public void run(ImageProcessor ip) {
IndexColorModel icm = (IndexColorModel) ip.getColorModel();
// IJ.write("Color Model=" + ip.getColorModel() + " " + ip.isColorLut());
int pixBits = icm.getPixelSize();
int mapSize = icm.getMapSize();
// retrieve the current lookup tables (maps) for R,G,B
byte[] Rmap = new byte[mapSize];
icm.getReds(Rmap);
byte[] Gmap = new byte[mapSize];
icm.getGreens(Gmap);
byte[] Bmap = new byte[mapSize];
icm.getBlues(Bmap);
// modify the lookup tables
for (int idx = 0; idx < mapSize; idx++) {
int r = 0xff & Rmap[idx]; // mask to treat as unsigned byte
int g = 0xff & Gmap[idx];
int b = 0xff & Bmap[idx];
Rmap[idx] = (byte) Math.min(r + 10, 255);
Gmap[idx] = (byte) Math.min(g + 10, 255);
Bmap[idx] = (byte) Math.min(b + 10, 255);
}
// create a new color model and apply to the image
IndexColorModel icm2 = new IndexColorModel(pixBits, mapSize, Rmap, Gmap, Bmap);
ip.setColorModel(icm2);
WindowManager.getCurrentImage().updateAndDraw();
}
private static Image5D createImage5D(CMMCore core, String wndTitle) throws Exception {
core_ = core;
ImageProcessor ip;
int type = 0;
int width_ = (int) core_.getImageWidth();
int height_ = (int) core_.getImageHeight();
long byteDepth = core_.getBytesPerPixel();
long channels = core_.getNumberOfChannels();
if (byteDepth == 1 && channels == 1) {
type = ImagePlus.GRAY8;
ip = new ByteProcessor(width_, height_);
if (contrastSettings8_.getRange() == 0.0) ip.setMinAndMax(0, 255);
else ip.setMinAndMax(contrastSettings8_.min, contrastSettings8_.max);
} else if (byteDepth == 2 && channels == 1) {
type = ImagePlus.GRAY16;
ip = new ShortProcessor(width_, height_);
if (contrastSettings16_.getRange() == 0.0) ip.setMinAndMax(0, 65535);
else ip.setMinAndMax(contrastSettings16_.min, contrastSettings16_.max);
} else if (byteDepth == 0) {
throw (new Exception(logError("Imaging device not initialized")));
} else if (byteDepth == 1 && channels == 4) {
// assuming RGB32 format
ip = new ColorProcessor(width_, height_);
if (contrastSettings8_.getRange() == 0.0) ip.setMinAndMax(0, 255);
else ip.setMinAndMax(contrastSettings8_.min, contrastSettings8_.max);
} else {
String message =
"Unsupported pixel depth: "
+ core_.getBytesPerPixel()
+ " byte(s) and "
+ channels
+ " channel(s).";
throw (new Exception(logError(message)));
}
ip.setColor(Color.black);
if (currentColorModel_ != null) ip.setColorModel(currentColorModel_);
ip.fill();
Image5D img5d = new Image5D(wndTitle, type, width_, height_, 1, 1, 1, false);
@SuppressWarnings("unused")
Image5DWindow i5dw = new Image5DWindow(img5d);
return img5d;
}
/**
* 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;
}
public synchronized void updateImage() {
int imageSize = width * height;
int nChannels = getNChannels();
int redValue, greenValue, blueValue;
int ch = getChannel();
// IJ.log("updateImage: "+ch+"/"+nChannels+" "+currentSlice+" "+currentFrame);
if (ch > nChannels) ch = nChannels;
boolean newChannel = false;
if (ch - 1 != currentChannel) {
previousChannel = currentChannel;
currentChannel = ch - 1;
newChannel = true;
}
ImageProcessor ip = getProcessor();
if (mode != COMPOSITE) {
if (newChannel) {
setupLuts(nChannels);
LUT cm = lut[currentChannel];
if (mode == COLOR) ip.setColorModel(cm);
if (!(cm.min == 0.0 && cm.max == 0.0)) ip.setMinAndMax(cm.min, cm.max);
if (!IJ.isMacro()) ContrastAdjuster.update();
for (int i = 0; i < MAX_CHANNELS; i++) active[i] = i == currentChannel ? true : false;
Channels.updateChannels();
}
if (ip != null) img = ip.createImage();
return;
}
if (nChannels == 1) {
cip = null;
rgbPixels = null;
awtImage = null;
if (ip != null) img = ip.createImage();
return;
}
if (cip == null
|| cip[0].getWidth() != width
|| cip[0].getHeight() != height
|| getBitDepth() != bitDepth) {
setup(nChannels, getImageStack());
rgbPixels = null;
rgbSampleModel = null;
if (currentChannel >= nChannels) {
setSlice(1);
currentChannel = 0;
newChannel = true;
}
bitDepth = getBitDepth();
}
if (newChannel) {
getProcessor().setMinAndMax(cip[currentChannel].getMin(), cip[currentChannel].getMax());
if (!IJ.isMacro()) ContrastAdjuster.update();
}
// IJ.log(nChannels+" "+ch+" "+currentChannel+" "+newChannel);
if (getSlice() != currentSlice || getFrame() != currentFrame) {
currentSlice = getSlice();
currentFrame = getFrame();
int position = getStackIndex(1, currentSlice, currentFrame);
if (cip == null) return;
for (int i = 0; i < nChannels; ++i)
cip[i].setPixels(getImageStack().getProcessor(position + i).getPixels());
}
if (rgbPixels == null) {
rgbPixels = new int[imageSize];
newPixels = true;
imageSource = null;
rgbRaster = null;
rgbImage = null;
}
cip[currentChannel].setMinAndMax(ip.getMin(), ip.getMax());
if (singleChannel && nChannels <= 3) {
switch (currentChannel) {
case 0:
cip[0].updateComposite(rgbPixels, 1);
break;
case 1:
cip[1].updateComposite(rgbPixels, 2);
break;
case 2:
cip[2].updateComposite(rgbPixels, 3);
break;
}
} else {
if (cip == null) return;
if (syncChannels) {
ImageProcessor ip2 = getProcessor();
double min = ip2.getMin(), max = ip2.getMax();
for (int i = 0; i < nChannels; i++) {
cip[i].setMinAndMax(min, max);
lut[i].min = min;
lut[i].max = max;
}
syncChannels = false;
}
if (active[0]) cip[0].updateComposite(rgbPixels, 4);
else {
for (int i = 1; i < imageSize; i++) rgbPixels[i] = 0;
}
if (cip == null || nChannels > cip.length) return;
for (int i = 1; i < nChannels; i++) if (active[i]) cip[i].updateComposite(rgbPixels, 5);
}
if (IJ.isJava16()) createBufferedImage();
else createImage();
if (img == null && awtImage != null) img = awtImage;
singleChannel = false;
}
