private String readLine(InputStream in) throws IOException { StringBuffer buf = new StringBuffer(); while (true) { int i = in.read(); if ((i == -1) || (i == '\n') || (i == '\r')) { return buf.toString(); } buf.append((char) i); } // return new BufferedReader (new InputStreamReader (in)).readLine (); }
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(); }
/** * Create a new reader. * * @param in the input * @param out the output * @param bindings the key bindings to use * @param term the terminal to use */ public ConsoleReader(InputStream in, Writer out, InputStream bindings, Terminal term) throws IOException { this.terminal = term; setInput(in); this.out = out; if (bindings == null) { try { String bindingFile = System.getProperty( "jline.keybindings", new File(System.getProperty("user.home", ".jlinebindings.properties")) .getAbsolutePath()); if (new File(bindingFile).isFile()) { bindings = new FileInputStream(new File(bindingFile)); } } catch (Exception e) { // swallow exceptions with option debugging if (debugger != null) { e.printStackTrace(debugger); } } } if (bindings == null) { bindings = terminal.getDefaultBindings(); } this.keybindings = new short[Character.MAX_VALUE * 2]; Arrays.fill(this.keybindings, UNKNOWN); /** * Loads the key bindings. Bindings file is in the format: * * <p>keycode: operation name */ if (bindings != null) { Properties p = new Properties(); p.load(bindings); bindings.close(); for (Iterator i = p.keySet().iterator(); i.hasNext(); ) { String val = (String) i.next(); try { Short code = new Short(val); String op = (String) p.getProperty(val); Short opval = (Short) KEYMAP_NAMES.get(op); if (opval != null) { keybindings[code.shortValue()] = opval.shortValue(); } } catch (NumberFormatException nfe) { consumeException(nfe); } } // hardwired arrow key bindings // keybindings[VK_UP] = PREV_HISTORY; // keybindings[VK_DOWN] = NEXT_HISTORY; // keybindings[VK_LEFT] = PREV_CHAR; // keybindings[VK_RIGHT] = NEXT_CHAR; } }