/** Generate output image whose type is same as input image. */
private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
int width = imp.getWidth();
int height = imp.getHeight();
float[] pixels = (float[]) fp.getPixels();
ImageProcessor oip = null;
// Create output image consistent w/ type of input image.
int size = pixels.length;
switch (ptype) {
case BYTE_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
byte[] pixels8 = (byte[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
break;
case SHORT_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
short[] pixels16 = (short[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
break;
case FLOAT_TYPE:
oip = new FloatProcessor(width, height, pixels, null);
break;
}
// Adjust for display.
// Calling this on non-ByteProcessors ensures image
// processor is set up to correctly display image.
oip.resetMinAndMax();
// Create new image plus object. Don't use
// ImagePlus.createImagePlus here because there may be
// attributes of input image that are not appropriate for
// projection.
return new ImagePlus(makeTitle(), oip);
}
/** Constructs a Wand object from an ImageProcessor. */
public Wand(ImageProcessor ip) {
this.ip = ip;
if (ip instanceof ByteProcessor) bpixels = (byte[]) ip.getPixels();
else if (ip instanceof ColorProcessor) cpixels = (int[]) ip.getPixels();
else if (ip instanceof ShortProcessor) spixels = (short[]) ip.getPixels();
else if (ip instanceof FloatProcessor) fpixels = (float[]) ip.getPixels();
width = ip.getWidth();
height = ip.getHeight();
}
void reset(ImagePlus imp, ImageProcessor ip) {
// Assign the pixels of ip to the data in the restore array, while
// taking care to not give the address the restore array to the
// image processor.
int[] pixels = (int[]) ip.getPixels();
for (int i = 0; i < numPixels; i++) pixels[i] = restore[i];
}
/*------------------------------------------------------------------*/
void putRow(ImageProcessor ip, int y, double[] row) {
int rowLength = ip.getWidth();
if (rowLength != row.length) {
throw new IndexOutOfBoundsException("Incoherent array sizes");
}
y *= rowLength;
if (ip.getPixels() instanceof float[]) {
float[] floatPixels = (float[]) ip.getPixels();
for (int i = 0; (i < rowLength); i++) {
floatPixels[y++] = (float) row[i];
}
} else {
throw new IllegalArgumentException("Float image required");
}
} /* end putRow */
/*------------------------------------------------------------------*/
void putColumn(ImageProcessor ip, int x, double[] column) {
int width = ip.getWidth();
if (ip.getHeight() != column.length) {
throw new IndexOutOfBoundsException("Incoherent array sizes");
}
if (ip.getPixels() instanceof float[]) {
float[] floatPixels = (float[]) ip.getPixels();
for (int i = 0; (i < column.length); i++) {
floatPixels[x] = (float) column[i];
x += width;
}
} else {
throw new IllegalArgumentException("Float image required");
}
} /* end putColumn */
/*------------------------------------------------------------------*/
public void getHorizontalGradient(ImageProcessor ip, double tolerance) {
if (!(ip.getPixels() instanceof float[])) {
throw new IllegalArgumentException("Float image required");
}
float[] floatPixels = (float[]) ip.getPixels();
int width = ip.getWidth();
int height = ip.getHeight();
double line[] = new double[width];
for (int y = 0; (y < height); y++) {
getRow(ip, y, line);
getSplineInterpolationCoefficients(line, tolerance);
getGradient(line);
putRow(ip, y, line);
stepProgressBar();
}
} /* end getHorizontalGradient */
/*------------------------------------------------------------------*/
public void getVerticalHessian(ImageProcessor ip, double tolerance) {
if (!(ip.getPixels() instanceof float[])) {
throw new IllegalArgumentException("Float image required");
}
float[] floatPixels = (float[]) ip.getPixels();
int width = ip.getWidth();
int height = ip.getHeight();
double line[] = new double[height];
for (int x = 0; (x < width); x++) {
getColumn(ip, x, line);
getSplineInterpolationCoefficients(line, tolerance);
getHessian(line);
putColumn(ip, x, line);
stepProgressBar();
}
} /* end getVerticalHessian */
/** Adds the image in 'ip' to the end of the stack. */
public void addSlice(String sliceLabel, ImageProcessor ip) {
if (ip.getWidth() != width || ip.getHeight() != height)
throw new IllegalArgumentException("Dimensions do not match");
if (nSlices == 0) {
cm = ip.getColorModel();
min = ip.getMin();
max = ip.getMax();
}
addSlice(sliceLabel, ip.getPixels());
}
// Binary fill by Gabriel Landini, G.Landini at bham.ac.uk
// 21/May/2008
void fill(ImageProcessor ip, int foreground, int background) {
int width = ip.getWidth();
int height = ip.getHeight();
FloodFiller ff = new FloodFiller(ip);
ip.setColor(127);
for (int y = 0; y < height; y++) {
if (ip.getPixel(0, y) == background) ff.fill(0, y);
if (ip.getPixel(width - 1, y) == background) ff.fill(width - 1, y);
}
for (int x = 0; x < width; x++) {
if (ip.getPixel(x, 0) == background) ff.fill(x, 0);
if (ip.getPixel(x, height - 1) == background) ff.fill(x, height - 1);
}
byte[] pixels = (byte[]) ip.getPixels();
int n = width * height;
for (int i = 0; i < n; i++) {
if (pixels[i] == 127) pixels[i] = (byte) background;
else pixels[i] = (byte) foreground;
}
}
public ImageProcessor getMask() {
if (cachedMask != null && cachedMask.getPixels() != null) return cachedMask;
ImageProcessor mask = new ByteProcessor(width, height);
double a = width / 2.0, b = height / 2.0;
double a2 = a * a, b2 = b * b;
a -= 0.5;
b -= 0.5;
double xx, yy;
int offset;
byte[] pixels = (byte[]) mask.getPixels();
for (int y = 0; y < height; y++) {
offset = y * width;
for (int x = 0; x < width; x++) {
xx = x - a;
yy = y - b;
if ((xx * xx / a2 + yy * yy / b2) <= 1.0) pixels[offset + x] = -1;
}
}
cachedMask = mask;
return mask;
}
/**
* Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
* there is an error.
*/
public boolean analyze(ImagePlus imp, ImageProcessor ip) {
if (this.imp == null) this.imp = imp;
showResults = (options & SHOW_RESULTS) != 0;
excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
resetCounter = (options & CLEAR_WORKSHEET) != 0;
showProgress = (options & SHOW_PROGRESS) != 0;
floodFill = (options & INCLUDE_HOLES) == 0;
recordStarts = (options & RECORD_STARTS) != 0;
addToManager = (options & ADD_TO_MANAGER) != 0;
displaySummary = (options & DISPLAY_SUMMARY) != 0;
inSituShow = (options & IN_SITU_SHOW) != 0;
outputImage = null;
ip.snapshot();
ip.setProgressBar(null);
if (Analyzer.isRedirectImage()) {
redirectImp = Analyzer.getRedirectImage(imp);
if (redirectImp == null) return false;
int depth = redirectImp.getStackSize();
if (depth > 1 && depth == imp.getStackSize()) {
ImageStack redirectStack = redirectImp.getStack();
redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
} else redirectIP = redirectImp.getProcessor();
} else if (imp.getType() == ImagePlus.COLOR_RGB) {
ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
if (original != null
&& original.getWidth() == imp.getWidth()
&& original.getHeight() == imp.getHeight()) {
redirectImp = original;
redirectIP = original.getProcessor();
}
}
if (!setThresholdLevels(imp, ip)) return false;
width = ip.getWidth();
height = ip.getHeight();
if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
blackBackground = Prefs.blackBackground && inSituShow;
if (slice == 1) outlines = new ImageStack(width, height);
if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
else drawIP = new ByteProcessor(width, height);
drawIP.setLineWidth(lineWidth);
if (showChoice == ROI_MASKS) {
} // Place holder for now...
else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
else if (showChoice == OUTLINES) {
if (!inSituShow) {
if (customLut == null) makeCustomLut();
drawIP.setColorModel(customLut);
}
drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
}
outlines.addSlice(null, drawIP);
if (showChoice == ROI_MASKS || blackBackground) {
drawIP.setColor(Color.black);
drawIP.fill();
drawIP.setColor(Color.white);
} else {
drawIP.setColor(Color.white);
drawIP.fill();
drawIP.setColor(Color.black);
}
}
calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();
if (rt == null) {
rt = Analyzer.getResultsTable();
analyzer = new Analyzer(imp);
} else analyzer = new Analyzer(imp, measurements, rt);
if (resetCounter && slice == 1) {
if (!Analyzer.resetCounter()) return false;
}
beginningCount = Analyzer.getCounter();
byte[] pixels = null;
if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
if (r == null) {
r = ip.getRoi();
mask = ip.getMask();
if (displaySummary) {
if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
}
}
minX = r.x;
maxX = r.x + r.width;
minY = r.y;
maxY = r.y + r.height;
if (r.width < width || r.height < height || mask != null) {
if (!eraseOutsideRoi(ip, r, mask)) return false;
}
int offset;
double value;
int inc = Math.max(r.height / 25, 1);
int mi = 0;
ImageWindow win = imp.getWindow();
if (win != null) win.running = true;
if (measurements == 0) measurements = Analyzer.getMeasurements();
if (showChoice == ELLIPSES) measurements |= ELLIPSE;
measurements &= ~LIMIT; // ignore "Limit to Threshold"
roiNeedsImage =
(measurements & PERIMETER) != 0
|| (measurements & SHAPE_DESCRIPTORS) != 0
|| (measurements & FERET) != 0;
particleCount = 0;
wand = new Wand(ip);
pf = new PolygonFiller();
if (floodFill) {
ImageProcessor ipf = ip.duplicate();
ipf.setValue(fillColor);
ff = new FloodFiller(ipf);
}
roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;
for (int y = r.y; y < (r.y + r.height); y++) {
offset = y * width;
for (int x = r.x; x < (r.x + r.width); x++) {
if (pixels != null) value = pixels[offset + x] & 255;
else if (imageType == SHORT) value = ip.getPixel(x, y);
else value = ip.getPixelValue(x, y);
if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
}
if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
if (win != null) canceled = !win.running;
if (canceled) {
Macro.abort();
break;
}
}
if (showProgress) IJ.showProgress(1.0);
if (showResults) rt.updateResults();
imp.killRoi();
ip.resetRoi();
ip.reset();
if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
totalCount += particleCount;
if (!canceled) showResults();
return true;
}
ImageProcessor setup(ImagePlus imp) {
ImageProcessor ip;
int type = imp.getType();
if (type != ImagePlus.COLOR_RGB) return null;
ip = imp.getProcessor();
int id = imp.getID();
int slice = imp.getCurrentSlice();
if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
flag = false; // if true, flags a change from HSB to RGB or viceversa
numSlices = imp.getStackSize();
stack = imp.getStack();
width = stack.getWidth();
height = stack.getHeight();
numPixels = width * height;
hSource = new byte[numPixels];
sSource = new byte[numPixels];
bSource = new byte[numPixels];
// restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
// long way:
int[] temp = (int[]) ip.getPixels();
restore = new int[numPixels];
for (int i = 0; i < numPixels; i++) restore[i] = temp[i];
fillMask = new int[numPixels];
// Get hsb or rgb from image.
ColorProcessor cp = (ColorProcessor) ip;
IJ.showStatus("Gathering data");
if (isRGB) cp.getRGB(hSource, sSource, bSource);
else cp.getHSB(hSource, sSource, bSource);
IJ.showStatus("done");
// Create a spectrum ColorModel for the Hue histogram plot.
Color c;
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
for (int i = 0; i < 256; i++) {
c = Color.getHSBColor(i / 255f, 1f, 1f);
reds[i] = (byte) c.getRed();
greens[i] = (byte) c.getGreen();
blues[i] = (byte) c.getBlue();
}
ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);
// Make an image with just the hue from the RGB image and the spectrum LUT.
// This is just for a hue histogram for the plot. Do not show it.
// ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
ImagePlus impHue = new ImagePlus("Hue", bpHue);
// impHue.show();
ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
ImagePlus impSat = new ImagePlus("Sat", bpSat);
// impSat.show();
ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
ImagePlus impBri = new ImagePlus("Bri", bpBri);
// impBri.show();
plot.setHistogram(impHue, 0);
splot.setHistogram(impSat, 1);
bplot.setHistogram(impBri, 2);
updateLabels();
updatePlot();
updateScrollBars();
imp.updateAndDraw();
}
previousImageID = id;
previousSlice = slice;
return ip;
}
/*------------------------------------------------------------------*/
void doIt(ImageProcessor ip) {
int width = ip.getWidth();
int height = ip.getHeight();
double hLine[] = new double[width];
double vLine[] = new double[height];
if (!(ip.getPixels() instanceof float[])) {
throw new IllegalArgumentException("Float image required");
}
switch (operation) {
case GRADIENT_MAGNITUDE:
{
ImageProcessor h = ip.duplicate();
ImageProcessor v = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsH = (float[]) h.getPixels();
float[] floatPixelsV = (float[]) v.getPixels();
getHorizontalGradient(h, FLT_EPSILON);
getVerticalGradient(v, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
floatPixels[k] =
(float)
Math.sqrt(
floatPixelsH[k] * floatPixelsH[k] + floatPixelsV[k] * floatPixelsV[k]);
}
stepProgressBar();
}
}
break;
case GRADIENT_DIRECTION:
{
ImageProcessor h = ip.duplicate();
ImageProcessor v = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsH = (float[]) h.getPixels();
float[] floatPixelsV = (float[]) v.getPixels();
getHorizontalGradient(h, FLT_EPSILON);
getVerticalGradient(v, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
floatPixels[k] = (float) Math.atan2(floatPixelsH[k], floatPixelsV[k]);
}
stepProgressBar();
}
}
break;
case LAPLACIAN:
{
ImageProcessor hh = ip.duplicate();
ImageProcessor vv = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsHH = (float[]) hh.getPixels();
float[] floatPixelsVV = (float[]) vv.getPixels();
getHorizontalHessian(hh, FLT_EPSILON);
getVerticalHessian(vv, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
floatPixels[k] = (float) (floatPixelsHH[k] + floatPixelsVV[k]);
}
stepProgressBar();
}
}
break;
case LARGEST_HESSIAN:
{
ImageProcessor hh = ip.duplicate();
ImageProcessor vv = ip.duplicate();
ImageProcessor hv = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsHH = (float[]) hh.getPixels();
float[] floatPixelsVV = (float[]) vv.getPixels();
float[] floatPixelsHV = (float[]) hv.getPixels();
getHorizontalHessian(hh, FLT_EPSILON);
getVerticalHessian(vv, FLT_EPSILON);
getCrossHessian(hv, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
floatPixels[k] =
(float)
(0.5
* (floatPixelsHH[k]
+ floatPixelsVV[k]
+ Math.sqrt(
4.0 * floatPixelsHV[k] * floatPixelsHV[k]
+ (floatPixelsHH[k] - floatPixelsVV[k])
* (floatPixelsHH[k] - floatPixelsVV[k]))));
}
stepProgressBar();
}
}
break;
case SMALLEST_HESSIAN:
{
ImageProcessor hh = ip.duplicate();
ImageProcessor vv = ip.duplicate();
ImageProcessor hv = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsHH = (float[]) hh.getPixels();
float[] floatPixelsVV = (float[]) vv.getPixels();
float[] floatPixelsHV = (float[]) hv.getPixels();
getHorizontalHessian(hh, FLT_EPSILON);
getVerticalHessian(vv, FLT_EPSILON);
getCrossHessian(hv, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
floatPixels[k] =
(float)
(0.5
* (floatPixelsHH[k]
+ floatPixelsVV[k]
- Math.sqrt(
4.0 * floatPixelsHV[k] * floatPixelsHV[k]
+ (floatPixelsHH[k] - floatPixelsVV[k])
* (floatPixelsHH[k] - floatPixelsVV[k]))));
}
stepProgressBar();
}
}
break;
case HESSIAN_ORIENTATION:
{
ImageProcessor hh = ip.duplicate();
ImageProcessor vv = ip.duplicate();
ImageProcessor hv = ip.duplicate();
float[] floatPixels = (float[]) ip.getPixels();
float[] floatPixelsHH = (float[]) hh.getPixels();
float[] floatPixelsVV = (float[]) vv.getPixels();
float[] floatPixelsHV = (float[]) hv.getPixels();
getHorizontalHessian(hh, FLT_EPSILON);
getVerticalHessian(vv, FLT_EPSILON);
getCrossHessian(hv, FLT_EPSILON);
for (int y = 0, k = 0; (y < height); y++) {
for (int x = 0; (x < width); x++, k++) {
if (floatPixelsHV[k] < 0.0) {
floatPixels[k] =
(float)
(-0.5
* Math.acos(
(floatPixelsHH[k] - floatPixelsVV[k])
/ Math.sqrt(
4.0 * floatPixelsHV[k] * floatPixelsHV[k]
+ (floatPixelsHH[k] - floatPixelsVV[k])
* (floatPixelsHH[k] - floatPixelsVV[k]))));
} else {
floatPixels[k] =
(float)
(0.5
* Math.acos(
(floatPixelsHH[k] - floatPixelsVV[k])
/ Math.sqrt(
4.0 * floatPixelsHV[k] * floatPixelsHV[k]
+ (floatPixelsHH[k] - floatPixelsVV[k])
* (floatPixelsHH[k] - floatPixelsVV[k]))));
}
}
stepProgressBar();
}
}
break;
default:
throw new IllegalArgumentException("Invalid operation");
}
ip.resetMinAndMax();
imp.updateAndDraw();
} /* end doIt */