public boolean getParticlesTableFile() {
java.lang.String ptable_dir = prefs.get("QuickPALM.ptable_dir", ".");
java.lang.String ptable_file = prefs.get("QuickPALM.ptable_file", "Particles Table.xls");
OpenDialog chooser = new OpenDialog("Load Particles Table", ptable_dir, ptable_file);
ptablefile = chooser.getDirectory() + chooser.getFileName();
prefs.set("QuickPALM.ptable_dir", chooser.getDirectory());
prefs.set("QuickPALM.ptable_file", chooser.getFileName());
return true;
}
public boolean getCalibrationFile() {
java.lang.String cal_dir = prefs.get("QuickPALM.cal_dir", ".");
java.lang.String cal_file = prefs.get("QuickPALM.cal_file", "Astigmatism calibration.xls");
OpenDialog chooser = new OpenDialog("Astigmatism calibration", cal_dir, cal_file);
calfile = chooser.getDirectory() + chooser.getFileName();
prefs.set("QuickPALM.cal_dir", chooser.getDirectory());
prefs.set("QuickPALM.cal_file", chooser.getFileName());
return true;
}
public void run(String arg) {
String ijDir = System.getProperty("ij.dir");
if (!ijDir.endsWith("/")) ijDir += "/";
if (arg == null || "".equals(arg)) {
OpenDialog dialog = new OpenDialog("Which Fiji component", ijDir + "plugins", "");
if (dialog.getDirectory() == null) return;
arg = dialog.getDirectory() + dialog.getFileName();
}
if (arg.startsWith(ijDir)) arg = arg.substring(ijDir.length());
final JFrame frame = new JFrame("Building " + arg + "...");
Container panel = frame.getContentPane();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
JTextArea textArea = new JTextArea("Calling Fiji Build\n", 25, 80);
textArea.setFont(new Font("Courier", Font.PLAIN, 12));
textArea.setEditable(false);
panel.add(new JScrollPane(textArea));
final JButton okay = new JButton("okay");
okay.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
frame.dispose();
}
});
okay.setEnabled(false);
okay.setAlignmentX(Component.CENTER_ALIGNMENT);
panel.add(okay);
frame.pack();
frame.setLocationRelativeTo(null);
okay.requestFocus();
frame.setVisible(true);
try {
Fake fake = new Fake();
fake.out = fake.err = new PrintStream(new JTextAreaOutputStream(textArea));
Parser parser = fake.parse(new FileInputStream(ijDir + "/Fakefile"), new File(ijDir));
final Rule all = parser.parseRules(Arrays.asList(arg.split("\\s+")));
all.make();
fake.out.println("Finished.");
frame.setTitle("Built " + arg);
okay.setEnabled(true);
} catch (Exception e) {
IJ.handleException(e);
}
}
public void run(String arg) {
OpenDialog od = new OpenDialog("Install Plugin, Macro or Script...", arg);
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) return;
if (!validExtension(name)) {
IJ.error("Plugin Installer", errorMessage());
return;
}
String path = directory + name;
install(path);
}
String showDialog() {
if (defaultDir == null) defaultDir = Menus.getMacrosPath();
OpenDialog od = new OpenDialog("Install Macros", defaultDir, fileName);
String name = od.getFileName();
if (name == null) return null;
String dir = od.getDirectory();
if (!(name.endsWith(".txt") || name.endsWith(".ijm"))) {
IJ.showMessage("Macro Installer", "File name must end with \".txt\" or \".ijm\" .");
return null;
}
fileName = name;
defaultDir = dir;
return dir + name;
}
public void run(String arg) {
boolean display = false;
File test = new File(arg);
display = !test.exists();
OpenDialog od = new OpenDialog("Open mkt file...", arg);
if (od != null) {
String file = od.getFileName();
if (file == null) return;
String directory = od.getDirectory();
directory = directory.replace('\\', '/'); // Windows safe
if (!directory.endsWith("/")) directory += "/";
arg = directory + file;
}
try {
FileProjectionSource fileSource = new MKTProjectionSource();
fileSource.initStream(arg);
ImagePlusDataSink sink = new ImagePlusDataSink();
Grid2D imp = fileSource.getNextProjection();
int i = 0;
while (imp != null) {
sink.process(imp, i);
i++;
imp = fileSource.getNextProjection();
}
sink.close();
setStack(ImageUtil.wrapGrid3D(sink.getResult(), "").getStack());
setTitle(new File(arg).getName());
fileSource.close();
if (display) show();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
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();
}
}
