/**
* Closes dialog box when the OK button is pressed, sets variables and calls algorithm.
*
* @param event Event that triggers function.
*/
public void actionPerformed(ActionEvent event) {
String command = event.getActionCommand();
Object source = event.getSource();
if (command.equals("OK")) {
if (setVariables()) {
callAlgorithm();
}
} else if (command.equals("Cancel")) {
dispose();
} else if (command.equals("Help")) {
// MipavUtil.showHelp("");
} else if (source.equals(doRicianCheckBox)) {
if (doRicianCheckBox.isSelected()) {
labelDegree.setEnabled(true);
textDegree.setEnabled(true);
} else {
labelDegree.setEnabled(false);
textDegree.setEnabled(false);
}
} else { // else if (source == thresholdCheckbox)
super.actionPerformed(event);
}
}
/**
* Closes dialog box when the OK button is pressed and calls the algorithm.
*
* @param event Event that triggers function.
*/
public void actionPerformed(ActionEvent event) {
String command = event.getActionCommand();
Object source = event.getSource();
if (command.equals("OK")) {
if (setVariables()) {
callAlgorithm();
}
} else if (command.equals("Script")) {
callAlgorithm();
} else if (command.equals("Cancel")) {
dispose();
} else if (source == blueSmoothBox) {
if (blueSmoothBox.isSelected()) {
interpolationLabel.setEnabled(true);
interpolationText.setEnabled(true);
} else {
interpolationLabel.setEnabled(false);
interpolationText.setEnabled(false);
}
} else {
super.actionPerformed(event);
}
}
/** Loads the default settings from Preferences to set up the dialog. */
public void legacyLoadDefaults() {
String defaultsString = Preferences.getDialogDefaults(getDialogName());
if ((defaultsString != null) && (newImage != null)) {
try {
StringTokenizer st = new StringTokenizer(defaultsString, ",");
textSearchWindowSide.setText("" + MipavUtil.getInt(st));
textSimilarityWindowSide.setText("" + MipavUtil.getInt(st));
textNoiseStandardDeviation.setText("" + MipavUtil.getFloat(st));
textDegree.setText("" + MipavUtil.getFloat(st));
doRician = MipavUtil.getBoolean(st);
doRicianCheckBox.setSelected(doRician);
textDegree.setEnabled(doRician);
labelDegree.setEnabled(doRician);
image25DCheckBox.setSelected(MipavUtil.getBoolean(st));
if (MipavUtil.getBoolean(st)) {
newImage.setSelected(true);
} else {
replaceImage.setSelected(true);
}
} catch (Exception ex) {
// since there was a problem parsing the defaults string, start over with the original
// defaults
Preferences.debug("Resetting defaults for dialog: " + getDialogName());
Preferences.removeProperty(getDialogName());
}
}
}
/**
* Initializes the GUI by creating the components, placing them in the dialog, and displaying
* them.
*/
private void init() {
setForeground(Color.black);
setTitle("Nonlocal Means Filter");
JPanel mainPanel;
mainPanel = new JPanel();
mainPanel.setBorder(BorderFactory.createEmptyBorder(3, 3, 3, 3));
mainPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridwidth = 1;
gbc.gridheight = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.weightx = 1;
gbc.insets = new Insets(3, 3, 3, 3);
gbc.gridx = 0;
gbc.gridy = 0;
gbc.fill = GridBagConstraints.HORIZONTAL;
paramPanel = new JPanel(new GridBagLayout());
paramPanel.setForeground(Color.black);
paramPanel.setBorder(buildTitledBorder("Parameters"));
mainPanel.add(paramPanel, gbc);
GridBagConstraints gbc2 = new GridBagConstraints();
gbc2.gridwidth = 1;
gbc2.gridheight = 1;
gbc2.anchor = GridBagConstraints.WEST;
gbc2.weightx = 1;
gbc2.insets = new Insets(3, 3, 3, 3);
gbc2.gridx = 0;
gbc2.gridy = 0;
gbc2.fill = GridBagConstraints.HORIZONTAL;
labelSearchWindowSide = createLabel("Search window side (odd)");
paramPanel.add(labelSearchWindowSide, gbc2);
gbc2.gridx = 1;
textSearchWindowSide = createTextField("15");
paramPanel.add(textSearchWindowSide, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 1;
labelSimilarityWindowSide = createLabel("Similarity window side (odd) ");
paramPanel.add(labelSimilarityWindowSide, gbc2);
gbc2.gridx = 1;
textSimilarityWindowSide = createTextField("7");
paramPanel.add(textSimilarityWindowSide, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 2;
labelNoiseStandardDeviation = createLabel("Noise standard deviation ");
paramPanel.add(labelNoiseStandardDeviation, gbc2);
gbc2.gridx = 1;
textNoiseStandardDeviation = createTextField("10.0");
paramPanel.add(textNoiseStandardDeviation, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 3;
labelDegree = createLabel("Degree of filtering ");
labelDegree.setEnabled(doRician);
paramPanel.add(labelDegree, gbc2);
gbc2.gridx = 1;
textDegree = createTextField("1.414");
textDegree.setEnabled(doRician);
paramPanel.add(textDegree, gbc2);
gbc2.gridx = 0;
gbc2.gridy = 4;
doRicianCheckBox = new JCheckBox("Deal with Rician noise in MRI");
doRicianCheckBox.setFont(serif12);
doRicianCheckBox.setSelected(false);
doRicianCheckBox.addActionListener(this);
paramPanel.add(doRicianCheckBox, gbc2);
if (image.getNDims() > 2) {
gbc2.gridx = 0;
gbc2.gridy = 5;
gbc2.gridwidth = 2;
image25DCheckBox = new JCheckBox("Process each slice independently (2.5D)");
image25DCheckBox.setFont(serif12);
paramPanel.add(image25DCheckBox, gbc2);
image25DCheckBox.setSelected(false);
} // if (image.getNDims > 2)
JPanel outputOptPanel = new JPanel(new GridLayout(1, 2));
destinationPanel = new JPanel(new BorderLayout());
destinationPanel.setForeground(Color.black);
destinationPanel.setBorder(buildTitledBorder("Destination"));
outputOptPanel.add(destinationPanel);
destinationGroup = new ButtonGroup();
newImage = new JRadioButton("New image", true);
newImage.setBounds(10, 16, 120, 25);
newImage.setFont(serif12);
destinationGroup.add(newImage);
destinationPanel.add(newImage, BorderLayout.NORTH);
replaceImage = new JRadioButton("Replace image", false);
replaceImage.setFont(serif12);
destinationGroup.add(replaceImage);
destinationPanel.add(replaceImage, BorderLayout.CENTER);
// Only if the image is unlocked can it be replaced.
if (image.getLockStatus() == ModelStorageBase.UNLOCKED) {
replaceImage.setEnabled(true);
} else {
replaceImage.setEnabled(false);
}
gbc.gridx = 0;
gbc.gridy = 1;
mainPanel.add(outputOptPanel, gbc);
mainDialogPanel.add(mainPanel, BorderLayout.CENTER);
mainDialogPanel.add(buildButtons(), BorderLayout.SOUTH);
getContentPane().add(mainDialogPanel);
pack();
setResizable(true);
// setVisible(true);
System.gc();
}
/** Sets up the GUI (panels, buttons, etc) and displays it on the screen. */
private void init() {
DecimalFormat df;
int xUnits;
String unitStr;
String distStr;
setForeground(Color.black);
setTitle("Center Distances version 2 07/14/08");
df = new DecimalFormat("0.000E0");
GridBagConstraints gbc = new GridBagConstraints();
int yPos = 0;
gbc.gridwidth = 1;
gbc.gridheight = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.weightx = 1;
gbc.insets = new Insets(3, 3, 3, 3);
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.gridx = 0;
gbc.gridy = yPos++;
JPanel mainPanel = new JPanel(new GridBagLayout());
mainPanel.setForeground(Color.black);
mainPanel.setBorder(buildTitledBorder("Input parameters"));
blueMinLabel = new JLabel("Minimum number of blue pixels per nucleus");
blueMinLabel.setForeground(Color.black);
blueMinLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(blueMinLabel, gbc);
blueMinText = new JTextField(5);
if (image.getNDims() == 2) {
blueMinText.setText("1000");
} else {
blueMinText.setText("20000");
}
blueMinText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(blueMinText, gbc);
redMinLabel = new JLabel("Minimum red pixel count");
redMinLabel.setForeground(Color.black);
redMinLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(redMinLabel, gbc);
redMinText = new JTextField(5);
redMinText.setText("50");
redMinText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(redMinText, gbc);
redFractionLabel = new JLabel("Fraction of red pixels to consider");
redFractionLabel.setForeground(Color.black);
redFractionLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(redFractionLabel, gbc);
redFractionText = new JTextField(5);
redFractionText.setText("0.15");
redFractionText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(redFractionText, gbc);
xUnits = image.getFileInfo(0).getUnitsOfMeasure()[0];
if (xUnits != Unit.UNKNOWN_MEASURE.getLegacyNum()) {
unitStr = (Unit.getUnitFromLegacyNum(xUnits)).toString();
greenMergingLabel = new JLabel("Green merging radius around peak (" + unitStr + ")");
} else {
greenMergingLabel = new JLabel("Green merging radius around peak");
}
greenMergingLabel.setForeground(Color.black);
greenMergingLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(greenMergingLabel, gbc);
if (image.getNDims() == 2) {
// mergingDistance = 8.0f * image.getFileInfo(0).getResolutions()[0];
mergingDistance = 0.0f;
} else {
// mergingDistance = 4.0f * image.getFileInfo(0).getResolutions()[0];
mergingDistance = 0.0f;
}
distStr = df.format(mergingDistance);
greenMergingText = new JTextField(10);
greenMergingText.setText(distStr);
greenMergingText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(greenMergingText, gbc);
greenMinLabel = new JLabel("Minimum green pixel count");
greenMinLabel.setForeground(Color.black);
greenMinLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(greenMinLabel, gbc);
greenMinText = new JTextField(5);
greenMinText.setText("10");
greenMinText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(greenMinText, gbc);
greenFractionLabel = new JLabel("Fraction of green pixels to consider");
greenFractionLabel.setForeground(Color.black);
greenFractionLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(greenFractionLabel, gbc);
greenFractionText = new JTextField(5);
greenFractionText.setText("0.01");
greenFractionText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(greenFractionText, gbc);
greenRegionsLabel = new JLabel("Green regions per cell");
greenRegionsLabel.setForeground(Color.black);
greenRegionsLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(greenRegionsLabel, gbc);
JPanel buttonPanel = new JPanel(new GridBagLayout());
greenGroup = new ButtonGroup();
oneButton = new JRadioButton("1", false);
oneButton.setForeground(Color.black);
oneButton.setFont(serif12);
greenGroup.add(oneButton);
gbc.gridx = 0;
gbc.gridy = 0;
buttonPanel.add(oneButton, gbc);
twoButton = new JRadioButton("2", true);
twoButton.setForeground(Color.black);
twoButton.setFont(serif12);
greenGroup.add(twoButton);
gbc.gridx = 1;
gbc.gridy = 0;
buttonPanel.add(twoButton, gbc);
threeButton = new JRadioButton("3", false);
threeButton.setForeground(Color.black);
threeButton.setFont(serif12);
greenGroup.add(threeButton);
gbc.gridx = 2;
gbc.gridy = 0;
buttonPanel.add(threeButton, gbc);
fourButton = new JRadioButton("4", false);
fourButton.setForeground(Color.black);
fourButton.setFont(serif12);
greenGroup.add(fourButton);
gbc.gridx = 3;
gbc.gridy = 0;
buttonPanel.add(fourButton, gbc);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(buttonPanel, gbc);
twoBox = new JCheckBox("Use 2 top gray levels in green segmentation", true);
twoBox.setForeground(Color.black);
twoBox.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos++;
mainPanel.add(twoBox, gbc);
blueValueLabel =
new JLabel("Fraction of blue transition from image min to max at nucleus boundary");
blueValueLabel.setForeground(Color.black);
blueValueLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(blueValueLabel, gbc);
blueValueText = new JTextField(5);
blueValueText.setText("0.15");
blueValueText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(blueValueText, gbc);
blueSmoothBox = new JCheckBox("Smooth blue VOI contours with AlgorithmBSmooth", true);
blueSmoothBox.setForeground(Color.black);
blueSmoothBox.setFont(serif12);
blueSmoothBox.addActionListener(this);
gbc.gridx = 0;
gbc.gridy = yPos++;
mainPanel.add(blueSmoothBox, gbc);
interpolationLabel = new JLabel("Number of interpolation points determined by divisor (> 1.0)");
interpolationLabel.setForeground(Color.black);
interpolationLabel.setFont(serif12);
gbc.gridx = 0;
gbc.gridy = yPos;
mainPanel.add(interpolationLabel, gbc);
interpolationText = new JTextField(5);
interpolationText.setText("24.0");
interpolationText.setFont(serif12);
gbc.gridx = 1;
gbc.gridy = yPos++;
mainPanel.add(interpolationText, gbc);
getContentPane().add(mainPanel, BorderLayout.CENTER);
getContentPane().add(buildButtons(), BorderLayout.SOUTH);
pack();
setVisible(true);
setResizable(false);
System.gc();
} // end init()
/** Sets up the GUI (panels, buttons, etc) and displays it on the screen. */
private void init() {
if (image.getFileInfo(0).getFileFormat() == FileUtility.DICOM) {
FileInfoDicom dicomInfo = (FileInfoDicom) image.getFileInfo(0);
FileDicomTagTable tagTable = dicomInfo.getTagTable();
if (tagTable.getValue("0018,1310") != null) {
// Acquisition matrix
FileDicomTag tag = tagTable.get(new FileDicomKey("0018,1310"));
Object[] values = tag.getValueList();
int valNumber = values.length;
if ((valNumber == 4) && (values instanceof Short[])) {
int frequencyRows = ((Short) values[0]).intValue();
Preferences.debug("frequencyRows = " + frequencyRows + "\n");
int frequencyColumns = ((Short) values[1]).intValue();
Preferences.debug("frequencyColumns = " + frequencyColumns + "\n");
int phaseRows = ((Short) values[2]).intValue();
Preferences.debug("phaseRows = " + phaseRows + "\n");
int phaseColumns = ((Short) values[3]).intValue();
Preferences.debug("phaseColumns = " + phaseColumns + "\n");
if ((frequencyRows > 0) && (phaseRows == 0)) {
subYDim = frequencyRows;
} else if ((frequencyRows == 0) && (phaseRows > 0)) {
subYDim = phaseRows;
}
if ((frequencyColumns > 0) && (phaseColumns == 0)) {
subXDim = frequencyColumns;
} else if ((frequencyColumns == 0) && (phaseColumns > 0)) {
subXDim = phaseColumns;
}
}
} // if (tagTable.getValue("0018,1310") != null)
if (tagTable.getValue("0019,100A") != null) {
FileDicomTag tag = tagTable.get(new FileDicomKey("0019,100A"));
Object value = tag.getValue(false);
if (value instanceof Short) {
numberOfImagesInMosaic = ((Short) value).intValue();
Preferences.debug("Number of images in mosaic = " + numberOfImagesInMosaic + "\n");
}
} // if (tagTable.getValue("0019,100A") != null)
} // if (image.getFileInfo(0).getFileFormat() == FileUtility.DICOM)*/
setForeground(Color.black);
setTitle("Mosaic To 3D Volume");
JPanel inputPanel = new JPanel(new GridBagLayout());
inputPanel.setForeground(Color.black);
inputPanel.setBorder(buildTitledBorder("Image"));
JLabel labelUse = new JLabel("Image:");
labelUse.setForeground(Color.black);
labelUse.setFont(serif12);
JLabel labelImage = new JLabel(image.getImageName());
labelImage.setForeground(Color.black);
labelImage.setFont(serif12);
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.gridheight = 1;
gbc.gridwidth = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.weightx = 1;
gbc.insets = new Insets(5, 5, 5, 5);
inputPanel.add(labelUse, gbc);
gbc.gridx = 1;
gbc.fill = GridBagConstraints.HORIZONTAL;
inputPanel.add(labelImage, gbc);
JPanel dimensionPanel = new JPanel(new GridBagLayout());
dimensionPanel.setForeground(Color.black);
dimensionPanel.setBorder(buildTitledBorder("X and Y Dimensions of Result"));
JLabel labelXDim = new JLabel("X dimension of slices");
labelXDim.setForeground(Color.black);
labelXDim.setFont(serif12);
textXDim = new JTextField(10);
if (subXDim != 0) {
textXDim.setText(String.valueOf(subXDim));
}
textXDim.setFont(serif12);
textXDim.setForeground(Color.black);
JLabel labelYDim = new JLabel("Y dimension of slices");
labelYDim.setForeground(Color.black);
labelYDim.setFont(serif12);
textYDim = new JTextField(10);
if (subYDim != 0) {
textYDim.setText(String.valueOf(subYDim));
}
textYDim.setFont(serif12);
textYDim.setForeground(Color.black);
JLabel labelNumberImages = new JLabel("Number of images in mosaic");
labelNumberImages.setForeground(Color.black);
labelNumberImages.setFont(serif12);
textNumberImages = new JTextField(10);
if (numberOfImagesInMosaic != 0) {
textNumberImages.setText(String.valueOf(numberOfImagesInMosaic));
}
textNumberImages.setFont(serif12);
textNumberImages.setForeground(Color.black);
gbc.gridx = 0;
gbc.gridy = 0;
dimensionPanel.add(labelXDim, gbc);
gbc.gridx = 1;
dimensionPanel.add(textXDim, gbc);
gbc.gridx = 0;
gbc.gridy = 1;
dimensionPanel.add(labelYDim, gbc);
gbc.gridx = 1;
dimensionPanel.add(textYDim, gbc);
gbc.gridx = 0;
gbc.gridy = 2;
dimensionPanel.add(labelNumberImages, gbc);
gbc.gridx = 1;
dimensionPanel.add(textNumberImages, gbc);
JPanel mainPanel = new JPanel(new BorderLayout());
mainPanel.add(inputPanel, BorderLayout.NORTH);
mainPanel.add(dimensionPanel, BorderLayout.CENTER);
mainPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
JPanel buttonPanel = new JPanel();
buttonPanel.add(buildButtons());
getContentPane().add(mainPanel);
getContentPane().add(buttonPanel, BorderLayout.SOUTH);
pack();
setVisible(true);
}