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