/** 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); }
public String[] getOpenImageNames() { int[] imageIDList = WindowManager.getIDList(); String[] imageNames = new String[imageIDList.length]; // imageNames[0] = "None"; if (!imageIDList.equals(null) && imageIDList.length > 1) { for (int i = 0; i < imageIDList.length; i++) { ImagePlus tempIMP = WindowManager.getImage(imageIDList[i]); imageNames[i] = tempIMP.getTitle(); } return imageNames; } else { imageNames[0] = "None"; return imageNames; } }
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; }
void addImage() { ImagePlus imp = IJ.getImage(); int[] wList = WindowManager.getIDList(); if (wList == null || wList.length < 2) { IJ.error("Add Image...", "The command requires at least two open images."); return; } String[] titles = new String[wList.length]; for (int i = 0; i < wList.length; i++) { ImagePlus imp2 = WindowManager.getImage(wList[i]); titles[i] = imp2 != null ? imp2.getTitle() : ""; } int x = 0, y = 0; Roi roi = imp.getRoi(); if (roi != null && roi.isArea()) { Rectangle r = roi.getBounds(); x = r.x; y = r.y; } int index = 0; if (wList.length == 2) { ImagePlus i1 = WindowManager.getImage(wList[0]); ImagePlus i2 = WindowManager.getImage(wList[1]); if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1; } else if (imp.getID() == wList[0]) index = 1; GenericDialog gd = new GenericDialog("Add Image..."); gd.addChoice("Image to add:", titles, titles[index]); gd.addNumericField("X location:", x, 0); gd.addNumericField("Y location:", y, 0); gd.addNumericField("Opacity (0-100%):", 100, 0); gd.addCheckbox("Create image selection", createImageRoi); gd.showDialog(); if (gd.wasCanceled()) return; index = gd.getNextChoiceIndex(); x = (int) gd.getNextNumber(); y = (int) gd.getNextNumber(); double opacity = gd.getNextNumber() / 100.0; createImageRoi = gd.getNextBoolean(); ImagePlus overlay = WindowManager.getImage(wList[index]); if (wList.length == 2) { ImagePlus i1 = WindowManager.getImage(wList[0]); ImagePlus i2 = WindowManager.getImage(wList[1]); if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) { imp = i1; overlay = i2; } } if (overlay == imp) { IJ.error( "Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\"."); return; } if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) { IJ.error( "Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\"."); return; } if (createImageRoi && x == 0 && y == 0) { x = imp.getWidth() / 2 - overlay.getWidth() / 2; y = imp.getHeight() / 2 - overlay.getHeight() / 2; } roi = new ImageRoi(x, y, overlay.getProcessor()); roi.setName(overlay.getShortTitle()); if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity); if (createImageRoi) imp.setRoi(roi); else { Overlay overlayList = imp.getOverlay(); if (overlayList == null) overlayList = new Overlay(); overlayList.add(roi); imp.setOverlay(overlayList); overlay2 = overlayList; Undo.setup(Undo.OVERLAY_ADDITION, imp); } }
public void run(String arg) { int[] wList = WindowManager.getIDList(); if (wList==null) { IJ.error("No images are open."); return; } double kernel=3; double kernelsum = 0; double kernelvarsum =0; double kernalvar = 0; double sigmawidth = 2; int kernelindex, minpixnumber; String[] kernelsize = { "3�,"5�, "7�, "9�}; GenericDialog gd = new GenericDialog("Sigma Filter"); gd.addChoice("Kernel size", kernelsize, kernelsize[0]); gd.addNumericField("Sigma width",sigmawidth , 2); gd.addNumericField("Minimum number of pixels", 1, 0); gd.addCheckbox("Keep source:",true); gd.addCheckbox("Do all stack:",true); gd.addCheckbox("Modified Lee's FIlter:",true); gd.showDialog(); if (gd.wasCanceled()) return ; kernelindex = gd.getNextChoiceIndex(); sigmawidth = gd.getNextNumber(); minpixnumber = ((int)gd.getNextNumber()); boolean keep = gd.getNextBoolean(); boolean doallstack = gd.getNextBoolean(); boolean modified = gd.getNextBoolean(); if (kernelindex==0) kernel = 3; if (kernelindex==1) kernel = 5; if (kernelindex==2) kernel = 7; if (kernelindex==3) kernel = 9; long start = System.currentTimeMillis(); if (minpixnumber> (kernel*kernel)){ IJ.showMessage("Sigma filter", "There must be more pixels in the kernel than+\n" + "the minimum number to be included"); return; } double v, midintensity; int x, y, ix, iy; double sum = 0; double backupsum =0; int count = 0; int n = 0; if (keep) {IJ.run("Select All"); IJ.run("Duplicate...", "title='Sigma filtered' duplicate");} int radius = (int)(kernel-1)/2; ImagePlus imp = WindowManager.getCurrentImage(); ImageStack stack1 = imp.getStack(); int width = imp.getWidth(); int height = imp.getHeight(); int nslices = stack1.getSize(); int cslice = imp.getCurrentSlice(); double status = width*height*nslices; ImageProcessor ip = imp.getProcessor(); int sstart = 1; if (!doallstack) {sstart = cslice; nslices=sstart;status = status/nslices;}; for (int i=sstart; i<=nslices; i++) { imp.setSlice(i); for (x=radius;x<width+radius;x++) { for (y=radius;y<height+radius;y++) { midintensity = ip.getPixelValue(x,y); count = 0; sum = 0; kernelsum =0; kernalvar =0; kernelvarsum =0; backupsum = 0; //calculate mean of kernel value for (ix=0;ix<kernel;ix++) { for (iy=0;iy<kernel;iy++) { v = ip.getPixelValue(x+ix-radius,y+iy-radius); kernelsum = kernelsum+v; } } double sigmacalcmean = (kernelsum/(kernel*kernel)); //calculate variance of kernel for (ix=0;ix<kernel;ix++) { for (iy=0;iy<kernel;iy++) { v = ip.getPixelValue(x+ix-radius,y+iy-radius); kernalvar = (v-sigmacalcmean)*(v-sigmacalcmean); kernelvarsum = kernelvarsum + kernalvar; } } //double variance = kernelvarsum/kernel; double sigmacalcvar = kernelvarsum/((kernel*kernel)-1); //calcuate sigma range = sqrt(variance/(mean^2)) � sigmawidth double sigmarange = sigmawidth*(Math.sqrt((sigmacalcvar) /(sigmacalcmean*sigmacalcmean))); //calulate sigma top value and bottom value double sigmatop = midintensity*(1+sigmarange); double sigmabottom = midintensity*(1-sigmarange); //calculate mean of values that differ are in sigma range. for (ix=0;ix<kernel;ix++) { for (iy=0;iy<kernel;iy++) { v = ip.getPixelValue(x+ix-radius,y+iy-radius); if ((v>=sigmabottom)&&(v<=sigmatop)){ sum = sum+v; count = count+1; } backupsum = v+ backupsum; } } //if there are too few pixels in the kernal that are within sigma range, the //mean of the entire kernal is taken. My modification of Lee's filter is to exclude the central value //from the calculation of the mean as I assume it to be spuriously high or low if (!(count>(minpixnumber))) {sum = (backupsum-midintensity); count = (int)((kernel*kernel)-1); if (!modified) {sum = (backupsum); count = (int)(kernel*kernel);} } double val = (sum/count); ip.putPixelValue(x,y, val); n = n+1; double percentage = (((double)n/status)*100); IJ.showStatus(IJ.d2s(percentage,0) +"% done"); } // IJ.showProgress(i, status); }} imp.updateAndDraw(); IJ.showStatus(IJ.d2s((System.currentTimeMillis()-start)/1000.0, 2)+" seconds"); }