/** 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); }
// Conversion Options void conversions() { double[] weights = ColorProcessor.getWeightingFactors(); boolean weighted = !(weights[0] == 1d / 3d && weights[1] == 1d / 3d && weights[2] == 1d / 3d); // boolean weighted = !(Math.abs(weights[0]-1d/3d)<0.0001 && Math.abs(weights[1]-1d/3d)<0.0001 // && Math.abs(weights[2]-1d/3d)<0.0001); GenericDialog gd = new GenericDialog("Conversion Options"); gd.addCheckbox("Scale when converting", ImageConverter.getDoScaling()); String prompt = "Weighted RGB conversions"; if (weighted) prompt += " (" + IJ.d2s(weights[0]) + "," + IJ.d2s(weights[1]) + "," + IJ.d2s(weights[2]) + ")"; gd.addCheckbox(prompt, weighted); gd.showDialog(); if (gd.wasCanceled()) return; ImageConverter.setDoScaling(gd.getNextBoolean()); Prefs.weightedColor = gd.getNextBoolean(); if (!Prefs.weightedColor) ColorProcessor.setWeightingFactors(1d / 3d, 1d / 3d, 1d / 3d); else if (Prefs.weightedColor && !weighted) ColorProcessor.setWeightingFactors(0.299, 0.587, 0.114); return; }
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(); } }
// Input/Output options void io() { GenericDialog gd = new GenericDialog("I/O Options"); gd.addNumericField("JPEG quality (0-100):", FileSaver.getJpegQuality(), 0, 3, ""); gd.addNumericField("GIF and PNG transparent index:", Prefs.getTransparentIndex(), 0, 3, ""); gd.addStringField( "File extension for tables (.txt, .xls or .csv):", Prefs.get("options.ext", ".csv"), 4); gd.addCheckbox("Use JFileChooser to open/save", Prefs.useJFileChooser); if (!IJ.isMacOSX()) gd.addCheckbox("Use_file chooser to import sequences", Prefs.useFileChooser); gd.addCheckbox("Save TIFF and raw in Intel byte order", Prefs.intelByteOrder); gd.addCheckbox("Skip dialog when opening .raw files", Prefs.skipRawDialog); gd.setInsets(15, 20, 0); gd.addMessage("Results Table Options"); gd.setInsets(3, 40, 0); gd.addCheckbox("Copy_column headers", Prefs.copyColumnHeaders); gd.setInsets(0, 40, 0); gd.addCheckbox("Copy_row numbers", !Prefs.noRowNumbers); gd.setInsets(0, 40, 0); gd.addCheckbox("Save_column headers", !Prefs.dontSaveHeaders); gd.setInsets(0, 40, 0); gd.addCheckbox("Save_row numbers", !Prefs.dontSaveRowNumbers); gd.showDialog(); if (gd.wasCanceled()) return; int quality = (int) gd.getNextNumber(); if (quality < 0) quality = 0; if (quality > 100) quality = 100; FileSaver.setJpegQuality(quality); int transparentIndex = (int) gd.getNextNumber(); Prefs.setTransparentIndex(transparentIndex); String extension = gd.getNextString(); if (!extension.startsWith(".")) extension = "." + extension; Prefs.set("options.ext", extension); Prefs.useJFileChooser = gd.getNextBoolean(); if (!IJ.isMacOSX()) Prefs.useFileChooser = gd.getNextBoolean(); Prefs.intelByteOrder = gd.getNextBoolean(); Prefs.skipRawDialog = gd.getNextBoolean(); Prefs.copyColumnHeaders = gd.getNextBoolean(); Prefs.noRowNumbers = !gd.getNextBoolean(); Prefs.dontSaveHeaders = !gd.getNextBoolean(); Prefs.dontSaveRowNumbers = !gd.getNextBoolean(); return; }
// Miscellaneous Options void miscOptions() { String key = IJ.isMacintosh() ? "command" : "control"; GenericDialog gd = new GenericDialog("Miscellaneous Options", IJ.getInstance()); gd.addStringField("Divide by zero value:", "" + FloatBlitter.divideByZeroValue, 10); gd.addCheckbox("Use pointer cursor", Prefs.usePointerCursor); gd.addCheckbox("Hide \"Process Stack?\" dialog", IJ.hideProcessStackDialog); gd.addCheckbox("Require " + key + " key for shortcuts", Prefs.requireControlKey); gd.addCheckbox("Move isolated plugins to Misc. menu", Prefs.moveToMisc); if (!IJ.isMacOSX()) gd.addCheckbox("Run single instance listener", Prefs.runSocketListener); gd.addCheckbox("Enhanced line tool", Prefs.enhancedLineTool); gd.addCheckbox("Reverse CZT order of \">\" and \"<\"", Prefs.reverseNextPreviousOrder); gd.addCheckbox("Debug mode", IJ.debugMode); gd.addHelp(IJ.URL + "/docs/menus/edit.html#misc"); gd.showDialog(); if (gd.wasCanceled()) return; String divValue = gd.getNextString(); if (divValue.equalsIgnoreCase("infinity") || divValue.equalsIgnoreCase("infinite")) FloatBlitter.divideByZeroValue = Float.POSITIVE_INFINITY; else if (divValue.equalsIgnoreCase("NaN")) FloatBlitter.divideByZeroValue = Float.NaN; else if (divValue.equalsIgnoreCase("max")) FloatBlitter.divideByZeroValue = Float.MAX_VALUE; else { Float f; try { f = new Float(divValue); } catch (NumberFormatException e) { f = null; } if (f != null) FloatBlitter.divideByZeroValue = f.floatValue(); } IJ.register(FloatBlitter.class); Prefs.usePointerCursor = gd.getNextBoolean(); IJ.hideProcessStackDialog = gd.getNextBoolean(); Prefs.requireControlKey = gd.getNextBoolean(); Prefs.moveToMisc = gd.getNextBoolean(); if (!IJ.isMacOSX()) Prefs.runSocketListener = gd.getNextBoolean(); Prefs.enhancedLineTool = gd.getNextBoolean(); Prefs.reverseNextPreviousOrder = gd.getNextBoolean(); IJ.setDebugMode(gd.getNextBoolean()); }
// DICOM options void dicom() { GenericDialog gd = new GenericDialog("DICOM Options"); gd.addCheckbox("Open as 32-bit float", Prefs.openDicomsAsFloat); // gd.addCheckbox("Calculate voxel depth", Prefs.calculateDicomVoxelDepth); gd.addMessage("Orthogonal Views"); gd.setInsets(5, 40, 0); gd.addCheckbox("Rotate YZ", Prefs.rotateYZ); gd.setInsets(0, 40, 0); gd.addCheckbox("Flip XZ", Prefs.flipXZ); gd.showDialog(); if (gd.wasCanceled()) return; Prefs.openDicomsAsFloat = gd.getNextBoolean(); // Prefs.calculateDicomVoxelDepth = gd.getNextBoolean(); Prefs.rotateYZ = gd.getNextBoolean(); Prefs.flipXZ = gd.getNextBoolean(); }
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 void openDirectory(File f, String path) { if (path == null) return; if (!(path.endsWith(File.separator) || path.endsWith("/"))) path += File.separator; String[] names = f.list(); names = (new FolderOpener()).trimFileList(names); if (names == null) return; String msg = "Open all " + names.length + " images in \"" + f.getName() + "\" as a stack?"; GenericDialog gd = new GenericDialog("Open Folder"); gd.setInsets(10, 5, 0); gd.addMessage(msg); gd.setInsets(15, 35, 0); gd.addCheckbox("Convert to RGB", convertToRGB); gd.setInsets(0, 35, 0); gd.addCheckbox("Use Virtual Stack", virtualStack); gd.enableYesNoCancel(); gd.showDialog(); if (gd.wasCanceled()) return; if (gd.wasOKed()) { convertToRGB = gd.getNextBoolean(); virtualStack = gd.getNextBoolean(); String options = " sort"; if (convertToRGB) options += " convert_to_rgb"; if (virtualStack) options += " use"; IJ.run("Image Sequence...", "open=[" + path + "]" + options); DirectoryChooser.setDefaultDirectory(path); } else { for (int k = 0; k < names.length; k++) { IJ.redirectErrorMessages(); if (!names[k].startsWith(".")) (new Opener()).open(path + names[k]); } } IJ.register(DragAndDrop.class); }
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 analyseParticles(MyFunctions f) { GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles"); gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2); gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0); gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2); gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true)); gd.addCheckbox( "3D PALM (astigmatism) - will require calibration file", prefs.get("QuickPALM.is3d", false)); gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true)); gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false)); gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true)); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Online rendering settings (used only if selected) --"); gd.addMessage("\n"); gd.addNumericField("Pixel size of rendered image (nm)", 30, 2); gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0); gd.addNumericField("Update every (frames)", 10, 0); // gd.addNumericField("Allow color saturation (%)", 50, 0); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Attach to running acquisition settings (used only if selected) --"); gd.addMessage("\n"); gd.addStringField( "_Image name pattern (NN...NN represents the numerical change)", prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"), 20); gd.addNumericField("Start NN...NN with", 0, 0); gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0); gd.addMessage("\n"); // ----------------------------------------- gd.addMessage("-- Advanced settings (don't normally need to be changed) --"); gd.addMessage("\n"); gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0); gd.addNumericField( "Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0); gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0); gd.addNumericField( "Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0); gd.addMessage("\n\nDon't forget to save the table in the end..."); gd.showDialog(); if (gd.wasCanceled()) return false; snr = (int) gd.getNextNumber(); prefs.set("QuickPALM.snr", snr); fwhm = gd.getNextNumber(); prefs.set("QuickPALM.fwhm", fwhm); pixelsize = gd.getNextNumber(); prefs.set("QuickPALM.pixelsize", pixelsize); smartsnr = gd.getNextBoolean(); prefs.set("QuickPALM.smartsnr", smartsnr); is3d = gd.getNextBoolean(); prefs.set("QuickPALM.is3d", is3d); view = gd.getNextBoolean(); prefs.set("QuickPALM.view", view); attach = gd.getNextBoolean(); prefs.set("QuickPALM.attach", attach); if (gd.getNextBoolean()) { f.psave = new ParticleSaver(); f.psave.setup(); prefs.set("QuickPALM.stream", true); } else prefs.set("QuickPALM.stream", false); // -- magn = pixelsize / gd.getNextNumber(); viewer_accumulate = (int) gd.getNextNumber(); viewer_update = (int) gd.getNextNumber(); // -- pattern = gd.getNextString().trim(); prefs.set("QuickPALM.pattern", pattern); prefix = pattern.substring(0, pattern.indexOf("N")); sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length()); nimchars = pattern.split("N").length - 1; nimstart = (int) gd.getNextNumber(); waittime = (int) gd.getNextNumber(); // -- symmetry = gd.getNextNumber() / 100; prefs.set("QuickPALM.symmetry", symmetry); pthrsh = gd.getNextNumber() / 100; prefs.set("QuickPALM.lthreshold", pthrsh * 100); maxpart = (int) gd.getNextNumber(); prefs.set("QuickPALM.maxiter", maxpart); threads = (int) gd.getNextNumber(); prefs.set("QuickPALM.nthreads", threads); return true; }
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; }
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; }