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);
}
}
}
}
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);
}