/** This function produces the Laplacian of input image. */
private void calcStoreInDest3D() {
int i;
int length;
float[] buffer;
float lap;
try {
destImage.setLock();
} catch (IOException error) {
displayError("Algorithm Laplacian: Image(s) locked");
setCompleted(false);
destImage.releaseLock();
return;
}
try {
length = srcImage.getSliceSize() * srcImage.getExtents()[2];
buffer = new float[length];
srcImage.exportData(0, length, buffer); // locks and releases lock
fireProgressStateChanged(srcImage.getImageName(), "Calculating the Laplacian ...");
} catch (IOException error) {
buffer = null;
errorCleanUp("Algorithm Laplacian exportData: Image(s) locked", true);
return;
} catch (OutOfMemoryError e) {
buffer = null;
errorCleanUp("Algorithm Laplacian exportData: Out of memory", true);
return;
}
int mod = length / 100; // mod is 1 percent of length
float min, max;
min = Float.MAX_VALUE;
max = -Float.MAX_VALUE;
float minL, maxL;
minL = Float.MAX_VALUE;
maxL = -Float.MAX_VALUE;
if (entireImage == false) {
for (i = 0; i < length; i++) {
if (mask.get(i)) {
if (buffer[i] > max) {
max = buffer[i];
} else if (buffer[i] < min) {
min = buffer[i];
}
}
}
}
for (i = 0; (i < length) && !threadStopped; i++) {
if (((i % mod) == 0)) {
fireProgressStateChanged(Math.round((float) i / (length - 1) * 100));
}
if ((entireImage == true) || mask.get(i)) {
lap = AlgorithmConvolver.convolve3DPt(i, srcImage.getExtents(), buffer, kExtents, GxxData);
if (entireImage == false) {
if (mask.get(i)) {
if (lap > maxL) {
maxL = lap;
} else if (lap < minL) {
minL = lap;
}
}
}
destImage.set(i, lap);
} else {
destImage.set(i, buffer[i]);
}
}
if (entireImage == false) {
for (i = 0; i < length; i++) {
if (mask.get(i)) {
lap = destImage.getFloat(i);
lap = (((lap - minL) / (maxL - minL)) * (max - min)) + min;
destImage.set(i, lap);
}
}
}
if (threadStopped) {
finalize();
return;
}
destImage.calcMinMax();
destImage.releaseLock();
setCompleted(true);
}
/**
* Calculates the Laplacian image and replaces the source image with the new image.
*
* @param buffer DOCUMENT ME!
* @param extents DOCUMENT ME!
* @return resultBuffer
*/
@SuppressWarnings("unused")
private float[] calcInPlace3DBuffer(float[] buffer, int[] extents) {
int i, s;
int length;
float[] resultBuffer;
float lap;
try {
if (buffer == null) {
length = srcImage.getSliceSize() * srcImage.getExtents()[2];
buffer = new float[length];
} else {
length = buffer.length;
}
resultBuffer = new float[length];
sBuffer = new byte[length];
if (srcImage != null) {
fireProgressStateChanged(srcImage.getImageName(), "Calculating the Laplacian ...");
} else {
fireProgressStateChanged("Medialness", "Calculating the Laplacian ...");
}
} catch (OutOfMemoryError e) {
buffer = null;
resultBuffer = null;
sBuffer = null;
errorCleanUp("Algorithm Laplacian exportData: Out of memory", true);
return null;
}
try {
if (srcImage != null) {
srcImage.exportData(0, length, buffer); // locks and releases lock
}
} catch (IOException error) {
buffer = null;
resultBuffer = null;
System.gc();
errorCleanUp("Algorithm Laplacian: " + error, false);
return null;
}
float[] sigs = new float[3];
for (s = 1; (s <= 8) && !threadStopped; s++) {
sigs[0] = s;
sigs[1] = s;
sigs[2] = s;
makeKernels3D(sigs);
fireProgressStateChanged(Math.round((float) (s) / 8 * 100));
for (i = 0; (i < length) && !threadStopped; i++) {
// if (entireImage == true || mask.get(i)) {
lap = AlgorithmConvolver.convolve3DPtMed(i, extents, buffer, kExtents, GxxData);
if (lap > resultBuffer[i]) {
resultBuffer[i] = lap;
}
sBuffer[i] = (byte) s;
// }
// else {
// resultBuffer[i] = 0;
// }
}
}
return resultBuffer;
}
/**
* This function produces the Laplacian of input image. See this Neva
*
* @param nImages number of images to be blurred. 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.
*/
private void calcStoreInDest2D(int nImages) {
int i, s;
int length;
float[] buffer;
float[] resultBuffer;
float lap;
try {
length = srcImage.getSliceSize();
buffer = new float[length];
resultBuffer = new float[length];
fireProgressStateChanged(srcImage.getImageName(), "Calculating the Laplacian ...");
} catch (OutOfMemoryError e) {
buffer = null;
resultBuffer = null;
errorCleanUp("Algorithm Laplacian exportData: Out of memory", true);
return;
}
try {
srcImage.exportData(0, length, buffer); // locks and releases lock
} catch (IOException error) {
displayError("Algorithm Gaussian Blur: Image(s) locked");
setCompleted(false);
destImage.releaseLock();
return;
}
float[] sigs = new float[2];
for (s = 1; (s <= 8) && !threadStopped; s++) {
sigs[0] = s;
sigs[1] = s;
makeKernels2D(sigs);
fireProgressStateChanged(Math.round((float) (s) / 8 * 100));
for (i = 0; (i < length) && !threadStopped; i++) {
lap =
AlgorithmConvolver.convolve2DPtMed(i, srcImage.getExtents(), buffer, kExtents, GxxData);
if (lap > resultBuffer[i]) {
resultBuffer[i] = lap;
}
}
}
if (threadStopped) {
finalize();
return;
}
try {
destImage.importData(0, resultBuffer, true);
} catch (IOException error) {
errorCleanUp("Algorithm Gaussian Blur: Image(s) locked", false);
return;
}
setCompleted(true);
}
/** Calculates the Laplacian and replaces the source image with the new image. */
private void calcInPlace3D() {
int i;
int length;
float[] buffer;
float[] resultBuffer;
float lap;
try {
length = srcImage.getSliceSize() * srcImage.getExtents()[2];
buffer = new float[length];
resultBuffer = new float[length];
srcImage.exportData(0, length, buffer); // locks and releases lock
fireProgressStateChanged(srcImage.getImageName(), "Calculating the Laplacian ...");
} catch (IOException error) {
buffer = null;
resultBuffer = null;
errorCleanUp("Algorithm Laplacian exportData: Image(s) locked", true);
return;
} catch (OutOfMemoryError e) {
errorCleanUp("Algorithm Laplacian exportData: Out of memory", true);
return;
}
int mod = length / 100; // mod is 1 percent of length
for (i = 0; (i < length) && !threadStopped; i++) {
if (((i % mod) == 0)) {
fireProgressStateChanged(Math.round((float) i / (length - 1) * 100));
}
if ((entireImage == true) || mask.get(i)) {
lap = AlgorithmConvolver.convolve3DPt(i, srcImage.getExtents(), buffer, kExtents, GxxData);
resultBuffer[i] = lap;
} else {
resultBuffer[i] = buffer[i];
}
}
buffer = null;
System.gc();
if (threadStopped) {
finalize();
return;
}
try {
srcImage.importData(0, resultBuffer, true);
} catch (IOException error) {
buffer = null;
resultBuffer = null;
errorCleanUp("Algorithm Laplacian importData: Image(s) locked", true);
return;
}
setCompleted(true);
}
