示例#1
0
 /**
  * @return true if min-max is set
  * @throws FormatException
  * @throws IOException
  */
 @SuppressWarnings("unchecked")
 public boolean isMinMaxSet() throws FormatException, IOException {
   if (minMaxSet == null) {
     MetadataStore store = reader.getMetadataStore();
     int series = reader.getSeries();
     List<Pixels> pixels = (List<Pixels>) store.getRoot();
     if (pixels == null) {
       return minMaxSet = true;
     }
     Pixels p = pixels.get(series);
     Channel c = p.getChannel(p.getSizeC().getValue() - 1);
     if (c.getStatsInfo() == null) {
       minMaxSet = false;
     } else {
       minMaxSet = true;
     }
   }
   return minMaxSet;
 }
  private void parseROIs(MetadataStore store) throws FormatException, IOException {
    if (MetadataTools.isOMEXMLMetadata(store) || MetadataTools.isOMEXMLRoot(store.getRoot())) {
      return;
    }

    String roiID = MetadataTools.createLSID("ROI", 0, 0);
    String maskID = MetadataTools.createLSID("Shape", 0, 0);

    store.setROIID(roiID, 0);
    store.setMaskID(maskID, 0, 0);

    String positionData = DataTools.readFile(roiDrawFile);
    String[] coordinates = positionData.split("[ ,]");

    double x1 = Double.parseDouble(coordinates[1]);
    double y1 = Double.parseDouble(coordinates[2]);
    double x2 = Double.parseDouble(coordinates[3]);
    double y2 = Double.parseDouble(coordinates[5]);

    store.setMaskX(x1, 0, 0);
    store.setMaskY(y1, 0, 0);
    store.setMaskWidth(x2 - x1, 0, 0);
    store.setMaskHeight(y2 - y1, 0, 0);

    store.setImageROIRef(roiID, 0, 0);

    ImageReader roiReader = new ImageReader();
    roiReader.setId(roiFile);
    byte[] roiPixels = roiReader.openBytes(0);
    roiReader.close();

    BitWriter bits = new BitWriter(roiPixels.length / 8);
    for (int i = 0; i < roiPixels.length; i++) {
      bits.write(roiPixels[i] == 0 ? 0 : 1, 1);
    }
    store.setMaskBinData(bits.toByteArray(), 0, 0);
  }