/*
* This test is illustrative of an issue in IJ1 where the internal stack gets
* deleted in certain cases. If you setProcessor() on an ImagePlus with a
* stack of 1 slice the stack gets deleted. A subsequent call to getStack()
* will hatch a new one using the pixels of the current ImageProcessor.
* Basically to avoid problems the legacy layer should never call
* setProcessor() or if it does it should do a getStack() rather than cache
* calls to previous getStack() calls.
*/
@Test
public void testStackKiller() {
final ImageStack stack = new ImageStack(2, 2);
final byte[] slice = new byte[] {1, 2, 3, 4};
stack.addSlice("one slice", slice);
final ImagePlus imp = new ImagePlus("fred", stack);
assertEquals(stack, imp.getStack());
final byte[] slice2 = new byte[] {5, 6, 7, 8};
final ByteProcessor proc = new ByteProcessor(2, 2, slice2, null);
imp.setProcessor(proc);
final ImageStack secondStack = imp.getStack();
assertNotSame(stack, secondStack);
assertEquals(slice, stack.getPixels(1));
assertEquals(slice2, secondStack.getPixels(1));
}
/** Performs actual projection using specified method. */
public void doProjection() {
if (imp == null) return;
sliceCount = 0;
if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD;
for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++;
if (method == MEDIAN_METHOD) {
projImage = doMedianProjection();
return;
}
// Create new float processor for projected pixels.
FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight());
ImageStack stack = imp.getStack();
RayFunction rayFunc = getRayFunction(method, fp);
if (IJ.debugMode == true) {
IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice);
}
// Determine type of input image. Explicit determination of
// processor type is required for subsequent pixel
// manipulation. This approach is more efficient than the
// more general use of ImageProcessor's getPixelValue and
// putPixel methods.
int ptype;
if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE;
else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE;
else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE;
else {
IJ.error("Z Project", "Non-RGB stack required");
return;
}
// Do the projection.
for (int n = startSlice; n <= stopSlice; n += increment) {
IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice);
IJ.showProgress(n - startSlice, stopSlice - startSlice);
projectSlice(stack.getPixels(n), rayFunc, ptype);
}
// Finish up projection.
if (method == SUM_METHOD) {
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else if (method == SD_METHOD) {
rayFunc.postProcess();
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else {
rayFunc.postProcess();
projImage = makeOutputImage(imp, fp, ptype);
}
if (projImage == null) IJ.error("Z Project", "Error computing projection.");
}
private byte getPixel(
final ImageStack image,
final int x,
final int y,
final int z,
final int w,
final int h,
final int d) {
if (x >= 0 && x < w && y >= 0 && y < h && z >= 0 && z < d)
return ((byte[]) image.getPixels(z + 1))[x + y * w];
return (byte) 255;
} /* end getPixel */
private ImagePlus findSurfaceVoxels(final ImagePlus imp) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack surfaceStack = new ImageStack(w, h, d);
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final byte[] pixels = (byte[]) stack.getPixels(z + 1);
surfaceStack.setPixels(pixels.clone(), z + 1);
final ImageProcessor surfaceIP = surfaceStack.getProcessor(z + 1);
for (int y = 0; y < h; y++) {
checkNeighbours:
for (int x = 0; x < w; x++) {
if (getPixel(stack, x, y, z, w, h, d) == (byte) 0) continue;
for (int nz = -1; nz < 2; nz++) {
final int znz = z + nz;
for (int ny = -1; ny < 2; ny++) {
final int yny = y + ny;
for (int nx = -1; nx < 2; nx++) {
final int xnx = x + nx;
final byte pixel = getPixel(stack, xnx, yny, znz, w, h, d);
if (pixel == (byte) 0) continue checkNeighbours;
}
}
}
// we checked all the neighbours for a 0
// but didn't find one, so this is not a surface voxel
surfaceIP.set(x, y, (byte) 1);
}
}
}
// turn all the 1's into 0's
final int wh = w * h;
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final ImageProcessor ip = surfaceStack.getProcessor(z + 1);
for (int i = 0; i < wh; i++) {
if (ip.get(i) == (byte) 1) ip.set(i, (byte) 0);
}
}
final ImagePlus surfaceImp = new ImagePlus("Surface");
surfaceImp.setStack(surfaceStack);
surfaceImp.setCalibration(imp.getCalibration());
return surfaceImp;
}
/**
* Saito-Toriwaki algorithm for Euclidian Distance Transformation. Direct application of Algorithm
* 1. Bob Dougherty 8/8/2006
*
* <ul>
* <li>Version S1A: lower memory usage.
* <li>Version S1A.1 A fixed indexing bug for 666-bin data set
* <li>Version S1A.2 Aug. 9, 2006. Changed noResult value.
* <li>Version S1B Aug. 9, 2006. Faster.
* <li>Version S1B.1 Sept. 6, 2006. Changed comments.
* <li>Version S1C Oct. 1, 2006. Option for inverse case. <br>
* Fixed inverse behavior in y and z directions.
* <li>Version D July 30, 2007. Multithread processing for step 2.
* </ul>
*
* <p>This version assumes the input stack is already in memory, 8-bit, and outputs to a new
* 32-bit stack. Versions that are more stingy with memory may be forthcoming.
*
* @param imp 8-bit (binary) ImagePlus
*/
private float[][] geometryToDistanceMap(ImagePlus imp, boolean inv) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getStackSize();
int nThreads = Runtime.getRuntime().availableProcessors();
// Create references to input data
ImageStack stack = imp.getStack();
byte[][] data = new byte[d][];
for (int k = 0; k < d; k++) data[k] = (byte[]) stack.getPixels(k + 1);
// Create 32 bit floating point stack for output, s. Will also use it
// for g in Transformation 1.
float[][] s = new float[d][];
for (int k = 0; k < d; k++) {
ImageProcessor ipk = new FloatProcessor(w, h);
s[k] = (float[]) ipk.getPixels();
}
float[] sk;
// Transformation 1. Use s to store g.
IJ.showStatus("EDT transformation 1/3");
Step1Thread[] s1t = new Step1Thread[nThreads];
for (int thread = 0; thread < nThreads; thread++) {
s1t[thread] = new Step1Thread(thread, nThreads, w, h, d, inv, s, data);
s1t[thread].start();
}
try {
for (int thread = 0; thread < nThreads; thread++) {
s1t[thread].join();
}
} catch (InterruptedException ie) {
IJ.error("A thread was interrupted in step 1 .");
}
// Transformation 2. g (in s) -> h (in s)
IJ.showStatus("EDT transformation 2/3");
Step2Thread[] s2t = new Step2Thread[nThreads];
for (int thread = 0; thread < nThreads; thread++) {
s2t[thread] = new Step2Thread(thread, nThreads, w, h, d, s);
s2t[thread].start();
}
try {
for (int thread = 0; thread < nThreads; thread++) {
s2t[thread].join();
}
} catch (InterruptedException ie) {
IJ.error("A thread was interrupted in step 2 .");
}
// Transformation 3. h (in s) -> s
IJ.showStatus("EDT transformation 3/3");
Step3Thread[] s3t = new Step3Thread[nThreads];
for (int thread = 0; thread < nThreads; thread++) {
s3t[thread] = new Step3Thread(thread, nThreads, w, h, d, inv, s, data);
s3t[thread].start();
}
try {
for (int thread = 0; thread < nThreads; thread++) {
s3t[thread].join();
}
} catch (InterruptedException ie) {
IJ.error("A thread was interrupted in step 3 .");
}
// Find the largest distance for scaling
// Also fill in the background values.
float distMax = 0;
final int wh = w * h;
float dist;
for (int k = 0; k < d; k++) {
sk = s[k];
for (int ind = 0; ind < wh; ind++) {
if (((data[k][ind] & 255) < 128) ^ inv) {
sk[ind] = 0;
} else {
dist = (float) Math.sqrt(sk[ind]);
sk[ind] = dist;
distMax = (dist > distMax) ? dist : distMax;
}
}
}
IJ.showProgress(1.0);
IJ.showStatus("Done");
return s;
}
public void Calc_5Fr(ImagePlus imp1, ImagePlus imp2) {
if (imp1.getType() != imp2.getType()) {
error();
return;
}
if (imp1.getType() == 0) { // getType returns 0 for 8-bit, 1 for 16-bit
bitDepth = "8-bit";
Prefs.set("ps.bitDepth", bitDepth);
} else {
bitDepth = "16-bit";
Prefs.set("ps.bitDepth", bitDepth);
}
int width = imp1.getWidth();
int height = imp1.getHeight();
if (width != imp2.getWidth() || height != imp2.getHeight()) {
error();
return;
}
ImageStack stack1 = imp1.getStack();
// if (bgStackTitle != "NoBg") ImageStack stack2 = imp2.getStack();
ImageStack stack2 = imp2.getStack();
ImageProcessor ip = imp1.getProcessor();
int dimension = width * height;
byte[] pixB;
short[] pixS;
float[][] pixF = new float[5][dimension];
float[][] pixFBg = new float[5][dimension];
float a;
float b;
float den;
float aSmp;
float bSmp;
float denSmp;
float aBg;
float bBg;
float denBg;
float retF;
float azimF;
byte[] retB = new byte[dimension];
short[] retS = new short[dimension];
byte[] azimB = new byte[dimension];
short[] azimS = new short[dimension];
// Derived Variables:
float swingAngle = 2f * (float) Math.PI * swing;
float tanSwingAngleDiv2 = (float) Math.tan(swingAngle / 2.f);
float tanSwingAngleDiv2DivSqrt2 = (float) (Math.tan(swingAngle / 2.f) / Math.sqrt(2));
float wavelengthDiv2Pi = wavelength / (2f * (float) Math.PI);
// get the pixels of each slice in the stack and convert to float
for (int i = 0; i < 5; i++) {
if (bitDepth == "8-bit") {
pixB = (byte[]) stack1.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixF[i][j] = 0xff & pixB[j];
if (bgStackTitle != "NoBg") {
pixB = (byte[]) stack2.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixFBg[i][j] = 0xff & pixB[j];
}
} else {
pixS = (short[]) stack1.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixF[i][j] = (float) pixS[j];
if (bgStackTitle != "NoBg") {
pixS = (short[]) stack2.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixFBg[i][j] = (float) pixS[j];
}
}
}
// Algorithm
// terms a and b
for (int j = 0; j < dimension; j++) {
denSmp = (pixF[1][j] + pixF[2][j] + pixF[3][j] + pixF[4][j] - 4 * pixF[0][j]) / 2;
denBg = denSmp;
a = (pixF[4][j] - pixF[1][j]);
aSmp = a;
aBg = a;
b = (pixF[2][j] - pixF[3][j]);
bSmp = b;
bBg = b;
if (bgStackTitle != "NoBg") {
denBg = (pixFBg[1][j] + pixFBg[2][j] + pixFBg[3][j] + pixFBg[4][j] - 4 * pixFBg[0][j]) / 2;
aBg = pixFBg[4][j] - pixFBg[1][j];
bBg = pixFBg[2][j] - pixFBg[3][j];
}
// Special case of sample retardance half wave, denSmp = 0
if (denSmp == 0) {
retF = (float) wavelength / 4;
azimF =
(float) (a == 0 & b == 0 ? 0 : (azimRef + 90 + 90 * Math.atan2(a, b) / Math.PI) % 180);
} else {
// Retardance, the background correction can be improved by separately considering sample
// retardance values larger than a quarter wave
if (bgStackTitle != "NoBg") {
a = aSmp / denSmp - aBg / denBg;
b = bSmp / denSmp - bBg / denBg;
} else {
a = aSmp / denSmp;
b = bSmp / denSmp;
}
retF = (float) Math.atan(tanSwingAngleDiv2 * Math.sqrt(a * a + b * b));
if (denSmp < 0) retF = (float) Math.PI - retF;
retF = retF * wavelengthDiv2Pi; // convert to nm
if (retF > retCeiling) retF = retCeiling;
// Orientation
if ((bgStackTitle == "NoBg") || ((bgStackTitle != "NoBg") && (Math.abs(denSmp) < 1))) {
a = aSmp;
b = bSmp;
}
azimF =
(float) (a == 0 & b == 0 ? 0 : (azimRef + 90 + 90 * Math.atan2(a, b) / Math.PI) % 180);
}
if (bitDepth == "8-bit") retB[j] = (byte) (((int) (255 * retF / retCeiling)) & 0xff);
else retS[j] = (short) (4095 * retF / retCeiling);
if (mirror == "Yes") azimF = 180 - azimF;
if (bitDepth == "8-bit") azimB[j] = (byte) (((int) azimF) & 0xff);
else azimS[j] = (short) (azimF * 10f);
}
// show the resulting images in slice 1 and 2
imp1.setSlice(3);
if (bitDepth == "8-bit") {
stack1.setPixels(retB, 1);
stack1.setPixels(azimB, 2);
} else {
stack1.setPixels(retS, 1);
stack1.setPixels(azimS, 2);
}
imp1.setSlice(1);
IJ.selectWindow(imp1.getTitle());
Prefs.set("ps.sampleStackTitle", sampleStackTitle);
Prefs.set("ps.bgStackTitle", bgStackTitle);
Prefs.set("ps.mirror", mirror);
Prefs.set("ps.wavelength", wavelength);
Prefs.set("ps.swing", swing);
Prefs.set("ps.retCeiling", retCeiling);
Prefs.set("ps.azimRef", azimRef);
Prefs.savePreferences();
}
