/**
* Extract blob.
*
* @param id ID.
* @param fastBitmap Image to be processed.
* @return Image with the extracted blob.
*/
public FastBitmap Extract(int id, FastBitmap fastBitmap) {
// Check if blobs list is null.
if (this.blobs == null) this.blobs = new BlobDetection().ProcessImage(fastBitmap);
FastBitmap image;
if (fastBitmap.isGrayscale()) {
image =
new FastBitmap(
fastBitmap.getWidth(), fastBitmap.getHeight(), FastBitmap.ColorSpace.Grayscale);
for (IntPoint p : blobs.get(id).getPoints()) {
image.setGray(p.x, p.y, fastBitmap.getGray(p.x, p.y));
}
} else {
image =
new FastBitmap(fastBitmap.getWidth(), fastBitmap.getHeight(), FastBitmap.ColorSpace.RGB);
for (IntPoint p : blobs.get(id).getPoints()) {
image.setRed(p.x, p.y, fastBitmap.getRed(p.x, p.y));
image.setGreen(p.x, p.y, fastBitmap.getGreen(p.x, p.y));
image.setBlue(p.x, p.y, fastBitmap.getBlue(p.x, p.y));
}
}
return image;
}
/**
* Computes histograms.
*
* @param fastBitmap Image.
*/
private void ProcessImage(FastBitmap fastBitmap) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
if (fastBitmap.isGrayscale()) {
int[] g = new int[width];
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
g[y] += fastBitmap.getGray(x, y);
}
}
gray = new Histogram(g);
}
if (fastBitmap.isRGB()) {
int[] r = new int[width];
int[] g = new int[width];
int[] b = new int[width];
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
r[y] += fastBitmap.getRed(x, y);
g[y] += fastBitmap.getGreen(x, y);
b[y] += fastBitmap.getBlue(x, y);
}
}
red = new Histogram(r);
green = new Histogram(g);
blue = new Histogram(b);
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
if (fastBitmap.isRGB()) {
int size = fastBitmap.getWidth() * fastBitmap.getHeight();
for (int i = 0; i < size; i++) {
int r = fastBitmap.getRed(i);
int g = fastBitmap.getGreen(i);
int b = fastBitmap.getBlue(i);
float[] color = ColorConverter.RGBtoHLS(r, g, b);
int[] newColor = ColorConverter.HSLtoRGB(degree, color[1], color[2]);
newColor[0] = newColor[0] > 255 ? 255 : newColor[0];
newColor[0] = newColor[0] < 0 ? 0 : newColor[0];
newColor[1] = newColor[1] > 255 ? 255 : newColor[1];
newColor[1] = newColor[1] < 0 ? 0 : newColor[1];
newColor[2] = newColor[2] > 255 ? 255 : newColor[2];
newColor[2] = newColor[2] < 0 ? 0 : newColor[2];
fastBitmap.setRGB(i, newColor);
}
} else {
throw new IllegalArgumentException("Hue modifier only works in RGB images.");
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
int noise = (width * height * noiseAmount) / 200;
if (fastBitmap.isGrayscale()) {
for (int i = 0; i < noise; i++) {
int x = random.nextInt(height);
int y = random.nextInt(width);
int[] c = new int[] {0, 255};
int color = random.nextInt(2);
fastBitmap.setGray(x, y, c[color]);
}
} else if (fastBitmap.isRGB()) {
for (int i = 0; i < noise; i++) {
int x = random.nextInt(height);
int y = random.nextInt(width);
int[] c = new int[] {0, 255};
int band = random.nextInt(2);
int color = random.nextInt(2);
if (band == 0) {
fastBitmap.setRed(x, y, c[color]);
} else if (band == 1) {
fastBitmap.setGreen(x, y, c[color]);
} else if (band == 2) {
fastBitmap.setBlue(x, y, c[color]);
}
}
}
}
private static void watershedPostProcess(FastBitmap ip) {
byte[] pixels = ip.getGrayData();
int size = ip.getWidth() * ip.getHeight();
for (int i = 0; i < size; i++) {
if ((pixels[i] & 255) < 255) pixels[i] = (byte) 0;
}
}
private void CalculateNewSize(FastBitmap fastBitmap) {
// return same size if original image size should be kept
if (keepSize) {
this.newWidth = fastBitmap.getWidth();
this.newHeight = fastBitmap.getHeight();
return;
}
// angle's sine and cosine
double angleRad = -angle * Math.PI / 180;
double angleCos = Math.cos(angleRad);
double angleSin = Math.sin(angleRad);
// calculate half size
double halfWidth = (double) fastBitmap.getWidth() / 2;
double halfHeight = (double) fastBitmap.getHeight() / 2;
// rotate corners
double cx1 = halfWidth * angleCos;
double cy1 = halfWidth * angleSin;
double cx2 = halfWidth * angleCos - halfHeight * angleSin;
double cy2 = halfWidth * angleSin + halfHeight * angleCos;
double cx3 = -halfHeight * angleSin;
double cy3 = halfHeight * angleCos;
double cx4 = 0;
double cy4 = 0;
// recalculate image size
halfWidth =
Math.max(Math.max(cx1, cx2), Math.max(cx3, cx4))
- Math.min(Math.min(cx1, cx2), Math.min(cx3, cx4));
halfHeight =
Math.max(Math.max(cy1, cy2), Math.max(cy3, cy4))
- Math.min(Math.min(cy1, cy2), Math.min(cy3, cy4));
this.newWidth = (int) (halfWidth * 2 + 0.5);
this.newHeight = (int) (halfHeight * 2 + 0.5);
}
private void Watershed(FastBitmap fastBitmap) {
DistanceTransform dt = new DistanceTransform(distance);
float[][] distance = dt.Compute(fastBitmap);
// Convert 2D to 1D - ImageJ Compatibility
float[] distance1D = new float[distance.length * distance[0].length];
int p = 0;
for (int i = 0; i < fastBitmap.getHeight(); i++) {
for (int j = 0; j < fastBitmap.getWidth(); j++) {
distance1D[p++] = distance[i][j];
}
}
// Make directions offsets
makeDirectionOffsets(distance[0].length);
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
FastBitmap back = new FastBitmap(width, height, FastBitmap.ColorSpace.Grayscale);
// Pegue as maxima
long[] maxPoints =
getSortedMaxPoints(distance, distance1D, back, 0, dt.getMaximumDistance(), -808080.0);
// Analise e marque as maxima em imagem de background
float maxSortingError = 1.1f * SQRT2 / 2f;
analyseAndMarkMaxima(distance1D, back, maxPoints, tolerance, maxSortingError);
// Transform em 8bit 0..255
FastBitmap outImage = make8Bit(distance, back, dt.getMaximumDistance(), -808080.0);
cleanupMaxima(outImage, back, maxPoints);
watershedSegment(outImage);
watershedPostProcess(outImage);
fastBitmap.setImage(outImage);
}
@Override
public void applyInPlace(FastBitmap sourceImage) {
int width = overlayImage.getWidth();
int height = overlayImage.getHeight();
int[] rgbO;
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
rgbO = overlayImage.getRGB(x, y);
if (rgbO[0] >= _replaceColor[0]
&& rgbO[1] >= _replaceColor[1]
&& rgbO[2] >= _replaceColor[2]) {
// x and y is reverted
sourceImage.setRGB(x + getyOffset(), y + getxOffset(), rgbO);
}
}
}
}
@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;
}
private int processLevel(
int pass,
FastBitmap ip,
int[] fateTable,
int levelStart,
int levelNPoints,
int[] coordinates,
int[] setPointList) {
int width = ip.getWidth();
int height = ip.getHeight();
int xmax = width - 1;
int ymax = height - 1;
byte[] pixels = ip.getGrayData();
int nChanged = 0;
int nUnchanged = 0;
for (int i = 0, p = levelStart; i < levelNPoints; i++, p++) {
int xy = coordinates[p];
int x = xy & intEncodeXMask;
int y = (xy & intEncodeYMask) >> intEncodeShift;
int offset = x + y * width;
int index = 0; // neighborhood pixel ocupation: index in fateTable
if (y > 0 && (pixels[offset - width] & 255) == 255) index ^= 1;
if (x < xmax && y > 0 && (pixels[offset - width + 1] & 255) == 255) index ^= 2;
if (x < xmax && (pixels[offset + 1] & 255) == 255) index ^= 4;
if (x < xmax && y < ymax && (pixels[offset + width + 1] & 255) == 255) index ^= 8;
if (y < ymax && (pixels[offset + width] & 255) == 255) index ^= 16;
if (x > 0 && y < ymax && (pixels[offset + width - 1] & 255) == 255) index ^= 32;
if (x > 0 && (pixels[offset - 1] & 255) == 255) index ^= 64;
if (x > 0 && y > 0 && (pixels[offset - width - 1] & 255) == 255) index ^= 128;
int mask = 1 << pass;
if ((fateTable[index] & mask) == mask)
setPointList[nChanged++] = offset; // remember to set pixel to 255
else coordinates[levelStart + (nUnchanged++)] = xy; // keep this pixel for future passes
} // for pixel i
for (int i = 0; i < nChanged; i++) pixels[setPointList[i]] = (byte) 255;
return nChanged;
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
if (fastBitmap.isRGB() && overlay.isRGB()) {
int w = fastBitmap.getWidth();
int h = fastBitmap.getHeight();
switch (algorithm) {
case Lighten:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) > fastBitmap.getRed(i, j)) {
fastBitmap.setRed(i, j, overlay.getRed(i, j));
}
if (overlay.getGreen(i, j) > fastBitmap.getGreen(i, j)) {
fastBitmap.setGreen(i, j, overlay.getGreen(i, j));
}
if (overlay.getBlue(i, j) > fastBitmap.getBlue(i, j)) {
fastBitmap.setBlue(i, j, overlay.getBlue(i, j));
}
}
}
break;
case Darken:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) < fastBitmap.getRed(i, j)) {
fastBitmap.setRed(i, j, overlay.getRed(i, j));
}
if (overlay.getGreen(i, j) < fastBitmap.getGreen(i, j)) {
fastBitmap.setGreen(i, j, overlay.getGreen(i, j));
}
if (overlay.getBlue(i, j) < fastBitmap.getBlue(i, j)) {
fastBitmap.setBlue(i, j, overlay.getBlue(i, j));
}
}
}
break;
case Multiply:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r = fastBitmap.getRed(i, j) * overlay.getRed(i, j) / 255;
int g = fastBitmap.getGreen(i, j) * overlay.getGreen(i, j) / 255;
int b = fastBitmap.getBlue(i, j) * overlay.getBlue(i, j) / 255;
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Average:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r = fastBitmap.getRed(i, j) + overlay.getRed(i, j) / 2;
int g = fastBitmap.getGreen(i, j) + overlay.getGreen(i, j) / 2;
int b = fastBitmap.getBlue(i, j) + overlay.getBlue(i, j) / 2;
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Add:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r = Math.min(fastBitmap.getRed(i, j) + overlay.getRed(i, j), 255);
int g = Math.min(fastBitmap.getGreen(i, j) + overlay.getGreen(i, j), 255);
int b = Math.min(fastBitmap.getBlue(i, j) + overlay.getBlue(i, j), 255);
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Subtract:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int temp = fastBitmap.getRed(i, j) + overlay.getRed(i, j);
if (temp < 255) {
fastBitmap.setRed(i, j, 0);
} else {
fastBitmap.setRed(i, j, temp - 255);
}
temp = fastBitmap.getGreen(i, j) + overlay.getGreen(i, j);
if (temp < 255) {
fastBitmap.setGreen(i, j, 0);
} else {
fastBitmap.setGreen(i, j, temp - 255);
}
temp = fastBitmap.getBlue(i, j) + overlay.getBlue(i, j);
if (temp < 255) {
fastBitmap.setBlue(i, j, 0);
} else {
fastBitmap.setBlue(i, j, temp - 255);
}
}
}
break;
case Difference:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r = Math.abs(fastBitmap.getRed(i, j) - overlay.getRed(i, j));
int g = Math.abs(fastBitmap.getGreen(i, j) - overlay.getGreen(i, j));
int b = Math.abs(fastBitmap.getBlue(i, j) - overlay.getBlue(i, j));
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Negation:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r = 255 - Math.abs(255 - fastBitmap.getRed(i, j) - overlay.getRed(i, j));
int g = 255 - Math.abs(255 - fastBitmap.getGreen(i, j) - overlay.getGreen(i, j));
int b = 255 - Math.abs(255 - fastBitmap.getBlue(i, j) - overlay.getBlue(i, j));
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Screen:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r =
((255 - (((255 - fastBitmap.getRed(i, j)) * (255 - overlay.getRed(i, j))) >> 8)));
int g =
((255
- (((255 - fastBitmap.getGreen(i, j)) * (255 - overlay.getGreen(i, j)))
>> 8)));
int b =
((255
- (((255 - fastBitmap.getBlue(i, j)) * (255 - overlay.getBlue(i, j))) >> 8)));
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Exclusion:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r =
((fastBitmap.getRed(i, j)
+ overlay.getRed(i, j)
- 2 * fastBitmap.getRed(i, j) * overlay.getRed(i, j) / 255));
int g =
((fastBitmap.getGreen(i, j)
+ overlay.getGreen(i, j)
- 2 * fastBitmap.getGreen(i, j) * overlay.getGreen(i, j) / 255));
int b =
((fastBitmap.getBlue(i, j)
+ overlay.getBlue(i, j)
- 2 * fastBitmap.getBlue(i, j) * overlay.getBlue(i, j) / 255));
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
case Overlay:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int temp;
if (overlay.getRed(i, j) < 128) {
temp = (2 * fastBitmap.getRed(i, j) * overlay.getRed(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setRed(i, j, temp);
} else {
temp =
(255
- 2 * (255 - fastBitmap.getRed(i, j)) * (255 - overlay.getRed(i, j)) / 255);
temp = Math.min(255, temp);
fastBitmap.setRed(i, j, temp);
}
if (overlay.getGreen(i, j) < 128) {
temp = (2 * fastBitmap.getGreen(i, j) * overlay.getGreen(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setGreen(i, j, temp);
} else {
temp =
(255
- 2
* (255 - fastBitmap.getGreen(i, j))
* (255 - overlay.getGreen(i, j))
/ 255);
temp = Math.min(255, temp);
fastBitmap.setGreen(i, j, temp);
}
if (overlay.getBlue(i, j) < 128) {
temp = (2 * fastBitmap.getBlue(i, j) * overlay.getBlue(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setBlue(i, j, temp);
} else {
temp =
(255
- 2
* (255 - fastBitmap.getBlue(i, j))
* (255 - overlay.getBlue(i, j))
/ 255);
temp = Math.min(255, temp);
fastBitmap.setBlue(i, j, temp);
}
}
}
break;
case SoftLight:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int temp;
if (fastBitmap.getRed(i, j) < 128) {
temp = (2 * overlay.getRed(i, j) * fastBitmap.getRed(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setRed(i, j, temp);
} else {
temp =
(255
- 2 * (255 - overlay.getRed(i, j)) * (255 - fastBitmap.getRed(i, j)) / 255);
temp = Math.min(255, temp);
overlay.setRed(i, j, temp);
}
if (fastBitmap.getGreen(i, j) < 128) {
temp = (2 * overlay.getGreen(i, j) * fastBitmap.getGreen(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setGreen(i, j, temp);
} else {
temp =
(255
- 2
* (255 - overlay.getGreen(i, j))
* (255 - fastBitmap.getGreen(i, j))
/ 255);
temp = Math.min(255, temp);
fastBitmap.setGreen(i, j, temp);
}
if (fastBitmap.getBlue(i, j) < 128) {
temp = (2 * overlay.getBlue(i, j) * fastBitmap.getBlue(i, j) / 255);
temp = Math.min(255, temp);
fastBitmap.setBlue(i, j, temp);
} else {
temp =
(255
- 2
* (255 - overlay.getBlue(i, j))
* (255 - fastBitmap.getBlue(i, j))
/ 255);
temp = Math.min(255, temp);
fastBitmap.setBlue(i, j, temp);
}
}
}
break;
case HardLight:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
float temp;
if (overlay.getRed(i, j) < 128) {
temp =
(2 * ((fastBitmap.getRed(i, j) >> 1) + 64))
* ((float) overlay.getRed(i, j) / 255);
fastBitmap.setRed(i, j, (int) temp);
} else {
temp =
(255
- (2
* (255 - ((fastBitmap.getRed(i, j) >> 1) + 64))
* (float) (255 - overlay.getRed(i, j))
/ 255));
fastBitmap.setRed(i, j, (int) temp);
}
if (overlay.getGreen(i, j) < 128) {
temp =
(2 * ((fastBitmap.getGreen(i, j) >> 1) + 64))
* ((float) overlay.getGreen(i, j) / 255);
fastBitmap.setGreen(i, j, (int) temp);
} else {
temp =
(255
- (2
* (255 - ((fastBitmap.getGreen(i, j) >> 1) + 64))
* (float) (255 - overlay.getGreen(i, j))
/ 255));
fastBitmap.setGreen(i, j, (int) temp);
}
if (overlay.getBlue(i, j) < 128) {
temp =
(2 * ((fastBitmap.getBlue(i, j) >> 1) + 64))
* ((float) overlay.getBlue(i, j) / 255);
fastBitmap.setBlue(i, j, (int) temp);
} else {
temp =
(255
- (2
* (255 - ((fastBitmap.getBlue(i, j) >> 1) + 64))
* (float) (255 - overlay.getBlue(i, j))
/ 255));
fastBitmap.setBlue(i, j, (int) temp);
}
}
}
break;
case ColorDodge:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) == 255) {
fastBitmap.setRed(i, j, 255);
} else {
int x =
Math.min(255, ((fastBitmap.getRed(i, j) << 8) / (255 - overlay.getRed(i, j))));
fastBitmap.setRed(i, j, x);
}
if (overlay.getGreen(i, j) == 255) {
fastBitmap.setGreen(i, j, 255);
} else {
int x =
Math.min(
255, ((fastBitmap.getGreen(i, j) << 8) / (255 - overlay.getGreen(i, j))));
fastBitmap.setGreen(i, j, x);
}
if (overlay.getBlue(i, j) == 255) {
fastBitmap.setBlue(i, j, 255);
} else {
int x =
Math.min(
255, ((fastBitmap.getBlue(i, j) << 8) / (255 - overlay.getBlue(i, j))));
fastBitmap.setBlue(i, j, x);
}
}
}
break;
case ColorBurn:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) == 0) {
fastBitmap.setRed(i, j, overlay.getRed(i, j));
} else {
int x =
Math.max(
0, (255 - ((255 - fastBitmap.getRed(i, j)) << 8) / overlay.getRed(i, j)));
fastBitmap.setRed(i, j, x);
}
if (overlay.getGreen(i, j) == 0) {
fastBitmap.setGreen(i, j, overlay.getGreen(i, j));
} else {
int x =
Math.max(
0,
(255 - ((255 - fastBitmap.getGreen(i, j)) << 8) / overlay.getGreen(i, j)));
fastBitmap.setGreen(i, j, x);
}
if (overlay.getBlue(i, j) == 0) {
fastBitmap.setBlue(i, j, overlay.getBlue(i, j));
} else {
int x =
Math.max(
0, (255 - ((255 - fastBitmap.getBlue(i, j)) << 8) / overlay.getBlue(i, j)));
fastBitmap.setBlue(i, j, x);
}
}
}
break;
case LinearLight:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int temp;
if (overlay.getRed(i, j) < 128) {
temp = fastBitmap.getRed(i, j) + (2 * overlay.getRed(i, j));
if (temp < 255) {
fastBitmap.setRed(i, j, 0);
} else {
fastBitmap.setRed(i, j, (temp - 255));
}
} else {
int x = Math.min(fastBitmap.getRed(i, j) + (2 * (overlay.getRed(i, j) - 128)), 255);
fastBitmap.setRed(i, j, x);
}
if (overlay.getGreen(i, j) < 128) {
temp = fastBitmap.getGreen(i, j) + (2 * overlay.getGreen(i, j));
if (temp < 255) {
fastBitmap.setGreen(i, j, 0);
} else {
fastBitmap.setGreen(i, j, (temp - 255));
}
} else {
int x =
Math.min(fastBitmap.getGreen(i, j) + (2 * (overlay.getGreen(i, j) - 128)), 255);
fastBitmap.setGreen(i, j, x);
}
if (overlay.getBlue(i, j) < 128) {
temp = fastBitmap.getBlue(i, j) + (2 * overlay.getBlue(i, j));
if (temp < 255) {
fastBitmap.setBlue(i, j, 0);
} else {
fastBitmap.setBlue(i, j, (temp - 255));
}
} else {
int x =
Math.min(fastBitmap.getBlue(i, j) + (2 * (overlay.getBlue(i, j) - 128)), 255);
fastBitmap.setBlue(i, j, x);
}
}
}
break;
case VividLight:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) < 128) {
// Color Burn
int o = overlay.getRed(i, j) * 2;
if (o == 0) {
fastBitmap.setRed(i, j, o);
} else {
int x = Math.max(0, (255 - ((255 - fastBitmap.getRed(i, j)) << 8) / o));
fastBitmap.setRed(i, j, x);
}
} else {
// Color Dodge
int o = 2 * (overlay.getRed(i, j) - 128);
if (o == 255) {
fastBitmap.setRed(i, j, 255);
} else {
int x = Math.min(255, ((fastBitmap.getRed(i, j) << 8) / (255 - o)));
fastBitmap.setRed(i, j, x);
}
}
if (overlay.getGreen(i, j) < 128) {
// Color Burn
int o = overlay.getGreen(i, j) * 2;
if (o == 0) {
fastBitmap.setGreen(i, j, o);
} else {
int x = Math.max(0, (255 - ((255 - fastBitmap.getGreen(i, j)) << 8) / o));
fastBitmap.setGreen(i, j, x);
}
} else {
// Color Dodge
int o = 2 * (overlay.getGreen(i, j) - 128);
if (o == 255) {
fastBitmap.setGreen(i, j, 255);
} else {
int x = Math.min(255, ((fastBitmap.getGreen(i, j) << 8) / (255 - o)));
fastBitmap.setGreen(i, j, x);
}
}
if (overlay.getBlue(i, j) < 128) {
// Color Burn
int o = overlay.getBlue(i, j) * 2;
if (o == 0) {
fastBitmap.setBlue(i, j, o);
} else {
int x = Math.max(0, (255 - ((255 - fastBitmap.getBlue(i, j)) << 8) / o));
fastBitmap.setBlue(i, j, x);
}
} else {
// Color Dodge
int o = 2 * (overlay.getBlue(i, j) - 128);
if (o == 255) {
fastBitmap.setGreen(i, j, 255);
} else {
int x = Math.min(255, ((fastBitmap.getBlue(i, j) << 8) / (255 - o)));
fastBitmap.setBlue(i, j, x);
}
}
}
}
break;
case PinLight:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int o = overlay.getRed(i, j) * 2;
if (overlay.getRed(i, j) < 128) {
// Darken
if (o < fastBitmap.getRed(i, j)) {
fastBitmap.setRed(i, j, o);
}
} else {
// Lighten
if (o > fastBitmap.getRed(i, j)) {
fastBitmap.setRed(i, j, o);
}
}
o = overlay.getGreen(i, j) * 2;
if (overlay.getGreen(i, j) < 128) {
// Darken
if (o < fastBitmap.getGreen(i, j)) {
fastBitmap.setGreen(i, j, o);
}
} else {
// Lighten
if (o > fastBitmap.getGreen(i, j)) {
fastBitmap.setGreen(i, j, o);
}
}
o = overlay.getBlue(i, j) * 2;
if (overlay.getBlue(i, j) < 128) {
// Darken
if (o < fastBitmap.getBlue(i, j)) {
fastBitmap.setBlue(i, j, o);
}
} else {
// Lighten
if (o > fastBitmap.getBlue(i, j)) {
fastBitmap.setBlue(i, j, o);
}
}
}
}
break;
case Reflect:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
if (overlay.getRed(i, j) == 255) {
fastBitmap.setRed(i, j, 255);
} else {
int x =
Math.min(
255,
(fastBitmap.getRed(i, j)
* fastBitmap.getRed(i, j)
/ (255 - overlay.getRed(i, j))));
fastBitmap.setRed(i, j, x);
}
if (overlay.getGreen(i, j) == 255) {
fastBitmap.setGreen(i, j, 255);
} else {
int x =
Math.min(
255,
(fastBitmap.getGreen(i, j)
* fastBitmap.getGreen(i, j)
/ (255 - overlay.getGreen(i, j))));
fastBitmap.setGreen(i, j, x);
}
if (overlay.getBlue(i, j) == 255) {
fastBitmap.setBlue(i, j, 255);
} else {
int x =
Math.min(
255,
(fastBitmap.getBlue(i, j)
* fastBitmap.getBlue(i, j)
/ (255 - overlay.getBlue(i, j))));
fastBitmap.setBlue(i, j, x);
}
}
}
break;
case Phoenix:
for (int i = 0; i < h; i++) {
for (int j = 0; j < w; j++) {
int r =
((Math.min(fastBitmap.getRed(i, j), overlay.getRed(i, j))
- Math.max(fastBitmap.getRed(i, j), overlay.getRed(i, j))
+ 255));
int g =
((Math.min(fastBitmap.getGreen(i, j), overlay.getGreen(i, j))
- Math.max(fastBitmap.getGreen(i, j), overlay.getGreen(i, j))
+ 255));
int b =
((Math.min(fastBitmap.getBlue(i, j), overlay.getBlue(i, j))
- Math.max(fastBitmap.getBlue(i, j), overlay.getBlue(i, j))
+ 255));
fastBitmap.setRGB(i, j, r, g, b);
}
}
break;
}
} else {
throw new IllegalArgumentException("Blend only works in RGB images.");
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
FastBitmap copy = new FastBitmap(fastBitmap);
if (fastBitmap.isGrayscale()) {
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
double mean = 0;
double var = 0;
int total = 0;
for (int i = x - radius; i <= x + radius; i++) {
for (int j = y - radius; j <= y + radius; j++) {
if (i >= 0 && i < height && j >= 0 && j < width) {
mean += copy.getGray(i, j);
total++;
}
}
}
mean /= total;
for (int i = x - radius; i <= x + radius; i++) {
for (int j = y - radius; j <= y + radius; j++) {
if (i >= 0 && i < height && j >= 0 && j < width)
var += Math.pow(copy.getGray(i, j) - mean, 2);
}
}
var /= total - 1;
if (var < 0) var = 0;
if (var > 255) var = 255;
fastBitmap.setGray(x, y, (int) var);
}
}
}
if (fastBitmap.isRGB()) {
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
double meanR = 0, meanG = 0, meanB = 0;
double varR = 0, varG = 0, varB = 0;
int total = 0;
for (int i = x - radius; i <= x + radius; i++) {
for (int j = y - radius; j <= y + radius; j++) {
if (i >= 0 && i < height && j >= 0 && j < width) {
meanR += copy.getRed(i, j);
meanG += copy.getGreen(i, j);
meanB += copy.getBlue(i, j);
total++;
}
}
}
meanR /= total;
meanG /= total;
meanB /= total;
for (int i = x - radius; i <= x + radius; i++) {
for (int j = y - radius; j <= y + radius; j++) {
if (i >= 0 && i < height && j >= 0 && j < width) {
varR += Math.pow(copy.getRed(i, j) - meanR, 2);
varG += Math.pow(copy.getGreen(i, j) - meanG, 2);
varB += Math.pow(copy.getBlue(i, j) - meanB, 2);
}
}
}
varR /= total - 1;
varG /= total - 1;
varB /= total - 1;
if (varR < 0) varR = 0;
if (varG < 0) varG = 0;
if (varB < 0) varB = 0;
if (varR > 255) varR = 255;
if (varG > 255) varG = 255;
if (varB > 255) varB = 255;
fastBitmap.setRGB(x, y, (int) varR, (int) varG, (int) varB);
}
}
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
int Xline, Yline;
int radiusI = (weight.length - 1) / 2;
int radiusJ = (weight[0].length - 1) / 2;
int maxArray = calcMax(weight);
int c;
FastBitmap copy = new FastBitmap(fastBitmap);
if (fastBitmap.isGrayscale()) {
int[] avgL = new int[maxArray];
int median;
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
c = 0;
for (int i = 0; i < weight.length; i++) {
Xline = x + (i - radiusI);
for (int j = 0; j < weight[0].length; j++) {
Yline = y + (j - radiusJ);
if ((Xline >= 0) && (Xline < height) && (Yline >= 0) && (Yline < width)) {
if (weight[i][j] > 0) {
for (int k = 0; k < weight[i][j]; k++) {
avgL[c] = copy.getGray(Xline, Yline);
c++;
}
}
}
}
}
Arrays.sort(avgL, 0, c);
// median
median = c / 2;
fastBitmap.setGray(x, y, avgL[median]);
}
}
} else if (fastBitmap.isRGB()) {
int[] avgR = new int[maxArray];
int[] avgG = new int[maxArray];
int[] avgB = new int[maxArray];
int median;
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
c = 0;
for (int i = 0; i < weight.length; i++) {
Xline = x + (i - radiusI);
for (int j = 0; j < weight[0].length; j++) {
Yline = y + (j - radiusJ);
if ((Xline >= 0) && (Xline < height) && (Yline >= 0) && (Yline < width)) {
if (weight[i][j] > 0) {
for (int k = 0; k < weight[i][j]; k++) {
avgR[c] = copy.getRed(Xline, Yline);
avgG[c] = copy.getGreen(Xline, Yline);
avgB[c] = copy.getBlue(Xline, Yline);
c++;
}
}
}
}
}
Arrays.sort(avgR, 0, c);
Arrays.sort(avgG, 0, c);
Arrays.sort(avgB, 0, c);
// median
median = c / 2;
fastBitmap.setRGB(x, y, avgR[median], avgG[median], avgB[median]);
}
}
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
if (fastBitmap.isGrayscale()) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
double oldIradius = (double) (height - 1) / 2;
double oldJradius = (double) (width - 1) / 2;
CalculateNewSize(fastBitmap);
FastBitmap destinationData =
new FastBitmap(newWidth, newHeight, FastBitmap.ColorSpace.Grayscale);
// get destination image size
double newIradius = (double) (newHeight - 1) / 2;
double newJradius = (double) (newWidth - 1) / 2;
// angle's sine and cosine
double angleRad = -angle * Math.PI / 180;
double angleCos = Math.cos(angleRad);
double angleSin = Math.sin(angleRad);
// destination pixel's coordinate relative to image center
double ci, cj;
// coordinates of source points and cooefficiens
double oi, oj, di, dj, k1, k2;
int oi1, oj1, oi2, oj2;
// width and height decreased by 1
int imax = height - 1;
int jmax = width - 1;
ci = -newIradius;
for (int i = 0; i < newHeight; i++) {
cj = -newJradius;
for (int j = 0; j < newWidth; j++) {
// coordinate of the nearest point
oi = angleCos * ci + angleSin * cj + oldIradius;
oj = -angleSin * ci + angleCos * cj + oldJradius;
oi1 = (int) oi;
oj1 = (int) oj;
// validate source pixel's coordinates
if ((oi1 < 0) || (oj1 < 0) || (oi1 >= height) || (oj1 >= width)) {
// fill destination image with filler
destinationData.setGray(i, j, fillGray);
} else {
di = oi - (double) oi1;
dj = oj - (double) oj1;
// initial pixel value
int g = 0;
for (int n = -1; n < 3; n++) {
// get Y cooefficient
k1 = Interpolation.BiCubicKernel(dj - (double) n);
oj2 = oj1 + n;
if (oj2 < 0) oj2 = 0;
if (oj2 > jmax) oj2 = jmax;
for (int m = -1; m < 3; m++) {
// get X cooefficient
k2 = k1 * Interpolation.BiCubicKernel((double) m - di);
oi2 = oi1 + m;
if (oi2 < 0) oi2 = 0;
if (oi2 > imax) oi2 = imax;
g += k2 * fastBitmap.getGray(oi2, oj2);
}
}
destinationData.setGray(i, j, Math.max(0, Math.min(255, g)));
}
cj++;
}
ci++;
}
fastBitmap.setImage(destinationData);
destinationData.recycle();
} else if (fastBitmap.isRGB()) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
double oldIradius = (double) (height - 1) / 2;
double oldJradius = (double) (width - 1) / 2;
CalculateNewSize(fastBitmap);
FastBitmap destinationData = new FastBitmap(newWidth, newHeight, FastBitmap.ColorSpace.RGB);
// get destination image size
double newIradius = (double) (newHeight - 1) / 2;
double newJradius = (double) (newWidth - 1) / 2;
// angle's sine and cosine
double angleRad = -angle * Math.PI / 180;
double angleCos = Math.cos(angleRad);
double angleSin = Math.sin(angleRad);
// destination pixel's coordinate relative to image center
double ci, cj;
// coordinates of source points and cooefficiens
double oi, oj, di, dj, k1, k2;
int oi1, oj1, oi2, oj2;
// width and height decreased by 1
int imax = height - 1;
int jmax = width - 1;
ci = -newIradius;
for (int i = 0; i < newHeight; i++) {
cj = -newJradius;
for (int j = 0; j < newWidth; j++) {
// coordinate of the nearest point
oi = angleCos * ci + angleSin * cj + oldIradius;
oj = -angleSin * ci + angleCos * cj + oldJradius;
oi1 = (int) oi;
oj1 = (int) oj;
// validate source pixel's coordinates
if ((oi < 0) || (oj < 0) || (oi >= height) || (oj >= width)) {
// fill destination image with filler
destinationData.setRGB(i, j, fillRed, fillGreen, fillBlue);
} else {
di = oi - (double) oi1;
dj = oj - (double) oj1;
// initial pixel value
int r = 0;
int g = 0;
int b = 0;
for (int n = -1; n < 3; n++) {
// get Y cooefficient
k1 = Interpolation.BiCubicKernel(dj - (double) n);
oj2 = oj1 + n;
if (oj2 < 0) oj2 = 0;
if (oj2 > jmax) oj2 = jmax;
for (int m = -1; m < 3; m++) {
// get X cooefficient
k2 = k1 * Interpolation.BiCubicKernel((double) m - di);
oi2 = oi1 + m;
if (oi2 < 0) oi2 = 0;
if (oi2 > imax) oi2 = imax;
r += k2 * fastBitmap.getRed(oi2, oj2);
g += k2 * fastBitmap.getGreen(oi2, oj2);
b += k2 * fastBitmap.getBlue(oi2, oj2);
}
}
r = Math.max(0, Math.min(255, r));
g = Math.max(0, Math.min(255, g));
b = Math.max(0, Math.min(255, b));
destinationData.setRGB(i, j, r, g, b);
}
cj++;
}
ci++;
}
fastBitmap.setImage(destinationData);
destinationData.recycle();
}
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
int Xline, Yline;
int lines = CalcLines(radius);
int maxArray = lines * lines;
int c;
FastBitmap copy = new FastBitmap(fastBitmap);
if (fastBitmap.isGrayscale()) {
int[] avgL = new int[maxArray];
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
c = 0;
for (int i = 0; i < lines; i++) {
Xline = x + (i - radius);
for (int j = 0; j < lines; j++) {
Yline = y + (j - radius);
if ((Xline >= 0) && (Xline < height) && (Yline >= 0) && (Yline < width)) {
avgL[c] = copy.getGray(Xline, Yline);
} else {
avgL[c] = copy.getGray(x, y);
}
c++;
}
}
Arrays.sort(avgL);
// alpha trimmed mean
double mean = 0;
for (int i = t; i < c - t; i++) {
mean += avgL[i];
}
fastBitmap.setGray(x, y, (int) (mean / (avgL.length - 2 * t)));
}
}
} else if (fastBitmap.isRGB()) {
int[] avgR = new int[maxArray];
int[] avgG = new int[maxArray];
int[] avgB = new int[maxArray];
for (int x = 0; x < height; x++) {
for (int y = 0; y < width; y++) {
c = 0;
for (int i = 0; i < lines; i++) {
Xline = x + (i - radius);
for (int j = 0; j < lines; j++) {
Yline = y + (j - radius);
if ((Xline >= 0) && (Xline < height) && (Yline >= 0) && (Yline < width)) {
avgR[c] = copy.getRed(Xline, Yline);
avgG[c] = copy.getGreen(Xline, Yline);
avgB[c] = copy.getBlue(Xline, Yline);
} else {
avgR[c] = copy.getRed(x, y);
avgG[c] = copy.getGreen(x, y);
avgB[c] = copy.getBlue(x, y);
}
c++;
}
}
Arrays.sort(avgR);
Arrays.sort(avgG);
Arrays.sort(avgB);
// alpha trimmed mean
double meanR = 0, meanG = 0, meanB = 0;
for (int i = t; i < c - t; i++) {
meanR += avgR[i];
meanG += avgG[i];
meanB += avgB[i];
}
meanR /= (avgR.length - 2 * t);
meanG /= (avgG.length - 2 * t);
meanB /= (avgB.length - 2 * t);
fastBitmap.setRGB(x, y, (int) meanR, (int) meanG, (int) meanB);
}
}
}
}
private void analyseAndMarkMaxima(
float[] edmPixels,
FastBitmap back,
long[] maxPoints,
float tolerance,
float maxSortingError) {
int width = back.getWidth();
int height = back.getHeight();
byte[] types = (byte[]) back.getGrayData();
int nMax = maxPoints.length;
int[] pList = new int[width * height]; // here we enter points starting from a maximum
for (int iMax = nMax - 1;
iMax >= 0;
iMax--) { // process all maxima now, starting from the highest
int offset0 =
(int) maxPoints[iMax]; // type cast gets 32 lower bits, where pixel index is encoded
// int offset0 = maxPoints[iMax].offset;
if ((types[offset0] & (byte) 4)
!= 0) // this maximum has been reached from another one, skip it
continue;
// we create a list of connected points and start the list at the current maximum
int x0 = offset0 % width;
int y0 = offset0 / width;
float v0 = trueEdmHeight(x0, y0, edmPixels, width, height);
boolean sortingError;
do { // repeat if we have encountered a sortingError
pList[0] = offset0;
types[offset0] |=
((byte) 16 | (byte) 2); // mark first point as equal height (to itself) and listed
int listLen = 1; // number of elements in the list
int listI = 0; // index of current element in the list
sortingError = false; // if sorting was inaccurate: a higher maximum was not handled so far
boolean maxPossible = true; // it may be a true maximum
double xEqual = x0; // for creating a single point: determine average over the
double yEqual = y0; // coordinates of contiguous equal-height points
int nEqual = 1; // counts xEqual/yEqual points that we use for averaging
do { // while neigbor list is not fully processed (to listLen)
int offset = pList[listI];
int x = offset % width;
int y = offset / width;
boolean isInner =
(y != 0 && y != height - 1)
&& (x != 0 && x != width - 1); // not necessary, but faster than isWithin
for (int d = 0; d < 8; d++) { // analyze all neighbors (in 8 directions) at the same level
int offset2 = offset + dirOffset[d];
if ((isInner || isWithin(x, y, d, width, height)) && (types[offset2] & (byte) 2) == 0) {
if (edmPixels[offset2] <= 0) continue; // ignore the background (non-particles)
if ((types[offset2] & (byte) 4) != 0) {
maxPossible =
false; // we have reached a point processed previously, thus it is no maximum
// now
break;
}
int x2 = x + DIR_X_OFFSET[d];
int y2 = y + DIR_Y_OFFSET[d];
float v2 = trueEdmHeight(x2, y2, edmPixels, width, height);
if (v2 > v0 + maxSortingError) {
maxPossible = false; // we have reached a higher point, thus it is no maximum
// if(x0<25&&y0<20)IJ.write("x0,y0="+x0+","+y0+":stop at higher neighbor from
// x,y="+x+","+y+", dir="+d+",value,value2,v2-v="+v0+","+v2+","+(v2-v0));
break;
} else if (v2 >= v0 - (float) tolerance) {
if (v2 > v0) { // maybe this point should have been treated earlier
sortingError = true;
offset0 = offset2;
v0 = v2;
x0 = x2;
y0 = y2;
}
pList[listLen] = offset2;
listLen++; // we have found a new point within the tolerance
types[offset2] |= (byte) 2;
if (v2
== v0) { // prepare finding center of equal points (in case single point needed)
types[offset2] |= (byte) 16;
xEqual += x2;
yEqual += y2;
nEqual++;
}
}
} // if isWithin & not (byte)2
} // for directions d
listI++;
} while (listI < listLen);
if (sortingError) { // if x0,y0 was not the true maximum but we have reached a higher one
for (listI = 0; listI < listLen; listI++)
types[pList[listI]] = 0; // reset all points encountered, then retry
} else {
int resetMask = ~(maxPossible ? (byte) 2 : ((byte) 2 | (byte) 16));
xEqual /= nEqual;
yEqual /= nEqual;
double minDist2 = 1e20;
int nearestI = 0;
for (listI = 0; listI < listLen; listI++) {
int offset = pList[listI];
int x = offset % width;
int y = offset / width;
types[offset] &= resetMask; // reset attributes no longer needed
types[offset] |= (byte) 4; // mark as processed
if (maxPossible) {
types[offset] |= (byte) 8;
if ((types[offset] & (byte) 16) != 0) {
double dist2 =
(xEqual - x) * (double) (xEqual - x) + (yEqual - y) * (double) (yEqual - y);
if (dist2 < minDist2) {
minDist2 = dist2; // this could be the best "single maximum" point
nearestI = listI;
}
}
}
} // for listI
if (maxPossible) {
int offset = pList[nearestI];
types[offset] |= (byte) 32;
}
} // if !sortingError
} while (sortingError); // redo if we have encountered a higher maximum: handle it now.
} // for all maxima iMax
}
/**
* Compute GLRLM.
*
* @param fastBitmap Image to be processed.
* @return GLRLM.
*/
public double[][] Compute(FastBitmap fastBitmap) {
int maxGray = 255;
if (autoGray) maxGray = ImageStatistics.Maximum(fastBitmap);
int height = fastBitmap.getHeight();
int width = fastBitmap.getWidth();
double[][] runMatrix = new double[maxGray + 1][width + 1];
switch (degree) {
case Degree_0:
for (int i = 0; i < height; i++) {
int runs = 1;
for (int j = 1; j < width; j++) {
int g1 = fastBitmap.getGray(i, j - 1);
int g2 = fastBitmap.getGray(i, j);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (j == width - 1)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (j == width - 1)) {
runMatrix[g2][1]++;
}
}
}
break;
case Degree_45:
// Compute I(0,0) and I(height,width)
runMatrix[0][1]++;
runMatrix[height - 1][width - 1]++;
// Compute height
for (int i = 1; i < height; i++) {
int runs = 1;
int steps = i;
for (int j = 0; j < steps; j++) {
int g1 = fastBitmap.getGray(i - j, j);
int g2 = fastBitmap.getGray(i - j - 1, j + 1);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (j == steps - 1)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (j == steps - 1)) {
runMatrix[g2][1]++;
}
}
}
// Compute width
for (int j = 1; j < width - 1; j++) {
int runs = 1;
int steps = height - j;
for (int i = 1; i < steps; i++) {
int g1 = fastBitmap.getGray(height - i, j + i - 1);
int g2 = fastBitmap.getGray(height - i - 1, j + i);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (i == steps - 1)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (i == steps - 1)) {
runMatrix[g2][1]++;
}
}
}
break;
case Degree_90:
for (int j = 0; j < width; j++) {
int runs = 1;
for (int i = 0; i < height - 1; i++) {
int g1 = fastBitmap.getGray(height - i - 1, j);
int g2 = fastBitmap.getGray(height - i - 2, j);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (i == height - 2)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (i == height - 2)) {
runMatrix[g2][1]++;
}
}
}
break;
case Degree_135:
// Compute I(0,width) and I(height,0)
runMatrix[0][width - 1]++;
runMatrix[height - 1][0]++;
// Compute height
for (int i = 1; i < width; i++) {
int runs = 1;
int steps = i;
int w = width - 1;
for (int j = 0; j < steps; j++) {
int g1 = fastBitmap.getGray(i - j, w);
int g2 = fastBitmap.getGray(i - j - 1, --w);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (j == steps - 1)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (j == steps - 1)) {
runMatrix[g2][1]++;
}
}
}
// Compute width
for (int j = 1; j < width - 1; j++) {
int runs = 1;
int steps = height - j;
int w = width - 1 - j;
for (int i = 1; i < steps; i++) {
int g1 = fastBitmap.getGray(height - i, w);
int g2 = fastBitmap.getGray(height - i - 1, --w);
if (g1 == g2) {
runs++;
} else {
runMatrix[g1][runs]++;
numPrimitives++;
runs = 1;
}
if ((g1 == g2) && (i == steps - 1)) {
runMatrix[g1][runs]++;
}
if ((g1 != g2) && (i == steps - 1)) {
runMatrix[g2][1]++;
}
}
}
break;
}
return runMatrix;
}
@Override
public void applyInPlace(FastBitmap fastBitmap) {
if (fastBitmap.isRGB()) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
LinkedList<IntPoint> examList = new LinkedList();
Color old = new Color(fastBitmap.getRGB(startPoint));
switch (algorithm) {
case FourWay:
if (!Color.isEqual(old, replace)) {
examList.addFirst(new IntPoint(startPoint));
while (examList.size() > 0) {
IntPoint p = examList.removeLast();
old = new Color(fastBitmap.getRGB(p));
if (!Color.isEqual(old, replace)) {
int x = p.x;
int y = p.y;
fastBitmap.setRGB(x, y, replace);
if (y - 1 > 0) {
examList.addFirst(new IntPoint(x, y - 1)); // check west neighbor
}
if (y + 1 < width) {
examList.addFirst(new IntPoint(x, y + 1)); // check east neighbor
}
if (x + 1 < height) {
examList.addFirst(new IntPoint(x + 1, y)); // check south neighbor
}
if (x - 1 > 0) {
examList.addFirst(new IntPoint(x - 1, y)); // check north neighbor
}
}
}
}
break;
case EightWay:
if (!Color.isEqual(old, replace)) {
examList.addFirst(new IntPoint(startPoint));
while (examList.size() > 0) {
IntPoint p = examList.removeFirst();
if (Color.isEqual(old, replace)) {
int x = p.x;
int y = p.y;
fastBitmap.setRGB(x, y, replace);
if ((x - 1 > 0) && (y - 1 > 0)) {
examList.addFirst(new IntPoint(x - 1, y - 1)); // check north-west neighbor
}
if (x - 1 > 0) {
examList.addFirst(new IntPoint(x - 1, y)); // check north neighbor
}
if ((x + 1 < height) && (y + 1 < width)) {
examList.addFirst(new IntPoint(x + 1, y + 1)); // check north-east neighbor
}
if (y - 1 > 0) {
examList.addFirst(new IntPoint(x, y - 1)); // check west neighbor
}
if (y + 1 < width) {
examList.addFirst(new IntPoint(x, y + 1)); // check east neighbor
}
if ((x + 1 < height) && (y - 1 > 0)) {
examList.addFirst(new IntPoint(x + 1, y - 1)); // check south-west neighbor
}
if (x + 1 < height) {
examList.addFirst(new IntPoint(x + 1, y)); // check south neighbor
}
if ((x + 1 < height) && (y + 1 < width)) {
examList.addFirst(new IntPoint(x + 1, y + 1)); // check south-east neighbor
}
}
}
}
break;
}
} else if (fastBitmap.isGrayscale()) {
int width = fastBitmap.getWidth();
int height = fastBitmap.getHeight();
LinkedList<IntPoint> examList = new LinkedList();
int iGray = fastBitmap.getGray(startPoint);
int _gray = gray;
int _Gray = _gray;
switch (algorithm) {
case FourWay:
if (iGray != _Gray) {
examList.addFirst(new IntPoint(startPoint));
while (examList.size() > 0) {
IntPoint p = examList.removeLast();
_gray = fastBitmap.getGray(p.x, p.y);
_Gray = _gray;
if (_Gray == iGray) {
int x = p.x;
int y = p.y;
fastBitmap.setGray(x, y, gray);
if (y - 1 > 0) {
examList.addFirst(new IntPoint(x, y - 1)); // check west neighbor
}
if (y + 1 < width) {
examList.addFirst(new IntPoint(x, y + 1)); // check east neighbor
}
if (x + 1 < height) {
examList.addFirst(new IntPoint(x + 1, y)); // check south neighbor
}
if (x - 1 > 0) {
examList.addFirst(new IntPoint(x - 1, y)); // check north neighbor
}
}
}
}
break;
case EightWay:
if (iGray != _Gray) {
examList.addFirst(new IntPoint(startPoint));
while (examList.size() > 0) {
IntPoint p = examList.removeFirst();
_gray = fastBitmap.getGray(p.x, p.y);
_Gray = _gray;
if (_Gray == iGray) {
int x = p.x;
int y = p.y;
fastBitmap.setGray(x, y, gray);
if ((x - 1 > 0) && (y - 1 > 0)) {
examList.addFirst(new IntPoint(x - 1, y - 1)); // check north-west neighbor
}
if (x - 1 > 0) {
examList.addFirst(new IntPoint(x - 1, y)); // check north neighbor
}
if ((x + 1 < height) && (y + 1 < width)) {
examList.addFirst(new IntPoint(x + 1, y + 1)); // check north-east neighbor
}
if (y - 1 > 0) {
examList.addFirst(new IntPoint(x, y - 1)); // check west neighbor
}
if (y + 1 < width) {
examList.addFirst(new IntPoint(x, y + 1)); // check east neighbor
}
if ((x + 1 < height) && (y - 1 > 0)) {
examList.addFirst(new IntPoint(x + 1, y - 1)); // check south-west neighbor
}
if (x + 1 < height) {
examList.addFirst(new IntPoint(x + 1, y)); // check south neighbor
}
if ((x + 1 < height) && (y + 1 < width)) {
examList.addFirst(new IntPoint(x + 1, y + 1)); // check south-east neighbor
}
}
}
}
break;
}
} else {
throw new IllegalArgumentException("Flood fill only works in RGB and grayscale images.");
}
}
private void cleanupMaxima(FastBitmap outIp, FastBitmap typeP, long[] maxPoints) {
int width = outIp.getWidth();
int height = outIp.getHeight();
byte[] pixels = outIp.getGrayData();
byte[] types = typeP.getGrayData();
int nMax = maxPoints.length;
int[] pList = new int[width * height];
for (int iMax = nMax - 1; iMax >= 0; iMax--) {
int offset0 =
(int) maxPoints[iMax]; // type cast gets lower 32 bits where pixel offset is encoded
if ((types[offset0] & ((byte) 8 | (byte) 64)) != 0) continue;
int level = pixels[offset0] & 255;
int loLevel = level + 1;
pList[0] = offset0; // we start the list at the current maximum
types[offset0] |= (byte) 2; // mark first point as listed
int listLen = 1; // number of elements in the list
int lastLen = 1;
int listI = 0; // index of current element in the list
boolean saddleFound = false;
while (!saddleFound && loLevel > 0) {
loLevel--;
lastLen = listLen; // remember end of list for previous level
listI = 0; // in each level, start analyzing the neighbors of all pixels
do { // for all pixels listed so far
int offset = pList[listI];
int x = offset % width;
int y = offset / width;
boolean isInner =
(y != 0 && y != height - 1)
&& (x != 0 && x != width - 1); // not necessary, but faster than isWithin
for (int d = 0; d < 8; d++) { // analyze all neighbors (in 8 directions) at the same level
int offset2 = offset + dirOffset[d];
if ((isInner || isWithin(x, y, d, width, height)) && (types[offset2] & (byte) 2) == 0) {
if ((types[offset2] & (byte) 8) != 0
|| (((types[offset2] & (byte) 64) != 0) && (pixels[offset2] & 255) >= loLevel)) {
saddleFound = true; // we have reached a point touching a "true" maximum...
// if (xList[0]==122) IJ.write("saddle found at level="+loLevel+";
// x,y="+xList[listI]+","+yList[listI]+", dir="+d);
break; // ...or a level not lower, but touching a "true" maximum
} else if ((pixels[offset2] & 255) >= loLevel && (types[offset2] & (byte) 64) == 0) {
pList[listLen] = offset2;
// xList[listLen] = x+DIR_X_OFFSET[d];
// yList[listLen] = x+DIR_Y_OFFSET[d];
listLen++; // we have found a new point to be processed
types[offset2] |= (byte) 2;
}
} // if isWithin & not (byte)2
} // for directions d
if (saddleFound) break; // no reason to search any further
listI++;
} while (listI < listLen);
} // while !levelFound && loLevel>=0
for (listI = 0;
listI < listLen;
listI++) // reset attribute since we may come to this place again
types[pList[listI]] &= ~(byte) 2;
for (listI = 0;
listI < lastLen;
listI++) { // for all points higher than the level of the saddle point
int offset = pList[listI];
pixels[offset] = (byte) loLevel; // set pixel value to the level of the saddle point
types[offset] |=
(byte) 64; // mark as processed: there can't be a local maximum in this area
}
} // for all maxima iMax
}
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;
}