/**
* Returns the name of an image output by this algorithm, the image returned depends on the
* parameter label given (which can be used to retrieve the image object from the image registry).
*
* @param imageParamName The output image parameter label for which to get the image name.
* @return The image name of the requested output image parameter label.
*/
public String getOutputImageName(final String imageParamName) {
if (imageParamName.equals(AlgorithmParameters.RESULT_IMAGE)) {
if (getResultImage() != null) {
// algo produced a new result image
return getResultImage().getImageName();
} else {
// algo was done in place
return image.getImageName();
}
}
Preferences.debug(
"Unrecognized output image parameter: " + imageParamName + "\n",
Preferences.DEBUG_SCRIPTING);
return null;
}
/**
* Once all the necessary variables are set, call the Gaussian Blur algorithm based on what type
* of image this is and whether or not there is a separate destination image.
*/
protected void callAlgorithm() {
try {
centerDistanceAlgo =
new PlugInAlgorithmCenterDistance2(
image,
blueMin,
redMin,
redFraction,
mergingDistance,
greenMin,
greenFraction,
greenRegionNumber,
twoGreenLevels,
blueBoundaryFraction,
blueSmooth,
interpolationDivisor);
// This is very important. Adding this object as a listener allows
// the algorithm to
// notify this object when it has completed or failed. See algorithm
// performed event.
// This is made possible by implementing AlgorithmedPerformed
// interface
centerDistanceAlgo.addListener(this);
createProgressBar(image.getImageName(), " ...", centerDistanceAlgo);
setVisible(false); // Hide dialog
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still
// have user interface work fast.
if (centerDistanceAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
centerDistanceAlgo.run();
}
} catch (OutOfMemoryError x) {
MipavUtil.displayError("Center Distance: unable to allocate enough memory");
return;
}
} // end callAlgorithm()
/**
* Once all the necessary variables are set, call the Nonlocal Means filter algorithm based on
* what type of image this is and whether or not there is a separate destination image.
*/
protected void callAlgorithm() {
String name = makeImageName(image.getImageName(), "_NonlocalMeans");
int[] destExtents;
if (image.getNDims() == 2) { // source image is 2D
destExtents = new int[2];
destExtents[0] = image.getExtents()[0]; // X dim
destExtents[1] = image.getExtents()[1]; // Y dim
} else {
destExtents = new int[3];
destExtents[0] = image.getExtents()[0];
destExtents[1] = image.getExtents()[1];
destExtents[2] = image.getExtents()[2];
}
if (displayLoc == NEW) {
try {
// Make result image of float type
if (image.isColorImage()) {
resultImage = new ModelImage(ModelImage.ARGB, destExtents, name);
} else {
resultImage = new ModelImage(ModelImage.FLOAT, destExtents, name);
}
// resultImage = (ModelImage)image.clone();
// resultImage.setImageName(name);
// Make algorithm
nlMeansFilterAlgo =
new AlgorithmNonlocalMeansFilter(
resultImage,
image,
searchWindowSide,
similarityWindowSide,
noiseStandardDeviation,
degreeOfFiltering,
doRician,
image25D);
// This is very important. Adding this object as a listener allows the algorithm to
// notify this object when it has completed of failed. See algorithm performed event.
// This is made possible by implementing AlgorithmedPerformed interface
nlMeansFilterAlgo.addListener(this);
createProgressBar(image.getImageName(), nlMeansFilterAlgo);
// Hide dialog
setVisible(false);
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still have user interface work
// fast
if (nlMeansFilterAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
nlMeansFilterAlgo.run();
}
} catch (OutOfMemoryError x) {
MipavUtil.displayError("Dialog Nonlocal Means Filter: unable to allocate enough memory");
if (resultImage != null) {
resultImage.disposeLocal(); // Clean up memory of result image
resultImage = null;
}
return;
}
} else {
try {
// No need to make new image space because the user has choosen to replace the source image
// Make the algorithm class
nlMeansFilterAlgo =
new AlgorithmNonlocalMeansFilter(
null,
image,
searchWindowSide,
similarityWindowSide,
noiseStandardDeviation,
degreeOfFiltering,
doRician,
image25D);
// This is very important. Adding this object as a listener allows the algorithm to
// notify this object when it has completed of failed. See algorithm performed event.
// This is made possible by implementing AlgorithmedPerformed interface
nlMeansFilterAlgo.addListener(this);
createProgressBar(image.getImageName(), nlMeansFilterAlgo);
// Hide the dialog since the algorithm is about to run.
setVisible(false);
// These next lines set the titles in all frames where the source image is displayed to
// "locked - " image name so as to indicate that the image is now read/write locked!
// The image frames are disabled and then unregisted from the userinterface until the
// algorithm has completed.
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
titles = new String[imageFrames.size()];
for (int i = 0; i < imageFrames.size(); i++) {
titles[i] = ((Frame) (imageFrames.elementAt(i))).getTitle();
((Frame) (imageFrames.elementAt(i))).setTitle("Locked: " + titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(false);
userInterface.unregisterFrame((Frame) (imageFrames.elementAt(i)));
}
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still have user interface work
// fast
if (nlMeansFilterAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
nlMeansFilterAlgo.run();
}
} catch (OutOfMemoryError x) {
MipavUtil.displayError("Dialog Nonlocal Means Filter: unable to allocate enough memory");
return;
}
}
}
/** 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);
}
/**
* Once all the necessary variables are set, call the Concat algorithm based on what type of image
* this is and whether or not there is a separate destination image.
*/
protected void callAlgorithm() {
int destExtents[] = new int[3];
ModelImage destImage = null;
destExtents[0] = subXDim;
destExtents[1] = subYDim;
destExtents[2] = numberOfImagesInMosaic;
destImage =
new ModelImage(
image.getType(), destExtents, makeImageName(image.getImageName(), "_mosaic_to_slices"));
try {
// Make algorithm
mathAlgo = new AlgorithmMosaicToSlices(image, destImage);
// This is very important. Adding this object as a listener allows the algorithm to
// notify this object when it has completed of failed. See algorithm performed event.
// This is made possible by implementing AlgorithmedPerformed interface
mathAlgo.addListener(this);
createProgressBar(image.getImageName(), mathAlgo);
// Hide dialog
setVisible(false);
if (displayLoc == REPLACE) {
// These next lines set the titles in all frames where the source image is displayed to
// "locked - " image name so as to indicate that the image is now read/write locked!
// The image frames are disabled and then unregisted from the userinterface until the
// algorithm has completed.
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
titles = new String[imageFrames.size()];
for (int i = 0; i < imageFrames.size(); i++) {
titles[i] = ((Frame) (imageFrames.elementAt(i))).getTitle();
((Frame) (imageFrames.elementAt(i))).setTitle("Locked: " + titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(false);
userInterface.unregisterFrame((Frame) (imageFrames.elementAt(i)));
}
}
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still have user interface work
// fast.
if (mathAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
mathAlgo.run();
}
} catch (OutOfMemoryError x) {
System.gc();
MipavUtil.displayError("Dialog Concatenation: unable to allocate enough memory");
return;
}
}