/** * Execute plugin functionality: stack FFT with window function, max projection over all slices * (phase, Z angle), blank out central 1/8 circle (set to min value), display min-max. */ public ResultSet exec(ImagePlus... imps) { ImagePlus imp = imps[0]; Util_StackFFT2D stackFFT2D = new Util_StackFFT2D(); stackFFT2D.resultTypeChoice = Util_StackFFT2D.resultType[1]; ImagePlus impF = stackFFT2D.exec(imp); IJ.run(impF, "Z Project...", "projection=[Max Intensity]"); ImagePlus impProjF = ij.WindowManager.getCurrentImage(); maskCentralRegion(impProjF); if (impProjF.isComposite()) { // display grayscale, not colored composite CompositeImage ci = (CompositeImage) impProjF; ci.setMode(IJ.GRAYSCALE); impProjF.updateAndDraw(); } displayMinToMax(impProjF); impProjF.setTitle(I1l.makeTitle(imps[0], TLA)); String shortInfo = "Maximum intensity projection of log" + " (amplitude^2) 2D FFT stack, central region masked," + " rescaled (min-max) to improve contrast of the relevant" + " frequency range."; results.addImp(shortInfo, impProjF); results.addInfo( "How to interpret", "look for clean 1st & 2nd" + " order spots, similar across angles. Note that spot" + " intensity depends on image content."); return results; }
/** * Prepare for processing; also called at the very end with argument 'final' to show any newly * created output image. */ public int setup(String arg, ImagePlus imp) { if (arg.equals("final")) { showOutput(); return DONE; } this.imp = imp; // 'arg' is processing type; default is 'EDM' (0) if (arg.equals("watershed")) { processType = WATERSHED; flags += KEEP_THRESHOLD; } else if (arg.equals("points")) processType = UEP; else if (arg.equals("voronoi")) processType = VORONOI; // output type if (processType != WATERSHED) // Watershed always has output BYTE_OVERWRITE=0 outImageType = outputType; // otherwise use the static variable from setOutputType if (outImageType != BYTE_OVERWRITE) flags |= NO_CHANGES; // check image and prepare if (imp != null) { ImageProcessor ip = imp.getProcessor(); if (!ip.isBinary()) { IJ.error("8-bit binary image (0 and 255) required."); return DONE; } ip.resetRoi(); // processing routines assume background=0; image may be otherwise boolean invertedLut = imp.isInvertedLut(); background255 = (invertedLut && Prefs.blackBackground) || (!invertedLut && !Prefs.blackBackground); } return flags; } // public int setup
void showDialog() { int width = imp.getWidth(); int height = imp.getHeight(); Calibration cal = imp.getCalibration(); int places; if (cal.scaled()) { pixelWidth = cal.pixelWidth; pixelHeight = cal.pixelHeight; units = cal.getUnits(); places = 2; } else { pixelWidth = 1.0; pixelHeight = 1.0; units = "pixels"; places = 0; } if (areaPerPoint == 0.0) areaPerPoint = (width * cal.pixelWidth * height * cal.pixelHeight) / 81.0; // default to 9x9 grid ImageWindow win = imp.getWindow(); GenericDialog gd = new GenericDialog("Grid..."); gd.addChoice("Grid Type:", types, type); gd.addNumericField("Area per Point:", areaPerPoint, places, 6, units + "^2"); gd.addChoice("Color:", colors, color); gd.addCheckbox("Random Offset", randomOffset); gd.addDialogListener(this); gd.showDialog(); if (gd.wasCanceled()) showGrid(null); }
private ImagePlus duplicateImage(ImageProcessor iProcessor) { int w = iProcessor.getWidth(); int h = iProcessor.getHeight(); ImagePlus iPlus = NewImage.createByteImage("Image", w, h, 1, NewImage.FILL_BLACK); ImageProcessor imageProcessor = iPlus.getProcessor(); imageProcessor.copyBits(iProcessor, 0, 0, Blitter.COPY); return iPlus; }
void Bernsen(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) { // Bernsen recommends WIN_SIZE = 31 and CONTRAST_THRESHOLD = 15. // 1) Bernsen J. (1986) "Dynamic Thresholding of Grey-Level Images" // Proc. of the 8th Int. Conf. on Pattern Recognition, pp. 1251-1255 // 2) Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding // Techniques and Quantitative Performance Evaluation" Journal of // Electronic Imaging, 13(1): 146-165 // http://citeseer.ist.psu.edu/sezgin04survey.html // Ported to ImageJ plugin from E Celebi's fourier_0.8 routines // This version uses a circular local window, instead of a rectagular one ImagePlus Maximp, Minimp; ImageProcessor ip = imp.getProcessor(), ipMax, ipMin; int contrast_threshold = 15; int local_contrast; int mid_gray; byte object; byte backg; int temp; if (par1 != 0) { IJ.log("Bernsen: changed contrast_threshold from :" + contrast_threshold + " to:" + par1); contrast_threshold = (int) par1; } if (doIwhite) { object = (byte) 0xff; backg = (byte) 0; } else { object = (byte) 0; backg = (byte) 0xff; } Maximp = duplicateImage(ip); ipMax = Maximp.getProcessor(); RankFilters rf = new RankFilters(); rf.rank(ipMax, radius, rf.MAX); // Maximum // Maximp.show(); Minimp = duplicateImage(ip); ipMin = Minimp.getProcessor(); rf.rank(ipMin, radius, rf.MIN); // Minimum // Minimp.show(); byte[] pixels = (byte[]) ip.getPixels(); byte[] max = (byte[]) ipMax.getPixels(); byte[] min = (byte[]) ipMin.getPixels(); for (int i = 0; i < pixels.length; i++) { local_contrast = (int) ((max[i] & 0xff) - (min[i] & 0xff)); mid_gray = (int) ((min[i] & 0xff) + (max[i] & 0xff)) / 2; temp = (int) (pixels[i] & 0x0000ff); if (local_contrast < contrast_threshold) pixels[i] = (mid_gray >= 128) ? object : backg; // Low contrast region else pixels[i] = (temp >= mid_gray) ? object : backg; } // imp.updateAndDraw(); return; }
private boolean ignoreArrowKeys(ImagePlus imp) { Frame frame = WindowManager.getFrontWindow(); String title = frame.getTitle(); if (title != null && title.equals("ROI Manager")) return true; // Control Panel? if (frame != null && frame instanceof javax.swing.JFrame) return true; ImageWindow win = imp.getWindow(); // LOCI Data Browser window? if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci")) return true; return false; }
/** * Called by the PlugInFilterRunner after setup. Asks the user in case of a stack and prepares a * separate ouptut stack if required */ public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) { this.pfr = pfr; int width = imp.getWidth(); int height = imp.getHeight(); // ask whether to process all slices of stack & prepare stack // (if required) for writing into it in parallel threads flags = IJ.setupDialog(imp, flags); if ((flags & DOES_STACKS) != 0 && outImageType != BYTE_OVERWRITE) { outStack = new ImageStack(width, height, imp.getStackSize()); maxFinder.setNPasses(imp.getStackSize()); } return flags; } // public int showDialog
/** * Attempts to open the specified path with the given plugin. If the plugin extends the ImagePlus * class (e.g., BioRad_Reader), set extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it * to false. * * @return A reference to the plugin, if it was successful. */ private Object tryPlugIn(String className, String path) { Object o = IJ.runPlugIn(className, path); if (o instanceof ImagePlus) { // plugin extends ImagePlus class ImagePlus imp = (ImagePlus) o; if (imp.getWidth() == 0) o = null; // invalid image else width = IMAGE_OPENED; // success } else { // plugin does not extend ImagePlus; assume success width = IMAGE_OPENED; } return o; }
/** Set display range for each channel to min-max. */ private static void displayMinToMax(ImagePlus imp) { if (imp.isComposite()) { for (int c = 1; c <= imp.getNChannels(); c++) { double min = I1l.getStatsForChannel(imp, c).min; double max = I1l.getStatsForChannel(imp, c).max; imp.setC(c); IJ.setMinAndMax(imp, min, max); } imp.setC(1); } else { double min = imp.getStatistics().min; double max = imp.getStatistics().max; IJ.setMinAndMax(imp, min, max); } }
void drawLines() { GeneralPath path = new GeneralPath(); int width = imp.getWidth(); int height = imp.getHeight(); for (int i = 0; i < linesV; i++) { float xoff = (float) (xstart + i * tileWidth); path.moveTo(xoff, 0f); path.lineTo(xoff, height); } for (int i = 0; i < linesH; i++) { float yoff = (float) (ystart + i * tileHeight); path.moveTo(0f, yoff); path.lineTo(width, yoff); } showGrid(path); }
void Contrast(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) { // G. Landini, 2013 // Based on a simple contrast toggle. This procedure does not have user-provided paramters other // than the kernel radius // Sets the pixel value to either white or black depending on whether its current value is // closest to the local Max or Min respectively // The procedure is similar to Toggle Contrast Enhancement (see Soille, Morphological Image // Analysis (2004), p. 259 ImagePlus Maximp, Minimp; ImageProcessor ip = imp.getProcessor(), ipMax, ipMin; int c_value = 0; int mid_gray; byte object; byte backg; if (doIwhite) { object = (byte) 0xff; backg = (byte) 0; } else { object = (byte) 0; backg = (byte) 0xff; } Maximp = duplicateImage(ip); ipMax = Maximp.getProcessor(); RankFilters rf = new RankFilters(); rf.rank(ipMax, radius, rf.MAX); // Maximum // Maximp.show(); Minimp = duplicateImage(ip); ipMin = Minimp.getProcessor(); rf.rank(ipMin, radius, rf.MIN); // Minimum // Minimp.show(); byte[] pixels = (byte[]) ip.getPixels(); byte[] max = (byte[]) ipMax.getPixels(); byte[] min = (byte[]) ipMin.getPixels(); for (int i = 0; i < pixels.length; i++) { pixels[i] = ((Math.abs((int) (max[i] & 0xff - pixels[i] & 0xff)) <= Math.abs((int) (pixels[i] & 0xff - min[i] & 0xff)))) ? object : backg; } // imp.updateAndDraw(); return; }
/** * Execute the plugin functionality: duplicate and scale the given image. * * @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image; * just returns it. */ public Object[] exec( ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) { // 0 - Check validity of parameters if (null == imp) return null; ImageProcessor ip = imp.getProcessor(); int xe = ip.getWidth(); int ye = ip.getHeight(); // int [] data = (ip.getHistogram()); IJ.showStatus("Thresholding..."); long startTime = System.currentTimeMillis(); // 1 Do it if (imp.getStackSize() == 1) { ip.snapshot(); Undo.setup(Undo.FILTER, imp); } // Apply the selected algorithm if (myMethod.equals("Bernsen")) { Bernsen(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Contrast")) { Contrast(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Mean")) { Mean(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Median")) { Median(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("MidGrey")) { MidGrey(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Niblack")) { Niblack(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Otsu")) { Otsu(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Phansalkar")) { Phansalkar(imp, radius, par1, par2, doIwhite); } else if (myMethod.equals("Sauvola")) { Sauvola(imp, radius, par1, par2, doIwhite); } // IJ.showProgress((double)(255-i)/255); imp.updateAndDraw(); imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE); // 2 - Return the threshold and the image IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0); return new Object[] {imp}; }
void MidGrey(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) { // See: Image Processing Learning Resourches HIPR2 // http://homepages.inf.ed.ac.uk/rbf/HIPR2/adpthrsh.htm ImagePlus Maximp, Minimp; ImageProcessor ip = imp.getProcessor(), ipMax, ipMin; int c_value = 0; int mid_gray; byte object; byte backg; if (par1 != 0) { IJ.log("MidGrey: changed c_value from :" + c_value + " to:" + par1); c_value = (int) par1; } if (doIwhite) { object = (byte) 0xff; backg = (byte) 0; } else { object = (byte) 0; backg = (byte) 0xff; } Maximp = duplicateImage(ip); ipMax = Maximp.getProcessor(); RankFilters rf = new RankFilters(); rf.rank(ipMax, radius, rf.MAX); // Maximum // Maximp.show(); Minimp = duplicateImage(ip); ipMin = Minimp.getProcessor(); rf.rank(ipMin, radius, rf.MIN); // Minimum // Minimp.show(); byte[] pixels = (byte[]) ip.getPixels(); byte[] max = (byte[]) ipMax.getPixels(); byte[] min = (byte[]) ipMin.getPixels(); for (int i = 0; i < pixels.length; i++) { pixels[i] = ((int) (pixels[i] & 0xff) > (int) (((max[i] & 0xff) + (min[i] & 0xff)) / 2) - c_value) ? object : backg; } // imp.updateAndDraw(); return; }
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 showDialog() { String[] types = {"RAW", "JPEG", "ZLIB"}; GenericDialog gd = new GenericDialog("Generate Bricks"); gd.addChoice("FileType", types, filetype); gd.addNumericField("JPEG quality", jpeg_quality, 0); gd.addNumericField("Max file size (MB)", bdsizelimit, 0); int[] wlist = WindowManager.getIDList(); if (wlist == null) return false; String[] titles = new String[wlist.length]; for (int i = 0; i < wlist.length; i++) titles[i] = ""; int tnum = 0; for (int i = 0; i < wlist.length; i++) { ImagePlus imp = WindowManager.getImage(wlist[i]); if (imp != null) { titles[tnum] = imp.getTitle(); tnum++; } } gd.addChoice("Source image: ", titles, titles[0]); gd.showDialog(); if (gd.wasCanceled()) return false; filetype = types[gd.getNextChoiceIndex()]; jpeg_quality = (int) gd.getNextNumber(); if (jpeg_quality > 100) jpeg_quality = 100; if (jpeg_quality < 0) jpeg_quality = 0; bdsizelimit = (int) gd.getNextNumber(); int id = gd.getNextChoiceIndex(); lvImgTitle = new ArrayList<String>(); lvImgTitle.add(titles[id]); Prefs.set("filetype.string", filetype); Prefs.set("jpeg_quality.int", jpeg_quality); Prefs.set("bdsizelimit.int", bdsizelimit); return true; }
private boolean deleteOverlayRoi(ImagePlus imp) { if (imp == null) return false; Overlay overlay = null; ImageCanvas ic = imp.getCanvas(); if (ic != null) overlay = ic.getShowAllList(); if (overlay == null) overlay = imp.getOverlay(); if (overlay == null) return false; Roi roi = imp.getRoi(); for (int i = 0; i < overlay.size(); i++) { Roi roi2 = overlay.get(i); if (roi2 == roi) { overlay.remove(i); imp.deleteRoi(); ic = imp.getCanvas(); if (ic != null) ic.roiManagerSelect(roi, true); return true; } } return false; }
ImagePlus duplicateStack(ImagePlus img1) { ImageStack stack1 = img1.getStack(); int width = stack1.getWidth(); int height = stack1.getHeight(); int n = stack1.getSize(); ImageStack stack2 = img1.createEmptyStack(); try { for (int i = 1; i <= n; i++) { ImageProcessor ip1 = stack1.getProcessor(i); ip1.resetRoi(); ImageProcessor ip2 = ip1.crop(); stack2.addSlice(stack1.getSliceLabel(i), ip2); } } catch (OutOfMemoryError e) { stack2.trim(); stack2 = null; return null; } return new ImagePlus("Duplicate", stack2); }
void abortPluginOrMacro(ImagePlus imp) { if (imp != null) { ImageWindow win = imp.getWindow(); if (win != null) { win.running = false; win.running2 = false; } } Macro.abort(); Interpreter.abort(); if (Interpreter.getInstance() != null) IJ.beep(); }
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; }
public void run(String arg) { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.noImage(); return; } if (imp.getStackSize() > 1) { IJ.error("This command requires a montage"); return; } GenericDialog gd = new GenericDialog("Stack Maker"); gd.addNumericField("Images_per_row: ", w, 0); gd.addNumericField("Images_per_column: ", h, 0); gd.addNumericField("Border width: ", b, 0); gd.showDialog(); if (gd.wasCanceled()) return; w = (int) gd.getNextNumber(); h = (int) gd.getNextNumber(); b = (int) gd.getNextNumber(); ImageStack stack = makeStack(imp.getProcessor(), w, h, b); new ImagePlus("Stack", stack).show(); }
public void run() { while (!done) { synchronized (this) { try { wait(); } catch (InterruptedException e) { } reset(imp, ip); // GL apply(imp, ip); // GL imp.updateAndDraw(); // GL } } }
void Mean(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) { // See: Image Processing Learning Resourches HIPR2 // http://homepages.inf.ed.ac.uk/rbf/HIPR2/adpthrsh.htm ImagePlus Meanimp; ImageProcessor ip = imp.getProcessor(), ipMean; int c_value = 0; byte object; byte backg; if (par1 != 0) { IJ.log("Mean: changed c_value from :" + c_value + " to:" + par1); c_value = (int) par1; } if (doIwhite) { object = (byte) 0xff; backg = (byte) 0; } else { object = (byte) 0; backg = (byte) 0xff; } Meanimp = duplicateImage(ip); ImageConverter ic = new ImageConverter(Meanimp); ic.convertToGray32(); ipMean = Meanimp.getProcessor(); RankFilters rf = new RankFilters(); rf.rank(ipMean, radius, rf.MEAN); // Mean // Meanimp.show(); byte[] pixels = (byte[]) ip.getPixels(); float[] mean = (float[]) ipMean.getPixels(); for (int i = 0; i < pixels.length; i++) pixels[i] = ((int) (pixels[i] & 0xff) > (int) (mean[i] - c_value)) ? object : backg; // imp.updateAndDraw(); return; }
public void actionPerformed(ActionEvent e) { Button b = (Button) e.getSource(); if (b == null) return; boolean imageThere = checkImage(); if (imageThere) { if (b == originalB) { reset(imp, ip); filteredB.setEnabled(true); } else if (b == filteredB) { apply(imp, ip); } else if (b == sampleB) { reset(imp, ip); sample(); apply(imp, ip); } else if (b == stackB) { applyStack(); } else if (b == helpB) { IJ.showMessage( "Help", "Threshold Colour v1.0\n \n" + "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n" + "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n" + "or Red, Green and Blue components.\n \n" + "Pass: Band-pass filter (anything within range is displayed).\n \n" + "Stop: Band-reject filter (anything within range is NOT displayed).\n \n" + "Original: Shows the original image and updates the buffer when\n" + " switching to another image.\n \n" + "Filtered: Shows the filtered image.\n \n" + "Stack: Processes the rest of the slices in the stack (if any)\n" + " using the current settings.\n \n" + "Threshold: Shows the object/background in the foreground and\n" + " background colours selected in the ImageJ toolbar.\n \n" + "Invert: Swaps the fore/background colours.\n \n" + "Sample: (experimental) Sets the ranges of the filters based on the\n" + " pixel value componentd in a rectangular, user-defined, ROI.\n \n" + "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n" + "Note that the \'thresholded\' image is RGB, not 8 bit grey."); } updatePlot(); updateLabels(); imp.updateAndDraw(); } else { IJ.beep(); IJ.showStatus("No Image"); } notify(); }
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) { int width = imp.getWidth(); int height = imp.getHeight(); type = gd.getNextChoice(); areaPerPoint = gd.getNextNumber(); color = gd.getNextChoice(); randomOffset = gd.getNextBoolean(); double minArea = (width * height) / 50000.0; if (type.equals(types[1]) && minArea < 144.0) minArea = 144.0; else if (minArea < 16) minArea = 16.0; if (areaPerPoint / (pixelWidth * pixelHeight) < minArea) { String err = "\"Area per Point\" too small"; if (gd.wasOKed()) IJ.error("Grid", err); else IJ.showStatus(err); return true; } double tileSize = Math.sqrt(areaPerPoint); tileWidth = tileSize / pixelWidth; tileHeight = tileSize / pixelHeight; if (randomOffset) { xstart = (int) (random.nextDouble() * tileWidth); ystart = (int) (random.nextDouble() * tileHeight); } else { xstart = (int) (tileWidth / 2.0 + 0.5); ystart = (int) (tileHeight / 2.0 + 0.5); } linesV = (int) ((width - xstart) / tileWidth) + 1; linesH = (int) ((height - ystart) / tileHeight) + 1; if (gd.invalidNumber()) return true; if (type.equals(types[0])) drawLines(); else if (type.equals(types[1])) drawCrosses(); else if (type.equals(types[2])) drawPoints(); else showGrid(null); return true; }
void setHistogram(ImagePlus imp, int j) { ImageProcessor ip = imp.getProcessor(); ImageStatistics stats = ImageStatistics.getStatistics(ip, AREA + MODE, null); int maxCount2 = 0; histogram = stats.histogram; for (int i = 0; i < stats.nBins; i++) if ((histogram[i] > maxCount2) && (i != stats.mode)) maxCount2 = histogram[i]; hmax = stats.maxCount; if ((hmax > (maxCount2 * 1.5)) && (maxCount2 != 0)) { // GL 1.5 was 2 hmax = (int) (maxCount2 * 1.1); // GL 1.1 was 1.5 histogram[stats.mode] = hmax; } os = null; ColorModel cm = ip.getColorModel(); if (!(cm instanceof IndexColorModel)) return; IndexColorModel icm = (IndexColorModel) cm; int mapSize = icm.getMapSize(); if (mapSize != 256) return; byte[] r = new byte[256]; byte[] g = new byte[256]; byte[] b = new byte[256]; icm.getReds(r); icm.getGreens(g); icm.getBlues(b); hColors = new Color[256]; if (isRGB) { if (j == 0) { for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, 0 & 255, 0 & 255); } else if (j == 1) { for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, i & 255, 0 & 255); } else if (j == 2) { for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, 0 & 255, i & 255); } } else { if (j == 0) { for (int i = 0; i < 256; i++) hColors[i] = new Color(r[i] & 255, g[i] & 255, b[i] & 255); } else if (j == 1) { for (int i = 0; i < 256; i++) // hColors[i] = new Color(127-i/2&255, 127+i/2&255, 127-i/2&255); hColors[i] = new Color(192 - i / 4 & 255, 192 + i / 4 & 255, 192 - i / 4 & 255); } else if (j == 2) { for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, i & 255, 0 & 255); } } }
// at the very end - show output image (if the is a separate one) private void showOutput() { if (interrupted) return; if (outStack != null) { outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outStack); int[] d = imp.getDimensions(); outImp.setDimensions(d[2], d[3], d[4]); for (int i = 1; i <= imp.getStackSize(); i++) outStack.setSliceLabel(imp.getStack().getSliceLabel(i), i); } if (outImageType != BYTE_OVERWRITE) { ImageProcessor ip = outImp.getProcessor(); if (!Prefs.blackBackground) ip.invertLut(); ip.resetMinAndMax(); outImp.show(); } }
void applyStack() { // int minKeepH = minHue, maxKeepH = maxHue; //GL not needed? // int minKeepS = minSat, maxKeepS = maxSat; // int minKeepB = minBri, maxKeepB = maxBri; for (int i = 1; i <= numSlices; i++) { imp.setSlice(i); if (!checkImage()) { IJ.beep(); IJ.showStatus("No Image"); return; } // minHue = minKeepH; // maxHue = maxKeepH; // minSat = minKeepS; // maxSat = maxKeepS; // minBri = minKeepB; // maxBri = maxKeepB; apply(imp, ip); } }
/** Mask central offset / low freq spike to better use display range. */ private void maskCentralRegion(ImagePlus imp) { int w = imp.getWidth(); double d = this.maskDiameter * w; if (w % 2 == 0) { d += 1; // tweak to centre the mask about zero freq stripes } // N.B. we assume the image is square! (FFT result) OvalRoi mask = new OvalRoi(w / 2 - d / 2 + 1, w / 2 - d / 2 + 1, d, d); imp.setRoi(mask); for (int c = 1; c <= imp.getNChannels(); c++) { imp.setC(c); double min = I1l.getStatsForChannel(imp, c).min; IJ.run(imp, "Set...", "value=" + min + " slice"); } imp.setC(1); imp.deleteRoi(); }
void showGrid(Shape shape) { ImageCanvas ic = imp.getCanvas(); if (ic == null) return; if (shape == null) ic.setDisplayList(null); else ic.setDisplayList(shape, getColor(), null); }
public void keyPressed(KeyEvent e) { // if (e.isConsumed()) return; int keyCode = e.getKeyCode(); IJ.setKeyDown(keyCode); hotkey = false; if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return; char keyChar = e.getKeyChar(); int flags = e.getModifiers(); if (IJ.debugMode) IJ.log( "keyPressed: code=" + keyCode + " (" + KeyEvent.getKeyText(keyCode) + "), char=\"" + keyChar + "\" (" + (int) keyChar + "), flags=" + KeyEvent.getKeyModifiersText(flags)); boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0; boolean control = (flags & KeyEvent.CTRL_MASK) != 0; boolean alt = (flags & KeyEvent.ALT_MASK) != 0; boolean meta = (flags & KeyEvent.META_MASK) != 0; String cmd = null; ImagePlus imp = WindowManager.getCurrentImage(); boolean isStack = (imp != null) && (imp.getStackSize() > 1); if (imp != null && !control && ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) { Roi roi = imp.getRoi(); if (roi instanceof TextRoi) { if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return; if (alt) { switch (keyChar) { case 'u': case 'm': keyChar = IJ.micronSymbol; break; case 'A': keyChar = IJ.angstromSymbol; break; default: } } ((TextRoi) roi).addChar(keyChar); return; } } // Handle one character macro shortcuts if (!control && !meta) { Hashtable macroShortcuts = Menus.getMacroShortcuts(); if (macroShortcuts.size() > 0) { if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200)); else cmd = (String) macroShortcuts.get(new Integer(keyCode)); if (cmd != null) { // MacroInstaller.runMacroCommand(cmd); commandName = cmd; MacroInstaller.runMacroShortcut(cmd); return; } } } if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') { Hashtable shortcuts = Menus.getShortcuts(); if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200)); else cmd = (String) shortcuts.get(new Integer(keyCode)); } if (cmd == null) { switch (keyChar) { case '<': case ',': if (isStack) cmd = "Previous Slice [<]"; break; case '>': case '.': case ';': if (isStack) cmd = "Next Slice [>]"; break; case '+': case '=': cmd = "In [+]"; break; case '-': cmd = "Out [-]"; break; case '/': cmd = "Reslice [/]..."; break; default: } } if (cmd == null) { switch (keyCode) { case KeyEvent.VK_TAB: WindowManager.putBehind(); return; case KeyEvent.VK_BACK_SPACE: // delete if (deleteOverlayRoi(imp)) return; cmd = "Clear"; hotkey = true; break; // case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start // Animation"; break; case KeyEvent.VK_EQUALS: cmd = "In [+]"; break; case KeyEvent.VK_MINUS: cmd = "Out [-]"; break; case KeyEvent.VK_SLASH: case 0xbf: cmd = "Reslice [/]..."; break; case KeyEvent.VK_COMMA: case 0xbc: if (isStack) cmd = "Previous Slice [<]"; break; case KeyEvent.VK_PERIOD: case 0xbe: if (isStack) cmd = "Next Slice [>]"; break; case KeyEvent.VK_LEFT: case KeyEvent.VK_RIGHT: case KeyEvent.VK_UP: case KeyEvent.VK_DOWN: // arrow keys if (imp == null) return; Roi roi = imp.getRoi(); if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return; boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown()); boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown(); if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]"; else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]"; else if (zoomKey && keyCode == KeyEvent.VK_DOWN && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]"; else if (zoomKey && keyCode == KeyEvent.VK_UP && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]"; else if (roi != null) { if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode); else roi.nudge(keyCode); return; } break; case KeyEvent.VK_ESCAPE: abortPluginOrMacro(imp); return; case KeyEvent.VK_ENTER: WindowManager.toFront(this); return; default: break; } } if (cmd != null && !cmd.equals("")) { commandName = cmd; if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true; if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd); else { doCommand(cmd); keyPressedTime = System.currentTimeMillis(); lastKeyCommand = cmd; } } }