/**
* Calculates the zero crossing mask of a 2D image and returns it as a BitSet buffer.
*
* @param buffer the slice to work with
* @param extents the extents of the image
* @return BitSet buffer with mask set when a zero crossing is detected
*/
public BitSet calcZeroXMaskBitset(float[] buffer, int[] extents) {
setStartTime();
makeKernels2D();
float[] xResultBuffer;
float[] yResultBuffer;
AlgorithmSeparableConvolver xConvolver =
new AlgorithmSeparableConvolver(
buffer, extents, GxxData, kExtents, false); // assume not color
xConvolver.run();
xResultBuffer = xConvolver.getOutputBuffer();
xConvolver.finalize();
xConvolver = null;
AlgorithmSeparableConvolver yConvolver =
new AlgorithmSeparableConvolver(
buffer, extents, GyyData, kExtents, false); // assume not color
yConvolver.run();
yResultBuffer = yConvolver.getOutputBuffer();
yConvolver.finalize();
yConvolver = null;
for (int i = 0; i < buffer.length; i++) {
xResultBuffer[i] = -(xResultBuffer[i] + yResultBuffer[i]);
}
computeElapsedTime();
return genLevelMask(extents[0], extents[1], xResultBuffer, 0, zeroDetectionType);
}
/**
* 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);
}
/**
* 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);
}