Exemplo n.º 1
0
  private void parseROIs(MetadataStore store) throws IOException {
    if (roiFile == null) return;
    String roiData = DataTools.readFile(roiFile);
    String[] lines = roiData.split("\r\n");

    int firstRow = 0;
    while (firstRow < lines.length && !lines[firstRow].startsWith("ROI")) {
      firstRow++;
    }
    firstRow += 2;
    if (firstRow >= lines.length) return;

    for (int i = firstRow; i < lines.length; i++) {
      String[] cols = lines[i].split("\t");
      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);
        store.setRectangleHeight(new Double(cols[5]), i - firstRow, 0);
        String roiID = MetadataTools.createLSID("ROI", i - firstRow);
        store.setROIID(roiID, i - firstRow);
        for (int s = 0; s < getSeriesCount(); s++) {
          store.setImageROIRef(roiID, s, i - firstRow);
        }
      }
    }
  }
Exemplo n.º 2
0
  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);
  }