/** 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;
}
}
/** 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;
}
}
}
/**
* 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;
}
/**
* 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());
}
/**
* 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()
/** 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;
}
/**
* 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;
}
/**
* 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;
}