@Override
public void applyInPlace(FastBitmap fastBitmap) {
if (fastBitmap.isRGB()) {
fastBitmap.toGrayscale();
}
if (invert) new Invert().applyInPlace(fastBitmap);
int size = fastBitmap.getWidth() * fastBitmap.getHeight();
int min = ImageStatistics.Minimum(fastBitmap);
int max = ImageStatistics.Maximum(fastBitmap);
fastBitmap.toRGB();
for (int i = 0; i < size; i++) {
int[] rgb = GrayscaleToHeatMap(fastBitmap.getRed(i), min, max);
fastBitmap.setRGB(i, rgb);
}
}
/**
* Calculate binarization threshold for the given image.
*
* @param fastBitmap FastBitmap.
* @return Threshold value.
*/
public int CalculateThreshold(FastBitmap fastBitmap) {
ImageStatistics stat = new ImageStatistics(fastBitmap);
Histogram hist = stat.getHistogramGray();
int[] histogram = hist.getValues();
int total = fastBitmap.getWidth() * fastBitmap.getHeight();
double sum = 0;
for (int i = 0; i < 256; i++) sum += i * histogram[i];
double sumB = 0;
int wB = 0;
int wF = 0;
double varMax = 0;
int threshold = 0;
for (int i = 0; i < 256; i++) {
wB += histogram[i];
if (wB == 0) continue;
wF = total - wB;
if (wF == 0) break;
sumB += (double) (i * histogram[i]);
double mB = sumB / wB;
double mF = (sum - sumB) / wF;
double varBetween = (double) wB * (double) wF * (mB - mF) * (mB - mF);
if (varBetween > varMax) {
varMax = varBetween;
threshold = i;
}
}
return threshold;
}
/**
* Calculate binarization threshold for the given image.
*
* @param fastBitmap FastBitmap.
* @return Threshold value.
*/
public int CalculateThreshold(FastBitmap fastBitmap) {
ImageStatistics stat = new ImageStatistics(fastBitmap);
ImageHistogram hist = stat.getHistogramGray();
int[] histogram = hist.getValues();
// Normalize histogram, that is makes the sum of all bins equal to 1.
double sum = 0;
for (int i = 0; i < histogram.length; ++i) {
sum += histogram[i];
}
if (sum == 0) {
// This should not normally happen, but...
throw new IllegalArgumentException("Empty histogram: sum of all bins is zero.");
}
double[] normalizedHist = new double[histogram.length];
for (int i = 0; i < histogram.length; i++) {
normalizedHist[i] = histogram[i] / sum;
}
//
double[] pT = new double[histogram.length];
pT[0] = normalizedHist[0];
for (int i = 1; i < histogram.length; i++) {
pT[i] = pT[i - 1] + normalizedHist[i];
}
// Entropy for black and white parts of the histogram
final double epsilon = Double.MIN_VALUE;
double[] hB = new double[histogram.length];
double[] hW = new double[histogram.length];
for (int t = 0; t < histogram.length; t++) {
// Black entropy
if (pT[t] > epsilon) {
double hhB = 0;
for (int i = 0; i <= t; i++) {
if (normalizedHist[i] > epsilon) {
hhB -= normalizedHist[i] / pT[t] * Math.log(normalizedHist[i] / pT[t]);
}
}
hB[t] = hhB;
} else {
hB[t] = 0;
}
// White entropy
double pTW = 1 - pT[t];
if (pTW > epsilon) {
double hhW = 0;
for (int i = t + 1; i < histogram.length; ++i) {
if (normalizedHist[i] > epsilon) {
hhW -= normalizedHist[i] / pTW * Math.log(normalizedHist[i] / pTW);
}
}
hW[t] = hhW;
} else {
hW[t] = 0;
}
}
// Find histogram index with maximum entropy
double jMax = hB[0] + hW[0];
int tMax = 0;
for (int t = 1; t < histogram.length; ++t) {
double j = hB[t] + hW[t];
if (j > jMax) {
jMax = j;
tMax = t;
}
}
return tMax;
}
private boolean watershedSegment(FastBitmap ip) {
int width = ip.getWidth();
int height = ip.getHeight();
byte[] pixels = ip.getGrayData();
// Create an array with the coordinates of all points between value 1 and 254
// This method, suggested by Stein Roervik (stein_at_kjemi-dot-unit-dot-no),
// greatly speeds up the watershed segmentation routine.
ImageStatistics is = new ImageStatistics(ip);
int[] histogram = is.getHistogramGray().getValues();
int arraySize = width * height - histogram[0] - histogram[255];
int[] coordinates = new int[arraySize]; // from pixel coordinates, low bits x, high bits y
int highestValue = 0;
int maxBinSize = 0;
int offset = 0;
int[] levelStart = new int[256];
for (int v = 1; v < 255; v++) {
levelStart[v] = offset;
offset += histogram[v];
if (histogram[v] > 0) highestValue = v;
if (histogram[v] > maxBinSize) maxBinSize = histogram[v];
}
int[] levelOffset = new int[highestValue + 1];
for (int y = 0, i = 0; y < height; y++) {
for (int x = 0; x < width; x++, i++) {
int v = pixels[i] & 255;
if (v > 0 && v < 255) {
offset = levelStart[v] + levelOffset[v];
coordinates[offset] = x | y << intEncodeShift;
levelOffset[v]++;
}
} // for x
} // for y
// Create an array of the points (pixel offsets) that we set to 255 in one pass.
// If we remember this list we need not create a snapshot of the ImageProcessor.
int[] setPointList = new int[Math.min(maxBinSize, (width * height + 2) / 3)];
// now do the segmentation, starting at the highest level and working down.
// At each level, dilate the particle (set pixels to 255), constrained to pixels
// whose values are at that level and also constrained (by the fateTable)
// to prevent features from merging.
int[] table = makeFateTable();
final int[] directionSequence = new int[] {7, 3, 1, 5, 0, 4, 2, 6}; // diagonal directions first
for (int level = highestValue; level >= 1; level--) {
int remaining =
histogram[level]; // number of points in the level that have not been processed
int idle = 0;
while (remaining > 0 && idle < 8) {
int dIndex = 0;
do { // expand each level in 8 directions
int n =
processLevel(
directionSequence[dIndex % 8],
ip,
table,
levelStart[level],
remaining,
coordinates,
setPointList);
// IJ.log("level="+level+" direction="+directionSequence[dIndex%8]+"
// remain="+remaining+"-"+n);
remaining -= n; // number of points processed
if (n > 0) idle = 0; // nothing processed in this direction?
dIndex++;
} while (remaining > 0 && idle++ < 8);
}
if (remaining > 0 && level > 1) { // any pixels that we have not reached?
int nextLevel = level; // find the next level to process
do nextLevel--;
while (nextLevel > 1 && histogram[nextLevel] == 0);
// in principle we should add all unprocessed pixels of this level to the
// tasklist of the next level. This would make it very slow for some images,
// however. Thus we only add the pixels if they are at the border (of the
// image or a thresholded area) and correct unprocessed pixels at the very
// end by CleanupExtraLines
if (nextLevel > 0) {
int newNextLevelEnd = levelStart[nextLevel] + histogram[nextLevel];
for (int i = 0, p = levelStart[level]; i < remaining; i++, p++) {
int xy = coordinates[p];
int x = xy & intEncodeXMask;
int y = (xy & intEncodeYMask) >> intEncodeShift;
int pOffset = x + y * width;
boolean addToNext = false;
if (x == 0 || y == 0 || x == width - 1 || y == height - 1)
addToNext = true; // image border
else
for (int d = 0; d < 8; d++)
if (isWithin(x, y, d, width, height) && pixels[pOffset + dirOffset[d]] == 0) {
addToNext = true; // border of area below threshold
break;
}
if (addToNext) coordinates[newNextLevelEnd++] = xy;
}
// tasklist for the next level to process becomes longer by this:
histogram[nextLevel] = newNextLevelEnd - levelStart[nextLevel];
}
}
}
return true;
}