More OME-XML validation fixes, see #520.

components/bio-formats/src/loci/formats/MetadataTools.java

@@ -118,22 +118,31 @@ public static void populatePixels(MetadataStore store, IFormatReader r,
       store.setPixelsSizeZ(new PositiveInteger(r.getSizeZ()), i);
       store.setPixelsSizeC(new PositiveInteger(r.getSizeC()), i);
       store.setPixelsSizeT(new PositiveInteger(r.getSizeT()), i);
-      store.setPixelsBinDataBigEndian(new Boolean(!r.isLittleEndian()), i, 0);
 
+      int tiffDataCount = 0;
+      OMEXMLService service = null;
       try {
-        OMEXMLService service =
-          new ServiceFactory().getInstance(OMEXMLService.class);
+        service = new ServiceFactory().getInstance(OMEXMLService.class);
         if (service.isOMEXMLRoot(store.getRoot())) {
           OME root = (OME) store.getRoot();
-          BinData bin = root.getImage(i).getPixels().getBinData(0);
-          bin.setLength(new NonNegativeLong(0L));
-          store.setRoot(root);
+          tiffDataCount = root.getImage(i).getPixels().sizeOfTiffDataList();
         }
       }
       catch (DependencyException exc) {
         LOGGER.debug("Failed to set BinData.Length", exc);
       }
 
+      if (tiffDataCount == 0) {
+        store.setPixelsBinDataBigEndian(new Boolean(!r.isLittleEndian()), i, 0);
+
+        if (service != null && service.isOMEXMLRoot(store.getRoot())) {
+          OME root = (OME) store.getRoot();
+          BinData bin = root.getImage(i).getPixels().getBinData(0);
+          bin.setLength(new NonNegativeLong(0L));
+          store.setRoot(root);
+        }
+      }
+
       try {
         store.setPixelsType(PixelType.fromString(
           FormatTools.getPixelTypeString(r.getPixelType())), i);

components/bio-formats/src/loci/formats/in/BDReader.java

@@ -279,9 +279,12 @@ protected void initFile(String id) throws FormatException, IOException {
       String row = name.substring(0, 1);
       Integer col = Integer.parseInt(name.substring(1));
 
+      store.setWellID(MetadataTools.createLSID("Well", 0, i), 0, i);
       store.setWellColumn(new NonNegativeInteger(col - 1), 0, i);
       store.setWellRow(new NonNegativeInteger(row.charAt(0) - 'A'), 0, i);
 
+      String wellSampleID = MetadataTools.createLSID("WellSample", 0, i, 0);
+      store.setWellSampleID(wellSampleID, 0, i, 0);
       store.setWellSampleIndex(new NonNegativeInteger(i), 0, i, 0);
 
       String imageID = MetadataTools.createLSID("Image", i);
@@ -346,6 +349,7 @@ protected void initFile(String id) throws FormatException, IOException {
         }
       }
 
+      store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
       store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
       store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
       store.setPlateName(plateName, 0);
@@ -523,6 +527,8 @@ private void parseROIs(MetadataStore store) throws IOException {
       if (cols.length < 6) break;
 
       if (cols[2].trim().length() > 0) {
+        String rectangleID = MetadataTools.createLSID("Shape", i - firstRow, 0);
+        store.setRectangleID(rectangleID, i - firstRow, 0);
         store.setRectangleX(new Double(cols[2]), i - firstRow, 0);
         store.setRectangleY(new Double(cols[3]), i - firstRow, 0);
         store.setRectangleWidth(new Double(cols[4]), i - firstRow, 0);

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

@@ -411,6 +411,8 @@ protected void initMetadataStore() throws FormatException {
         store.setExperimenterFirstName(firstName, 0);
         store.setExperimenterLastName(lastName, 0);
         store.setExperimenterEmail(email, 0);
+        store.setExperimenterDisplayName(artist, 0);
+        store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
       }
 
       store.setImageDescription(firstIFD.getComment(), 0);

components/bio-formats/src/loci/formats/in/InCellReader.java

@@ -435,6 +435,9 @@ protected void initFile(String id) throws FormatException, IOException {
       if (timepoint < 0) timepoint = 0;
       int sampleIndex = (field - 1) * totalTimepoints + timepoint;
 
+      String wellSampleID =
+        MetadataTools.createLSID("WellSample", 0, well, sampleIndex);
+      store.setWellSampleID(wellSampleID, 0 ,well, sampleIndex);
       store.setWellSampleIndex(new NonNegativeInteger(i), 0, well, sampleIndex);
       store.setWellSampleImageRef(imageID, 0, well, sampleIndex);
       if (field < posX.size()) {
@@ -503,6 +506,7 @@ protected void initFile(String id) throws FormatException, IOException {
       String colNaming =
         Character.isDigit(colName.charAt(0)) ? "Number" : "Letter";
 
+      store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
       store.setPlateRowNamingConvention(getNamingConvention(rowNaming), 0);
       store.setPlateColumnNamingConvention(getNamingConvention(colNaming), 0);
       store.setPlateWellOriginX(0.5, 0);
@@ -872,6 +876,8 @@ else if (qName.equals("Plate")) {
         for (int r=0; r<wellRows; r++) {
           for (int c=0; c<wellCols; c++) {
             int well = r * wellCols + c;
+            String wellID = MetadataTools.createLSID("Well", nextPlate, well);
+            store.setWellID(wellID, nextPlate, well);
             store.setWellRow(new NonNegativeInteger(r), nextPlate, well);
             store.setWellColumn(new NonNegativeInteger(c), nextPlate, well);
           }

components/bio-formats/src/loci/formats/in/LEOReader.java

@@ -29,6 +29,7 @@
 import loci.common.RandomAccessInputStream;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
+import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.TiffParser;
@@ -120,6 +121,12 @@ protected void initMetadataStore() throws FormatException {
     if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
       store.setPixelsPhysicalSizeX(xSize, 0);
       store.setPixelsPhysicalSizeY(xSize, 0);
+
+      String instrument = MetadataTools.createLSID("Instrument", 0);
+      store.setInstrumentID(instrument, 0);
+      store.setImageInstrumentRef(instrument, 0);
+
+      store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
       store.setObjectiveWorkingDistance(workingDistance, 0, 0);
       store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
       store.setObjectiveCorrection(getCorrection("Other"), 0, 0);

components/bio-formats/src/loci/formats/in/MIASReader.java

@@ -677,10 +677,13 @@ else if (nWells == 384) {
       int wellCol = (wellIndex % wellColumns) + 1;
       char wellRow = (char) ('A' + row);
 
+      store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
       store.setWellRow(new NonNegativeInteger(row), 0, well);
       store.setWellColumn(new NonNegativeInteger(wellCol - 1), 0, well);
 
       String imageID = MetadataTools.createLSID("Image", well);
+      String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, 0);
+      store.setWellSampleID(wellSampleID, 0, well, 0);
       store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0);
 
       store.setImageID(imageID, well);
@@ -693,10 +696,13 @@ else if (nWells == 384) {
     MetadataLevel level = getMetadataOptions().getMetadataLevel();
 
     if (level != MetadataLevel.MINIMUM) {
-      store.setExperimentID("Experiment:" + experiment.getName(), 0);
+      String experimentID = MetadataTools.createLSID("Experiment", 0);
+      store.setExperimentID(experimentID, 0);
       store.setExperimentType(getExperimentType("Other"), 0);
+      store.setExperimentDescription(experiment.getName(), 0);
 
       // populate SPW metadata
+      store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
       store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
       store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
 
@@ -708,7 +714,7 @@ else if (nWells == 384) {
 
       for (int well=0; well<nWells; well++) {
         // populate Image/Pixels metadata
-        store.setImageExperimentRef("Experiment:" + experiment.getName(), well);
+        store.setImageExperimentRef(experimentID, well);
 
         String instrumentID = MetadataTools.createLSID("Instrument", 0);
         store.setInstrumentID(instrumentID, 0);
@@ -848,6 +854,7 @@ private void populateROI(List<String> columns, String[] data, int series,
     store.setROIID(roiID, roi);
     store.setImageROIRef(roiID, series, roi);
 
+    store.setEllipseID(MetadataTools.createLSID("Shape", roi, 0), roi, 0);
     store.setEllipseTheT(new NonNegativeInteger(tv), roi, 0);
     store.setEllipseTheZ(new NonNegativeInteger(zv), roi, 0);
     store.setEllipseX(new Double(data[columns.indexOf("Col")]), roi, 0);
@@ -915,6 +922,8 @@ else if (key.equals("Pixel_Y")) {
           physicalSizeY = new Double(value);
         }
         else if (key.equals("Objective_ID")) {
+          store.setObjectiveID(
+            MetadataTools.createLSID("Objective", 0, 0), 0, 0);
           store.setObjectiveModel(value, 0, 0);
         }
         else if (key.equals("Magnification")) {
@@ -969,13 +978,17 @@ private int parseMasks(MetadataStore store, int series, int roi,
     int nOverlays = 0;
     for (int i=0; i<3; i++) {
       String roiId = MetadataTools.createLSID("ROI", series, roi + nOverlays);
-      String maskId = MetadataTools.createLSID("Mask", series, roi + nOverlays, 0);
+      String maskId =
+        MetadataTools.createLSID("Mask", series, roi + nOverlays, 0);
       overlayFiles.put(maskId, overlayTiff);
       overlayPlanes.put(maskId, new Integer(i));
 
       boolean validMask = populateMaskPixels(series, roi + nOverlays, 0);
       if (validMask) {
         store.setROIID(roiId, roi + nOverlays);
+
+        String maskID = MetadataTools.createLSID("Shape", roi + nOverlays, 0);
+        store.setMaskID(maskID, roi + nOverlays, 0);
         store.setMaskX(new Double(0), roi + nOverlays, 0);
         store.setMaskY(new Double(0), roi + nOverlays, 0);
         store.setMaskWidth(new Double(getSizeX()), roi + nOverlays, 0);

components/bio-formats/src/loci/formats/in/OMETiffReader.java

@@ -44,6 +44,7 @@
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
+import loci.formats.MetadataTools;
 import loci.formats.MissingLibraryException;
 import loci.formats.ome.OMEXMLMetadata;
 import loci.formats.services.OMEXMLService;
@@ -607,6 +608,8 @@ else if (core[s].sizeC == core[s].imageCount) {
     }
     core = series.toArray(new CoreMetadata[series.size()]);
     info = planeInfo.toArray(new OMETiffPlane[0][0]);
+
+    MetadataTools.populatePixels(metadataStore, this);
   }
 
   // -- Helper methods --

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

@@ -461,6 +461,7 @@ public void testSaneOMEXML() {
         // if CreationDate is before 1995, it's probably invalid
         String date = retrieve.getImageAcquiredDate(i);
         if (date != null) {
+          date = date.trim();
           long acquiredDate = DateTools.getTime(date, DateTools.ISO8601_FORMAT);
           long saneDate =
             DateTools.getTime("1995-01-01T00:00:00", DateTools.ISO8601_FORMAT);
@@ -943,7 +944,6 @@ private boolean initFile() {
     if (reader == null) {
       reader = new BufferedImageReader(new FileStitcher());
       reader.setNormalized(true);
-      reader.setOriginalMetadataPopulated(true);
       reader.setMetadataFiltered(true);
       MetadataStore store = null;
       try {