

components/formats-bsd/src/loci/formats/in/BaseTiffReader.java

@@ -230,15 +230,8 @@ protected void initStandardMetadata() throws FormatException, IOException {
     putInt("MinSampleValue", firstIFD, IFD.MIN_SAMPLE_VALUE);
     putInt("MaxSampleValue", firstIFD, IFD.MAX_SAMPLE_VALUE);
 
-    TiffRational xResolution = firstIFD.getIFDRationalValue(IFD.X_RESOLUTION);
-    TiffRational yResolution = firstIFD.getIFDRationalValue(IFD.Y_RESOLUTION);
-
-    if (xResolution != null) {
-      put("XResolution", xResolution.doubleValue());
-    }
-    if (yResolution != null) {
-      put("YResolution", yResolution.doubleValue());
-    }
+    putDouble("XResolution", firstIFD, IFD.X_RESOLUTION);
+    putDouble("YResolution", firstIFD, IFD.Y_RESOLUTION);
 
     int planar = firstIFD.getIFDIntValue(IFD.PLANAR_CONFIGURATION);
     String planarConfig = null;
@@ -252,8 +245,8 @@ protected void initStandardMetadata() throws FormatException, IOException {
     }
     put("PlanarConfiguration", planarConfig);
 
-    putInt("XPosition", firstIFD, IFD.X_POSITION);
-    putInt("YPosition", firstIFD, IFD.Y_POSITION);
+    putDouble("XPosition", firstIFD, IFD.X_POSITION);
+    putDouble("YPosition", firstIFD, IFD.Y_POSITION);
     putInt("FreeOffsets", firstIFD, IFD.FREE_OFFSETS);
     putInt("FreeByteCounts", firstIFD, IFD.FREE_BYTE_COUNTS);
     putInt("GrayResponseUnit", firstIFD, IFD.GRAY_RESPONSE_UNIT);
@@ -575,6 +568,15 @@ protected void putString(String key, IFD ifd, int tag) {
     put(key, value);
   }
 
+  protected void putDouble(String key, IFD ifd, int tag) {
+    if (ifd.getIFDValue(tag) instanceof Number) {
+      Number number = (Number) ifd.getIFDValue(tag);
+      if (number != null) {
+        put(key, number.doubleValue());
+      }
+    }
+  }
+
   // -- Internal FormatReader API methods --
 
   /* @see loci.formats.FormatReader#initFile(String) */

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

@@ -26,12 +26,16 @@
 package loci.formats.in;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import loci.common.DataTools;
+import loci.common.Location;
 import loci.common.RandomAccessInputStream;
 import loci.common.xml.XMLTools;
 import loci.formats.CoreMetadata;
@@ -42,6 +46,7 @@
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.PhotoInterp;
 import loci.formats.tiff.TiffParser;
+import loci.formats.tiff.TiffRational;
 import ome.xml.model.primitives.Color;
 import ome.xml.model.primitives.NonNegativeInteger;
 
@@ -68,10 +73,17 @@ public class VectraReader extends BaseTiffReader {
   /** TIFF image description prefix for PerkinElmer Vectra/QPTIFF files. */
   private static final String SOFTWARE_CHECK = "PerkinElmer-QPI";
 
+  private static final String ANNOTATION_SUFFIX = "_annotations.xml";
+  private static final List<String> EXTRA_FILES = Arrays.asList(
+    "CoverslipMask.tif", "FocusMap.tif", "Label.tif",
+    "OverviewBF.tif", "OverviewFL.tif", "SampleMask.tif"
+  );
+
   // -- Fields --
 
   private int pyramidDepth = 1;
   private String profileXML;
+  private List<String> allFiles = new ArrayList<String>();
 
   // -- Constructor --
 
@@ -82,6 +94,7 @@ public VectraReader() {
     noSubresolutions = true;
     suffixSufficient = false;
     canSeparateSeries = false;
+    hasCompanionFiles = true;
   }
 
   // -- IFormatReader API methods --
@@ -114,6 +127,19 @@ public boolean isThisType(String name, boolean open) {
     }
   }
 
+  /* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
+  @Override
+  public String[] getSeriesUsedFiles(boolean noPixels) {
+    if (allFiles.size() == 1) {
+      return super.getSeriesUsedFiles(noPixels);
+    }
+    if (noPixels) {
+      return allFiles.subList(
+        1, allFiles.size()).toArray(new String[allFiles.size() - 1]);
+    }
+    return allFiles.toArray(new String[allFiles.size()]);
+  }
+
   /**
    * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
    */
@@ -150,6 +176,9 @@ public void close(boolean fileOnly) throws IOException {
     if (!fileOnly) {
       pyramidDepth = 1;
       profileXML = null;
+      if (allFiles != null) {
+        allFiles.clear();
+      }
     }
   }
 
@@ -188,6 +217,21 @@ public int getOptimalTileHeight() {
   protected void initStandardMetadata() throws FormatException, IOException {
     super.initStandardMetadata();
 
+    // look for companion files
+
+    Location currentFile = new Location(currentId).getAbsoluteFile();
+    allFiles.add(currentFile.getAbsolutePath());
+    Location parent = currentFile.getParentFile();
+    String[] list = parent.list(true);
+    Arrays.sort(list);
+    for (String f : list) {
+      if (f.endsWith(ANNOTATION_SUFFIX) || EXTRA_FILES.contains(f)) {
+        allFiles.add(new Location(parent, f).getAbsolutePath());
+      }
+    }
+
+    // set up IFDs
+
     ifds = tiffParser.getMainIFDs();
     thumbnailIFDs = null;
 
@@ -276,6 +320,7 @@ protected void initMetadataStore() throws FormatException {
     MetadataStore store = makeFilterMetadata();
 
     for (int i=0; i<getSeriesCount(); i++) {
+      setSeries(i);
       int coreIndex = seriesToCoreIndex(i);
       store.setImageName(getImageName(coreIndex), i);
       store.setImageDescription("", i);
@@ -287,11 +332,31 @@ protected void initMetadataStore() throws FormatException {
 
       store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(x), i);
       store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(y), i);
+
+      TiffRational xPos = ifd.getIFDRationalValue(IFD.X_POSITION);
+      TiffRational yPos = ifd.getIFDRationalValue(IFD.Y_POSITION);
+      int unitMultiplier = ifd.getResolutionMultiplier();
+
+      for (int c=0; c<getEffectiveSizeC(); c++) {
+        store.setPlaneTheZ(new NonNegativeInteger(0), i, c);
+        store.setPlaneTheT(new NonNegativeInteger(0), i, c);
+        store.setPlaneTheC(new NonNegativeInteger(c), i, c);
+
+        if (xPos != null) {
+          double position = xPos.doubleValue() * unitMultiplier;
+          store.setPlanePositionX(FormatTools.getPhysicalSizeX(position), i, c);
+        }
+        if (yPos != null) {
+          double position = yPos.doubleValue() * unitMultiplier;
+          store.setPlanePositionY(FormatTools.getPhysicalSizeY(position), i, c);
+        }
+      }
     }
+    setSeries(0);
 
     // each high-resolution IFD has an XML description that needs to be parsed
 
-    for (int c=0; c<getSizeC(); c++) {
+    for (int c=0; c<getEffectiveSizeC(); c++) {
       String xml = getIFDComment(c);
       try {
         Element root = XMLTools.parseDOM(xml).getDocumentElement();
@@ -375,9 +440,6 @@ else if (name.equals("Objective") && c == 0) {
           else if (name.equals("ExposureTime")) {
             Time exposure = new Time(DataTools.parseDouble(value), UNITS.MICROSECOND);
             store.setPlaneExposureTime(exposure, 0, c);
-            store.setPlaneTheZ(new NonNegativeInteger(0), 0, c);
-            store.setPlaneTheT(new NonNegativeInteger(0), 0, c);
-            store.setPlaneTheC(new NonNegativeInteger(c), 0, c);
           }
         }
       }