public void drawPixels(ImageProcessor ip) { int saveWidth = ip.getLineWidth(); if (getStrokeWidth() > 1f) ip.setLineWidth((int) Math.round(getStrokeWidth())); double offset = getOffset(0.5); if (xSpline != null) { ip.moveTo( x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset)); for (int i = 1; i < splinePoints; i++) ip.lineTo( x + (int) (Math.round(xSpline[i]) + offset), y + (int) Math.round(ySpline[i] + offset)); if (type == POLYGON || type == FREEROI || type == TRACED_ROI) ip.lineTo( x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset)); } else if (xpf != null) { ip.moveTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset)); for (int i = 1; i < nPoints; i++) ip.lineTo(x + (int) (Math.round(xpf[i]) + offset), y + (int) Math.round(ypf[i] + offset)); if (type == POLYGON || type == FREEROI || type == TRACED_ROI) ip.lineTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset)); } else { ip.moveTo(x + xp[0], y + yp[0]); for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]); if (type == POLYGON || type == FREEROI || type == TRACED_ROI) ip.lineTo(x + xp[0], y + yp[0]); } ip.setLineWidth(saveWidth); updateFullWindow = true; }
/** Draws an outline of this OvalRoi on the image. */ public void drawPixels(ImageProcessor ip) { Polygon p = getPolygon(); if (p.npoints > 0) { int saveWidth = ip.getLineWidth(); if (getStrokeWidth() > 1f) ip.setLineWidth((int) Math.round(getStrokeWidth())); ip.drawPolygon(p); ip.setLineWidth(saveWidth); } if (Line.getWidth() > 1 || getStrokeWidth() > 1) updateFullWindow = true; }
void lineWidth() { int width = (int) IJ.getNumber("Line Width:", Line.getWidth()); if (width == IJ.CANCELED) return; Line.setWidth(width); LineWidthAdjuster.update(); ImagePlus imp = WindowManager.getCurrentImage(); if (imp != null && imp.isProcessor()) { ImageProcessor ip = imp.getProcessor(); ip.setLineWidth(Line.getWidth()); Roi roi = imp.getRoi(); if (roi != null && roi.isLine()) imp.draw(); } }
public void mousePressed(MouseEvent e) { // super.mousePressed(e); ImageProcessor ip = imp.getProcessor(); ip.setLineWidth(1); if (Toolbar.getToolId() == Toolbar.DROPPER) IJ.setTool(Toolbar.RECTANGLE); Rectangle flipperRect = new Rectangle(86, 268, 18, 18); Rectangle resetRect = new Rectangle(86, 294, 18, 18); Rectangle foreground1Rect = new Rectangle(9, 266, 45, 10); Rectangle foreground2Rect = new Rectangle(9, 276, 23, 25); Rectangle background1Rect = new Rectangle(33, 302, 45, 10); Rectangle background2Rect = new Rectangle(56, 277, 23, 25); int x = offScreenX(e.getX()); int y = offScreenY(e.getY()); long difference = System.currentTimeMillis() - mouseDownTime; boolean doubleClick = (difference <= 250); mouseDownTime = System.currentTimeMillis(); if (flipperRect.contains(x, y)) { Color c = Toolbar.getBackgroundColor(); Toolbar.setBackgroundColor(Toolbar.getForegroundColor()); Toolbar.setForegroundColor(c); } else if (resetRect.contains(x, y)) { Toolbar.setForegroundColor(new Color(0x000000)); Toolbar.setBackgroundColor(new Color(0xffffff)); } else if ((background1Rect.contains(x, y)) || (background2Rect.contains(x, y))) { background = true; if (doubleClick) editColor(); ((ColorGenerator) ip).refreshForeground(); ((ColorGenerator) ip).refreshBackground(); } else if ((foreground1Rect.contains(x, y)) || (foreground2Rect.contains(x, y))) { background = false; if (doubleClick) editColor(); ((ColorGenerator) ip).refreshBackground(); ((ColorGenerator) ip).refreshForeground(); } else { // IJ.log(" " + difference + " " + doubleClick); if (doubleClick) editColor(); else { setDrawingColor(offScreenX(e.getX()), offScreenY(e.getY()), background); } } if (ip instanceof ColorGenerator) { if (background) { ((ColorGenerator) ip).refreshForeground(); ((ColorGenerator) ip).refreshBackground(); } else { ((ColorGenerator) ip).refreshBackground(); ((ColorGenerator) ip).refreshForeground(); } } }
/** * 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; }