void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() == 1) {
IJ.error("Line to Area", "Straight line width must be > 1");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE) ip2.fillPolygon(roi.getPolygon());
else {
roi.drawPixels(ip2);
// BufferedImage bi = new BufferedImage(imp.getWidth(), imp.getHeight(),
// BufferedImage.TYPE_BYTE_GRAY);
// Graphics g = bi.getGraphics();
// Roi roi2 = (Roi)roi.clone();
// roi2.setStrokeColor(Color.white);
// roi2.drawOverlay(g);
// ip2 = new ByteProcessor(bi);
}
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
Undo.setup(Undo.ROI, imp);
Roi roi2 = null;
if (roi.getType() == Roi.LINE) {
double width = roi.getStrokeWidth();
if (width <= 1.0) roi.setStrokeWidth(1.0000001);
FloatPolygon p = roi.getFloatPolygon();
roi.setStrokeWidth(width);
roi2 = new PolygonRoi(p, Roi.POLYGON);
roi2.setDrawOffset(roi.getDrawOffset());
} else {
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
roi2 = tts.convert(ip2);
}
transferProperties(roi, roi2);
roi2.setStrokeWidth(0);
Color c = roi2.getStrokeColor();
if (c != null) // remove any transparency
roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue()));
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
public ImageProcessor expandImage(ImageProcessor ipOld, int wNew, int hNew, int xOff, int yOff) {
ImageProcessor ipNew = ipOld.createProcessor(wNew, hNew);
if (zeroFill) ipNew.setValue(0.0);
else ipNew.setColor(Toolbar.getBackgroundColor());
ipNew.fill();
ipNew.insert(ipOld, xOff, yOff);
return ipNew;
}
ImageProcessor expand(ImageProcessor ip, boolean hasEdgePixels) {
if (hasEdgePixels) {
ImageProcessor ip2 = ip.createProcessor(ip.getWidth() + 2, ip.getHeight() + 2);
if (foreground == 0) {
ip2.setColor(255);
ip2.fill();
}
ip2.insert(ip, 1, 1);
// new ImagePlus("ip2", ip2).show();
return ip2;
} else return ip;
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() > 1) ip2.fillPolygon(roi.getPolygon());
else roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
public ImageStack expandStack(ImageStack stackOld, int wNew, int hNew, int xOff, int yOff) {
int nFrames = stackOld.getSize();
ImageProcessor ipOld = stackOld.getProcessor(1);
java.awt.Color colorBack = Toolbar.getBackgroundColor();
ImageStack stackNew = new ImageStack(wNew, hNew, stackOld.getColorModel());
ImageProcessor ipNew;
for (int i = 1; i <= nFrames; i++) {
IJ.showProgress((double) i / nFrames);
ipNew = ipOld.createProcessor(wNew, hNew);
if (zeroFill) ipNew.setValue(0.0);
else ipNew.setColor(colorBack);
ipNew.fill();
ipNew.insert(stackOld.getProcessor(i), xOff, yOff);
stackNew.addSlice(stackOld.getSliceLabel(i), ipNew);
}
return stackNew;
}
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;
}
// 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;
}
}
/**
* 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;
}
void apply(ImagePlus imp, ImageProcessor ip) {
// this.setCursor(wait);
// IJ.showStatus("Bandpassing slice "+previousSlice);
java.awt.Color col;
if (invert.getState()) col = Toolbar.getForegroundColor();
else col = Toolbar.getBackgroundColor();
ip.setColor(col);
int fill = ip.BLACK;
int keep = 0;
if (bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // PPP All pass
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState()
&& !bandPassS.getState()
&& !bandPassB.getState()) { // SSS All stop
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // PPS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // SSP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && !bandPassS.getState() && !bandPassB.getState()) { // PSS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // SPP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (!bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // SPS
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue >= minHue) && (hue <= maxHue))
|| ((sat < minSat) || (sat > maxSat))
|| ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
} else if (bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // PSP
for (int j = 0; j < numPixels; j++) {
int hue = hSource[j] & 0xff;
int sat = sSource[j] & 0xff;
int bri = bSource[j] & 0xff;
if (((hue < minHue) || (hue > maxHue))
|| ((sat >= minSat) && (sat <= maxSat))
|| ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
else fillMask[j] = keep;
}
}
ip.fill(fillMask);
if (threshold.getState()) {
ip.invert();
for (int j = 0; j < numPixels; j++) {
if (fillMask[j] == fill) fillMask[j] = keep;
else fillMask[j] = fill;
}
ip.fill(fillMask);
ip.invert();
}
}