/**
* Common event handling code - can handle desirable actions (such as buttons being clicked) and
* undesirable actions (the window being closed) all in a common location.
*
* @param command a String representing the action that occurred.
*/
private void processCommand(String command) {
dialog.setVisible(false);
if (CONNECT.equals(command)) {
options.setValue(JOptionPane.OK_OPTION);
} else {
options.setValue(JOptionPane.CANCEL_OPTION);
}
}
/**
* Sets the dialog's value for further reference before changing its visibility status to
* invisible.
*
* @param command the previously set command string to identify the source of this method
* invocation
*/
private void leaveDialog(final String command) {
JOptionPane optionPane = (JOptionPane) getContentPane();
if (Text.OK.equals(command)) {
optionPane.setValue(JOptionPane.OK_OPTION);
} else {
optionPane.setValue(JOptionPane.CANCEL_OPTION);
}
setVisible(false);
}
public void actionPerformed(ActionEvent e) {
if (getName() == CLOSE) {
JOptionPane optionPane = (JOptionPane) e.getSource();
optionPane.setValue(Integer.valueOf(JOptionPane.CLOSED_OPTION));
}
}
@Override
public void actionPerformed(ActionEvent arg0) {
if (!dialog.username.getText().isEmpty() && Utils.validIP(dialog.serverIp.getText())) {
try {
serverIP = InetAddress.getByName(dialog.serverIp.getText());
username = dialog.username.getText();
LOGIN_RESULT result = Actions.login(serverIP, serverPort);
if (result == LOGIN_RESULT.SUCCESSFUL) pane.setValue(JOptionPane.OK_OPTION);
else if (result == LOGIN_RESULT.USERNAME_USED) {
dialog.usernameLabel.setText("Username already in use.");
dialog.username.setBorder(BorderFactory.createLineBorder(Color.RED));
} else if (result == LOGIN_RESULT.INVALID_IP || result == null) {
dialog.serverIpLabel.setText("Server IP is invalid.");
dialog.serverIp.setBorder(BorderFactory.createLineBorder(Color.RED));
}
} catch (IOException e) {
e.printStackTrace();
} catch (InterruptedException e) {
e.printStackTrace();
}
} else {
if (dialog.username.getText().isEmpty())
dialog.username.setBorder(BorderFactory.createLineBorder(Color.RED));
if (!Utils.validIP(dialog.serverIp.getText()))
dialog.serverIp.setBorder(BorderFactory.createLineBorder(Color.RED));
}
}
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible()
&& (e.getSource() == optionPane)
&& (JOptionPane.VALUE_PROPERTY.equals(prop)
|| JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) {
Object value = optionPane.getValue();
if (value == JOptionPane.UNINITIALIZED_VALUE) return;
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
if (button1.equals(value)) {
try {
double a = Double.parseDouble(left.getText());
double b = Double.parseDouble(right.getText());
double err = Double.parseDouble(error.getText());
if (a > b) {
JOptionPane.showMessageDialog(this, "A < B!!!", null, JOptionPane.ERROR_MESSAGE);
} else {
hideIt();
graphic.startApplyingMethod(parentFrame.getSelectedMethod(), err, a, b);
}
} catch (Exception ex) {
JOptionPane.showMessageDialog(
this, "Trebuie sa fie numar real!", null, JOptionPane.ERROR_MESSAGE);
}
} else if (button2.equals(value)) {
hideIt();
}
}
}
/** This method reacts to state changes in the option pane. */
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible()
&& (e.getSource() == optionPane)
&& (JOptionPane.VALUE_PROPERTY.equals(prop)
|| JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) {
Object value = optionPane.getValue();
if (value == JOptionPane.UNINITIALIZED_VALUE) {
// ignore reset
return;
}
// Reset the JOptionPane's value.
// If you don't do this, then if the user
// presses the same button next time, no
// property change event will be fired.
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
if (btnString1.equals(value)) {
String[] strings = new String[1];
strings[0] = numPlatesTextField.getText();
// make sure the inputed values are numbers only
if (tools.MathOps.areNumbers(strings)) {
int numP = Integer.parseInt(strings[0]);
if (numRows != -1 && numCols != -1) {
Model_Main TheMainModel = models.Model_Main.getModel();
if (TheMainModel == null) TheMainModel = new Model_Main();
boolean worked = TheMainModel.initNewPlates(numP, numRows, numCols);
if (worked) {
if (ParentFrame != null) ParentFrame.setVisible(false);
MainGUI TheMainGUI = new MainGUI(TheMainModel);
if (TheMainGUI != null)
TheMainGUI.setTitle("Project: " + TheMainModel.getInputProjectPath());
TheMainGUI.setVisible(true);
}
}
} else {
JOptionPane.showMessageDialog(
null, "Please Enter a Valid Number of Plates ", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
clearAndHide();
} else { // user closed dialog or clicked cancel
clearAndHide();
}
}
}
/** This method reacts to state changes in the option pane. */
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible()
&& (e.getSource() == optionPane)
&& (JOptionPane.VALUE_PROPERTY.equals(prop)
|| JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) {
Object value = optionPane.getValue();
if (value == JOptionPane.UNINITIALIZED_VALUE) {
// ignore reset
return;
}
// Reset the JOptionPane's value.
// If you don't do this, then if the user
// presses the same button next time, no
// property change event will be fired.
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
if (btnString1.equals(value)) {
typedText = textField1.getText();
String ucText = typedText.toUpperCase();
if (magicWord.equals(ucText)) {
// we're done; clear and dismiss the dialog
clearAndHide();
} else {
// text was invalid
textField1.selectAll();
JOptionPane.showMessageDialog(
iRuleDialog.this,
"Sorry, \""
+ typedText
+ "\" "
+ "isn't a valid response.\n"
+ "Please enter "
+ magicWord
+ ".",
"Try again",
JOptionPane.ERROR_MESSAGE);
typedText = null;
textField1.requestFocusInWindow();
}
} else { // user closed dialog or clicked cancel
mainGuiWindow.setLabel("It's OK.");
typedText = null;
clearAndHide();
}
}
}
/** This method reacts to state changes in the option pane. */
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible()
&& (e.getSource() == optionPane)
&& (JOptionPane.VALUE_PROPERTY.equals(prop)
|| JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) {
Object value = optionPane.getValue();
if (value == JOptionPane.UNINITIALIZED_VALUE) {
// ignore reset
return;
}
// Reset the JOptionPane's value.
// If you don't do this, then if the user
// presses the same button next time, no
// property change event will be fired.
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
if (btnString1.equals(value)) {
String[] strings = null;
strings = new String[1];
strings[0] = textField[0].getText().trim(); // zScore thresh
// make sure the inputed values are numbers only
if (tools.MathOps.areNumbers(strings)) {
zScore_channel = (String) channelBox.getSelectedItem();
zScore_threshold = Float.parseFloat(strings[0].trim());
clearAndHide();
} else {
JOptionPane.showMessageDialog(
null,
"Error with inputed bounds! Make sure numbers make sense ",
"Thresholds",
JOptionPane.ERROR_MESSAGE);
}
} else {
// user closed dialog or clicked cancel
typedText = null;
clearAndHide();
}
}
}
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible() && (e.getSource() == optionPane) && (prop.equals(JOptionPane.VALUE_PROPERTY))) {
Object value = optionPane.getValue();
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
// If you were going to check something
// before closing the window, you'd do
// it here.
if (value.equals("Close")) {
setVisible(false);
dispose();
} else if (value.equals("Print")) {
cp.createChartPrintJob();
}
}
}
private static void createNativesFolder(File folder) {
if (folder.exists() && !folder.isDirectory()) {
Desktop desktop = Desktop.getDesktop();
JButton browseFolder;
JButton ok = new JButton(UIManager.getString("OptionPane.okButtonText"));
Object[] options;
if (desktop.isSupported(Action.BROWSE)) {
browseFolder = new JButton("Browse Folder");
options = new Object[] {browseFolder, ok};
} else {
browseFolder = null;
options = new Object[] {ok};
}
JOptionPane msg =
new JOptionPane(
"We must create this folder \""
+ folder
+ "\" and there is a file called natives in its place.\n"
+ "Rename or move at this time or it will be deleted. Resistance is futile.",
JOptionPane.INFORMATION_MESSAGE,
JOptionPane.DEFAULT_OPTION,
null,
options);
if (browseFolder != null) {
browseFolder.addActionListener(
action -> {
try {
Desktop.getDesktop().browse(folder.getParentFile().toURI());
} catch (Exception e) {
UIUtils.displayException("Unable to browse folder", e);
}
});
}
ok.addActionListener(action -> msg.setValue(0));
JDialog dialog = msg.createDialog("Slyther");
try (InputStream icon = ClientMain.class.getResourceAsStream("/textures/icon_32.png")) {
dialog.setIconImage(ImageIO.read(icon));
} catch (IOException e) {
}
dialog.setVisible(true);
dialog.dispose();
folder.delete();
}
folder.mkdirs();
}
@Override
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible() && (e.getSource() == optionPane) && (prop.equals(JOptionPane.VALUE_PROPERTY))) {
Object value = optionPane.getValue();
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
// If you were going to check something
// before closing the window, you'd do
// it here.
if (value.equals("Close")) {
setVisible(false);
dispose();
} else if (value.equals("Print")) {
chartPanel.createChartPrintJob();
} else if (value.equals("Export GRAPH")) {
File exportFile =
GraphUtil.saveGraphics(chartPanel, XMAX.getConfiguration().getUserDir("GRAPH"));
if (exportFile != null) {
XMAX.getConfiguration().setUserDir("GRAPH", exportFile.getParent());
}
}
}
}
/** This method handles events for the text field. */
public void actionPerformed(ActionEvent e) {
optionPane.setValue(btnString1);
}
/** This method reacts to state changes in the option pane. */
public void propertyChange(PropertyChangeEvent e) {
String prop = e.getPropertyName();
if (isVisible()
&& (e.getSource() == optionPane)
&& (JOptionPane.VALUE_PROPERTY.equals(prop)
|| JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) {
Object value = optionPane.getValue();
if (value == JOptionPane.UNINITIALIZED_VALUE) {
// ignore reset
return;
}
// Reset the JOptionPane's value.
// If you don't do this, then if the user
// presses the same button next time, no
// property change event will be fired.
optionPane.setValue(JOptionPane.UNINITIALIZED_VALUE);
if (btnString1.equals(value)) {
String[] strings = null;
strings = new String[3];
strings[0] = textField[0].getText(); // Nuc thresh
strings[1] = textField[1].getText(); // Cyt Thresh
strings[2] = textField[2].getText(); // Bkgd thresh
// make sure the inputed values are numbers only
if (tools.MathOps.areNumbers(strings)) {
int NucBoundaryChannel = channelBox_nuc.getSelectedIndex();
int CytoBoundaryChannel = channelBox_cyto.getSelectedIndex();
float Thresh_Nuc_Value = Float.parseFloat(strings[0]);
float Thresh_CellBoundary = Float.parseFloat(strings[1]);
float Thresh_Bkgd_Value = Float.parseFloat(strings[2]);
// Storing the Parameters for each Model_Field
int len = TheWells.length;
for (int i = 0; i < len; i++) {
Model_Well well = TheWells[i];
Model_Field[] fields = well.getFields();
for (int p = 0; p < fields.length; p++) {
Model_ParameterSet pset = fields[p].getParameterSet();
pset.setParameter("Algorithm", "DefaultSegmentor_v1");
// Threshold Channel Nucleus
pset.setParameter(
"Thresh_Nuc_ChannelName",
"" + models.Model_Main.getModel().getTheChannelNames()[NucBoundaryChannel]);
// Threshold Channel Cytoplasm
pset.setParameter(
"Thresh_Cyt_ChannelName",
models.Model_Main.getModel().getTheChannelNames()[CytoBoundaryChannel]);
// Nuc bound threshold
pset.setParameter("Thresh_Nuc_Value", "" + Thresh_Nuc_Value);
// Cell bound Threshold
pset.setParameter("Thresh_Cyt_Value", "" + Thresh_CellBoundary);
// Bkgd threshold
pset.setParameter("Thresh_Bkgd_Value", "" + Thresh_Bkgd_Value);
if (CoordsToSave == 0) pset.setParameter("CoordsToSaveToHDF", "BoundingBox");
else if (CoordsToSave == 1) pset.setParameter("CoordsToSaveToHDF", "Centroid");
else if (CoordsToSave == 2) pset.setParameter("CoordsToSaveToHDF", "Outlines");
else if (CoordsToSave == 3) pset.setParameter("CoordsToSaveToHDF", "Everything");
// Finding the index of this channel name
for (int j = 0; j < models.Model_Main.getModel().getTheChannelNames().length; j++)
if (models.Model_Main.getModel()
.getTheChannelNames()[j]
.equalsIgnoreCase(pset.getParameter_String("Thresh_Nuc_ChannelName")))
pset.setParameter("Thresh_Nuc_ChannelIndex", "" + j);
// Finding the index of this channel name
for (int j = 0; j < models.Model_Main.getModel().getTheChannelNames().length; j++)
if (models.Model_Main.getModel()
.getTheChannelNames()[j]
.equalsIgnoreCase(pset.getParameter_String("Thresh_Cyt_ChannelName")))
pset.setParameter("Thresh_Cyt_ChannelIndex", "" + j);
// Storing Parameters used to process this field
String hdfPath = models.Model_Main.getModel().getOutputProjectPath() + "/Data.h5";
try {
pset.writeParameters(
hdfPath,
well.getPlate().getID(),
well.getWellIndex(),
fields[p].getIndexInWell());
} catch (H5IO_Exception e1) {
e1.printStackTrace();
}
}
}
if (Thresh_Bkgd_Value > 0) models.Model_Main.getModel().setBackgroundSubtract(true);
// Only getting wells with Images that we can process
int numWells = TheWells.length;
ArrayList<Model_Well> wellsWIm = new ArrayList<Model_Well>();
for (int i = 0; i < numWells; i++)
if (TheWells[i].getFields() != null && TheWells[i].getFields().length > 0)
wellsWIm.add(TheWells[i]);
int numW = wellsWIm.size();
Model_Well[] wellsWithImages = new Model_Well[numW];
for (int i = 0; i < numW; i++) wellsWithImages[i] = wellsWIm.get(i);
// File dir = models.Model_Main.getModel()
// .getProjectDirectory();
// File f = new File(dir.getAbsolutePath() + "/BatchJobs");
// if (f.exists())
// deleteDir(f);
//
// f = new File(dir.getAbsolutePath() + "/BatchJobs");
// f.mkdir();
// File f2 = new File(dir.getAbsolutePath() +
// "/BatchResults");
// if (f2.exists())
// deleteDir(f2);
// f2 = new File(dir.getAbsolutePath() + "/BatchResults");
// f2.mkdir();
if (models.Model_Main.getModel().isProcessing()) {
JOptionPane.showMessageDialog(
null,
"Please wait till segmentation is complete before starting another process",
"Be Patient",
JOptionPane.ERROR_MESSAGE);
return;
}
// Single thread run
Processor_WriteParameters tasker = new Processor_WriteParameters(wellsWithImages, null);
tasker.start();
} else {
JOptionPane.showMessageDialog(
null,
"Error with inputed bounds! Make sure numbers make sense ",
"Thresholds",
JOptionPane.ERROR_MESSAGE);
return;
}
clearAndHide();
} else { // user closed dialog or clicked cancel
clearAndHide();
}
}
}