void scale(ImageProcessor ip) { if (newWindow) { Rectangle r = ip.getRoi(); ImagePlus imp2 = imp.createImagePlus(); imp2.setProcessor(title, ip.resize(newWidth, newHeight)); Calibration cal = imp2.getCalibration(); if (cal.scaled()) { cal.pixelWidth *= 1.0 / xscale; cal.pixelHeight *= 1.0 / yscale; } imp2.show(); imp.trimProcessor(); imp2.trimProcessor(); imp2.changes = true; } else { if (processStack && imp.getStackSize() > 1) { Undo.reset(); StackProcessor sp = new StackProcessor(imp.getStack(), ip); sp.scale(xscale, yscale, bgValue); } else { ip.snapshot(); Undo.setup(Undo.FILTER, imp); ip.setSnapshotCopyMode(true); ip.scale(xscale, yscale); ip.setSnapshotCopyMode(false); } imp.killRoi(); imp.updateAndDraw(); imp.changes = true; } }
void createNewStack(ImagePlus imp, ImageProcessor ip) { int nSlices = imp.getStackSize(); int w = imp.getWidth(), h = imp.getHeight(); ImagePlus imp2 = imp.createImagePlus(); Rectangle r = ip.getRoi(); boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight(); ImageStack stack1 = imp.getStack(); ImageStack stack2 = new ImageStack(newWidth, newHeight); ImageProcessor ip1, ip2; int method = interpolationMethod; if (w == 1 || h == 1) method = ImageProcessor.NONE; for (int i = 1; i <= nSlices; i++) { IJ.showStatus("Scale: " + i + "/" + nSlices); ip1 = stack1.getProcessor(i); String label = stack1.getSliceLabel(i); if (crop) { ip1.setRoi(r); ip1 = ip1.crop(); } ip1.setInterpolationMethod(method); ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing); if (ip2 != null) stack2.addSlice(label, ip2); IJ.showProgress(i, nSlices); } imp2.setStack(title, stack2); Calibration cal = imp2.getCalibration(); if (cal.scaled()) { cal.pixelWidth *= 1.0 / xscale; cal.pixelHeight *= 1.0 / yscale; } IJ.showProgress(1.0); int[] dim = imp.getDimensions(); imp2.setDimensions(dim[2], dim[3], dim[4]); if (imp.isComposite()) { imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode()); ((CompositeImage) imp2).copyLuts(imp); } if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true); if (newDepth > 0 && newDepth != oldDepth) imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod); if (imp2 != null) { imp2.show(); imp2.changes = true; } }
void createNewStack(ImagePlus imp, ImageProcessor ip) { Rectangle r = ip.getRoi(); boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight(); int nSlices = imp.getStackSize(); ImageStack stack1 = imp.getStack(); ImageStack stack2 = new ImageStack(newWidth, newHeight); ImageProcessor ip1, ip2; boolean interp = interpolate; if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false; for (int i = 1; i <= nSlices; i++) { IJ.showStatus("Scale: " + i + "/" + nSlices); ip1 = stack1.getProcessor(i); String label = stack1.getSliceLabel(i); if (crop) { ip1.setRoi(r); ip1 = ip1.crop(); } ip1.setInterpolate(interp); ip2 = ip1.resize(newWidth, newHeight); if (ip2 != null) stack2.addSlice(label, ip2); IJ.showProgress(i, nSlices); } ImagePlus imp2 = imp.createImagePlus(); imp2.setStack(title, stack2); Calibration cal = imp2.getCalibration(); if (cal.scaled()) { cal.pixelWidth *= 1.0 / xscale; cal.pixelHeight *= 1.0 / yscale; } int[] dim = imp.getDimensions(); imp2.setDimensions(dim[2], dim[3], dim[4]); IJ.showProgress(1.0); if (imp.isComposite()) { imp2 = new CompositeImage(imp2, 0); ((CompositeImage) imp2).copyLuts(imp); } if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true); imp2.show(); imp2.changes = true; }
/** * 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; }
boolean showDialog(ImageProcessor ip) { int bitDepth = imp.getBitDepth(); boolean isStack = imp.getStackSize() > 1; r = ip.getRoi(); int width = newWidth; if (width == 0) width = r.width; int height = (int) ((double) width * r.height / r.width); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); if (xscale != 0.0 && yscale != 0.0) { width = (int) (r.width * xscale); height = (int) (r.height * yscale); } else { xstr = "-"; ystr = "-"; } GenericDialog gd = new GenericDialog("Scale"); gd.addStringField("X Scale (0.05-25):", xstr); gd.addStringField("Y Scale (0.05-25):", ystr); gd.setInsets(5, 0, 5); gd.addStringField("Width (pixels):", "" + width); gd.addStringField("Height (pixels):", "" + height); fields = gd.getStringFields(); for (int i = 0; i < 3; i++) { ((TextField) fields.elementAt(i)).addTextListener(this); ((TextField) fields.elementAt(i)).addFocusListener(this); } xField = (TextField) fields.elementAt(0); yField = (TextField) fields.elementAt(1); widthField = (TextField) fields.elementAt(2); heightField = (TextField) fields.elementAt(3); fieldWithFocus = xField; gd.addCheckbox("Interpolate", interpolate); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with Background Color", fillWithBackground); if (isStack) gd.addCheckbox("Process Entire Stack", processStack); gd.addCheckbox("Create New Window", newWindow); title = WindowManager.getUniqueName(imp.getTitle()); gd.setInsets(10, 0, 0); gd.addStringField("Title:", title, 12); gd.showDialog(); if (gd.wasCanceled()) return false; xstr = gd.getNextString(); ystr = gd.getNextString(); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); String wstr = gd.getNextString(); newWidth = (int) Tools.parseDouble(wstr, 0); newHeight = (int) Tools.parseDouble(gd.getNextString(), 0); if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0"))) newWidth = (int) (newHeight * (double) r.width / r.height); if (newWidth == 0 || newHeight == 0) { IJ.error("Invalid width or height entered"); return false; } if (xscale > 25.0) xscale = 25.0; if (yscale > 25.0) yscale = 25.0; if (xscale > 0.0 && yscale > 0.0) { newWidth = (int) (r.width * xscale); newHeight = (int) (r.height * yscale); } interpolate = gd.getNextBoolean(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); if (isStack) processStack = gd.getNextBoolean(); newWindow = gd.getNextBoolean(); if (!newWindow && xscale == 0.0) { xscale = (double) newWidth / r.width; yscale = (double) newHeight / r.height; } title = gd.getNextString(); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) bgValue = ip.getBestIndex(bgc); else if (bitDepth == 24) bgValue = bgc.getRGB(); } else { if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white else if (bitDepth == 24) bgValue = 0xffffffff; // white } return true; }
boolean showDialog(ImageProcessor ip) { String macroOptions = Macro.getOptions(); if (macroOptions != null) { if (macroOptions.indexOf(" interpolate") != -1) macroOptions.replaceAll(" interpolate", " interpolation=Bilinear"); else if (macroOptions.indexOf(" interpolation=") == -1) macroOptions = macroOptions + " interpolation=None"; Macro.setOptions(macroOptions); } int bitDepth = imp.getBitDepth(); int stackSize = imp.getStackSize(); boolean isStack = stackSize > 1; oldDepth = stackSize; if (isStack) { xstr = "1.0"; ystr = "1.0"; zstr = "1.0"; } r = ip.getRoi(); int width = newWidth; if (width == 0) width = r.width; int height = (int) ((double) width * r.height / r.width); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); zscale = 1.0; if (xscale != 0.0 && yscale != 0.0) { width = (int) (r.width * xscale); height = (int) (r.height * yscale); } else { xstr = "-"; ystr = "-"; } GenericDialog gd = new GenericDialog("Scale"); gd.addStringField("X Scale:", xstr); gd.addStringField("Y Scale:", ystr); if (isStack) gd.addStringField("Z Scale:", zstr); gd.setInsets(5, 0, 5); gd.addStringField("Width (pixels):", "" + width); gd.addStringField("Height (pixels):", "" + height); if (isStack) { String label = "Depth (images):"; if (imp.isHyperStack()) { int slices = imp.getNSlices(); int frames = imp.getNFrames(); if (slices == 1 && frames > 1) { label = "Depth (frames):"; oldDepth = frames; } else { label = "Depth (slices):"; oldDepth = slices; } } gd.addStringField(label, "" + oldDepth); } fields = gd.getStringFields(); for (int i = 0; i < fields.size(); i++) { ((TextField) fields.elementAt(i)).addTextListener(this); ((TextField) fields.elementAt(i)).addFocusListener(this); } xField = (TextField) fields.elementAt(0); yField = (TextField) fields.elementAt(1); if (isStack) { zField = (TextField) fields.elementAt(2); widthField = (TextField) fields.elementAt(3); heightField = (TextField) fields.elementAt(4); depthField = (TextField) fields.elementAt(5); } else { widthField = (TextField) fields.elementAt(2); heightField = (TextField) fields.elementAt(3); } fieldWithFocus = xField; gd.addChoice("Interpolation:", methods, methods[interpolationMethod]); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with background color", fillWithBackground); gd.addCheckbox("Average when downsizing", averageWhenDownsizing); boolean hyperstack = imp.isHyperStack() || imp.isComposite(); if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack); gd.addCheckbox("Create new window", newWindow); title = WindowManager.getUniqueName(imp.getTitle()); gd.setInsets(10, 0, 0); gd.addStringField("Title:", title, 12); gd.showDialog(); if (gd.wasCanceled()) return false; xstr = gd.getNextString(); ystr = gd.getNextString(); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); if (isStack) { zstr = gd.getNextString(); zscale = Tools.parseDouble(ystr, 0.0); } String wstr = gd.getNextString(); newWidth = (int) Tools.parseDouble(wstr, 0); newHeight = (int) Tools.parseDouble(gd.getNextString(), 0); if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0"))) newWidth = (int) (newHeight * (double) r.width / r.height); if (newWidth == 0 || newHeight == 0) { IJ.error("Scaler", "Width or height is 0"); return false; } if (xscale > 0.0 && yscale > 0.0) { newWidth = (int) (r.width * xscale); newHeight = (int) (r.height * yscale); } if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0); interpolationMethod = gd.getNextChoiceIndex(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); averageWhenDownsizing = gd.getNextBoolean(); if (isStack && !hyperstack) processStack = gd.getNextBoolean(); if (hyperstack) processStack = true; newWindow = gd.getNextBoolean(); if (xscale == 0.0) { xscale = (double) newWidth / r.width; yscale = (double) newHeight / r.height; } title = gd.getNextString(); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) bgValue = ip.getBestIndex(bgc); else if (bitDepth == 24) bgValue = bgc.getRGB(); } else bgValue = 0.0; return true; }
void sample() { byte[] hsSource, ssSource, bsSource; // ImageProcessor ip2; // ip2 = imp.getProcessor(); Rectangle myroi = ip.getRoi(); int swidth = myroi.width; int sheight = myroi.height; int sy = myroi.y; int sx = myroi.x; if (swidth == width && sheight == height) { IJ.showMessage("Select a rectangular ROI"); IJ.beep(); return; } IJ.run("Select None"); int snumPixels = swidth * sheight; hsSource = new byte[snumPixels]; ssSource = new byte[snumPixels]; bsSource = new byte[snumPixels]; int[] pixs = new int[snumPixels]; int[] bin = new int[256]; int counter = 0, pi = 0, rangePassH = 0, rangeStopH = 0, rangePassL = 0, rangeStopL = 0, i, j; for (i = sy; i < sy + sheight; i++) { for (j = sx; j < sx + swidth; j++) { pixs[counter++] = ip.getPixel(j, i); } } // Get hsb or rgb from roi. ColorProcessor cp2 = new ColorProcessor(swidth, sheight, pixs); int iminhue = 256, imaxhue = -1, iminsat = 256, imaxsat = -1, iminbri = 256, imaxbri = -1; int iminred = 256, imaxred = -1, imingre = 256, imaxgre = -1, iminblu = 256, imaxblu = -1; if (isRGB) cp2.getRGB(hsSource, ssSource, bsSource); else cp2.getHSB(hsSource, ssSource, bsSource); for (i = 0; i < snumPixels; i++) { bin[hsSource[i] & 255] = 1; if ((hsSource[i] & 255) > imaxhue) imaxhue = (hsSource[i] & 255); if ((hsSource[i] & 255) < iminhue) iminhue = (hsSource[i] & 255); if ((ssSource[i] & 255) > imaxsat) imaxsat = (ssSource[i] & 255); if ((ssSource[i] & 255) < iminsat) iminsat = (ssSource[i] & 255); if ((bsSource[i] & 255) > imaxbri) imaxbri = (bsSource[i] & 255); if ((bsSource[i] & 255) < iminbri) iminbri = (bsSource[i] & 255); // IJ.showMessage("h:"+minhue+"H:"+maxhue+"s:"+minsat+"S:"+maxsat+"b:"+minbri+"B:"+maxbri); } if (!isRGB) { // get pass or stop filter whichever has a narrower range for (i = 0; i < 256; i++) { if (bin[i] > 0) { rangePassL = i; break; } } for (i = 255; i >= 0; i--) { if (bin[i] > 0) { rangePassH = i; break; } } for (i = 0; i < 256; i++) { if (bin[i] == 0) { rangeStopL = i; break; } } for (i = 255; i >= 0; i--) { if (bin[i] == 0) { rangeStopH = i; break; } } if ((rangePassH - rangePassL) < (rangeStopH - rangeStopL)) { bandPassH.setState(true); bandStopH.setState(false); iminhue = rangePassL; imaxhue = rangePassH; } else { bandPassH.setState(false); bandStopH.setState(true); iminhue = rangeStopL; imaxhue = rangeStopH; } } else { bandPassH.setState(true); bandStopH.setState(false); } adjustMinHue(iminhue); minSlider.setValue(iminhue); adjustMaxHue(imaxhue); maxSlider.setValue(imaxhue); adjustMinSat(iminsat); minSlider2.setValue(iminsat); adjustMaxSat(imaxsat); maxSlider2.setValue(imaxsat); adjustMinBri(iminbri); minSlider3.setValue(iminbri); adjustMaxBri(imaxbri); maxSlider3.setValue(imaxbri); originalB.setEnabled(true); // IJ.showStatus("done"); }