/**
* Calculate the Rand index between some 2D original labels and the corresponding proposed labels.
* Both image are binarized. We follow the definition of Rand index as described by William M.
* Rand \cite{Rand71}.
*
* <p>BibTeX:
*
* <pre>
* @article{Rand71,
* author = {William M. Rand},
* title = {Objective criteria for the evaluation of clustering methods},
* journal = {Journal of the American Statistical Association},
* year = {1971},
* volume = {66},
* number = {336},
* pages = {846--850},
* doi = {10.2307/2284239)
* }
* </pre>
*
* @param label 2D image with the original labels
* @param proposal 2D image with the proposed labels
* @param binaryThreshold threshold value to binarize the input images
* @return rand index value and derived statistics
*/
public ClassificationStatistics randIndexStats(
ImageProcessor label, ImageProcessor proposal, double binaryThreshold) {
// Binarize inputs
ByteProcessor binaryLabel = new ByteProcessor(label.getWidth(), label.getHeight());
ByteProcessor binaryProposal = new ByteProcessor(label.getWidth(), label.getHeight());
for (int x = 0; x < label.getWidth(); x++)
for (int y = 0; y < label.getHeight(); y++) {
binaryLabel.set(x, y, label.getPixelValue(x, y) > binaryThreshold ? 255 : 0);
binaryProposal.set(x, y, proposal.getPixelValue(x, y) > binaryThreshold ? 255 : 0);
}
// Find components
ShortProcessor components1 =
(ShortProcessor)
Utils.connectedComponents(new ImagePlus("binary labels", binaryLabel), 4)
.allRegions
.getProcessor();
ShortProcessor components2 =
(ShortProcessor)
Utils.connectedComponents(new ImagePlus("proposal labels", binaryProposal), 4)
.allRegions
.getProcessor();
return getRandIndexStats(components1, components2);
}
protected synchronized void initialize(ImageProcessor projection) throws Exception {
if (!init) {
super.init();
// Precompute offsets
lineOffset = 0;
if (getGeometry().getDetectorWidth() != -1) {
System.out.println(
"row size projection: "
+ projection.getWidth()
+ "\nrow size detector: "
+ getGeometry().getDetectorWidth());
lineOffset = (projection.getWidth() - getGeometry().getDetectorWidth()) / 2;
}
maxI = getGeometry().getReconDimensionX();
maxJ = getGeometry().getReconDimensionY();
maxK = getGeometry().getReconDimensionZ();
maxU = getGeometry().getDetectorWidth(); // or it should be projection.getWidth();
maxV = getGeometry().getDetectorHeight();
dx = getGeometry().getVoxelSpacingX();
dy = getGeometry().getVoxelSpacingY();
dz = getGeometry().getVoxelSpacingZ();
time = System.currentTimeMillis();
// projectionViews = InitializeProjectionViews();
// volumeImage = InitializeVolumeImage();
}
}
private static final void prepareExtendedImage(
final ImageProcessor source, final ImageProcessor target) {
if (target.getWidth() > source.getWidth()) {
target.copyBits(source, source.getWidth(), 0, Blitter.COPY);
if (target.getHeight() > source.getHeight())
target.copyBits(source, source.getWidth(), 0, Blitter.COPY);
}
if (target.getHeight() > source.getHeight()) target.copyBits(source, 0, 1, Blitter.COPY);
target.copyBits(source, 0, 0, Blitter.COPY);
}
@Override
public final void run() {
while (!isInterrupted()) {
final boolean b;
synchronized (this) {
b = pleaseRepaint;
pleaseRepaint = keepPainting;
}
if (b) {
final long t = System.currentTimeMillis();
lambda += dt * dLambda;
phi += dt * dPhi;
this.camera.setOrientation(lambda, phi, rho);
mapper.map(temp);
final Object targetPixels = target.getPixels();
target.setPixels(temp.getPixels());
temp.setPixels(targetPixels);
impTarget.updateAndDraw();
if (visualize) visualize(impSource, temp.getWidth(), temp.getHeight(), p);
dt = (System.currentTimeMillis() - t) / 1000f;
}
synchronized (this) {
try {
if (!pleaseRepaint) wait();
} catch (final InterruptedException e) {
}
}
}
}
// set values in floatEdm to zero if pixel in mask equals 'resetOnThis'
private void resetMasked(FloatProcessor floatEdm, ImageProcessor mask, int resetOnThis) {
int width = mask.getWidth();
int height = mask.getHeight();
byte[] mPixels = (byte[]) mask.getPixels();
float[] fPixels = (float[]) floatEdm.getPixels();
for (int i = 0; i < width * height; i++) if (mPixels[i] == resetOnThis) fPixels[i] = 0;
}
public IJLineIteratorIP(ImageProcessor ip, int xdir) {
this.ip = ip;
if (xdir > 1) throw new IllegalArgumentException("illegal direction " + xdir);
dir = xdir;
final int width = ip.getWidth();
final int height = ip.getHeight();
switch (dir) {
case Ox:
{
size = height;
blength = width;
break;
}
case Oy:
{
size = width;
blength = height;
break;
}
} // end
Object pix = ip.getPixels();
setType(pix);
btype = ip.getBitDepth();
initbuffer(dir);
// System.out.println("\nbitedpth "+ btype);
}
/**
* Return an ImageRecord containing the images pixel dimensions.
*
* @param file absolute file path to image
* @return ImageRecord containing the images pixel dimensions
*/
public static ImageRecord getImageDimensions(final String file) {
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Getting image dimensions from: {}", file);
}
final ImageRecord dim = new ImageRecord(file);
final Opener o = new Opener();
final ImagePlus imp = o.openImage(file);
if (imp == null) {
return null;
}
ImageProcessor ip = imp.getProcessor();
final int width = ip.getWidth();
final int height = ip.getHeight();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"{} (width: {} | height: {})", file, Integer.toString(width), Integer.toString(height));
}
dim.setWidth(width);
dim.setHeight(height);
ip = null;
return dim;
}
private ImagePlus duplicateImage(ImageProcessor iProcessor) {
int w = iProcessor.getWidth();
int h = iProcessor.getHeight();
ImagePlus iPlus = NewImage.createByteImage("Image", w, h, 1, NewImage.FILL_BLACK);
ImageProcessor imageProcessor = iPlus.getProcessor();
imageProcessor.copyBits(iProcessor, 0, 0, Blitter.COPY);
return iPlus;
}
// constructor method
public ContourTracer(ImageProcessor ip) {
this.ip = ip;
this.width = ip.getWidth();
this.height = ip.getHeight();
makeAuxArrays();
findAllContours();
collectRegions();
}
/** Constructs a Wand object from an ImageProcessor. */
public Wand(ImageProcessor ip) {
this.ip = ip;
if (ip instanceof ByteProcessor) bpixels = (byte[]) ip.getPixels();
else if (ip instanceof ColorProcessor) cpixels = (int[]) ip.getPixels();
else if (ip instanceof ShortProcessor) spixels = (short[]) ip.getPixels();
else if (ip instanceof FloatProcessor) fpixels = (float[]) ip.getPixels();
width = ip.getWidth();
height = ip.getHeight();
}
ImageProcessor shrink(ImageProcessor ip, ImageProcessor ip2, boolean hasEdgePixels) {
if (hasEdgePixels) {
int width = ip.getWidth();
int height = ip.getHeight();
for (int y = 0; y < height; y++)
for (int x = 0; x < width; x++) ip.putPixel(x, y, ip2.getPixel(x + 1, y + 1));
}
return ip;
}
@Override
public BooleanImage getBinaryImage(ImageProcessor ip) {
if (th1 == null || !isSupported(ip)) return new BooleanImage(ip.getWidth(), ip.getHeight());
int width = ip.getWidth();
int height = ip.getHeight();
byte[] ch1, ch2, ch3;
ch1 = new byte[ip.getWidth() * ip.getHeight()];
ch2 = new byte[ip.getWidth() * ip.getHeight()];
ch3 = new byte[ip.getWidth() * ip.getHeight()];
ColorProcessor cp = (ColorProcessor) ip;
switch (colorspace) {
case RGB:
cp.getRGB(ch1, ch2, ch3);
break;
case HSB:
cp.getHSB(ch1, ch2, ch3);
break;
case Lab:
getLab(cp, ch1, ch2, ch3);
break;
case YUV:
getYUV(cp, ch1, ch2, ch3);
break;
default:
break;
}
boolean[] pix = new boolean[width * height];
for (int i = 0; i < ch1.length; i++) {
boolean c1 = th1[0] <= (ch1[i] & 0xff) && (ch1[i] & 0xff) <= th1[1];
if (pass1 ? !c1 : c1) continue;
boolean c2 = th2[0] <= (ch2[i] & 0xff) && (ch2[i] & 0xff) <= th2[1];
if (pass2 ? !c2 : c2) continue;
boolean c3 = th3[0] <= (ch3[i] & 0xff) && (ch3[i] & 0xff) <= th3[1];
if (pass3 ? !c3 : c3) continue;
pix[i] = true;
}
pix = applyMask(pix);
return new BooleanImage(width, height, pix);
}
/** Adds the image in 'ip' to the end of the stack. */
public void addSlice(String sliceLabel, ImageProcessor ip) {
if (ip.getWidth() != width || ip.getHeight() != height)
throw new IllegalArgumentException("Dimensions do not match");
if (nSlices == 0) {
cm = ip.getColorModel();
min = ip.getMin();
max = ip.getMax();
}
addSlice(sliceLabel, ip.getPixels());
}
// overwrite ip with floatEdm converted to bytes
private void byteFromFloat(ImageProcessor ip, FloatProcessor floatEdm) {
int width = ip.getWidth();
int height = ip.getHeight();
byte[] bPixels = (byte[]) ip.getPixels();
float[] fPixels = (float[]) floatEdm.getPixels();
for (int i = 0; i < width * height; i++) {
float v = fPixels[i];
bPixels[i] = v < 255f ? (byte) (v + 0.5) : (byte) 255;
}
}
private final void renderCubeFaces(final double hfov, final double vfov) {
/* fragile, but that's not public API and we know what we're doing... */
final double cubeSize = frontSource.getWidth() - 1;
/* prepare extended image */
ipSource =
ip.createProcessor(
hfov == 2.0 * Math.PI ? imp.getWidth() + 1 : imp.getWidth(),
vfov == Math.PI ? imp.getHeight() + 1 : imp.getHeight());
prepareExtendedImage(imp.getProcessor(), ipSource);
/* render cube faces */
final EquirectangularProjection q = p.clone();
q.resetOrientation();
q.setTargetWidth(cubeSize);
q.setTargetHeight(cubeSize);
q.setF(0.5f);
final InverseTransformMapping<EquirectangularProjection> qMapping =
new InverseTransformMapping<EquirectangularProjection>(q);
IJ.showStatus("Rendering cube faces...");
IJ.showProgress(0, 6);
qMapping.mapInterpolated(ipSource, frontSource);
IJ.showProgress(1, 6);
q.pan(Math.PI);
qMapping.mapInterpolated(ipSource, backSource);
IJ.showProgress(2, 6);
q.resetOrientation();
q.pan(Math.PI / 2);
qMapping.mapInterpolated(ipSource, leftSource);
IJ.showProgress(3, 6);
q.resetOrientation();
q.pan(-Math.PI / 2);
qMapping.mapInterpolated(ipSource, rightSource);
IJ.showProgress(4, 6);
q.resetOrientation();
q.tilt(-Math.PI / 2);
qMapping.mapInterpolated(ipSource, topSource);
IJ.showProgress(5, 6);
q.resetOrientation();
q.tilt(Math.PI / 2);
qMapping.mapInterpolated(ipSource, bottomSource);
IJ.showProgress(6, 6);
if (showCubefaces) {
new ImagePlus("front", frontSource).show();
new ImagePlus("back", backSource).show();
new ImagePlus("left", leftSource).show();
new ImagePlus("right", rightSource).show();
new ImagePlus("top", topSource).show();
new ImagePlus("bottom", bottomSource).show();
}
}
ImageProcessor expand(ImageProcessor ip, boolean hasEdgePixels) {
if (hasEdgePixels) {
ImageProcessor ip2 = ip.createProcessor(ip.getWidth() + 2, ip.getHeight() + 2);
if (foreground == 0) {
ip2.setColor(255);
ip2.fill();
}
ip2.insert(ip, 1, 1);
// new ImagePlus("ip2", ip2).show();
return ip2;
} else return ip;
}
public final void run(
final ImagePlus imp,
final int width,
final int height,
final double minLambda,
final double minPhi,
final double hfov,
final double vfov) {
ip = imp.getProcessor().createProcessor(width, height);
final ImagePlus impViewer = new ImagePlus("Panorama View", ip);
/* initialize projection */
p.setMinLambda(minLambda);
p.setMinPhi(minPhi);
p.setLambdaPiScale(Math.PI / hfov * imp.getWidth());
p.setPhiPiScale(Math.PI / vfov * (imp.getHeight() - 1));
p.setTargetWidth(ip.getWidth());
p.setTargetHeight(ip.getHeight());
p.setF(0.5);
System.out.println(p.getLambdaPiScale() + " " + p.getPhiPiScale());
/* TODO calculate proper size */
// final int cubeSize = 500;
final int cubeSize =
(int) Math.round(Math.max(p.getPhiPiScale(), p.getLambdaPiScale()) * 2.0 / Math.PI);
frontSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
backSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
leftSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
rightSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
topSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
bottomSource = ip.createProcessor(cubeSize + 1, cubeSize + 1);
renderCubeFaces(hfov, vfov);
/* instantiate and run mapper and painter */
final Mapper mapper =
new CubeFaceMapper(
frontSource, backSource, leftSource, rightSource, topSource, bottomSource, p);
painter = new MappingThread(imp, impViewer, mapper, ip, p);
impViewer.show();
gui = new GUI(impViewer);
gui.backupGui();
gui.takeOverGui();
painter.start();
update(false);
}
public void reset(ImageProcessor mask) {
if (mask == null || snapshotPixels == null) return;
if (mask.getWidth() != roiWidth || mask.getHeight() != roiHeight)
throw new IllegalArgumentException(maskSizeError(mask));
byte[] mpixels = (byte[]) mask.getPixels();
for (int y = roiY, my = 0; y < (roiY + roiHeight); y++, my++) {
int i = y * width + roiX;
int mi = my * roiWidth;
for (int x = roiX; x < (roiX + roiWidth); x++) {
if (mpixels[mi++] == 0) pixels[i] = snapshotPixels[i];
i++;
}
}
}
/**
* Creates the Euclidian Distance Map of a (binary) byte image.
*
* @param ip The input image, not modified; must be a ByteProcessor.
* @param backgroundValue Pixels in the input with this value are interpreted as background. Note:
* for pixel value 255, write either -1 or (byte)255.
* @param edgesAreBackground Whether out-of-image pixels are considered background
* @return The EDM, containing the distances to the nearest background pixel. Returns null if the
* thread is interrupted.
*/
public FloatProcessor makeFloatEDM(
ImageProcessor ip, int backgroundValue, boolean edgesAreBackground) {
int width = ip.getWidth();
int height = ip.getHeight();
FloatProcessor fp = new FloatProcessor(width, height);
byte[] bPixels = (byte[]) ip.getPixels();
float[] fPixels = (float[]) fp.getPixels();
final int progressInterval = 100;
int nProgressUpdates =
height
/ progressInterval; // how often the progress bar is updated when passing once through y
// range
double progressAddendum = (nProgressUpdates > 0) ? 0.5 / nProgressUpdates : 0;
for (int i = 0; i < width * height; i++)
if (bPixels[i] != backgroundValue) fPixels[i] = Float.MAX_VALUE;
int[][] pointBufs =
new int[2][width]; // two buffers for two passes; low short contains x, high short y
int yDist = Integer.MAX_VALUE; // this value is used only if edges are not background
// pass 1 & 2: increasing y
for (int x = 0; x < width; x++) {
pointBufs[0][x] = NO_POINT;
pointBufs[1][x] = NO_POINT;
}
for (int y = 0; y < height; y++) {
if (edgesAreBackground) yDist = y + 1; // distance to nearest background point (along y)
edmLine(bPixels, fPixels, pointBufs, width, y * width, y, backgroundValue, yDist);
if (y % progressInterval == 0) {
if (Thread.currentThread().isInterrupted()) return null;
addProgress(progressAddendum);
}
}
// pass 3 & 4: decreasing y
for (int x = 0; x < width; x++) {
pointBufs[0][x] = NO_POINT;
pointBufs[1][x] = NO_POINT;
}
for (int y = height - 1; y >= 0; y--) {
if (edgesAreBackground) yDist = height - y;
edmLine(bPixels, fPixels, pointBufs, width, y * width, y, backgroundValue, yDist);
if (y % progressInterval == 0) {
if (Thread.currentThread().isInterrupted()) return null;
addProgress(progressAddendum);
}
}
fp.sqrt();
return fp;
} // public FloatProcessor makeFloatEDM
@Override
public int[] getLineInt(int k, int dir) {
final int width = ip.getWidth();
final int height = ip.getHeight();
final int[] ret = (int[]) xget();
switch (dir) {
case Ox:
{
if (debug) System.out.println("fetching direction Ox");
final int lineno = height;
int offset = k * width;
int z = offset / (width * height);
if (z >= 0 && z < lineno) {
Object aux = ip.getPixels();
try {
System.arraycopy(aux, offset % height, ret, 0, ret.length);
// System.out.println(":"+offset/z);
} catch (Exception e) {
System.out.println("offset" + (offset % height));
e.printStackTrace();
}
}
return ret;
}
case Oy:
{
if (debug) System.out.println("fetching direction Oy");
final int lineno = width;
int offset = k * height;
k = k % width;
int z = offset / (width * height);
if (z >= 0 && z < lineno) {
try {
int[] pixels = (int[]) ip.getPixels();
if (pixels != null)
for (int y = 0; y < height; y++) {
ret[y] = pixels[k + y * width];
// System.out.print( "("+ k +" " +y +"),");
}
} catch (Exception e) {
// System.out.println("k "+ k );
e.printStackTrace();
}
}
return ret;
}
}
return null;
}
public void run(ImageProcessor image) {
/**
* ********************************************************************************* Initial
* phase *********************************************************************************
*/
int width = image.getWidth();
int heigh = image.getHeight();
ByteProcessor bp = Service.getByteProcessor(image);
/**
* ********************************************************************************* Convolve
* with LoG kernel
* *********************************************************************************
*/
Convolver convolver = new Convolver();
convolver.setNormalize(false);
convolver.convolve(bp, log, (int) Math.sqrt(log.length), (int) Math.sqrt(log.length));
ImagePlus outImg = new ImagePlus("Later Log kernel", bp);
outImg.show();
/**
* ********************************************************************************* threshold
* *********************************************************************************
*/
ByteProcessor bpThreshold = Service.getByteProcessor(bp);
int lut[] = new int[256];
int i = 0;
for (; i < threshold; i++) lut[i] = 0;
for (int j = i; j < lut.length; j++) lut[j] = 255;
bpThreshold.applyTable(lut);
ImagePlus outImg1 = new ImagePlus("Later threshold phase", bpThreshold);
outImg1.show();
/**
* ********************************************************************************* Find Zero
* crossing *********************************************************************************
*/
ByteProcessor out = new ByteProcessor(width, heigh);
for (i = 0; i < width; i++) for (int j = 0; j < heigh; j++) out.set(i, j, 255);
for (int x = 0; x < width - 1; x++) {
for (int y = 0; y < heigh - 1; y++) {
if (bpThreshold.get(x, y) != bpThreshold.get(x, y + 1)) out.set(x, y, 0);
if (bpThreshold.get(x, y) != bpThreshold.get(x + 1, y)) out.set(x, y, 0);
if (bpThreshold.get(x, y) != bpThreshold.get(x + 1, y + 1)) out.set(x, y, 0);
}
}
ImagePlus outImg2 = new ImagePlus("Edge Find", out);
outImg2.show();
}
ImageStack getRGBStack(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
int w = ip.getWidth();
int h = ip.getHeight();
int size = w * h;
byte[] r = new byte[size];
byte[] g = new byte[size];
byte[] b = new byte[size];
((ColorProcessor) ip).getRGB(r, g, b);
ImageStack stack = new ImageStack(w, h);
stack.addSlice("Red", r);
stack.addSlice("Green", g);
stack.addSlice("Blue", b);
stack.setColorModel(ip.getDefaultColorModel());
return stack;
}
/*------------------------------------------------------------------*/
void putRow(ImageProcessor ip, int y, double[] row) {
int rowLength = ip.getWidth();
if (rowLength != row.length) {
throw new IndexOutOfBoundsException("Incoherent array sizes");
}
y *= rowLength;
if (ip.getPixels() instanceof float[]) {
float[] floatPixels = (float[]) ip.getPixels();
for (int i = 0; (i < rowLength); i++) {
floatPixels[y++] = (float) row[i];
}
} else {
throw new IllegalArgumentException("Float image required");
}
} /* end putRow */
/*------------------------------------------------------------------*/
void putColumn(ImageProcessor ip, int x, double[] column) {
int width = ip.getWidth();
if (ip.getHeight() != column.length) {
throw new IndexOutOfBoundsException("Incoherent array sizes");
}
if (ip.getPixels() instanceof float[]) {
float[] floatPixels = (float[]) ip.getPixels();
for (int i = 0; (i < column.length); i++) {
floatPixels[x] = (float) column[i];
x += width;
}
} else {
throw new IllegalArgumentException("Float image required");
}
} /* end putColumn */
public MappingThread(
final ImagePlus impSource,
final ImagePlus impTarget,
final Mapper mapper,
final ImageProcessor target,
final PanoramaCamera<?> camera) {
this.impSource = impSource;
this.impTarget = impTarget;
this.mapper = mapper;
this.target = target;
this.temp = target.createProcessor(target.getWidth(), target.getHeight());
temp.snapshot();
this.camera = camera;
this.setName("MappingThread");
}
public void salt_and_pepper_NONE(ImageProcessor ip, double percent) {
setROIandPercent(ip, percent);
int width = ip.getWidth();
int xmin = roi.x;
int xmax = roi.x + roi.width - 1;
int ymin = roi.y;
int ymax = roi.y + roi.height - 1;
int rx, ry;
for (int i = 0; i < n / 2; i++) {
rx = rand(xmin, xmax);
ry = rand(ymin, ymax);
pixels[ry * width + rx] = (byte) 255;
rx = rand(xmin, xmax);
ry = rand(ymin, ymax);
pixels[ry * width + rx] = (byte) 0;
}
}
/**
* Execute the plugin functionality: duplicate and scale the given image.
*
* @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image;
* just returns it.
*/
public Object[] exec(
ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) {
// 0 - Check validity of parameters
if (null == imp) return null;
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
// int [] data = (ip.getHistogram());
IJ.showStatus("Thresholding...");
long startTime = System.currentTimeMillis();
// 1 Do it
if (imp.getStackSize() == 1) {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
}
// Apply the selected algorithm
if (myMethod.equals("Bernsen")) {
Bernsen(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Contrast")) {
Contrast(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Mean")) {
Mean(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Median")) {
Median(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("MidGrey")) {
MidGrey(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Niblack")) {
Niblack(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Otsu")) {
Otsu(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Phansalkar")) {
Phansalkar(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Sauvola")) {
Sauvola(imp, radius, par1, par2, doIwhite);
}
// IJ.showProgress((double)(255-i)/255);
imp.updateAndDraw();
imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
// 2 - Return the threshold and the image
IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0);
return new Object[] {imp};
}
public ImageStack makeStack(ImageProcessor ip, int w, int h, int b) {
int stackSize = w * h;
int width = ip.getWidth() / w;
int height = ip.getHeight() / h;
ImageStack stack = new ImageStack(width, height);
for (int y = 0; y < h; y++)
for (int x = 0; x < w; x++) {
ip.setRoi(x * width, y * height, width, height);
stack.addSlice(null, ip.crop());
}
if (b > 0) {
int cropwidth = width - b - b / 2;
int cropheight = height - b - b / 2;
StackProcessor sp = new StackProcessor(stack, ip);
stack = sp.crop(b, b, cropwidth, cropheight);
}
return stack;
}
public void run(String arg) {
imp = IJ.getImage();
Roi roi = imp.getRoi();
if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
ImageProcessor ip = imp.getProcessor();
if (!showDialog(ip)) return;
if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
else ip.setInterpolate(false);
ip.setBackgroundValue(bgValue);
imp.startTiming();
try {
if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
else scale(ip);
} catch (OutOfMemoryError o) {
IJ.outOfMemory("Scale");
}
IJ.showProgress(1.0);
}
public byte[] performExtraction() {
width = grayImage.getWidth();
height = grayImage.getHeight();
byte[] pixels = (byte[]) grayImage.getPixels();
byte[] result = new byte[width * height];
int offset, index;
for (int y = 1; y < height - 1; y++) {
offset = y * width;
for (int x = 1; x < width - 1; x++) {
index = offset + x;
result[index] = analyzeTexture(pixels, x, y, index);
}
}
return result;
}