/**
* This method is required if the AlgorithmPerformed interface is implemented. It is called by the
* algorithms when it has completed or failed to to complete, so that the dialog can be display
* the result image and/or clean up.
*
* @param algorithm Algorithm that caused the event.
*/
public void algorithmPerformed(AlgorithmBase algorithm) {
if (algorithm instanceof AlgorithmNonlocalMeansFilter) {
image.clearMask();
if ((nlMeansFilterAlgo.isCompleted() == true) && (resultImage != null)) {
updateFileInfo(image, resultImage);
resultImage.clearMask();
// The algorithm has completed and produced a new image to be displayed.
try {
new ViewJFrameImage(resultImage, null, new Dimension(610, 200));
} catch (OutOfMemoryError error) {
MipavUtil.displayError("Out of memory: unable to open new frame");
}
} else if (resultImage == null) {
// These next lines set the titles in all frames where the source image is displayed to
// image name so as to indicate that the image is now unlocked!
// The image frames are enabled and then registed to the userinterface.
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
for (int i = 0; i < imageFrames.size(); i++) {
((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(true);
if (((Frame) (imageFrames.elementAt(i))) != parentFrame) {
userInterface.registerFrame((Frame) (imageFrames.elementAt(i)));
}
}
if (parentFrame != null) {
userInterface.registerFrame(parentFrame);
}
image.notifyImageDisplayListeners(null, true);
} else if (resultImage != null) {
// algorithm failed but result image still has garbage
resultImage.disposeLocal(); // clean up memory
resultImage = null;
}
}
if (algorithm.isCompleted()) {
insertScriptLine();
}
// save the completion status for later
setComplete(algorithm.isCompleted());
nlMeansFilterAlgo.finalize();
nlMeansFilterAlgo = null;
dispose();
}
/**
* Creates a new JDialogNonlocalMeansFilter object.
*
* @param theParentFrame Parent frame.
* @param im Source image.
*/
public JDialogNonlocalMeansFilter(Frame theParentFrame, ModelImage im) {
super(theParentFrame, false);
image = im;
userInterface = ViewUserInterface.getReference();
init();
setVisible(true);
}
/** Construct the panel's GUI. */
private void initGUI() {
PanelManager mainPanelManager = new PanelManager(this);
PanelManager destPanelManager = new PanelManager("Destination");
PanelManager regionPanelManager = new PanelManager("Process");
ButtonGroup destinationGroup = new ButtonGroup();
ButtonGroup imageVOIGroup = new ButtonGroup();
newImageRadio = WidgetFactory.buildRadioButton("New image", true, destinationGroup);
destPanelManager.add(newImageRadio);
replaceImageRadio = WidgetFactory.buildRadioButton("Replace image", false, destinationGroup);
destPanelManager.addOnNextLine(replaceImageRadio);
// Only if the image is unlocked can it be replaced.
if (srcImage.getLockStatus() == ModelStorageBase.UNLOCKED) {
replaceImageRadio.setEnabled(true);
if (ViewUserInterface.getReference().doForceInPlace()) {
replaceImageRadio.setSelected(true);
newImageRadio.setEnabled(false);
}
} else {
replaceImageRadio.setEnabled(false);
}
wholeImageRadio = WidgetFactory.buildRadioButton("Whole image", true, imageVOIGroup);
regionPanelManager.add(wholeImageRadio);
voiRegionsRadio = WidgetFactory.buildRadioButton("VOI region(s)", false, imageVOIGroup);
regionPanelManager.addOnNextLine(voiRegionsRadio);
mainPanelManager.add(destPanelManager.getPanel());
mainPanelManager.add(regionPanelManager.getPanel());
}
/** {@inheritDoc} */
protected void setGUIFromParams() {
image = scriptParameters.retrieveInputImage();
userInterface = ViewUserInterface.getReference();
parentFrame = image.getParentFrame();
if (scriptParameters.doOutputNewImage()) {
setDisplayLocNew();
} else {
setDisplayLocReplace();
}
searchWindowSide = scriptParameters.getParams().getInt("search_window_side");
similarityWindowSide = scriptParameters.getParams().getInt("similarity_window_side");
noiseStandardDeviation = scriptParameters.getParams().getFloat("noise_standard_deviation");
degreeOfFiltering = scriptParameters.getParams().getFloat("degree_of_filtering");
doRician = scriptParameters.getParams().getBoolean("do_rician");
image25D = scriptParameters.doProcess3DAs25D();
}
/** {@inheritDoc} */
protected void setGUIFromParams() {
image = scriptParameters.retrieveInputImage(1);
userInterface = ViewUserInterface.getReference();
parentFrame = image.getParentFrame();
if (scriptParameters.doOutputNewImage()) {
setDisplayLocNew();
} else {
// replace processing not supported..
// setDisplayLocReplace();
setDisplayLocNew();
}
subXDim = scriptParameters.getParams().getInt("sub_x_dim");
subYDim = scriptParameters.getParams().getInt("sub_y_dim");
numberOfImagesInMosaic = scriptParameters.getParams().getInt("number_of_images_in_mosaic");
}
/** Starts the program. */
public void runAlgorithm() {
int i, j, k;
if (srcImage == null) {
displayError("Source Image is null");
finalize();
return;
}
if (threadStopped) {
finalize();
return;
}
trueVOIs = srcImage.getVOIs();
nTrueVOIs = trueVOIs.size();
testVOIs = testImage.getVOIs();
nTestVOIs = testVOIs.size();
length = srcImage.getExtents()[0];
for (i = 1; i < srcImage.getNDims(); i++) {
length *= srcImage.getExtents()[i];
}
testLength = testImage.getExtents()[0];
for (i = 1; i < testImage.getNDims(); i++) {
testLength *= testImage.getExtents()[i];
}
if (length != testLength) {
MipavUtil.displayError(
srcImage.getImageName()
+ " and "
+ testImage.getImageName()
+ " are unequal in dimensions");
setCompleted(false);
return;
}
trueMask = new short[length];
testMask = new short[length];
ViewUserInterface.getReference().setGlobalDataText(srcImage.getImageName() + " = true\n");
ViewUserInterface.getReference().setGlobalDataText(testImage.getImageName() + " = test\n");
for (i = 0; i < nTrueVOIs; i++) {
if ((trueVOIs.VOIAt(i).getCurveType() == VOI.CONTOUR)
|| (trueVOIs.VOIAt(i).getCurveType() == VOI.POLYLINE)) {
trueID = trueVOIs.VOIAt(i).getID();
for (j = 0; j < nTestVOIs; j++) {
testID = testVOIs.VOIAt(j).getID();
if (trueID == testID) {
for (k = 0; k < length; k++) {
trueMask[k] = -1;
testMask[k] = -1;
}
trueMask = srcImage.generateVOIMask(trueMask, i);
testMask = testImage.generateVOIMask(testMask, j);
absoluteTrue = 0;
trueFound = 0;
falseNegative = 0;
falsePositive = 0;
for (k = 0; k < length; k++) {
if (trueMask[k] == trueID) {
absoluteTrue++;
if (testMask[k] == trueID) {
trueFound++;
} else {
falseNegative++;
}
} // if (trueMask[k] == trueID)
else { // trueMask[k] != trueID
if (testMask[k] == trueID) {
falsePositive++;
}
} // else trueMask[k] != trueID
} // for (k = 0; k < length; k++)
ViewUserInterface.getReference()
.setGlobalDataText(
"Statistics for VOIs with ID = " + String.valueOf(trueID) + "\n");
fnvf = (float) falseNegative / (float) absoluteTrue;
ViewUserInterface.getReference()
.setGlobalDataText(
" False negative volume fraction = " + String.valueOf(fnvf) + "\n");
fpvf = (float) falsePositive / (float) absoluteTrue;
ViewUserInterface.getReference()
.setGlobalDataText(
" False positive volume fraction = " + String.valueOf(fpvf) + "\n");
tpvf = (float) trueFound / (float) absoluteTrue;
ViewUserInterface.getReference()
.setGlobalDataText(
" True Positive volume fraction = " + String.valueOf(tpvf) + "\n\n");
} // if (trueID == testID)
} // for (j = 0; j < nTestVOIs; j++)
} // if ((trueVOIs.VOIAt(i).getCurveType() == VOI.CONTOUR)
} // for (i = 0; i < nTrueVOIs; i++)
setCompleted(true);
}
/**
* 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;
}
}
}
/**
* Creates new Mosaic To Slices dialog.
*
* @param theParentFrame Parent frame.
* @param im Source image.
*/
public JDialogMosaicToSlices(Frame theParentFrame, ModelImage im) {
super(theParentFrame, false);
image = im;
userInterface = ViewUserInterface.getReference();
init();
}
/**
* 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;
}
}
/**
* This method is required if the AlgorithmPerformed interface is implemented. It is called by the
* algorithms when it has completed or failed to to complete, so that the dialog can be display
* the result image and/or clean up.
*
* @param algorithm Algorithm that caused the event.
*/
public void algorithmPerformed(AlgorithmBase algorithm) {
ViewJFrameImage imageFrame = null;
if (algorithm instanceof AlgorithmMosaicToSlices) {
if ((mathAlgo.isCompleted() == true) && (mathAlgo.getResultImage() != null)) {
// The algorithm has completed and produced a new image to be displayed.
if (displayLoc == NEW) {
try {
resultImage = mathAlgo.getResultImage();
new ViewJFrameImage(resultImage, null, new Dimension(610, 200));
} catch (OutOfMemoryError error) {
System.gc();
MipavUtil.displayError("Out of memory: unable to open new frame");
}
} else {
// These next lines set the titles in all frames where the source image is displayed to
// image name so as to indicate that the image is now unlocked!
// The image frames are enabled and then registed to the userinterface.
resultImage = mathAlgo.getResultImage();
Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector();
for (int i = 0; i < imageFrames.size(); i++) {
((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(true);
if ((((Frame) (imageFrames.elementAt(i))) != parentFrame) && (parentFrame != null)) {
userInterface.registerFrame((Frame) (imageFrames.elementAt(i)));
}
}
Point pt;
if (parentFrame != null) {
pt = ((ViewJFrameBase) parentFrame).getLocation();
} else {
pt =
new Point(
Toolkit.getDefaultToolkit().getScreenSize().width / 2,
Toolkit.getDefaultToolkit().getScreenSize().height / 2);
}
imageFrame = new ViewJFrameImage(resultImage, null, new Dimension(pt.x, pt.y));
if (parentFrame != null) {
((ViewJFrameBase) parentFrame).close();
} else {
((ViewJFrameBase) image.getParentFrame()).close();
}
// Not so sure about this.
if (image.getLightBoxFrame() != null) {
try {
pt = image.getLightBoxFrame().getLocation();
image.getLightBoxFrame().close();
new ViewJFrameLightBox(
imageFrame,
"LightBox",
resultImage,
imageFrame.getComponentImage().getLUTa(),
imageFrame.getComponentImage().getImageB(),
imageFrame.getComponentImage().getLUTb(),
imageFrame.getComponentImage().getResolutionX(),
imageFrame.getComponentImage().getResolutionY(),
new Dimension(pt.x, pt.y),
imageFrame.getControls(),
imageFrame.getVOIManager());
} catch (OutOfMemoryError error) {
MipavUtil.displayError("Out of memory: unable to open new frame");
}
}
}
} else if (resultImage == null) {
// These next lines set the titles in all frames where the source image is displayed to
// image name so as to indicate that the image is now unlocked!
// The image frames are enabled and then registered to the userinterface.
/*Vector imageFrames = imageA.getImageFrameVector();
for (int i = 0; i < imageFrames.size(); i++) {
((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]);
((Frame) (imageFrames.elementAt(i))).setEnabled(true);
if (((Frame) (imageFrames.elementAt(i))) != parentFrame) {
userInterface.registerFrame((Frame) (imageFrames.elementAt(i)));
}
}*/
if (parentFrame != null) {
userInterface.registerFrame(parentFrame);
}
image.notifyImageDisplayListeners(null, true);
} else if (resultImage != null) {
// algorithm failed but result image still has garbage
resultImage.disposeLocal(); // clean up memory
System.gc();
}
}
if (algorithm.isCompleted()) {
insertScriptLine();
}
mathAlgo.finalize();
mathAlgo = null;
dispose();
}