void createEllipse(ImagePlus imp) { IJ.showStatus("Fitting ellipse"); Roi roi = imp.getRoi(); if (roi == null) { noRoi("Fit Ellipse"); return; } if (roi.isLine()) { IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections"); return; } ImageProcessor ip = imp.getProcessor(); ip.setRoi(roi); int options = Measurements.CENTROID + Measurements.ELLIPSE; ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null); double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0; double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0; double x1 = stats.xCentroid - dx; double x2 = stats.xCentroid + dx; double y1 = stats.yCentroid - dy; double y2 = stats.yCentroid + dy; double aspectRatio = stats.minor / stats.major; imp.killRoi(); imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio)); }
void interpolate() { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Interpolate"); return; } if (roi.getType() == Roi.POINT) return; if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1"); GenericDialog gd = new GenericDialog("Interpolate"); gd.addNumericField("Interval:", 1.0, 1, 4, "pixel"); gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth); gd.showDialog(); if (gd.wasCanceled()) return; double interval = gd.getNextNumber(); smooth = gd.getNextBoolean(); Undo.setup(Undo.ROI, imp); FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth); int t = roi.getType(); int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI; if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON; if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0) type = Roi.POLYGON; if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE; if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE; ImageCanvas ic = imp.getCanvas(); if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0) type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON; Roi p = new PolygonRoi(poly, type); if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth()); p.setStrokeColor(roi.getStrokeColor()); p.setName(roi.getName()); transferProperties(roi, p); imp.setRoi(p); }
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(); }
/** Called by ImageJ when the user selects Quit. */ public void quit() { quitMacro = IJ.macroRunning(); Thread thread = new Thread(this, "Quit"); thread.setPriority(Thread.NORM_PRIORITY); thread.start(); IJ.wait(10); }
private void openDirectory(File f, String path) { if (path == null) return; if (!(path.endsWith(File.separator) || path.endsWith("/"))) path += File.separator; String[] names = f.list(); names = (new FolderOpener()).trimFileList(names); if (names == null) return; String msg = "Open all " + names.length + " images in \"" + f.getName() + "\" as a stack?"; GenericDialog gd = new GenericDialog("Open Folder"); gd.setInsets(10, 5, 0); gd.addMessage(msg); gd.setInsets(15, 35, 0); gd.addCheckbox("Convert to RGB", convertToRGB); gd.setInsets(0, 35, 0); gd.addCheckbox("Use Virtual Stack", virtualStack); gd.enableYesNoCancel(); gd.showDialog(); if (gd.wasCanceled()) return; if (gd.wasOKed()) { convertToRGB = gd.getNextBoolean(); virtualStack = gd.getNextBoolean(); String options = " sort"; if (convertToRGB) options += " convert_to_rgb"; if (virtualStack) options += " use"; IJ.run("Image Sequence...", "open=[" + path + "]" + options); DirectoryChooser.setDefaultDirectory(path); } else { for (int k = 0; k < names.length; k++) { IJ.redirectErrorMessages(); if (!names[k].startsWith(".")) (new Opener()).open(path + names[k]); } } IJ.register(DragAndDrop.class); }
void runMacro(String arg) { Roi roi = imp.getRoi(); if (IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } if (roi == null) { noRoi("Rotate>Selection"); return; } roi = (Roi) roi.clone(); if (arg.equals("rotate")) { double d = Tools.parseDouble(angle); if (Double.isNaN(d)) angle = "15"; String value = IJ.runMacroFile("ij.jar:RotateSelection", angle); if (value != null) angle = value; } else if (arg.equals("enlarge")) { String value = IJ.runMacroFile("ij.jar:EnlargeSelection", enlarge); if (value != null) enlarge = value; Roi.previousRoi = roi; } }
public int setup(String arg, ImagePlus imp) { this.arg = arg; this.imp = imp; IJ.register(ParticleAnalyzer.class); if (imp == null) { IJ.noImage(); return DONE; } if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) { IJ.error( "Particle Analyzer", "RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold."); return DONE; } if (!showDialog()) return DONE; int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO; int flags = IJ.setupDialog(imp, baseFlags); processStack = (flags & DOES_STACKS) != 0; slice = 0; saveRoi = imp.getRoi(); if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea()) polygon = saveRoi.getPolygon(); imp.startTiming(); nextFontSize = defaultFontSize; nextLineWidth = 1; return flags; }
void fitSpline() { Roi roi = imp.getRoi(); if (roi == null) { IJ.error("Spline", "Selection required"); return; } int type = roi.getType(); boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE; if (!(segmentedSelection || type == Roi.FREEROI || type == Roi.TRACED_ROI || type == Roi.FREELINE)) { IJ.error("Spline", "Polygon or polyline selection required"); return; } if (roi instanceof EllipseRoi) return; PolygonRoi p = (PolygonRoi) roi; if (!segmentedSelection) p = trimPolygon(p, p.getUncalibratedLength()); String options = Macro.getOptions(); if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening(); else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit(); else p.fitSpline(); imp.draw(); LineWidthAdjuster.update(); }
void loadTransformation(String filename, ResultsTable res) { try { String line; FileReader fr = new FileReader(filename); BufferedReader br = new BufferedReader(fr); if (!br.readLine().equals(" Z-Step Raw Width minus Heigh Calibration Width minus Height")) { IJ.error("File does not seam to be an Astigmatism calibration file"); return; } // java.lang.String [] elements = new java.lang.String [3]; java.lang.String[] elements; int counter = 1; res.reset(); while ((line = br.readLine()) != null) { IJ.showStatus("Loading element " + counter + "... sit back and relax."); counter++; line.trim(); elements = line.split("\t"); res.incrementCounter(); res.addValue("Z-Step", Double.parseDouble(elements[1])); res.addValue("Raw Width minus Heigh", Double.parseDouble(elements[2])); res.addValue("Calibration Width minus Height", Double.parseDouble(elements[3])); } fr.close(); } catch (FileNotFoundException e) { IJ.error("File not found exception" + e); return; } catch (IOException e) { IJ.error("IOException exception" + e); return; } catch (NumberFormatException e) { IJ.error("Number format exception" + e); return; } }
public void run(String arg) { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.noImage(); return; } ImageStack stack1 = imp.getStack(); String fileName = imp.getTitle(); int endslice = stack1.getSize(); ImagePlus imp2 = duplicateStack(imp); imp2.show(); String duplicateName = imp2.getTitle(); // IJ.showMessage("Box",fileName); ImageStack stack2 = imp2.getStack(); stack1.deleteSlice(1); stack2.deleteSlice(endslice); String calculatorstring = ("image1='" + fileName + "' operation=Subtract image2=" + imp2.getTitle() + " create stack"); IJ.run("Image Calculator...", calculatorstring); ImagePlus imp3 = WindowManager.getCurrentImage(); imp3.setTitle(fileName + " DeltaF up"); imp2.getWindow().close(); imp.getWindow().close(); }
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) { if (doOptions) { this.imp = imp; this.pfr = pfr; GenericDialog gd = new GenericDialog("Binary Options"); gd.addNumericField("Iterations (1-" + MAX_ITERATIONS + "):", iterations, 0, 3, ""); gd.addNumericField("Count (1-8):", count, 0, 3, ""); gd.addCheckbox("Black background", Prefs.blackBackground); gd.addCheckbox("Pad edges when eroding", Prefs.padEdges); gd.addChoice("EDM output:", outputTypes, outputTypes[EDM.getOutputType()]); if (imp != null) { gd.addChoice("Do:", operations, operation); gd.addPreviewCheckbox(pfr); gd.addDialogListener(this); previewing = true; } gd.addHelp(IJ.URL + "/docs/menus/process.html#options"); gd.showDialog(); previewing = false; if (gd.wasCanceled()) return DONE; if (imp == null) { // options dialog only, no do/preview dialogItemChanged(gd, null); // read dialog result return DONE; } return operation.equals(NO_OPERATION) ? DONE : IJ.setupDialog(imp, flags); } else { // no dialog, 'arg' is operation type if (!((ByteProcessor) imp.getProcessor()).isBinary()) { IJ.error("8-bit binary (black and white only) image required."); return DONE; } return IJ.setupDialog(imp, flags); } }
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) { this.pfr = pfr; 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); } gd = new GenericDialog("Rotate", IJ.getInstance()); gd.addNumericField("Angle (degrees):", angle, (int) angle == angle ? 1 : 2); gd.addNumericField("Grid Lines:", gridLines, 0); gd.addChoice("Interpolation:", methods, methods[interpolationMethod]); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with Background Color", fillWithBackground); if (canEnlarge) gd.addCheckbox("Enlarge Image to Fit Result", enlarge); else enlarge = false; gd.addPreviewCheckbox(pfr); gd.addDialogListener(this); gd.showDialog(); drawGridLines(0); if (gd.wasCanceled()) { return DONE; } if (!enlarge) flags |= KEEP_PREVIEW; // standard filter without enlarge else if (imp.getStackSize() == 1) flags |= NO_CHANGES; // undoable as a "compound filter" return IJ.setupDialog(imp, flags); }
/** Handle menu events. */ public void actionPerformed(ActionEvent e) { if ((e.getSource() instanceof MenuItem)) { MenuItem item = (MenuItem) e.getSource(); String cmd = e.getActionCommand(); commandName = cmd; ImagePlus imp = null; if (item.getParent() == Menus.getOpenRecentMenu()) { new RecentOpener(cmd); // open image in separate thread return; } else if (item.getParent() == Menus.getPopupMenu()) { Object parent = Menus.getPopupMenu().getParent(); if (parent instanceof ImageCanvas) imp = ((ImageCanvas) parent).getImage(); } int flags = e.getModifiers(); hotkey = false; actionPerformedTime = System.currentTimeMillis(); long ellapsedTime = actionPerformedTime - keyPressedTime; if (cmd != null && (ellapsedTime >= 200L || !cmd.equals(lastKeyCommand))) { if ((flags & Event.ALT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_ALT); if ((flags & Event.SHIFT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_SHIFT); new Executer(cmd, imp); } lastKeyCommand = null; if (IJ.debugMode) IJ.log("actionPerformed: time=" + ellapsedTime + ", " + e); } }
public void reduceHyperstack(ImagePlus imp, int factor, boolean reduceSlices) { int channels = imp.getNChannels(); int slices = imp.getNSlices(); int frames = imp.getNFrames(); int zfactor = reduceSlices ? factor : 1; int tfactor = reduceSlices ? 1 : factor; ImageStack stack = imp.getStack(); ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight()); boolean virtual = stack.isVirtual(); int slices2 = slices / zfactor + ((slices % zfactor) != 0 ? 1 : 0); int frames2 = frames / tfactor + ((frames % tfactor) != 0 ? 1 : 0); int n = channels * slices2 * frames2; int count = 1; for (int t = 1; t <= frames; t += tfactor) { for (int z = 1; z <= slices; z += zfactor) { for (int c = 1; c <= channels; c++) { int i = imp.getStackIndex(c, z, t); IJ.showProgress(i, n); ImageProcessor ip = stack.getProcessor(imp.getStackIndex(c, z, t)); // IJ.log(count++ +" "+i+" "+c+" "+z+" "+t); stack2.addSlice(stack.getSliceLabel(i), ip); } } } imp.setStack(stack2, channels, slices2, frames2); Calibration cal = imp.getCalibration(); if (cal.scaled()) cal.pixelDepth *= zfactor; if (virtual) imp.setTitle(imp.getTitle()); IJ.showProgress(1.0); }
public synchronized void adjustmentValueChanged(AdjustmentEvent e) { if (!checkImage()) { IJ.beep(); IJ.showStatus("No Image"); return; } if (e.getSource() == minSlider) { adjustMinHue((int) minSlider.getValue()); } else if (e.getSource() == maxSlider) { adjustMaxHue((int) maxSlider.getValue()); } else if (e.getSource() == minSlider2) { adjustMinSat((int) minSlider2.getValue()); } else if (e.getSource() == maxSlider2) { adjustMaxSat((int) maxSlider2.getValue()); } else if (e.getSource() == minSlider3) { adjustMinBri((int) minSlider3.getValue()); } else if (e.getSource() == maxSlider3) { adjustMaxBri((int) maxSlider3.getValue()); } originalB.setEnabled(true); updateLabels(); updatePlot(); notify(); }
public Channels() { super("Channels"); if (instance != null) { instance.toFront(); return; } WindowManager.addWindow(this); instance = this; GridBagLayout gridbag = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); setLayout(gridbag); int y = 0; c.gridx = 0; c.gridy = y++; c.gridwidth = 1; c.fill = GridBagConstraints.BOTH; c.anchor = GridBagConstraints.CENTER; int margin = 32; if (IJ.isMacOSX()) margin = 20; c.insets = new Insets(10, margin, 10, margin); choice = new Choice(); for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]); choice.select(0); choice.addItemListener(this); add(choice, c); CompositeImage ci = getImage(); int nCheckBoxes = ci != null ? ci.getNChannels() : 3; if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS; checkbox = new Checkbox[nCheckBoxes]; for (int i = 0; i < nCheckBoxes; i++) { checkbox[i] = new Checkbox("Channel " + (i + 1), true); c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5); c.gridy = y++; add(checkbox[i], c); checkbox[i].addItemListener(this); } c.insets = new Insets(0, 15, 10, 15); c.fill = GridBagConstraints.NONE; c.gridy = y++; moreButton = new Button(moreLabel); moreButton.addActionListener(this); add(moreButton, c); update(); pm = new PopupMenu(); for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]); add(pm); addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts setResizable(false); pack(); if (location == null) { GUI.center(this); location = getLocation(); } else setLocation(location); show(); }
public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command == null) return; if (command.equals(moreLabel)) { Point bloc = moreButton.getLocation(); pm.show(this, bloc.x, bloc.y); } else if (command.equals("Convert to RGB")) IJ.doCommand("Stack to RGB"); else IJ.doCommand(command); }
public void dragOver(DropTargetDragEvent e) { if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation()); Point loc = e.getLocation(); int buttonSize = Toolbar.getButtonSize(); int width = IJ.getInstance().getSize().width; openAsVirtualStack = width - loc.x <= buttonSize; if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>"); else IJ.showStatus("<<Drag and Drop>>"); }
public void run(String arg) { ImageWindow iw = WindowManager.getCurrentWindow(); pw = jutils.getPW4SelCopy(iw); String title = pw.getTitle(); float[][] yvals = pw.getYValues(); float[][] xvals = pw.getXValues(); int length = yvals[0].length; if (pw.getShowErrors()) errs = pw.getErrors(0, false); int[] colors = pw.getColors(); colors[0] = 0; ScriptEngineManager manager = new ScriptEngineManager(); engine = manager.getEngineByName("js"); ce = (Compilable) engine; // hitcounter=0; c2 = 0.0f; iterations = 0; checkc2 = false; double[] stats = new double[3]; tempx = new float[length]; tempdata = new float[length]; System.arraycopy(xvals[0], 0, tempx, 0, length); System.arraycopy(yvals[0], 0, tempdata, 0, length); pw.addPoints(tempx, new float[tempx.length], false); series = pw.getNpts().length - 1; double[] params = new double[10]; int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1}; init_options(params, fixes); if (!init_functions()) { return; } while (showoptions(params, fixes)) { NLLSfit_v2 fitclass; if (checkc2) { fitclass = new NLLSfit_v2(this, 0); } else { fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1); } float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true); pw.updateSeries(fit, series, false); c2 = (float) stats[1]; iterations = (int) stats[0]; } IJ.log("Chi Squared = " + (float) stats[1]); IJ.log("Iterations = " + (int) stats[0]); for (int i = 0; i < 10; i++) { IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]); } IJ.log("AIC = " + (float) stats[2]); // IJ.log("hits = "+hitcounter); set_options(params, fixes); }
public boolean beadCalibration3d() { imp = IJ.getImage(); if (imp == null) { IJ.noImage(); return false; } else if (imp.getStackSize() == 1) { IJ.error("Stack required"); return false; } else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) { // In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y); // requires a Float.intBitsToFloat() conversion IJ.error("8 or 16 bit greyscale image required"); return false; } width = imp.getWidth(); height = imp.getHeight(); nslices = imp.getStackSize(); imtitle = imp.getTitle(); models[0] = "*None*"; models[1] = "line"; models[2] = "2nd degree polynomial"; models[3] = "3rd degree polynomial"; models[4] = "4th degree polynomial"; GenericDialog gd = new GenericDialog("3D PALM calibration"); gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0); gd.addNumericField( "Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0); gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2); gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0); gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3])); gd.addCheckbox( "Show divergence of bead positions against model", prefs.get("QuickPALM.3Dcal_showDivergence", false)); gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false)); gd.addMessage("\n\nDon't forget to save the table in the end..."); gd.showDialog(); if (gd.wasCanceled()) return false; fwhm = gd.getNextNumber(); prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm); pthrsh = gd.getNextNumber() / 100; prefs.set("QuickPALM.pthrsh", pthrsh * 100); cal_z = gd.getNextNumber(); prefs.set("QuickPALM.z-step", cal_z); window = (int) gd.getNextNumber(); prefs.set("QuickPALM.window", window); model = gd.getNextChoice(); prefs.set("QuickPALM.model", model); part_divergence = gd.getNextBoolean(); prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence); part_extrainfo = gd.getNextBoolean(); prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo); return true; }
/** Performs actual projection using specified method. */ public void doProjection() { if (imp == null) return; sliceCount = 0; if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD; for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++; if (method == MEDIAN_METHOD) { projImage = doMedianProjection(); return; } // Create new float processor for projected pixels. FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight()); ImageStack stack = imp.getStack(); RayFunction rayFunc = getRayFunction(method, fp); if (IJ.debugMode == true) { IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice); } // Determine type of input image. Explicit determination of // processor type is required for subsequent pixel // manipulation. This approach is more efficient than the // more general use of ImageProcessor's getPixelValue and // putPixel methods. int ptype; if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE; else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE; else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE; else { IJ.error("Z Project", "Non-RGB stack required"); return; } // Do the projection. for (int n = startSlice; n <= stopSlice; n += increment) { IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice); IJ.showProgress(n - startSlice, stopSlice - startSlice); projectSlice(stack.getPixels(n), rayFunc, ptype); } // Finish up projection. if (method == SUM_METHOD) { fp.resetMinAndMax(); projImage = new ImagePlus(makeTitle(), fp); } else if (method == SD_METHOD) { rayFunc.postProcess(); fp.resetMinAndMax(); projImage = new ImagePlus(makeTitle(), fp); } else { rayFunc.postProcess(); projImage = makeOutputImage(imp, fp, ptype); } if (projImage == null) IJ.error("Z Project", "Error computing projection."); }
public void run(String arg) { int[] wList = WindowManager.getIDList(); if (wList == null) { IJ.error("No images are open."); return; } double thalf = 0.5; boolean keep; GenericDialog gd = new GenericDialog("Bleach correction"); gd.addNumericField("t½:", thalf, 1); gd.addCheckbox("Keep source stack:", true); gd.showDialog(); if (gd.wasCanceled()) return; long start = System.currentTimeMillis(); thalf = gd.getNextNumber(); keep = gd.getNextBoolean(); if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate"); ImagePlus imp1 = WindowManager.getCurrentImage(); int d1 = imp1.getStackSize(); double v1, v2; int width = imp1.getWidth(); int height = imp1.getHeight(); ImageProcessor ip1, ip2, ip3; int slices = imp1.getStackSize(); ImageStack stack1 = imp1.getStack(); ImageStack stack2 = imp1.getStack(); int currentSlice = imp1.getCurrentSlice(); for (int n = 1; n <= slices; n++) { ip1 = stack1.getProcessor(n); ip3 = stack1.getProcessor(1); ip2 = stack2.getProcessor(n); for (int x = 0; x < width; x++) { for (int y = 0; y < height; y++) { v1 = ip1.getPixelValue(x, y); v2 = ip3.getPixelValue(x, y); // =B8/(EXP(-C$7*A8)) v1 = (v1 / Math.exp(-n * thalf)); ip2.putPixelValue(x, y, v1); } } IJ.showProgress((double) n / slices); IJ.showStatus(n + "/" + slices); } // stack2.show(); imp1.updateAndDraw(); }
private boolean checkImage() { imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.beep(); IJ.showStatus("No image"); return false; } ip = setup(imp); if (ip == null) return false; return true; }
private void rotate(ImagePlus imp) { Roi roi = imp.getRoi(); if (IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } (new RoiRotator()).run(""); }
boolean setProperties(String title, Roi roi) { Frame f = WindowManager.getFrontWindow(); if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false; if (roi == null) { IJ.error("This command requires a selection."); return false; } RoiProperties rp = new RoiProperties(title, roi); boolean ok = rp.showDialog(); if (IJ.debugMode) IJ.log(roi.getDebugInfo()); return ok; }
void createMaskFromThreshold(ImagePlus imp) { ImageProcessor ip = imp.getProcessor(); if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) { IJ.error("Create Mask", "Area selection or thresholded image required"); return; } double t1 = ip.getMinThreshold(); double t2 = ip.getMaxThreshold(); IJ.run("Duplicate...", "title=mask"); ImagePlus imp2 = WindowManager.getCurrentImage(); ImageProcessor ip2 = imp2.getProcessor(); ip2.setThreshold(t1, t2, ImageProcessor.NO_LUT_UPDATE); IJ.run("Convert to Mask"); }
private String displayRanges(ImagePlus imp) { LUT[] luts = imp.getLuts(); if (luts == null) return ""; String s = "Display ranges\n"; int n = luts.length; if (n > 7) n = 7; for (int i = 0; i < n; i++) { double min = luts[i].min; double max = luts[i].max; int digits = (int) min == min && (int) max == max ? 0 : 2; s += " " + (i + 1) + ": " + IJ.d2s(min, digits) + "-" + IJ.d2s(max, digits) + "\n"; } return s; }
void doIterations(ImageProcessor ip, String mode) { if (escapePressed) return; if (!previewing && iterations > 1) IJ.showStatus(arg + "... press ESC to cancel"); for (int i = 0; i < iterations; i++) { if (Thread.currentThread().isInterrupted()) return; if (IJ.escapePressed()) { escapePressed = true; ip.reset(); return; } if (mode.equals("erode")) ((ByteProcessor) ip).erode(count, background); else ((ByteProcessor) ip).dilate(count, background); } }
/** Quit using a separate thread, hopefully avoiding thread deadlocks. */ public void run() { quitting = true; boolean changes = false; int[] wList = WindowManager.getIDList(); if (wList != null) { for (int i = 0; i < wList.length; i++) { ImagePlus imp = WindowManager.getImage(wList[i]); if (imp != null && imp.changes == true) { changes = true; break; } } } Frame[] frames = WindowManager.getNonImageWindows(); if (frames != null) { for (int i = 0; i < frames.length; i++) { if (frames[i] != null && (frames[i] instanceof Editor)) { if (((Editor) frames[i]).fileChanged()) { changes = true; break; } } } } if (windowClosed && !changes && Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS && !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) { GenericDialog gd = new GenericDialog("ImageJ", this); gd.addMessage("Are you sure you want to quit ImageJ?"); gd.showDialog(); quitting = !gd.wasCanceled(); windowClosed = false; } if (!quitting) return; if (!WindowManager.closeAllWindows()) { quitting = false; return; } // IJ.log("savePreferences"); if (applet == null) { saveWindowLocations(); Prefs.savePreferences(); } IJ.cleanup(); // setVisible(false); // IJ.log("dispose"); dispose(); if (exitWhenQuitting) System.exit(0); }
boolean init_functions() { GenericDialog gd = new GenericDialog("Fitting Options"); gd.addStringField("Extra Definitions", exdef, 50); gd.addCheckbox("Weight Using Plot Errors", false); gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50); gd.addStringField("Fit_Equation", function, 50); gd.showDialog(); if (gd.wasCanceled()) { return false; } exdef = gd.getNextString(); boolean errweights = gd.getNextBoolean(); weightfunction = gd.getNextString(); function = gd.getNextString(); // first initialize the weights weights = new float[tempdata.length]; if (errweights || weightfunction.equals("") || weightfunction == null || weightfunction == "1.0") { if (errweights) { for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]); } else { for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f; } } else { for (int i = 0; i < tempdata.length; i++) { String script = "y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";"; Double temp = new Double(0.0); try { temp = (Double) engine.eval(script); } catch (Exception e) { IJ.log(e.getMessage()); } if (!(temp.isInfinite() || temp.isNaN())) { weights[i] = temp.floatValue(); } } } // now compile the function script try { String script1 = exdef + "; retval=" + function + ";"; cs = ce.compile(script1); } catch (Exception e) { IJ.log(e.toString()); return false; } return true; }