/** Return the ROI Manager "Show All" list as an overlay. */ public Overlay getShowAllList() { if (!showAllROIs) return null; if (showAllList != null) return showAllList; RoiManager rm = RoiManager.getInstance(); if (rm == null) return null; Roi[] rois = rm.getRoisAsArray(); if (rois.length == 0) return null; Overlay overlay = new Overlay(); for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone()); return overlay; }
public boolean checkBeads() { rmanager = RoiManager.getInstance(); if (IJ.versionLessThan("1.26i")) return false; else if (rmanager == null) { IJ.error("Add bead ROIs to the RoiManager first (select region then press [t])."); return false; } nrois = rmanager.getCount(); if (nrois == 0) { IJ.error("Add bead ROIs to the RoiManager first (select region then press [t])."); return false; } rois = rmanager.getRoisAsArray(); return true; }
void fromRoiManager() { ImagePlus imp = IJ.getImage(); RoiManager rm = RoiManager.getInstance(); if (rm == null) { IJ.error("ROI Manager is not open"); return; } Roi[] rois = rm.getRoisAsArray(); if (rois.length == 0) { IJ.error("ROI Manager is empty"); return; } Overlay overlay = new Overlay(); for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone()); imp.setOverlay(overlay); ImageCanvas ic = imp.getCanvas(); if (ic != null) ic.setShowAllROIs(false); rm.setEditMode(imp, false); imp.killRoi(); }
public void run(ImageProcessor ip) { String[] imageNames = getOpenImageNames(); if (imageNames[0] == "None") { IJ.error("need at least 2 binary open images"); return; } double previousMinOverlap = Prefs.get("BVTB.BinaryFeatureExtractor.minOverlap", 0); boolean previousCombine = Prefs.get("BVTB.BinaryFeatureExtractor.combine", false); GenericDialog gd = new GenericDialog("Binary Feature Extractor"); gd.addChoice("Objects image", imageNames, imageNames[0]); gd.addChoice("Selector image", imageNames, imageNames[1]); gd.addNumericField("Object_overlap in % (0=off)", previousMinOverlap, 0, 9, ""); gd.addCheckbox("Combine objects and selectors", previousCombine); gd.addCheckbox("Count output", true); gd.addCheckbox("Analysis tables", false); gd.showDialog(); if (gd.wasCanceled()) { return; } String objectsImgTitle = gd.getNextChoice(); String selectorsImgTitle = gd.getNextChoice(); double minOverlap = gd.getNextNumber(); boolean combineImages = gd.getNextBoolean(); boolean showCountOutput = gd.getNextBoolean(); boolean showAnalysis = gd.getNextBoolean(); if (gd.invalidNumber() || minOverlap < 0 || minOverlap > 100) { IJ.error("invalid number"); return; } Prefs.set("BVTB.BinaryFeatureExtractor.minOverlap", minOverlap); Prefs.set("BVTB.BinaryFeatureExtractor.combine", combineImages); if (objectsImgTitle.equals(selectorsImgTitle)) { IJ.error("images need to be different"); return; } ImagePlus objectsImp = WindowManager.getImage(objectsImgTitle); ImageProcessor objectsIP = objectsImp.getProcessor(); ImagePlus selectorsImp = WindowManager.getImage(selectorsImgTitle); ImageProcessor selectorsIP = selectorsImp.getProcessor(); if (!objectsIP.isBinary() || !selectorsIP.isBinary()) { IJ.error("works with 8-bit binary images only"); return; } if ((objectsImp.getWidth() != selectorsImp.getWidth()) || objectsImp.getHeight() != selectorsImp.getHeight()) { IJ.error("images need to be of the same size"); return; } // close any existing RoiManager before instantiating a new one for this analysis RoiManager oldRM = RoiManager.getInstance2(); if (oldRM != null) { oldRM.close(); } RoiManager objectsRM = new RoiManager(true); ResultsTable objectsRT = new ResultsTable(); ParticleAnalyzer analyzeObjects = new ParticleAnalyzer(analyzerOptions, measurementFlags, objectsRT, 0.0, 999999999.9); analyzeObjects.setRoiManager(objectsRM); analyzeObjects.analyze(objectsImp); objectsRM.runCommand("Show None"); int objectNumber = objectsRT.getCounter(); Roi[] objectRoi = objectsRM.getRoisAsArray(); ResultsTable measureSelectorsRT = new ResultsTable(); Analyzer overlapAnalyzer = new Analyzer(selectorsImp, measurementFlags, measureSelectorsRT); ImagePlus outputImp = IJ.createImage("output", "8-bit black", objectsImp.getWidth(), objectsImp.getHeight(), 1); ImageProcessor outputIP = outputImp.getProcessor(); double[] measuredOverlap = new double[objectNumber]; outputIP.setValue(255.0); for (int o = 0; o < objectNumber; o++) { selectorsImp.killRoi(); selectorsImp.setRoi(objectRoi[o]); overlapAnalyzer.measure(); measuredOverlap[o] = measureSelectorsRT.getValue("%Area", o); if (minOverlap != 0.0 && measuredOverlap[o] >= minOverlap) { outputIP.fill(objectRoi[o]); finalCount++; } else if (minOverlap == 0.0 && measuredOverlap[o] > 0.0) { outputIP.fill(objectRoi[o]); finalCount++; } } // measureSelectorsRT.show("Objects"); selectorsImp.killRoi(); RoiManager selectorRM = new RoiManager(true); ResultsTable selectorRT = new ResultsTable(); ParticleAnalyzer.setRoiManager(selectorRM); ParticleAnalyzer analyzeSelectors = new ParticleAnalyzer(analyzerOptions, measurementFlags, selectorRT, 0.0, 999999999.9); analyzeSelectors.analyze(selectorsImp); selectorRM.runCommand("Show None"); int selectorNumber = selectorRT.getCounter(); if (combineImages) { outputImp.updateAndDraw(); Roi[] selectorRoi = selectorRM.getRoisAsArray(); ResultsTable measureObjectsRT = new ResultsTable(); Analyzer selectorAnalyzer = new Analyzer(outputImp, measurementFlags, measureObjectsRT); double[] selectorOverlap = new double[selectorNumber]; outputIP.setValue(255.0); for (int s = 0; s < selectorNumber; s++) { outputImp.killRoi(); outputImp.setRoi(selectorRoi[s]); selectorAnalyzer.measure(); selectorOverlap[s] = measureObjectsRT.getValue("%Area", s); if (selectorOverlap[s] > 0.0d) { outputIP.fill(selectorRoi[s]); } } selectorRoi = null; selectorAnalyzer = null; measureObjectsRT = null; } // selectorRT.show("Selectors"); outputImp.killRoi(); String outputImageTitle = WindowManager.getUniqueName("Extracted_" + objectsImgTitle); outputImp.setTitle(outputImageTitle); outputImp.show(); outputImp.changes = true; if (showCountOutput) { String[] openTextWindows = WindowManager.getNonImageTitles(); boolean makeNewTable = true; for (int w = 0; w < openTextWindows.length; w++) { if (openTextWindows[w].equals("BFE_Results")) { makeNewTable = false; } } TextWindow existingCountTable = ResultsTable.getResultsWindow(); if (makeNewTable) { countTable = new ResultsTable(); countTable.setPrecision(0); countTable.setValue("Image", 0, outputImageTitle); countTable.setValue("Objects", 0, objectNumber); countTable.setValue("Selectors", 0, selectorNumber); countTable.setValue("Extracted", 0, finalCount); countTable.show("BFE_Results"); } else { IJ.renameResults("BFE_Results", "Results"); countTable = ResultsTable.getResultsTable(); countTable.setPrecision(0); countTable.incrementCounter(); countTable.addValue("Image", outputImageTitle); countTable.addValue("Objects", objectNumber); countTable.addValue("Selectors", selectorNumber); countTable.addValue("Extracted", finalCount); IJ.renameResults("Results", "BFE_Results"); countTable.show("BFE_Results"); } } if (showAnalysis) { ResultsTable extractedRT = new ResultsTable(); ParticleAnalyzer analyzeExtracted = new ParticleAnalyzer( ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.RECORD_STARTS, measurementFlags, extractedRT, 0.0, 999999999.9); analyzeExtracted.analyze(outputImp); objectsRT.show("Objects"); selectorRT.show("Selectors"); extractedRT.show("Extracted"); } else { objectsRT = null; selectorRT = null; } objectsRM = null; measureSelectorsRT = null; analyzeObjects = null; overlapAnalyzer = null; objectRoi = null; selectorRM = null; objectsImp.killRoi(); objectsImp.changes = false; selectorsImp.changes = false; }
public void run(String arg) { String[] labels = { "Masked_Chromosomes", "Unmixed_Image", "Spectral_Image(optional)", "Spectra(optional)" }; ImagePlus[] imps = jutils.selectImages(true, 4, labels); if (imps == null) { return; } if (imps[0] == null) { return; } float[] mask = (float[]) imps[0].getStack().getPixels(2); findblobs3 fb = new findblobs3(imps[0].getWidth(), imps[0].getHeight()); float[] objects = fb.dofindblobs(mask, 0.5f); WaitForUserDialog dg = new WaitForUserDialog( "Optional Input", "Place RoiManager Points on Chromosome Segments (if desired)"); dg.show(); if (!dg.escPressed()) { RoiManager rman = RoiManager.getInstance(); while (rman != null && rman.getCount() > 1) { Roi[] rois = rman.getRoisAsArray(); int[] ids = new int[rois.length]; for (int i = 0; i < rois.length; i++) { Rectangle r = rois[i].getBounds(); ids[i] = (int) objects[r.x + fb.width * r.y]; } objects = fb.link_objects(objects, ids); rman.reset(); dg = new WaitForUserDialog( "Optional Input", "Place More RoiManager Points on Chromosome Segments (if desired)"); dg.show(); if (dg.escPressed()) break; } } int[] areas = fb.get_areas(objects); int[] temprank = jsort.get_javasort_order(areas); int[] arearank = jsort.get_javasort_order(temprank); for (int i = 0; i < fb.nobjects; i++) { arearank[i] = fb.nobjects - arearank[i] - 1; } // if the spectra are available, get them float[][][] spectra = null; Object[] data = null; if (imps[1] != null && imps[2] != null && imps[3] != null) { ImageWindow iw = imps[3].getWindow(); if (iw.getClass().getName().equals("jguis.PlotWindow4")) { float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues"); data = jutils.stack2array(imps[2].getStack()); Object[] coef = jutils.stack2array(imps[1].getStack()); spectra = new float[fb.nobjects][2][]; for (int i = 0; i < fb.nobjects; i++) { spectra[i][0] = fb.get_object_spectrum(objects, (i + 1), data, "Sum"); spectra[i][1] = new float[yvals[0].length]; float[] tempcoef = fb.get_object_spectrum(objects, (i + 1), coef, "Sum"); for (int j = 0; j < yvals[0].length; j++) { for (int k = 0; k < 5; k++) { spectra[i][1][j] += tempcoef[k] * yvals[k][j]; } } } } } CompositeImage imp = (CompositeImage) imps[0]; imp.setPosition(1, 1, 1); LUT graylut = jutils.get_lut_for_color(Color.white); imp.setChannelColorModel(graylut); imp.setPosition(2, 1, 1); LUT redlut = jutils.get_lut_for_color(Color.red); imp.setChannelColorModel(redlut); imp.setPosition(1, 1, 1); imp.updateAndRepaintWindow(); SkyPanel_v3 sp = new SkyPanel_v3(); int skychan = 6; if (imps[1] != null) skychan = imps[1].getNChannels(); // assume that the sky image has 6 channels and that the second is the unknown green // shift the unknown green to the end ImagePlus skyimp = null; if (imps[1] != null) { Object[] skystack = jutils.stack2array(imps[1].getStack()); // Object[] // skystack2={skystack[0],skystack[2],skystack[3],skystack[4],skystack[5],skystack[1]}; Object[] skystack2 = null; if (skychan == 6) skystack2 = new Object[] {skystack[0], skystack[2], skystack[3], skystack[4], skystack[5]}; else skystack2 = new Object[] {skystack[0], skystack[1], skystack[2], skystack[3], skystack[4]}; skyimp = new ImagePlus( "rearranged", jutils.array2stack(skystack2, imps[1].getWidth(), imps[1].getHeight())); } int nch = 5; if (skyimp != null) nch = skyimp.getStack().getSize(); GenericDialog gd2 = new GenericDialog("Options"); gd2.addNumericField("Area Accuracy (percent)", 30, 0); for (int i = 0; i < nch; i++) { gd2.addNumericField("Ch_" + (i + 1) + "_Contr_Thresh", 0.35, 5, 15, null); } // gd2.addNumericField("Contribution Threshold",0.35,5,15,null); gd2.addCheckbox("Mouse?", false); gd2.addNumericField("Box_Width", 150, 0); gd2.addNumericField("Box_Height", 100, 0); gd2.showDialog(); if (gd2.wasCanceled()) { return; } sp.areathresh = (float) gd2.getNextNumber(); sp.objthresh2 = new float[nch]; for (int i = 0; i < nch; i++) sp.objthresh2[i] = (float) gd2.getNextNumber(); // sp.objthresh=(float)gd2.getNextNumber(); boolean mouse = gd2.getNextBoolean(); int bwidth = (int) gd2.getNextNumber(); int bheight = (int) gd2.getNextNumber(); int[] colorindices = {4, 1, 2, 6, 3}; GenericDialog gd3 = new GenericDialog("Color Options"); for (int i = 0; i < 5; i++) gd3.addChoice( "Ch" + (i + 1) + " Color", SkyPanel_v3.colornames, SkyPanel_v3.colornames[colorindices[i]]); gd3.showDialog(); if (gd3.wasCanceled()) return; for (int i = 0; i < 5; i++) colorindices[i] = gd3.getNextChoiceIndex(); sp.colorindices = colorindices; sp.nch = 5; sp.dapilast = false; sp.cellwidth = bwidth; sp.cellheight = bheight; sp.init(imps[0], skyimp, objects, areas, arearank, fb, true, spectra, data, mouse); SkyPanel_v3.launch_frame(sp); }