/**
* Computes the geodesic distance function for each pixel in mask, using the given mask. Mask and
* marker should be ImageProcessor the same size and containing float values. The function returns
* a new Float processor the same size as the input, with values greater or equal to zero.
*/
@Override
public FloatProcessor geodesicDistanceMap(ImageProcessor marker, ImageProcessor mask) {
// size of image
width = mask.getWidth();
height = mask.getHeight();
// update mask
this.maskProc = mask;
// create new empty image, and fill it with black
FloatProcessor result = new FloatProcessor(width, height);
result.setValue(0);
result.fill();
// initialize empty image with either 0 (foreground) or Inf (background)
array = result.getFloatArray();
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
int val = marker.get(i, j) & 0x00ff;
array[i][j] = val == 0 ? backgroundValue : 0;
}
}
int iter = 0;
do {
modif = false;
// forward iteration
IJ.showStatus("Forward iteration " + iter);
forwardIteration();
// backward iteration
IJ.showStatus("Backward iteration " + iter);
backwardIteration();
// Iterate while pixels have been modified
iter++;
} while (modif);
// Normalize values by the first weight
if (this.normalizeMap) {
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
array[i][j] /= this.weights[0];
}
}
}
// Compute max value within the mask
float maxVal = 0;
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
if (maskProc.getPixel(i, j) != 0) maxVal = Math.max(maxVal, array[i][j]);
}
}
// update and return resulting Image processor
result.setFloatArray(array);
result.setMinAndMax(0, maxVal);
// Forces the display to non-inverted LUT
if (result.isInvertedLut()) result.invertLut();
return result;
}
/** 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;
}