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); }
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; }
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; }
public void run(String arg) { GenericDialog gd = new GenericDialog("Options"); double sfreq = 20000.0; gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null); String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"}; gd.addChoice("PSF Type?", psfchoice, psfchoice[0]); String[] filetypechoice = { "Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File" }; gd.addChoice("File Type?", filetypechoice, filetypechoice[0]); boolean ch2green = true; gd.addCheckbox("Ch2 is green?", ch2green); gd.showDialog(); if (gd.wasCanceled()) { return; } sfreq = gd.getNextNumber(); int psfflag = gd.getNextChoiceIndex(); int fileflag = gd.getNextChoiceIndex(); ch2green = gd.getNextBoolean(); int nfiles = 0; Object[] histograms = null; int xmax = 0; int ymax = 0; String[] names = null; if (fileflag < 2) { jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length / 2; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = organize_c3_files(filearray); for (int i = 0; i < nfiles; i++) { try { int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0); int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0); int length3 = (int) (((double) filearray[2 * i].length()) / 2.0); int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0); InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i])); InputStream instream2 = new BufferedInputStream(new FileInputStream(filearray[2 * i + 1])); if (fileflag == 0) { int[] pmdata = new int[length1]; int[] pmdata2 = new int[length2]; if (!ioclass.skipstreambytes(instream, 128)) { showioerror(); instream.close(); return; } if (!ioclass.skipstreambytes(instream2, 128)) { showioerror(); instream2.close(); return; } if (!ioclass.readintelintfile(instream, length1, pmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelintfile(instream2, length2, pmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000); } else { histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000); } } else { float[] tmdata = new float[length3]; float[] tmdata2 = new float[length4]; if (!ioclass.readintelshortfile(instream, length3, tmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata); } else { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2); } } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } instream.close(); instream2.close(); } catch (IOException e) { showioerror(); return; } } } else { if (fileflag == 2) { ImageWindow iw = WindowManager.getCurrentWindow(); float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues"); float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues"); sfreq = 1.0 / ((double) tempxvals[0][1]); nfiles = trajectories.length / 2; if (nfiles > 25) { nfiles = 25; } names = new String[nfiles + 1]; names[nfiles] = "avg"; histograms = new Object[nfiles]; for (int i = 0; i < nfiles; i++) { names[i] = "trajectory " + (i + 1); if (ch2green) { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]); } else { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]); } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } else { // here we read tab delimited lines from files jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = new String[nfiles + 1]; names[nfiles] = "avg"; for (int i = 0; i < nfiles; i++) { try { names[i] = filearray[i].getName(); BufferedReader d = new BufferedReader(new FileReader(filearray[i])); String[] lines = new String[256]; int counter = 0; do { lines[counter] = d.readLine(); counter++; } while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256); int numcolumns = 0; for (int j = 0; j < counter - 1; j++) { int temp = getncolumns(lines[j]); if (temp > numcolumns) { numcolumns = temp; } } float[][] temphist2 = null; if (ch2green) { temphist2 = new float[numcolumns][counter - 1]; } else { temphist2 = new float[counter - 1][numcolumns]; } for (int k = 0; k < counter - 1; k++) { float[] temp = tab_delim2float(lines[k]); for (int j = 0; j < numcolumns; j++) { if (ch2green) { temphist2[j][k] = temp[j]; } else { temphist2[k][j] = temp[j]; } } } histograms[i] = temphist2; d.close(); } catch (IOException e) { showioerror(); return; } } for (int i = 0; i < nfiles; i++) { if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } } // note that here x is green and y is red float[][][] pch = new float[nfiles][xmax][ymax]; for (int i = 0; i < nfiles; i++) { for (int j = 0; j < ((float[][]) histograms[i]).length; j++) { for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) { pch[i][j][k] = ((float[][]) histograms[i])[j][k]; } } } final PCH2DFitWindow cw = new PCH2DFitWindow(); cw.init(names, pch, psfflag); final Frame f = new Frame("PCH 2D Analysis"); f.setLocation(10, 10); f.addWindowListener( new WindowAdapter() { public void windowClosing(WindowEvent e) { f.dispose(); } }); f.add(cw); f.pack(); f.setResizable(false); Insets ins = f.getInsets(); cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65; cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right; f.setSize(cw.totalSize); f.setVisible(true); cw.requestFocus(); }
private void geterrors() { GenericDialog gd = new GenericDialog("Options"); float conf = 0.67f; gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null); gd.addChoice("Error Parameter", paramsnames, paramsnames[0]); double spacing = 0.01; gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null); boolean globalerror = false; gd.addCheckbox("Global Fit Error?", globalerror); int dataset = 0; gd.addNumericField("Data Set (for Global Error)", dataset, 0); gd.showDialog(); if (gd.wasCanceled()) { return; } conf = 0.01f * (float) gd.getNextNumber(); int paramindex = (int) gd.getNextChoiceIndex(); spacing = 0.01 * gd.getNextNumber(); globalerror = gd.getNextBoolean(); dataset = (int) gd.getNextNumber(); if (globalerror) { support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1); int[] erindeces = {paramindex, dataset}; // need to set up all the matrices int nsel = 0; int nparams = 11; for (int i = 0; i < ncurves; i++) { if (include[i]) { nsel++; } } double[][] params = new double[nsel][nparams]; String[][] tempformulas = new String[nsel][nparams]; double[][][] constraints = new double[2][nsel][nparams]; int[][] vflmatrix = new int[nsel][nparams]; float[][] tempdata = new float[nsel][xpts * ypts]; float[][] tempweights = new float[nsel][xpts * ypts]; int nfit = 0; int counter = 0; for (int i = 0; i < ncurves; i++) { if (include[i]) { for (int j = 0; j < nparams; j++) { params[counter][j] = globalparams[i][j]; tempformulas[counter][j] = globalformulas[i][j]; constraints[0][counter][j] = globalconstraints[0][i][j]; constraints[1][counter][j] = globalconstraints[1][i][j]; vflmatrix[counter][j] = globalvflmatrix[i][j]; if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) { nfit++; } } for (int j = 0; j < xpts; j++) { for (int k = 0; k < ypts; k++) { tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]); tempweights[counter][j + k * xpts] = weights[i][j][k]; } } counter++; } } int dofnum = xpts * ypts * nsel - (nfit - 1) - 1; int dofden = xpts * ypts * nsel - nfit - 1; // double flim=FLimit(dofnum,dofden,(double)conf); double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return; } double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing); double[][] c2plot = erclass.geterrorsglobal( params, vflmatrix, tempformulas, paramsnames, constraints, tempdata, tempweights, flim, truespacing, erindeces); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4( "c2 plot", paramsnames[paramindex] + "[" + dataset + "]", "Chi^2", c2plotf[0], c2plotf[1]) .draw(); } else { support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1); int errindex = paramindex; float[] tempdata = new float[xpts * ypts]; float[] tempweights = new float[xpts * ypts]; for (int i = 0; i < xpts; i++) { for (int j = 0; j < ypts; j++) { tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]); tempweights[i + j * xpts] = avgweights[i][j]; } } int nfit = 0; for (int i = 0; i < 7; i++) { if (avgfixes[i] == 0) { nfit++; } } int dofnum = xpts * ypts - (nfit - 1) - 1; int dofden = xpts * ypts - nfit - 1; double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return; } double truespacing = Math.abs(avgparams[errindex] * spacing); double[][] c2plot = erclass.geterrors( avgparams, avgfixes, avgconstraints, tempdata, tempweights, flim, truespacing, errindex); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw(); } }
public boolean get_errors(double[] params, int[] fixes) { GenericDialog gd = new GenericDialog("Error Options"); String[] methods = {"Support Plane", "Monte Carlo"}; gd.addChoice("Method", methods, methods[0]); float conf = 0.67f; gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null); String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"}; gd.addChoice("SP_Parameter", labels, labels[0]); double spacing = 0.01; gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null); int ntrials = 100; gd.addNumericField("MC_#_Trials", ntrials, 0); gd.showDialog(); if (gd.wasCanceled()) { return false; } int methodindex = gd.getNextChoiceIndex(); conf = 0.01f * (float) gd.getNextNumber(); int paramindex = gd.getNextChoiceIndex(); spacing = 0.01 * gd.getNextNumber(); ntrials = (int) gd.getNextNumber(); if (methodindex == 0) { support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1); int errindex = paramindex; int nfit = 0; for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) { nfit++; } } int npts = tempdata.length; int dofnum = npts - (nfit - 1) - 1; int dofden = npts - nfit - 1; double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return false; } double truespacing = Math.abs(params[errindex] * spacing); double[][] c2plot = erclass.geterrors( params, fixes, constraints, tempdata, weights, flim, truespacing, errindex); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); IJ.log( "upper error = " + (c2plot[1][0] - params[errindex]) + " lower error = " + (params[errindex] - c2plot[0][0])); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4("c2 plot", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw(); } else { StringBuffer sb = new StringBuffer(); sb.append("Trial\t"); for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) sb.append(labels[i] + "\t"); } sb.append("chi^2"); tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400); redirect = true; monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1); double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials); sb = new StringBuffer(); sb.append("StDev\t"); for (int i = 0; i < errors.length; i++) { float[] ferr = new float[errors[0].length]; for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j]; float stdev = jstatistics.getstatistic("StDev", ferr, null); sb.append("" + stdev); if (i < (errors.length - 1)) sb.append("\t"); } tw.append(sb.toString()); redirect = false; } return true; }
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"); }
public void run(String arg) { Frame[] niframes = WindowManager.getNonImageWindows(); String[] titles = new String[niframes.length + 1]; for (int i = 0; i < niframes.length; i++) { titles[i] = niframes[i].getTitle(); } titles[niframes.length] = "Clipboard"; GenericDialog gd = new GenericDialog("Windows"); boolean importfile = false; gd.addCheckbox("Import from file?", importfile); gd.addChoice("Windows", titles, titles[0]); boolean hasxvals = false; gd.addCheckbox("X Vals Column?", hasxvals); boolean multix = false; gd.addCheckbox("Multi_X_Columns?", multix); boolean skipendzeros = false; gd.addCheckbox("Skip_end_zeros?", skipendzeros); String[] delimiters = {"Tab", "Comma", "Space"}; gd.addChoice("Delimiter", delimiters, delimiters[0]); gd.showDialog(); if (gd.wasCanceled()) { return; } importfile = gd.getNextBoolean(); int index = gd.getNextChoiceIndex(); hasxvals = gd.getNextBoolean(); multix = gd.getNextBoolean(); skipendzeros = gd.getNextBoolean(); int delimindex = gd.getNextChoiceIndex(); if (multix) hasxvals = true; String textdata = ""; if (importfile) { OpenDialog od = new OpenDialog("Open File", "", ".txt"); String directory = od.getDirectory(); String name = od.getFileName(); if (name == null) { return; } try { File infile = new File(directory + name); BufferedReader b = new BufferedReader(new FileReader(infile)); textdata = (new jdataio()).readstringfile(b); b.close(); } catch (IOException e) { return; } } else { if (index == niframes.length) { // here we get the data from the clipboard Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null); try { if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) { textdata = (String) t.getTransferData(DataFlavor.stringFlavor); } } catch (UnsupportedFlavorException e) { } catch (IOException e) { } if (textdata.equals("")) { IJ.error("Error copying from clipboard."); return; } } else { if (niframes[index] instanceof Editor) { Editor tw = (Editor) niframes[index]; textdata = tw.getText(); } else { if (niframes[index] instanceof TextWindow) { TextWindow tw = (TextWindow) niframes[index]; textdata = tw.getTextPanel().getText(); } else { IJ.showMessage("Not a valid text window"); return; } } } } if (textdata == null) { IJ.showMessage("Error in Obtaining String"); return; } if (textdata.indexOf("\r") >= 0) { textdata = textdata.replace('\r', '\n'); } char[] delims = {'\t', ',', ' '}; delimit_string ds = new delimit_string(delims[delimindex]); String[] rows = ds.getrows(textdata); int lines = rows.length; int columns = ds.getnumcolumns(rows[0]); int ycolumns = columns; if (hasxvals) { if (multix) { ycolumns /= 2; } else { ycolumns--; } } if (multix) { float[][] ydata = new float[ycolumns][lines]; float[][] xdata = new float[ycolumns][lines]; for (int i = 0; i < lines; i++) { float[] temp = ds.delim2float(rows[i], columns); for (int j = 0; j < ycolumns; j++) { ydata[j][i] = temp[2 * j + 1]; xdata[j][i] = temp[2 * j]; } } int[] npts = new int[ycolumns]; for (int i = 0; i < ycolumns; i++) { npts[i] = lines; } if (skipendzeros) { for (int i = 0; i < ycolumns; i++) { int counter = lines - 1; while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) { xdata[i][counter] = 0.0f; ydata[i][counter] = 0.0f; npts[i]--; counter--; } } } (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw(); } else { float[][] tempydata = new float[ycolumns][lines]; float[] tempxdata = new float[lines]; float[][] xdata = null; float[][] ydata = null; int startcolumn = 0; if (hasxvals) startcolumn = 1; for (int i = 0; i < lines; i++) { float[] temp = ds.delim2float(rows[i], columns); if (hasxvals) { tempxdata[i] = temp[0]; } else { tempxdata[i] = (float) (i + 1); } for (int j = 0; j < ycolumns; j++) { tempydata[j][i] = temp[j + startcolumn]; } } int[] npts = new int[ycolumns]; npts[0] = lines; if (skipendzeros) { int maxpts = 0; for (int i = 0; i < ycolumns; i++) { int counter = lines - 1; npts[i] = lines; while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter])) && counter > 0) { npts[i]--; counter--; } if (npts[i] > maxpts) maxpts = npts[i]; IJ.log("" + npts[i]); } ydata = new float[ycolumns][maxpts]; xdata = new float[ycolumns][maxpts]; for (int i = 0; i < ycolumns; i++) { // npts[i]=npts[0]; System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]); System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]); } } else { ydata = tempydata; xdata = new float[ycolumns][]; for (int i = 0; i < ycolumns; i++) { npts[i] = npts[0]; xdata[i] = tempxdata.clone(); } } (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw(); } }
public boolean reconstructDataset() { view_modes[0] = "3D color"; view_modes[1] = "2D histogram"; view_modes[2] = "2D particle intensity (16-bit)"; view_modes[3] = "2D particle intensity (8-bit)"; GenericDialog gd = new GenericDialog("Reconstruct PALM/STORM Dataset"); gd.addNumericField( "Target pixel size for the rendered image (nm)", prefs.get("QuickPALM.viewer_tpixelsize", 30), 2); gd.addNumericField("Original image width (px)", prefs.get("QuickPALM.viewer_owidth", 512), 2); gd.addNumericField("Original image height (px)", prefs.get("QuickPALM.viewer_oheight", 512), 2); gd.addChoice("View mode", view_modes, prefs.get("QuickPALM.view_mode", view_modes[1])); // gd.addNumericField("Allow image saturation (%)", prefs.get("QuickPALM.saturation", 50), 0); gd.addCheckbox( "Simulate sub-difraction spot (gaussian convolution - only 2D)", prefs.get("QuickPALM.viewer_doConvolve", true)); // gd.addCheckbox("Make 3D stack", prefs.get("QuickPALM.viewer_do3d", false)); // gd.addCheckbox("Make movie", prefs.get("QuickPALM.viewer_doMovie", false)); gd.addCheckbox("Make 3D stack", false); gd.addCheckbox("Make movie", false); // gd.addCheckbox("Save only and don't show", prefs.get("QuickPALM.viewer_doSave", false)); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Simulate sub-difraction spot settings (used only if selected) --"); gd.addNumericField("FWHM of the spot", prefs.get("QuickPALM.viewer_fwhm", 30), 2); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Make 3D stack settings (used only if selected) --"); gd.addNumericField("Z-spacing between slices (nm)", prefs.get("QuickPALM.viewer_zstep", 50), 2); gd.addNumericField( "Merge particle Z-position above (nm - 0 for full Z range)", prefs.get("QuickPALM.viewer_mergeabove", 0), 2); gd.addNumericField( "Merge particle Z-position bellow (nm - 0 for full Z range)", prefs.get("QuickPALM.viewer_mergebellow", 0), 2); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Make movie settings (used only if selected) --"); gd.addNumericField( "Make a reconstruction in every N frames", prefs.get("QuickPALM.viewer_update", 10), 0); gd.addNumericField( "Accumulate N neighboring frames for each reconstruction\n(set to 0 to accumulate all the preceding frames)", prefs.get("QuickPALM.viewer_accumulate", 100), 0); gd.showDialog(); if (gd.wasCanceled()) return false; viewer_tpixelsize = gd.getNextNumber(); prefs.set("QuickPALM.viewer_tpixelsize", viewer_tpixelsize); viewer_owidth = (int) gd.getNextNumber(); prefs.set("QuickPALM.viewer_owidth", viewer_owidth); viewer_oheight = (int) gd.getNextNumber(); prefs.set("QuickPALM.viewer_oheight", viewer_oheight); view_mode = gd.getNextChoice(); prefs.set("QuickPALM.view_mode", view_mode); viewer_doConvolve = gd.getNextBoolean(); prefs.set("QuickPALM.viewer_doConvolve", viewer_doConvolve); viewer_do3d = gd.getNextBoolean(); prefs.set("QuickPALM.viewer_do3d", viewer_do3d); viewer_doMovie = gd.getNextBoolean(); prefs.set("QuickPALM.viewer_doMovie", viewer_doMovie); // viewer_doSave = gd.getNextBoolean(); // prefs.set("QuickPALM.viewer_doSave", viewer_doSave); // -- Simulate sub-difraction spot viewer_fwhm = gd.getNextNumber(); prefs.set("QuickPALM.viewer_fwhm", viewer_fwhm); // -- Show B&W // viewer_is8bit = gd.getNextBoolean(); // prefs.set("QuickPALM.viewer_is8bit", viewer_is8bit); // -- Make 3D stack viewer_zstep = gd.getNextNumber(); prefs.set("QuickPALM.viewer_zstep", viewer_zstep); viewer_mergeabove = gd.getNextNumber(); prefs.set("QuickPALM.viewer_mergeabove", viewer_mergeabove); viewer_mergebellow = gd.getNextNumber(); prefs.set("QuickPALM.viewer_mergebellow", viewer_mergebellow); // -- Make Movie viewer_update = (int) gd.getNextNumber(); prefs.set("QuickPALM.viewer_update", viewer_update); viewer_accumulate = (int) gd.getNextNumber(); prefs.set("QuickPALM.viewer_accumulate", viewer_accumulate); return true; }
/** Ask for parameters and then execute. */ public void run(String arg) { // 1 - Obtain the currently active image: ImagePlus imp = IJ.getImage(); if (null == imp) { IJ.showMessage("There must be at least one image open"); return; } if (imp.getBitDepth() != 8) { IJ.showMessage("Error", "Only 8-bit images are supported"); return; } // 2 - Ask for parameters: GenericDialog gd = new GenericDialog("Auto Local Threshold"); String[] methods = { "Try all", "Bernsen", "Contrast", "Mean", "Median", "MidGrey", "Niblack", "Otsu", "Phansalkar", "Sauvola" }; gd.addMessage("Auto Local Threshold v1.5"); gd.addChoice("Method", methods, methods[0]); gd.addNumericField("Radius", 15, 0); gd.addMessage("Special paramters (if different from default)"); gd.addNumericField("Parameter_1", 0, 0); gd.addNumericField("Parameter_2", 0, 0); gd.addCheckbox("White objects on black background", true); if (imp.getStackSize() > 1) { gd.addCheckbox("Stack", false); } gd.addMessage("Thresholded result is always shown in white [255]."); gd.showDialog(); if (gd.wasCanceled()) return; // 3 - Retrieve parameters from the dialog String myMethod = gd.getNextChoice(); int radius = (int) gd.getNextNumber(); double par1 = (double) gd.getNextNumber(); double par2 = (double) gd.getNextNumber(); boolean doIwhite = gd.getNextBoolean(); boolean doIstack = false; int stackSize = imp.getStackSize(); if (stackSize > 1) doIstack = gd.getNextBoolean(); // 4 - Execute! // long start = System.currentTimeMillis(); if (myMethod.equals("Try all")) { ImageProcessor ip = imp.getProcessor(); int xe = ip.getWidth(); int ye = ip.getHeight(); int ml = methods.length; ImagePlus imp2, imp3; ImageStack tstack = null, stackNew; if (stackSize > 1 && doIstack) { boolean doItAnyway = true; if (stackSize > 25) { YesNoCancelDialog d = new YesNoCancelDialog( IJ.getInstance(), "Auto Local Threshold", "You might run out of memory.\n \nDisplay " + stackSize + " slices?\n \n \'No\' will process without display and\noutput results to the log window."); if (!d.yesPressed()) { // doIlog=true; //will show in the log window doItAnyway = false; } if (d.cancelPressed()) return; } for (int j = 1; j <= stackSize; j++) { imp.setSlice(j); ip = imp.getProcessor(); tstack = new ImageStack(xe, ye); for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate()); imp2 = new ImagePlus("Auto Threshold", tstack); imp2.updateAndDraw(); for (int k = 1; k < ml; k++) { imp2.setSlice(k); Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite); } // if (doItAnyway){ CanvasResizer cr = new CanvasResizer(); stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1); imp3 = new ImagePlus("Auto Threshold", stackNew); imp3.updateAndDraw(); MontageMaker mm = new MontageMaker(); mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows } imp.setSlice(1); // if (doItAnyway) IJ.run("Images to Stack", "method=[Copy (center)] title=Montage"); return; } else { // single image try all tstack = new ImageStack(xe, ye); for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate()); imp2 = new ImagePlus("Auto Threshold", tstack); imp2.updateAndDraw(); for (int k = 1; k < ml; k++) { imp2.setSlice(k); // IJ.log("analyzing slice with "+methods[k]); Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite); } // imp2.setSlice(1); CanvasResizer cr = new CanvasResizer(); stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1); imp3 = new ImagePlus("Auto Threshold", stackNew); imp3.updateAndDraw(); MontageMaker mm = new MontageMaker(); mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); return; } } else { // selected a method if (stackSize > 1 && doIstack) { // whole stack // if (doIstackHistogram) {// one global histogram // Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog, // doIstackHistogram ); // } // else{ // slice by slice for (int k = 1; k <= stackSize; k++) { imp.setSlice(k); Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite); } // } imp.setSlice(1); } else { // just one slice Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite); } // 5 - If all went well, show the image: // not needed here as the source image is binarised } }
public boolean showDialog() { String bgChoice = "NoBg"; int[] wList = WindowManager.getIDList(); if (wList == null) { IJ.noImage(); return false; } String[] sampleTitles = new String[wList.length]; for (int i = 0; i < wList.length; i++) { ImagePlus imp = WindowManager.getImage(wList[i]); sampleTitles[i] = imp != null ? imp.getTitle() : ""; } String[] bgTitles = new String[wList.length + 1]; bgTitles[0] = "NoBg"; for (int i = 1; i < wList.length + 1; i++) { bgTitles[i] = sampleTitles[i - 1]; } for (int i = 1; i < (wList.length + 1); i++) { if (bgTitles[i] == bgStackTitle) bgChoice = bgStackTitle; } String sampleChoice = sampleTitles[0]; for (int i = 1; i < (wList.length); i++) { if (sampleTitles[i] == sampleStackTitle) sampleChoice = sampleStackTitle; } String[] mirrors = new String[2]; mirrors[0] = "No"; mirrors[1] = "Yes"; GenericDialog gd = new GenericDialog("PolScope 5Frame Calc"); gd.addChoice("Sample:", sampleTitles, sampleChoice); gd.addChoice("Background:", bgTitles, bgChoice); gd.addChoice("Mirror:", mirrors, mirror); gd.addNumericField("Wavelength: ", wavelength, 1, 8, " nm"); gd.addNumericField("Swing: ", swing, 3, 8, " wavelength"); gd.addNumericField("Ret. Ceiling: ", retCeiling, 1, 8, " nm"); gd.addNumericField("Orient. Ref.: ", azimRef, 1, 8, " degree"); gd.showDialog(); if (gd.wasCanceled()) return false; int index1 = gd.getNextChoiceIndex(); int index2 = gd.getNextChoiceIndex(); int index3 = gd.getNextChoiceIndex(); wavelength = (float) gd.getNextNumber(); swing = (float) gd.getNextNumber(); retCeiling = (float) gd.getNextNumber(); azimRef = (float) gd.getNextNumber(); imp1 = WindowManager.getImage(wList[index1]); sampleStackTitle = sampleTitles[index1]; bgStackTitle = bgTitles[index2]; if (bgStackTitle == "NoBg") { imp2 = WindowManager.getImage( wList[ index1]); // only to assign a valid ImagePlus to imp2 which is not used when NoBg } else { imp2 = WindowManager.getImage(wList[index2 - 1]); } mirror = mirrors[index3]; return true; }
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); }