/** Refine segmentation with ADD/SUB regions of interests */
private synchronized void refine() {
if (controlPanel.status != ControlJPanel.SEGMENTATED_STATUS) return;
if (controlPanel.addJRadioButton.isSelected()) addRoi = imp.getRoi();
else subRoi = imp.getRoi();
if (null != addRoi) {
final float alpha = controlPanel.addThreshold.getValue() / 100.0f;
final Shape shape = ShapeRoiHelper.getShape(new ShapeRoi(addRoi));
final AffineTransform trans = new AffineTransform();
trans.translate(addRoi.getBounds().getX(), addRoi.getBounds().getY());
final Area area = new Area(shape);
area.transform(trans);
siox.subpixelRefine(area, SioxSegmentator.ADD_EDGE, alpha, (float[]) confMatrix.getPixels());
}
if (null != subRoi) {
final float alpha = controlPanel.subThreshold.getValue() / 100.0f;
final Shape shape = ShapeRoiHelper.getShape(new ShapeRoi(subRoi));
final AffineTransform trans = new AffineTransform();
trans.translate(subRoi.getBounds().getX(), subRoi.getBounds().getY());
final Area area = new Area(shape);
area.transform(trans);
siox.subpixelRefine(area, SioxSegmentator.SUB_EDGE, alpha, (float[]) confMatrix.getPixels());
}
updateResult();
}
/** Segment image based on the current foreground and background ROIs */
private synchronized void segment() {
if (controlPanel.bgJRadioButton.isSelected()) backgroundRoi = imp.getRoi();
else foregroundRoi = imp.getRoi();
if (foregroundRoi == null) {
IJ.error("Siox Segmentation", "ERROR: no foreground selected!");
return;
}
// Create confidence matrix and initialize to unknown region of confidence
confMatrix = new FloatProcessor(imp.getWidth(), imp.getHeight());
final float[] imgData = (float[]) confMatrix.getPixels();
confMatrix.add(SioxSegmentator.UNKNOWN_REGION_CONFIDENCE);
// Set foreground ROI
if (foregroundRoi != null) {
confMatrix.setValue(SioxSegmentator.CERTAIN_FOREGROUND_CONFIDENCE);
confMatrix.fill(foregroundRoi);
}
// Set background ROI
if (backgroundRoi != null) {
confMatrix.setValue(SioxSegmentator.CERTAIN_BACKGROUND_CONFIDENCE);
confMatrix.fill(backgroundRoi);
} else {
// Workaround: select border pixels which are not foreground as background if no background
// was specified.
int w = imp.getWidth(), h = imp.getHeight();
for (int i = 0; i < w; i++) {
if (imgData[i] < 0.8f) imgData[i] = 0;
if (imgData[i + w * (h - 1)] < 0.8f) imgData[i + w * (h - 1)] = 0;
}
for (int i = 0; i < h; i++) {
if (imgData[w * i] < 0.8f) imgData[w * i] = 0;
if (imgData[w - 1 + w * i] < 0.8f) imgData[w - 1 + w * i] = 0;
}
}
// Call SIOX segmentation method
int[] pixels = (int[]) ip.getPixels();
final int smoothes = controlPanel.smoothness.getValue();
siox = new SioxSegmentator(imp.getWidth(), imp.getHeight(), null);
boolean success =
siox.segmentate(pixels, imgData, smoothes, controlPanel.multipart.isSelected() ? 4 : 0);
if (!success) IJ.error("Siox Segmentation", "The segmentation failed!");
updateResult();
// Set status flag to segmented
controlPanel.status = ControlJPanel.SEGMENTATED_STATUS;
controlPanel.updateComponentEnabling();
roiOverlay.setComposite(transparency100);
// Set up next panel components
controlPanel.subJRadioButton.setSelected(true);
controlPanel.addJRadioButton.setSelected(false);
lastButton = controlPanel.subJRadioButton;
}