Beispiel #1
0
 byte[] getJar(String address) {
   // System.out.println("getJar: "+address);
   byte[] data;
   try {
     URL url = new URL(address);
     IJ.showStatus("Connecting to " + IJ.URL);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
     if (len <= 0) return null;
     String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
     IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     if (IJ.debugMode) IJ.log("" + e);
     return null;
   }
   if (IJ.debugMode) IJ.wait(6000);
   return data;
 }
Beispiel #2
0
 /** Reads the pixel data from an image described by a FileInfo object. */
 Object readPixels(FileInfo fi) {
   Object pixels = null;
   try {
     InputStream is = createInputStream(fi);
     if (is == null) return null;
     ImageReader reader = new ImageReader(fi);
     pixels = reader.readPixels(is);
     minValue = reader.min;
     maxValue = reader.max;
     is.close();
   } catch (Exception e) {
     if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
   }
   return pixels;
 }
Beispiel #3
0
 String openUrlAsString(String address, int maxLines) {
   StringBuffer sb;
   try {
     URL url = new URL(address);
     InputStream in = url.openStream();
     BufferedReader br = new BufferedReader(new InputStreamReader(in));
     sb = new StringBuffer();
     int count = 0;
     String line;
     while ((line = br.readLine()) != null && count++ < maxLines) sb.append(line + "\n");
     in.close();
   } catch (IOException e) {
     sb = null;
   }
   return sb != null ? new String(sb) : null;
 }
Beispiel #4
0
 /** Opens a stack of images. */
 ImagePlus openStack(ColorModel cm, boolean show) {
   ImageStack stack = new ImageStack(fi.width, fi.height, cm);
   long skip = fi.getOffset();
   Object pixels;
   try {
     ImageReader reader = new ImageReader(fi);
     InputStream is = createInputStream(fi);
     if (is == null) return null;
     IJ.resetEscape();
     for (int i = 1; i <= fi.nImages; i++) {
       if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
       if (IJ.escapePressed()) {
         IJ.beep();
         IJ.showProgress(1.0);
         silentMode = false;
         return null;
       }
       pixels = reader.readPixels(is, skip);
       if (pixels == null) break;
       stack.addSlice(null, pixels);
       skip = fi.gapBetweenImages;
       if (!silentMode) IJ.showProgress(i, fi.nImages);
     }
     is.close();
   } catch (Exception e) {
     IJ.log("" + e);
   } catch (OutOfMemoryError e) {
     IJ.outOfMemory(fi.fileName);
     stack.trim();
   }
   if (!silentMode) IJ.showProgress(1.0);
   if (stack.getSize() == 0) return null;
   if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
     for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
   }
   ImagePlus imp = new ImagePlus(fi.fileName, stack);
   if (fi.info != null) imp.setProperty("Info", fi.info);
   if (show) imp.show();
   imp.setFileInfo(fi);
   setCalibration(imp);
   ImageProcessor ip = imp.getProcessor();
   if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
   setStackDisplayRange(imp);
   if (!silentMode) IJ.showProgress(1.0);
   silentMode = false;
   return imp;
 }
 public static byte[] download(String urlString, String name) {
   int maxLength = 52428800; // 50MB
   URL url = null;
   boolean unknownLength = false;
   byte[] data = null;
   ;
   int n = 0;
   try {
     url = new URL(urlString);
     if (IJ.debugMode) IJ.log("PluginInstaller: " + urlString + "  " + url);
     if (url == null) return null;
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     unknownLength = len < 0;
     if (unknownLength) len = maxLength;
     if (name != null) IJ.showStatus("Downloading " + url.getFile());
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int lenk = len / 1024;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) break;
       n += count;
       if (name != null)
         IJ.showStatus("Downloading " + name + " (" + (n / 1024) + "/" + lenk + "k)");
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (Exception e) {
     String msg = "" + e;
     if (!msg.contains("://")) msg += "\n   " + urlString;
     IJ.error("Plugin Installer", msg);
     return null;
   } finally {
     IJ.showProgress(1.0);
   }
   if (name != null) IJ.showStatus("");
   if (unknownLength) {
     byte[] data2 = data;
     data = new byte[n];
     for (int i = 0; i < n; i++) data[i] = data2[i];
   }
   return data;
 }
Beispiel #6
0
 public Properties decodeDescriptionString(FileInfo fi) {
   if (fi.description == null || fi.description.length() < 7) return null;
   if (IJ.debugMode) IJ.log("Image Description: " + new String(fi.description).replace('\n', ' '));
   if (!fi.description.startsWith("ImageJ")) return null;
   Properties props = new Properties();
   InputStream is = new ByteArrayInputStream(fi.description.getBytes());
   try {
     props.load(is);
     is.close();
   } catch (IOException e) {
     return null;
   }
   fi.unit = props.getProperty("unit", "");
   Double n = getNumber(props, "cf");
   if (n != null) fi.calibrationFunction = n.intValue();
   double c[] = new double[5];
   int count = 0;
   for (int i = 0; i < 5; i++) {
     n = getNumber(props, "c" + i);
     if (n == null) break;
     c[i] = n.doubleValue();
     count++;
   }
   if (count >= 2) {
     fi.coefficients = new double[count];
     for (int i = 0; i < count; i++) fi.coefficients[i] = c[i];
   }
   fi.valueUnit = props.getProperty("vunit");
   n = getNumber(props, "images");
   if (n != null && n.doubleValue() > 1.0) fi.nImages = (int) n.doubleValue();
   if (fi.nImages > 1) {
     double spacing = getDouble(props, "spacing");
     if (spacing != 0.0) {
       if (spacing < 0) spacing = -spacing;
       fi.pixelDepth = spacing;
     }
   }
   return props;
 }
Beispiel #7
0
 byte[] getJar(String address) {
   byte[] data;
   boolean gte133 = version().compareTo("1.33u") >= 0;
   try {
     URL url = new URL(address);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     String name = address.endsWith("ij/ij.jar") ? "daily build" : "ij.jar";
     IJ.showStatus("Downloading ij.jar (" + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       if (gte133) IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     return null;
   }
   return data;
 }
  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();
  }