protected void runScript(String[] cmd, JTextArea txaMsg) {
String strg = "";
if (cmd == null) return;
Process prcs = null;
try {
Messages.postDebug("Running script: " + cmd[2]);
Runtime rt = Runtime.getRuntime();
prcs = rt.exec(cmd);
if (prcs == null) return;
InputStream istrm = prcs.getInputStream();
if (istrm == null) return;
BufferedReader bfr = new BufferedReader(new InputStreamReader(istrm));
while ((strg = bfr.readLine()) != null) {
// System.out.println(strg);
strg = strg.trim();
// Messages.postDebug(strg);
strg = strg.toLowerCase();
if (txaMsg != null) {
txaMsg.append(strg);
txaMsg.append("\n");
}
}
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
Messages.postDebug(e.toString());
} finally {
// It is my understanding that these streams are left
// open sometimes depending on the garbage collector.
// So, close them.
try {
if (prcs != null) {
OutputStream os = prcs.getOutputStream();
if (os != null) os.close();
InputStream is = prcs.getInputStream();
if (is != null) is.close();
is = prcs.getErrorStream();
if (is != null) is.close();
}
} catch (Exception ex) {
Messages.writeStackTrace(ex);
}
}
}
private void onOK() {
try {
InputStream in = new FileInputStream(inputFile);
if (outputFile == null) {
outputFile = new File(inputFile.getAbsolutePath() + "_");
}
OutputStream out = new FileOutputStream(outputFile);
ANSIUnicodeConverter converter = new ANSIUnicodeConverter();
converter.setDirection(ANSIUnicodeConverter.ANSI2UNICODE);
StringBuffer output = new StringBuffer();
final int BUFFER_SIZE = 1024 * 1024; // 1M
byte[] buffer = new byte[BUFFER_SIZE];
int currentPosition = 0;
while (in.available() != 0) {
int currentBufferSize = BUFFER_SIZE;
if (in.available() < BUFFER_SIZE) {
currentBufferSize = in.available();
}
in.read(buffer, currentPosition, currentBufferSize);
currentBufferSize = currentBufferSize + currentBufferSize;
converter.setInput(new String(buffer));
out.write(converter.convert().getBytes());
}
in.close();
out.close();
} catch (Exception e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
}
/**
* Loads the drawing. By convention this method is invoked on a worker thread.
*
* @param progress A ProgressIndicator to inform the user about the progress of the operation.
* @return The Drawing that was loaded.
*/
protected Drawing loadDrawing(ProgressIndicator progress) throws IOException {
Drawing drawing = createDrawing();
if (getParameter("datafile") != null) {
URL url = new URL(getDocumentBase(), getParameter("datafile"));
URLConnection uc = url.openConnection();
// Disable caching. This ensures that we always request the
// newest version of the drawing from the server.
// (Note: The server still needs to set the proper HTTP caching
// properties to prevent proxies from caching the drawing).
if (uc instanceof HttpURLConnection) {
((HttpURLConnection) uc).setUseCaches(false);
}
// Read the data into a buffer
int contentLength = uc.getContentLength();
InputStream in = uc.getInputStream();
try {
if (contentLength != -1) {
in = new BoundedRangeInputStream(in);
((BoundedRangeInputStream) in).setMaximum(contentLength + 1);
progress.setProgressModel((BoundedRangeModel) in);
progress.setIndeterminate(false);
}
BufferedInputStream bin = new BufferedInputStream(in);
bin.mark(512);
// Read the data using all supported input formats
// until we succeed
IOException formatException = null;
for (InputFormat format : drawing.getInputFormats()) {
try {
bin.reset();
} catch (IOException e) {
uc = url.openConnection();
in = uc.getInputStream();
in = new BoundedRangeInputStream(in);
((BoundedRangeInputStream) in).setMaximum(contentLength + 1);
progress.setProgressModel((BoundedRangeModel) in);
bin = new BufferedInputStream(in);
bin.mark(512);
}
try {
bin.reset();
format.read(bin, drawing, true);
formatException = null;
break;
} catch (IOException e) {
formatException = e;
}
}
if (formatException != null) {
throw formatException;
}
} finally {
in.close();
}
}
return drawing;
}
private void seticon() {
Image icon;
try {
InputStream data = MainFrame.class.getResourceAsStream("icon.png");
icon = javax.imageio.ImageIO.read(data);
data.close();
} catch (IOException e) {
throw (new Error(e));
}
setIconImage(icon);
}
public void load(ActionEvent e) {
int returnVal = fc.showOpenDialog(this);
if (returnVal != JFileChooser.APPROVE_OPTION) {
return;
}
file = fc.getSelectedFile();
try {
InputStream in = new BufferedInputStream(new FileInputStream(file));
Properties newWl = new Properties();
newWl.load(in);
in.close();
setWordList(newWl);
} catch (IOException ex) {
handleException(ex);
}
}
public void setData(String text) {
if (text != null && text.length() > 0) {
InputStream in = null;
try {
Object result = null;
Drawing drawing = createDrawing();
// Try to read the data using all known input formats.
for (InputFormat fmt : drawing.getInputFormats()) {
try {
fmt.read(in, drawing);
in = new ByteArrayInputStream(text.getBytes("UTF8"));
result = drawing;
break;
} catch (IOException e) {
result = e;
}
}
if (result instanceof IOException) {
throw (IOException) result;
}
setDrawing(drawing);
} catch (Throwable e) {
getDrawing().removeAllChildren();
SVGTextFigure tf = new SVGTextFigure();
tf.setText(e.getMessage());
tf.setBounds(new Point2D.Double(10, 10), new Point2D.Double(100, 100));
getDrawing().add(tf);
e.printStackTrace();
} finally {
if (in != null) {
try {
in.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
}
}
}
public void ClosePort() {
if (portOpened) {
if (serialPort != null) {
try {
// Close the I/O streams.
out.close();
in.close();
// Close the port.
serialPort.removeEventListener();
serialPort.close();
} catch (IOException e) {
// Don't care
}
}
ClearLog();
portOpened = false;
portConfirmed = false;
previewPane.setConnected(false);
UpdateMenuBar();
}
}
private static void copyfile(String srFile, String dtFile) {
try {
File f1 = new File(srFile);
File f2 = new File(dtFile);
InputStream in = new FileInputStream(f1);
// For Overwrite the file.
OutputStream out = new FileOutputStream(f2);
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) > 0) {
out.write(buf, 0, len);
}
in.close();
out.close();
EIError.debugMsg("File copied " + srFile + " " + dtFile, EIError.ErrorLevel.Notice);
} catch (Exception e) {
EIError.debugMsg(
"Couldn't copy file" + srFile + " " + dtFile + " " + e.getMessage(),
EIError.ErrorLevel.Error);
}
}
public java.util.List<String> readTextFromJar(String s) {
InputStream is = null;
BufferedReader br = null;
String line;
ArrayList<String> list = new ArrayList<String>();
try {
is = getClass().getResourceAsStream(s);
br = new BufferedReader(new InputStreamReader(is));
while (null != (line = br.readLine())) {
list.add(line);
}
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
if (br != null) br.close();
if (is != null) is.close();
} catch (IOException e) {
e.printStackTrace();
}
}
return list;
}
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();
}
public void fetchExternalJSLibrary(String targetURLString) {
final URL targetURL;
String targetFile = "";
String s = null;
InputStream is = null;
BufferedReader dis = null;
try {
// ------------------------------------------------------------//
// Step 2: Create the URL. //
// ------------------------------------------------------------//
// Note: Put your real URL here, or better yet, read it as a //
// command-line arg, or read it from a file. //
// ------------------------------------------------------------//
targetURL = new URL(targetURLString);
// ----------------------------------------------//
// Step 3: Open an input stream from the url. //
// ----------------------------------------------//
is = targetURL.openStream();
// -------------------------------------------------------------//
// Step 4: //
// -------------------------------------------------------------//
// Convert the InputStream to BufferedReader //
// -------------------------------------------------------------//
dis = new BufferedReader(new InputStreamReader(is));
// ------------------------------------------------------------//
// Step 5: //
// ------------------------------------------------------------//
// Now just read each record of the input stream, and print //
// it out. Note that it's assumed that this problem is run //
// from a command-line, not from an application or applet. //
// ------------------------------------------------------------//
while ((s = dis.readLine()) != null) {
targetFile = targetFile + "\n" + s;
}
alert(targetFile);
System.out.println(targetFile);
} catch (MalformedURLException mue) {
alert("Ouch - a MalformedURLException happened.");
System.out.println("Ouch - a MalformedURLException happened.");
mue.printStackTrace();
System.exit(1);
} catch (IOException ioe) {
alert("Ouch - an IOException happened.");
System.out.println("Ouch - an IOException happened.");
ioe.printStackTrace();
System.exit(1);
} catch (Exception e) {
alert("Ouch - Something wrong happened.");
alert(e.toString());
alert(e.getMessage());
} finally {
// ---------------------------------//
// Step 6: Close the InputStream //
// ---------------------------------//
try {
is.close();
dis.close();
} catch (IOException ioe) {
// just going to ignore this one
}
} // end of 'finally' clause
}
/** Unpacks a resource to a temp. file */
public static File unpackInstaller(String resourceName) {
// Array to hold all results (this code is slightly more
// generally that it needs to be)
File[] results = new File[1];
URL[] urls = new URL[1];
// Determine size of download
ClassLoader cl = Main.class.getClassLoader();
urls[0] = cl.getResource(Config.getInstallerResource());
if (urls[0] == null) {
Config.trace("Could not find resource: " + Config.getInstallerResource());
return null;
}
int totalSize = 0;
int totalRead = 0;
for (int i = 0; i < urls.length; i++) {
if (urls[i] != null) {
try {
URLConnection connection = urls[i].openConnection();
totalSize += connection.getContentLength();
} catch (IOException ioe) {
Config.trace("Got exception: " + ioe);
return null;
}
}
}
// Unpack each file
for (int i = 0; i < urls.length; i++) {
if (urls[i] != null) {
// Create temp. file to store unpacked file in
InputStream in = null;
OutputStream out = null;
try {
// Use extension from URL (important for dll files)
String extension = new File(urls[i].getFile()).getName();
int lastdotidx = (extension != null) ? extension.lastIndexOf('.') : -1;
if (lastdotidx == -1) {
extension = ".dat";
} else {
extension = extension.substring(lastdotidx);
}
// Create output stream
results[i] = File.createTempFile("jre", extension);
results[i].deleteOnExit();
out = new FileOutputStream(results[i]);
// Create inputstream
URLConnection connection = urls[i].openConnection();
in = connection.getInputStream();
int read = 0;
byte[] buf = new byte[BUFFER_SIZE];
while ((read = in.read(buf)) != -1) {
out.write(buf, 0, read);
// Notify delegate
totalRead += read;
if (totalRead > totalSize && totalSize != 0) totalSize = totalRead;
// Update UI
if (totalSize != 0) {
int percent = (100 * totalRead) / totalSize;
setStepText(STEP_UNPACK, Config.getWindowStepProgress(STEP_UNPACK, percent));
}
}
} catch (IOException ie) {
Config.trace("Got exception while downloading resource: " + ie);
for (int j = 0; j < results.length; j++) {
if (results[j] != null) results[j].delete();
}
return null;
} finally {
try {
if (in != null) in.close();
if (out != null) out.close();
} catch (IOException io) {
/* ignore */
}
}
}
}
setStepText(STEP_UNPACK, Config.getWindowStep(STEP_UNPACK));
return results[0];
}