/**
* 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);
}
/** {@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);
}
/**
* 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();
}
