/**
* 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();
}
/** 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());
}
/** Starts the program. */
public void runAlgorithm() {
int[] destExtents = null;
if (srcImage == null) {
displayError("Source Image is null");
return;
}
if (srcImage.getNDims() == 2) {
makeKernels2D();
} else if ((srcImage.getNDims() == 3) && (image25D == false)) {
makeKernels3D();
} else if ((srcImage.getNDims() == 3) && (image25D == true)) {
makeKernels2D();
}
try {
if (srcImage.getNDims() == 2) {
destExtents = new int[2];
destExtents[0] = srcImage.getExtents()[0]; // X dim
destExtents[1] = srcImage.getExtents()[1]; // Y dim
} else if (srcImage.getNDims() == 3) {
destExtents = new int[3];
destExtents[0] = srcImage.getExtents()[0]; // X dim
destExtents[1] = srcImage.getExtents()[1]; // Y dim
destExtents[2] = srcImage.getExtents()[2]; // Z dim
}
zXMask = new ModelImage(ModelImage.UBYTE, destExtents, " Edges");
} catch (OutOfMemoryError e) {
destImage = null;
srcImage = null;
zXMask.disposeLocal();
zXMask = null;
errorCleanUp("Algorithm EdgeLapSep : Out of memory", true);
return;
}
if (destImage != null) { // NEW
if (srcImage.getNDims() == 2) {
calcStoreInDest2D(1, zeroDetectionType);
} else if ((srcImage.getNDims() == 3) && (image25D == false)) {
calcStoreInDest3D(zeroDetectionType);
} else if ((srcImage.getNDims() == 3) && (image25D == true)) {
calcStoreInDest2D(srcImage.getExtents()[2], zeroDetectionType);
}
}
if (threadStopped) {
finalize();
return;
}
}
/** dispose memory. */
public void disposeLocal() {
if (mathAlgo != null) {
mathAlgo.finalize();
mathAlgo = null;
}
if (image != null) {
image.disposeLocal();
}
image = null;
if (resultImage != null) {
resultImage.disposeLocal();
}
resultImage = null;
}
/** {@inheritDoc} */
protected void setGUIFromParams() {
image = scriptParameters.retrieveInputImage();
parentFrame = image.getParentFrame();
if (!image.isColorImage()) {
throw new ParameterException(
AlgorithmParameters.getInputImageLabel(1), "Source Image must be Color");
}
setBlueMin(scriptParameters.getParams().getInt("blue_min"));
setRedMin(scriptParameters.getParams().getInt("red_min"));
setRedFraction(scriptParameters.getParams().getFloat("red_fraction"));
setMergingDistance(scriptParameters.getParams().getFloat("merging_distance"));
setGreenMin(scriptParameters.getParams().getInt("green_min"));
setGreenFraction(scriptParameters.getParams().getFloat("green_fraction"));
setGreenRegionNumber(scriptParameters.getParams().getInt("green_region_number"));
setTwoGreenLevels(scriptParameters.getParams().getBoolean("two_green_levels"));
setBlueBoundaryFraction(scriptParameters.getParams().getFloat("blue_boundary_fraction"));
setBlueSmooth(scriptParameters.getParams().getBoolean("blue_smooth"));
setInterpolationDivisor(scriptParameters.getParams().getFloat("interpolation_divisor"));
}
/**
* Display string pass into the method. If the string is null no message is displayed. The
* completed flag is set to <code>false</code> and the progress bar is disposed;
*
* @param strErr the string that is to be displayed. If the string is null no message is
* displayed.
* @param gcFlag if <code>true</code> call the garbage collector.
*/
public void errorCleanUp(String strErr, boolean gcFlag) {
if (gcFlag == true) {
System.gc();
}
if (strErr != null) {
displayError(strErr);
}
setCompleted(false);
setThreadStopped(true);
if (destImage != null) {
destImage.releaseLock();
}
if (srcImage != null) {
srcImage.releaseLock();
}
}
/**
* Creates new dialog for distances within a cell from the geometric center using a plugin.
*
* @param theParentFrame Parent frame.
* @param im Source image.
*/
public PlugInDialogCenterDistance2(Frame theParentFrame, ModelImage im) {
super(theParentFrame, false);
if (!im.isColorImage()) {
MipavUtil.displayError("Source Image must be Color");
dispose();
return;
}
image = im;
init();
}
/**
* 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) {
imageA.clearMask();
if (algorithm instanceof PlugInAlgorithmISN) {
if (isnAlgo.isCompleted() == true) {
// The algorithm has completed and produced a new image to be displayed.
updateFileInfo(imageA, resultImage);
new ViewJFrameImage(resultImage, (ModelLUT) null);
}
}
}
/** Calls the algorithm. */
protected void callAlgorithm() {
try {
resultImage =
new ModelImage(imageA.getType(), imageA.getExtents(), (imageA.getImageName() + "_isn"));
resultImage.copyFileTypeInfo(imageA);
// Make algorithm
isnAlgo = new PlugInAlgorithmISN(resultImage, imageA);
// 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
isnAlgo.addListener(this);
createProgressBar(imageA.getImageName(), " ...", isnAlgo);
// Hide dialog
setVisible(false);
if (isRunInSeparateThread()) {
// Start the thread as a low priority because we wish to still have user interface work
// fast.
if (isnAlgo.startMethod(Thread.MIN_PRIORITY) == false) {
MipavUtil.displayError("A thread is already running on this object");
}
} else {
isnAlgo.run();
}
} catch (OutOfMemoryError x) {
System.gc();
MipavUtil.displayError("AlgorithmAbsoluteValue: unable to allocate enough memory");
return;
}
}
/**
* 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()
/**
* 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;
}
/**
* This method is required if the AlgorithmPerformed interface is implemented. It is called by the
* algorithm 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 PlugInAlgorithmCenterDistance2) {
image.clearMask();
if (algorithm.isCompleted()) {
insertScriptLine();
}
if (algorithm != null) {
algorithm.finalize();
algorithm = null;
}
dispose();
}
} // end AlgorithmPerformed()
/** {@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");
}
/**
* 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;
}
}
/**
* 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;
}
}
}
/**
* This function produces a new image that has been concatenated. Two 2D-images become one 3D
* image.
*/
private void cat2D_2D_3D() {
int length;
int xDim, yDim;
int i;
float[] buffer;
int cFactor = 1;
float[] resols = new float[3];
FileInfoBase[] fileInfo = null;
FileInfoDicom[] fileInfoDicom = null;
try {
resols = new float[3];
xDim = srcImage1.getExtents()[0];
yDim = srcImage1.getExtents()[1];
if (srcImage1.isColorImage()) {
cFactor = 4;
}
length = cFactor * xDim * yDim;
buffer = new float[length];
srcImage1.exportData(0, length, buffer);
destImage.importData(0, buffer, false);
srcImage2.exportData(0, length, buffer);
destImage.importData(buffer.length, buffer, true);
} catch (IOException error) {
buffer = null;
destImage.disposeLocal(); // Clean up memory of result image
destImage = null;
errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);
return;
} catch (OutOfMemoryError e) {
buffer = null;
destImage.disposeLocal(); // Clean up memory of result image
destImage = null;
errorCleanUp("Algorithm Concat. Images: Out of memory", true);
return;
}
resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
resols[2] = 1;
if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
&& (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2]];
fileInfoDicom[0] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[0]).clone());
fileInfoDicom[1] = (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[0]).clone());
destImage.setFileInfo(fileInfoDicom);
} else {
fileInfo = destImage.getFileInfo();
for (i = 0; (i < destImage.getExtents()[2]) && !threadStopped; i++) {
fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
fileInfo[i].setResolutions(resols);
fileInfo[i].setExtents(destImage.getExtents());
fileInfo[i].setMax(destImage.getMax());
fileInfo[i].setMin(destImage.getMin());
fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
}
if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {
if (((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[0])
.setPSetHashtable(((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable());
}
}
if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {
if (((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[1])
.setPSetHashtable(((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable());
}
}
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
setCompleted(true);
fileInfo = null;
fileInfoDicom = null;
}
/**
* This function produces the EdgeLap of input image.
*
* @param detectionType the type of zero crossing detection to perform
*/
private void calcStoreInDest3D(int detectionType) {
int nImages;
int length, totalLength;
float[] buffer, xResultBuffer, yResultBuffer, zResultBuffer;
int start;
float[] sliceBuffer;
try {
destImage.setLock();
} catch (IOException error) {
errorCleanUp("Algorithm EdgeLapSep: Image(s) locked", false);
return;
}
try {
length = srcImage.getSliceSize();
totalLength = srcImage.getSliceSize() * srcImage.getExtents()[2];
nImages = srcImage.getExtents()[2];
buffer = new float[totalLength];
sliceBuffer = new float[length];
srcImage.exportData(0, totalLength, buffer); // locks and releases lock
// fireProgressStateChanged(srcImage.getImageName(), "Calculating Zero X-ings ...");
} catch (IOException error) {
buffer = null;
sliceBuffer = null;
xResultBuffer = null;
yResultBuffer = null;
zResultBuffer = null;
errorCleanUp("Algorithm EdgeLapSep exportData: Image(s) locked", true);
return;
} catch (OutOfMemoryError e) {
buffer = null;
sliceBuffer = null;
xResultBuffer = null;
yResultBuffer = null;
zResultBuffer = null;
errorCleanUp("Algorithm EdgeLapSep: Out of memory", true);
return;
}
// initProgressBar();
fireProgressStateChanged(0, srcImage.getImageName(), "Convolving X dimension ...");
/** Minimum and maximum progress value for the convolving part */
int min = 0;
int max = min + Math.round(100 / 2.0f);
float stepPerDimension = ((float) (max - min)) / 3.0f;
AlgorithmSeparableConvolver xConvolver = null;
if (Math.round(stepPerDimension) > 1) {
xConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GxxData, kExtents, false); // assume not color
xConvolver.setProgressValues(generateProgressValues(min, min + Math.round(stepPerDimension)));
linkProgressToAlgorithm(xConvolver);
} else {
xConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GxxData, kExtents, false); // assume not color
}
if (!entireImage) {
xConvolver.setMask(mask);
}
xConvolver.run();
xResultBuffer = xConvolver.getOutputBuffer();
xConvolver.finalize();
xConvolver = null;
fireProgressStateChanged(
min + Math.round(stepPerDimension), srcImage.getImageName(), "Convolving Y dimension...");
AlgorithmSeparableConvolver yConvolver = null;
if ((Math.round(stepPerDimension * 2) - Math.round(stepPerDimension)) > 1) {
yConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GyyData, kExtents, false); // assume not color
yConvolver.setProgressValues(
generateProgressValues(
min + Math.round(stepPerDimension), min + Math.round(stepPerDimension * 2)));
linkProgressToAlgorithm(yConvolver);
} else {
yConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GyyData, kExtents, false); // assume not color
}
if (!entireImage) {
yConvolver.setMask(mask);
}
yConvolver.run();
yResultBuffer = yConvolver.getOutputBuffer();
yConvolver.finalize();
yConvolver = null;
fireProgressStateChanged(
min + Math.round(stepPerDimension * 2),
srcImage.getImageName(),
"Convolving Z dimension...");
AlgorithmSeparableConvolver zConvolver = null;
if ((Math.round(stepPerDimension * 3) - Math.round(stepPerDimension * 2)) > 1) {
zConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GzzData, kExtents, false); // assume not color
zConvolver.setProgressValues(
generateProgressValues(min + Math.round(stepPerDimension * 2), max));
linkProgressToAlgorithm(zConvolver);
} else {
zConvolver =
new AlgorithmSeparableConvolver(
buffer, srcImage.getExtents(), GzzData, kExtents, false); // assume not color
}
if (!entireImage) {
zConvolver.setMask(mask);
}
zConvolver.run();
zResultBuffer = zConvolver.getOutputBuffer();
zConvolver.finalize();
zConvolver = null;
min = max;
max = 100;
float stepPerImage = ((float) (max - min)) / nImages;
for (int s = 0; (s < nImages) && !threadStopped; s++) {
fireProgressStateChanged(
min + Math.round(stepPerImage * s),
srcImage.getImageName(),
"Calculating the edges of slice " + (s + 1) + "...");
start = s * length;
for (int i = start; (i < (start + length)) && !threadStopped; i++) {
if (entireImage || mask.get(i)) {
destImage.set(i, -(xResultBuffer[i] + yResultBuffer[i] + zResultBuffer[i]));
} else {
destImage.set(i, buffer[i]);
}
}
try {
destImage.exportDataNoLock(start, length, sliceBuffer);
} catch (IOException error) {
buffer = null;
sliceBuffer = null;
errorCleanUp("Algorithm EdgeLapSep exportData: " + error, true);
return;
}
genZeroXMask(s, sliceBuffer, detectionType);
}
if (threadStopped) {
finalize();
return;
}
zXMask.calcMinMax();
destImage.calcMinMax();
destImage.releaseLock();
setCompleted(true);
}
/**
* Working ... This function is never used. It doesn't modify any parameters or data members and
* returns void.
*
* @param image DOCUMENT ME!
* @param doColor DOCUMENT ME!
*/
public void calculatePrincipleAxis(ModelImage image, boolean doColor) {
int x, y, z;
int n = 0;
Matrix3f mat2 = new Matrix3f(); // Row,Col
Matrix3f meanProduct = new Matrix3f();
Vector3f mean = new Vector3f(); // Column vector
double voxVal = 0;
double total = 0;
double tot = 0;
// Moments first and second order
double mX = 0, mY = 0, mZ = 0, mXX = 0, mXY = 0, mXZ = 0, mYY = 0, mYZ = 0, mZZ = 0;
float min = (float) image.getMin();
int xEnd = image.getExtents()[0];
int yEnd = image.getExtents()[1];
int zEnd = image.getExtents()[2];
int nLim = (int) Math.sqrt((double) xEnd * yEnd * zEnd);
if (nLim < 1000) {
nLim = 1000;
}
for (z = 0; z < zEnd; z++) {
for (y = 0; y < yEnd; y++) {
for (x = 0; x < xEnd; x++) {
if (doColor) {
voxVal =
(double)
(image.getFloatC(x, y, z, 1)
+ image.getFloatC(x, y, z, 2)
+ image.getFloatC(x, y, z, 3));
} else {
voxVal = (double) (image.getFloat(x, y, z) - min);
}
mX += voxVal * x;
mY += voxVal * y;
mZ += voxVal * z;
mXX += voxVal * x * x;
mXY += voxVal * x * y;
mXZ += voxVal * x * z;
mYY += voxVal * y * y;
mYZ += voxVal * y * z;
mZZ += voxVal * z * z;
tot += voxVal;
n++;
if (n > nLim) { // Lets not over run the buffers during summation
n = 0;
total += tot;
mat2.M00 = (float) (mat2.M00 + mXX);
mat2.M01 = (float) (mat2.M01 + mXY);
mat2.M02 = (float) (mat2.M02 + mXZ);
mat2.M11 = (float) (mat2.M11 + mYY);
mat2.M12 = (float) (mat2.M12 + mYZ);
mat2.M22 = (float) (mat2.M22 + mZZ);
mean.X = (float) (mean.X + mX);
mean.Y = (float) (mean.Y + mY);
mean.Z = (float) (mean.Z + mZ);
tot = 0;
mX = 0;
mY = 0;
mZ = 0;
mXX = 0;
mXY = 0;
mXZ = 0;
mYY = 0;
mYZ = 0;
mZZ = 0;
}
}
}
}
total += tot;
if (Math.abs(total) < 1e-5) {
total = 1.0f;
}
mat2.M00 = (float) ((mat2.M00 + mXX) / total);
mat2.M01 = (float) ((mat2.M01 + mXY) / total);
mat2.M02 = (float) ((mat2.M02 + mXZ) / total);
mat2.M11 = (float) ((mat2.M11 + mYY) / total);
mat2.M12 = (float) ((mat2.M12 + mYZ) / total);
mat2.M22 = (float) ((mat2.M22 + mZZ) / total);
mean.X = (float) ((mean.X + mX) / total);
mean.Y = (float) ((mean.Y + mY) / total);
mean.Z = (float) ((mean.Z + mZ) / total);
// Now make it central (taking off the Center of Mass)
meanProduct.MakeTensorProduct(mean, mean);
mat2.M00 -= meanProduct.M00;
mat2.M01 -= meanProduct.M01;
mat2.M02 -= meanProduct.M02;
mat2.M10 -= meanProduct.M10;
mat2.M11 -= meanProduct.M11;
mat2.M12 -= meanProduct.M12;
mat2.M20 -= meanProduct.M20;
mat2.M21 -= meanProduct.M21;
mat2.M22 -= meanProduct.M22;
}
/** 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);
}
/**
* This function produces the EdgeLap of input image.
*
* @param nImages number of images on which to find zero crossings. If 2D image then nImage = 1.
* If 3D image where each image is to processed independently then nImages equals the number
* of images in the volume.
* @param detectionType the type of zero crossing detection to perform
*/
private void calcStoreInDest2D(int nImages, int detectionType) {
// int i, s, idx;
int length;
int start;
float[] buffer, xResultBuffer, yResultBuffer;
try {
destImage.setLock();
} catch (IOException error) {
errorCleanUp("Algorithm EdgeLapSep: Image(s) locked", false);
return;
}
try {
length = srcImage.getSliceSize();
buffer = new float[length];
// fireProgressStateChanged(srcImage.getImageName(), "Calculating the Edge ...");
} catch (OutOfMemoryError e) {
buffer = null;
errorCleanUp("Algorithm Edge Lap Sep: Out of memory", true);
return;
}
fireProgressStateChanged(0, srcImage.getImageName(), "Calculating the Edge ...");
float stepPerImage = 100f / nImages;
// initProgressBar();
for (int s = 0; (s < nImages) && !threadStopped; s++) {
fireProgressStateChanged(
Math.round(stepPerImage * s),
srcImage.getImageName(),
"Calculating the edges of slice " + (s + 1) + "...");
start = s * length;
try {
srcImage.exportData(start, length, buffer); // locks and releases lock
} catch (IOException error) {
errorCleanUp("Algorithm EdgeLapSep: Image(s) locked", false);
return;
}
int min = Math.round(stepPerImage * s);
int max = min + Math.round(((float) (Math.round(stepPerImage * (s + 1)) - min)) / 2.0f);
AlgorithmSeparableConvolver xConvolver = null;
if ((max - min) > 1) {
xConvolver =
new AlgorithmSeparableConvolver(
buffer,
new int[] {srcImage.getExtents()[0], srcImage.getExtents()[1]},
GxxData,
kExtents,
false);
xConvolver.setProgressValues(generateProgressValues(min, max));
linkProgressToAlgorithm(xConvolver);
} else {
xConvolver =
new AlgorithmSeparableConvolver(
buffer,
new int[] {srcImage.getExtents()[0], srcImage.getExtents()[1]},
GxxData,
kExtents,
false); // assume not color
}
if (!entireImage) {
xConvolver.setMask(mask);
}
xConvolver.run();
xResultBuffer = xConvolver.getOutputBuffer();
xConvolver.finalize();
xConvolver = null;
min = max;
max = Math.round(stepPerImage * (s + 1));
AlgorithmSeparableConvolver yConvolver = null;
if ((max - min) > 1) {
yConvolver =
new AlgorithmSeparableConvolver(
buffer,
new int[] {srcImage.getExtents()[0], srcImage.getExtents()[1]},
GyyData,
kExtents,
false);
yConvolver.setProgressValues(generateProgressValues(min, max));
linkProgressToAlgorithm(yConvolver);
} else {
yConvolver =
new AlgorithmSeparableConvolver(
buffer,
new int[] {srcImage.getExtents()[0], srcImage.getExtents()[1]},
GyyData,
kExtents,
false); // assume not color
}
if (!entireImage) {
yConvolver.setMask(mask);
}
yConvolver.run();
yResultBuffer = yConvolver.getOutputBuffer();
yConvolver.finalize();
yConvolver = null;
for (int i = 0, idx = start; (i < buffer.length) && !threadStopped; i++, idx++) {
if (entireImage || mask.get(i)) {
destImage.set(idx, -(xResultBuffer[i] + yResultBuffer[i]));
} else {
destImage.set(idx, buffer[i]);
}
}
try {
destImage.exportDataNoLock(start, length, buffer);
} catch (IOException error) {
errorCleanUp("Algorithm EdgeLapSep exportData: " + error, false);
return;
}
genZeroXMask(s, buffer, detectionType);
}
if (threadStopped) {
finalize();
return;
}
zXMask.calcMinMax();
destImage.calcMinMax();
destImage.releaseLock();
setCompleted(true);
}
/**
* Generates a zero crossing mask for a 2D function. Sets a ModelImage to 255 if a zero crossing
* is detected.
*
* @param slice the slice of the volume which we are working on (0 if from 2D image)
* @param buffer array in which to find zero crossing
* @param detectionType the type of zero crossing detection to perform
*/
public void genZeroXMask(int slice, float[] buffer, int detectionType) {
float x0, x1, x2, x3;
int i0, i1, i2, i3;
int i, j;
int indexY;
int length;
int xDim = srcImage.getExtents()[0];
int yDim = srcImage.getExtents()[1];
length = xDim * yDim;
int xxDim = xDim - 1;
int yyDim = yDim - 1;
float level = 0;
int offset = slice * length;
for (j = 0; j < yyDim; j++) {
indexY = j * xDim;
for (i = 0; i < xxDim; i++) {
i0 = indexY + i;
if (detectionType == MARCHING_SQUARES) {
i1 = i0 + 1;
i2 = i0 + xDim;
i3 = i0 + 1 + xDim;
x0 = buffer[i0];
x1 = buffer[i1];
x2 = buffer[i2];
x3 = buffer[i3];
if ((x0 >= level)
&& (x1 >= level)
&& (x2 >= level)
&& (x3 >= level)) { // case 0 - no edge
} else if ((x0 >= level) && (x1 >= level) && (x2 < level) && (x3 >= level)) {
// case 1 - edge in the lower left
zXMask.set(offset + i2, 255);
} else if ((x0 >= level) && (x1 >= level) && (x2 >= level) && (x3 < level)) {
// case 2 - edge in the lower right
zXMask.set(offset + i3, 255);
} else if ((x0 >= level) && (x1 >= level) && (x2 < level) && (x3 < level)) {
// case 3 - edge horizontally
zXMask.set(offset + i2, 255);
zXMask.set(offset + i3, 255);
} else if ((x0 >= level) && (x1 < level) && (x2 >= level) && (x3 >= level)) {
// case 4 - edge in the upper right
zXMask.set(offset + i1, 255);
} else if ((x0 >= level) && (x1 < level) && (x2 < level) && (x3 >= level)) {
// case 5 - ambiguous case; either edge in upper right and lower left or
// edge that goes from the upper right to the lower left
zXMask.set(offset + i1, 255);
zXMask.set(offset + i2, 255);
} else if ((x0 >= level) && (x1 < level) && (x2 >= level) && (x3 < level)) {
// case 6 - edge going vertically along the right
zXMask.set(offset + i1, 255);
zXMask.set(offset + i3, 255);
} else if ((x0 >= level) && (x1 < level) && (x2 < level) && (x3 < level)) {
// case 7 - edge in the upper left
zXMask.set(offset + i0, 255);
} else if ((x0 < level) && (x1 >= level) && (x2 >= level) && (x3 >= level)) {
// case 8 - edge in the upper left
zXMask.set(offset + i0, 255);
} else if ((x0 < level) && (x1 >= level) && (x2 < level) && (x3 >= level)) {
// case 9 - edge going vertically along the left
zXMask.set(offset + i0, 255);
zXMask.set(offset + i2, 255);
} else if ((x0 < level) && (x1 >= level) && (x2 >= level) && (x3 < level)) {
// case 10 - ambiguous case; either edge in upper left and lower right or
// edge that goes from the upper left to the lower right
zXMask.set(offset + i0, 255);
zXMask.set(offset + i3, 255);
} else if ((x0 < level) && (x1 >= level) && (x2 < level) && (x3 < level)) {
// case 11 - edge in the upper right
zXMask.set(offset + i1, 255);
} else if ((x0 < level) && (x1 < level) && (x2 >= level) && (x3 >= level)) {
// case 12 - edge going horizontally along the top
zXMask.set(offset + i0, 255);
zXMask.set(offset + i1, 255);
} else if ((x0 < level) && (x1 < level) && (x2 < level) && (x3 >= level)) {
// case 13 - edge in the lower right
zXMask.set(offset + i3, 255);
} else if ((x0 < level) && (x1 < level) && (x2 >= level) && (x3 < level)) {
// case 14 - edge in the lower left
zXMask.set(offset + i2, 255);
} else if ((x0 < level)
&& (x1 < level)
&& (x2 < level)
&& (x3 < level)) { // case 15 - no edge
}
} else if (detectionType == NEGATIVE_EDGES) {
if (buffer[i0] <= 1) {
zXMask.set(offset + i0, 255);
}
} else if (detectionType == OLD_DETECTION) {
i1 = i0 + 1;
i2 = i0 + xDim;
i3 = i0 + 1 + xDim;
x0 = buffer[i0];
x1 = buffer[i1];
x2 = buffer[i2];
x3 = buffer[i3];
if ((x0 > level) && (x1 > level) && (x2 > level) && (x3 > level)) {
zXMask.set(offset + i0, 0);
} else if ((x0 < level) && (x1 < level) && (x2 < level) && (x3 < level)) {
zXMask.set(offset + i0, 0);
} else {
zXMask.set(offset + i0, 255);
}
}
}
}
FileInfoBase[] fileInfo = zXMask.getFileInfo();
fileInfo[slice].setModality(srcImage.getFileInfo()[slice].getModality());
fileInfo[slice].setFileDirectory(srcImage.getFileInfo()[slice].getFileDirectory());
fileInfo[slice].setEndianess(srcImage.getFileInfo()[slice].getEndianess());
fileInfo[slice].setUnitsOfMeasure(srcImage.getFileInfo()[slice].getUnitsOfMeasure());
fileInfo[slice].setResolutions(srcImage.getFileInfo()[slice].getResolutions());
fileInfo[slice].setExtents(zXMask.getExtents());
fileInfo[slice].setMax(255);
fileInfo[slice].setMin(0);
fileInfo[slice].setPixelPadValue(srcImage.getFileInfo()[slice].getPixelPadValue());
fileInfo[slice].setPhotometric(srcImage.getFileInfo()[slice].getPhotometric());
}
/** Starts the program. */
public void runAlgorithm() {
if ((srcImage1 == null) || (srcImage2 == null) || (destImage == null)) {
displayError("Source Image(s) is null");
setCompleted(false);
return;
}
if (srcImage1.getType() != srcImage2.getType()) {
displayError("Source Images must be of the same data type.");
setCompleted(false);
return;
}
float[] resols1 = srcImage1.getResolutions(0);
float[] resols2 = srcImage2.getResolutions(0);
if ((srcImage1.getNDims() == 2) && (srcImage2.getNDims() == 2)) {
if (resols1[0] == resols2[0] && resols1[1] == resols2[1]) {
cat2D_2D_3D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else if (((srcImage1.getNDims() == 2) && (srcImage2.getNDims() == 3))
|| ((srcImage1.getNDims() == 3) && (srcImage2.getNDims() == 2))) {
if (resols1[0] == resols2[0] && resols1[1] == resols2[1]) {
cat2D_3D_3D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else if ((srcImage1.getNDims() == 3)
&& (srcImage2.getNDims() == 3)
&& (destImage.getNDims() == 3)) {
if (resols1[0] == resols2[0] && resols1[1] == resols2[1] && resols1[2] == resols2[2]) {
cat3D_3D_3D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else if ((srcImage1.getNDims() == 3)
&& (srcImage2.getNDims() == 3)
&& (destImage.getNDims() == 4)) {
if (resols1[0] == resols2[0] && resols1[1] == resols2[1] && resols1[2] == resols2[2]) {
cat3D_3D_4D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else if (((srcImage1.getNDims() == 3) && (srcImage2.getNDims() == 4))
|| ((srcImage1.getNDims() == 4) && (srcImage2.getNDims() == 3))) {
if (resols1[0] == resols2[0] && resols1[1] == resols2[1] && resols1[2] == resols2[2]) {
cat3D_4D_4D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else if ((srcImage1.getNDims() == 4) && (srcImage2.getNDims() == 4)) {
if (resols1[0] == resols2[0]
&& resols1[1] == resols2[1]
&& resols1[2] == resols2[2]
&& resols1[3] == resols2[3]) {
cat4D_4D_4D();
} else {
displayError("Resolutions must match up");
setCompleted(false);
return;
}
} else {
displayError("Source Image(s) dimensionality not supported.");
}
}
/**
* 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();
}
/** cat. */
private void cat3D_4D_4D() {
int length;
int xDim, yDim;
float[] buffer;
int cFactor = 1;
int i, j;
float[] resols = new float[3];
float[] origins = new float[3];
FileInfoBase[] fileInfo = null;
FileInfoDicom[] fileInfoDicom = null;
int srcALength, srcBLength;
try {
fireProgressStateChanged(srcImage1.getImageName(), "Concatenating images ...");
resols = new float[4];
origins = new float[4];
xDim = srcImage1.getExtents()[0];
yDim = srcImage1.getExtents()[1];
if (srcImage1.isColorImage()) {
cFactor = 4;
}
length = cFactor * xDim * yDim;
buffer = new float[length];
int nImages;
if (srcImage1.getNDims() > srcImage2.getNDims()) {
nImages =
(srcImage1.getExtents()[2] * srcImage1.getExtents()[3]) + srcImage2.getExtents()[2];
for (i = 0;
(i < (srcImage1.getExtents()[2] * srcImage1.getExtents()[3])) && !threadStopped;
i++) {
fireProgressStateChanged(Math.round((float) (i) / (nImages - 1) * 100));
srcImage1.exportData(i * length, length, buffer);
destImage.importData(i * length, buffer, false);
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
for (j = 0; (j < srcImage2.getExtents()[2]) && !threadStopped; j++) {
fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));
srcImage2.exportData(j * length, length, buffer);
destImage.importData((i + j) * length, buffer, false);
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
destImage.calcMinMax();
} else {
nImages =
(srcImage2.getExtents()[2] * srcImage2.getExtents()[3]) + srcImage1.getExtents()[2];
for (j = 0; (j < srcImage1.getExtents()[2]) && !threadStopped; j++) {
fireProgressStateChanged(Math.round((float) (j) / (nImages - 1) * 100));
srcImage1.exportData(j * length, length, buffer);
destImage.importData(j * length, buffer, false);
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
for (i = 0;
(i < (srcImage2.getExtents()[2] * srcImage2.getExtents()[3])) && !threadStopped;
i++) {
fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));
srcImage2.exportData(i * buffer.length, length, buffer);
destImage.importData((i + j) * buffer.length, buffer, false);
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
destImage.calcMinMax();
}
} catch (IOException error) {
buffer = null;
destImage.disposeLocal(); // Clean up memory of result image
destImage = null;
errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);
return;
} catch (OutOfMemoryError e) {
buffer = null;
destImage.disposeLocal(); // Clean up memory of result image
destImage = null;
errorCleanUp("Algorithm Concat. Images: Out of memory", true);
return;
}
resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
resols[2] = srcImage1.getFileInfo()[0].getResolutions()[2];
resols[3] = srcImage1.getFileInfo()[0].getResolutions()[3];
origins[0] = srcImage1.getFileInfo()[0].getOrigin()[0];
origins[1] = srcImage1.getFileInfo()[0].getOrigin()[1];
origins[2] = srcImage1.getFileInfo()[0].getOrigin()[2];
origins[3] = srcImage1.getFileInfo()[0].getOrigin()[3];
if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
&& (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2] * destImage.getExtents()[3]];
if (srcImage1.getNDims() > srcImage2.getNDims()) {
srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];
for (i = 0; (i < srcALength) && !threadStopped; i++) {
fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
fileInfoDicom[i].setOrigin(origins);
}
for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {
fileInfoDicom[srcALength + i] =
(FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
fileInfoDicom[srcALength + i].setOrigin(origins);
}
} else {
srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];
for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {
fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
fileInfoDicom[i].setOrigin(origins);
}
for (i = 0; (i < srcBLength) && !threadStopped; i++) {
fileInfoDicom[srcImage1.getExtents()[2] + i] =
(FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
fileInfoDicom[srcImage1.getExtents()[2] + i].setOrigin(origins);
}
}
destImage.setFileInfo(fileInfoDicom);
} else {
fileInfo = destImage.getFileInfo();
for (i = 0;
(i < (destImage.getExtents()[2] * destImage.getExtents()[3])) && !threadStopped;
i++) {
fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
fileInfo[i].setResolutions(resols);
fileInfo[i].setExtents(destImage.getExtents());
fileInfo[i].setMax(destImage.getMax());
fileInfo[i].setMin(destImage.getMin());
fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
}
if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {
if (srcImage1.getNDims() > srcImage2.getNDims()) {
srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];
for (i = 0; (i < srcALength) && !threadStopped; i++) {
if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[i])
.setPSetHashtable(
((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
}
}
} else {
for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {
if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[i])
.setPSetHashtable(
((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
}
}
}
}
if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {
if (srcImage1.getNDims() > srcImage2.getNDims()) {
srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];
for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {
if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[srcALength + i])
.setPSetHashtable(
((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
}
}
} else {
srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];
for (i = 0; (i < srcBLength) && !threadStopped; i++) {
if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
((FileInfoImageXML) fileInfo[srcImage1.getExtents()[2] + i])
.setPSetHashtable(
((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
}
}
}
}
}
if (threadStopped) {
buffer = null;
finalize();
return;
}
setCompleted(true);
fileInfo = null;
fileInfoDicom = null;
}
/**
* Use the GUI results to set up the variables needed to run the algorithm.
*
* @return <code>true</code> if parameters set successfully, <code>false</code> otherwise.
*/
private boolean setVariables() {
String tmpStr;
tmpStr = textXDim.getText();
try {
subXDim = Integer.parseInt(tmpStr);
} catch (NumberFormatException e) {
MipavUtil.displayError("New XDIM string is not a valid integer");
textXDim.requestFocus();
textXDim.selectAll();
return false;
}
if (subXDim < 3) {
MipavUtil.displayError("New XDIM must be at least 3");
textXDim.requestFocus();
textXDim.selectAll();
return false;
} else if (subXDim > image.getExtents()[0]) {
MipavUtil.displayError("New XDIM cannot exceed " + image.getExtents()[0]);
textXDim.requestFocus();
textXDim.selectAll();
return false;
}
tmpStr = textYDim.getText();
try {
subYDim = Integer.parseInt(tmpStr);
} catch (NumberFormatException e) {
MipavUtil.displayError("New YDIM string is not a valid integer");
textYDim.requestFocus();
textYDim.selectAll();
return false;
}
if (subYDim < 3) {
MipavUtil.displayError("New YDIM must be at least 3");
textYDim.requestFocus();
textYDim.selectAll();
return false;
} else if (subYDim > image.getExtents()[1]) {
MipavUtil.displayError("New YDIM cannot exceed " + image.getExtents()[1]);
textYDim.requestFocus();
textYDim.selectAll();
return false;
}
tmpStr = textNumberImages.getText();
try {
numberOfImagesInMosaic = Integer.parseInt(tmpStr);
} catch (NumberFormatException e) {
MipavUtil.displayError("New numberOfImagesInMosaic string is not a valid integer");
textNumberImages.requestFocus();
textNumberImages.selectAll();
return false;
}
if (numberOfImagesInMosaic < 1) {
MipavUtil.displayError("New numberOfImagesInMosaic must be at least 1");
textNumberImages.requestFocus();
textNumberImages.selectAll();
return false;
} else if (numberOfImagesInMosaic > (subXDim * subYDim)) {
MipavUtil.displayError("New numberOfImagesInMosaic cannot exceed (newXDim) * (newYDim)");
textNumberImages.requestFocus();
textNumberImages.selectAll();
return false;
}
displayLoc = NEW;
return true;
}
/**
* Use the GUI results to set up the variables needed to run the algorithm.
*
* @return <code>true</code> if parameters set successfully, <code>false</code> otherwise.
*/
private boolean setVariables() {
String tmpStr;
System.gc();
if (replaceImage.isSelected()) {
displayLoc = REPLACE;
} else if (newImage.isSelected()) {
displayLoc = NEW;
}
tmpStr = textSearchWindowSide.getText();
if (testParameter(tmpStr, 5, 101)) {
searchWindowSide = Integer.valueOf(tmpStr).intValue();
} else {
MipavUtil.displayError("Search window side must be between 5 and 101");
textSearchWindowSide.requestFocus();
textSearchWindowSide.selectAll();
return false;
}
if ((searchWindowSide % 2) == 0) {
MipavUtil.displayError("Search window side must be an odd number");
textSearchWindowSide.requestFocus();
textSearchWindowSide.selectAll();
return false;
}
tmpStr = textSimilarityWindowSide.getText();
if (testParameter(tmpStr, 3, 99)) {
similarityWindowSide = Integer.valueOf(tmpStr).intValue();
} else {
MipavUtil.displayError("Similarity window side must be between 3 and 99");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
if ((similarityWindowSide % 2) == 0) {
MipavUtil.displayError("Similarity window side must be an odd number");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
if (similarityWindowSide >= searchWindowSide) {
MipavUtil.displayError("Similarity window side must be less than search window side");
textSimilarityWindowSide.requestFocus();
textSimilarityWindowSide.selectAll();
return false;
}
tmpStr = textNoiseStandardDeviation.getText();
if (testParameter(tmpStr, 0.001, 1000.0)) {
noiseStandardDeviation = Float.valueOf(tmpStr).floatValue();
} else {
MipavUtil.displayError("Radius must be between 0.001 and 1000.0");
textNoiseStandardDeviation.requestFocus();
textNoiseStandardDeviation.selectAll();
return false;
}
doRician = doRicianCheckBox.isSelected();
if (doRician) {
tmpStr = textDegree.getText();
if (testParameter(tmpStr, 1.0, 10.0)) {
degreeOfFiltering = Float.valueOf(tmpStr).floatValue();
} else {
MipavUtil.displayError("Degree of filtering must be between 1.0 and 10.0");
textDegree.requestFocus();
textDegree.selectAll();
}
}
if (image.getNDims() > 2) {
image25D = image25DCheckBox.isSelected();
}
return true;
}
/**
* Use the GUI results to set up the variables needed to run the algorithm.
*
* @return <code>true</code> if parameters set successfully, <code>false</code> otherwise.
*/
private boolean setVariables() {
String tmpStr;
int i;
int totLength = image.getExtents()[0];
for (i = 1; i < image.getNDims(); i++) {
totLength *= image.getExtents()[i];
}
tmpStr = greenMergingText.getText();
mergingDistance = Float.parseFloat(tmpStr);
if (mergingDistance < 0.0f) {
MipavUtil.displayError("Merging distance cannot be less than 0");
greenMergingText.requestFocus();
greenMergingText.selectAll();
return false;
}
tmpStr = redMinText.getText();
redMin = Integer.parseInt(tmpStr);
if (redMin < 1) {
MipavUtil.displayError("red minimum must be at least 1");
redMinText.requestFocus();
redMinText.selectAll();
return false;
} else if (redMin > totLength) {
MipavUtil.displayError("red minimum must not exceed " + totLength);
redMinText.requestFocus();
redMinText.selectAll();
return false;
}
tmpStr = redFractionText.getText();
redFraction = Float.parseFloat(tmpStr);
if (redFraction <= 0.0f) {
MipavUtil.displayError("red fraction must be greater than zero");
redFractionText.requestFocus();
redFractionText.selectAll();
return false;
} else if (redFraction > 1.0f) {
MipavUtil.displayError("red fraction must not exceed one");
redFractionText.requestFocus();
redFractionText.selectAll();
return false;
}
tmpStr = greenMinText.getText();
greenMin = Integer.parseInt(tmpStr);
if (greenMin < 1) {
MipavUtil.displayError("green minimum must be at least 1");
greenMinText.requestFocus();
greenMinText.selectAll();
return false;
} else if (greenMin > totLength) {
MipavUtil.displayError("green minimum must not exceed " + totLength);
greenMinText.requestFocus();
greenMinText.selectAll();
return false;
}
tmpStr = greenFractionText.getText();
greenFraction = Float.parseFloat(tmpStr);
if (greenFraction <= 0.0f) {
MipavUtil.displayError("green fraction must be greater than zero");
greenFractionText.requestFocus();
greenFractionText.selectAll();
return false;
} else if (greenFraction > 1.0f) {
MipavUtil.displayError("green fraction must not exceed one");
greenFractionText.requestFocus();
greenFractionText.selectAll();
return false;
}
tmpStr = blueMinText.getText();
blueMin = Integer.parseInt(tmpStr);
if (blueMin <= 0) {
MipavUtil.displayError("Number of blue pixels must be greater than 0");
blueMinText.requestFocus();
blueMinText.selectAll();
return false;
} else if (blueMin > totLength) {
MipavUtil.displayError("blue minimum must not exceed " + totLength);
blueMinText.requestFocus();
blueMinText.selectAll();
return false;
}
if (oneButton.isSelected()) {
greenRegionNumber = 1;
} else if (twoButton.isSelected()) {
greenRegionNumber = 2;
} else if (threeButton.isSelected()) {
greenRegionNumber = 3;
} else {
greenRegionNumber = 4;
}
twoGreenLevels = twoBox.isSelected();
tmpStr = blueValueText.getText();
blueBoundaryFraction = Float.parseFloat(tmpStr);
if (blueBoundaryFraction < 0.0f) {
MipavUtil.displayError("Blue boundary fraction cannot be less than 0.0");
blueValueText.requestFocus();
blueValueText.selectAll();
return false;
} else if (blueBoundaryFraction > 1.0f) {
MipavUtil.displayError("Blue boundary value cannot be greater than 1.0");
blueValueText.requestFocus();
blueValueText.selectAll();
return false;
}
blueSmooth = blueSmoothBox.isSelected();
tmpStr = interpolationText.getText();
interpolationDivisor = Float.parseFloat(tmpStr);
if (interpolationDivisor <= 1.0f) {
MipavUtil.displayError("Interpolation divisor must be greater than 1");
interpolationText.requestFocus();
interpolationText.selectAll();
return false;
}
return true;
} // end setVariables()
/** 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);
}
/** 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()
