/** 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.");
}
/**
* Create ImagePlusExtended object from primary array (byte, short ....)
*
* @param title : title of the image
* @param object : array
* @param showImage : display image if true
* @return ImagePlusExtended
*/
public static ImagePlusExtended createImage(String title, Object object, boolean showImage) {
ImagePlusExtended imp = null;
int i = 0;
if (object instanceof byte[][]) {
byte[][] is = (byte[][]) object;
int height = is.length;
int width = is[0].length;
ByteProcessor byteprocessor = new ByteProcessor(width, height);
byte[] bp = (byte[]) byteprocessor.getPixels();
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
bp[i] = is[h][w];
w++;
i++;
}
i = ++h * width;
}
imp = new ImagePlusExtended(title, byteprocessor);
} else if (object instanceof short[][]) {
short[][] is = (short[][]) object;
int height = is.length;
int width = is[0].length;
ShortProcessor shortprocessor = new ShortProcessor(width, height);
short[] sp = (short[]) shortprocessor.getPixels();
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
sp[i] = is[h][w];
w++;
i++;
}
i = ++h * width;
}
imp = new ImagePlusExtended(title, shortprocessor);
} else if (object instanceof int[][]) {
int[][] is = (int[][]) object;
int height = is.length;
int width = is[0].length;
ShortProcessor shortprocessor = new ShortProcessor(width, height);
short[] sp = (short[]) shortprocessor.getPixels();
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
sp[i] = (short) is[h][w];
w++;
i++;
}
i = ++h * width;
}
imp = new ImagePlusExtended(title, shortprocessor);
} else if (object instanceof float[][]) {
float[][] fs = (float[][]) object;
int height = fs.length;
int width = fs[0].length;
FloatProcessor floatprocessor = new FloatProcessor(width, height);
float[] fp = (float[]) floatprocessor.getPixels();
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
fp[i] = fs[h][w];
w++;
i++;
}
i = ++h * width;
}
floatprocessor.resetMinAndMax();
imp = new ImagePlusExtended(title, floatprocessor);
} else if (object instanceof double[][]) {
double[][] ds = (double[][]) object;
int height = ds.length;
int width = ds[0].length;
FloatProcessor floatprocessor = new FloatProcessor(width, height);
float[] fp = (float[]) floatprocessor.getPixels();
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
fp[i] = (float) ds[h][w];
w++;
i++;
}
i = ++h * width;
}
floatprocessor.resetMinAndMax();
imp = new ImagePlusExtended(title, floatprocessor);
} else if (object instanceof byte[][][]) {
byte[][][] is = (byte[][][]) object;
int height = is.length;
int width = is[0].length;
int stackSize = is[0][0].length;
ImageStack imagestack = new ImageStack(width, height);
for (int sz = 0; sz < stackSize; sz++) {
ByteProcessor byteprocessor = new ByteProcessor(width, height);
byte[] bp = (byte[]) byteprocessor.getPixels();
i = 0;
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
bp[i] = is[h][w][sz];
w++;
i++;
}
i = ++h * width;
}
imagestack.addSlice("", byteprocessor);
}
imp = new ImagePlusExtended(title, imagestack);
} else if (object instanceof short[][][]) {
short[][][] is = (short[][][]) object;
int height = is.length;
int width = is[0].length;
int stackSize = is[0][0].length;
ImageStack imagestack = new ImageStack(width, height);
for (int sz = 0; sz < stackSize; sz++) {
ShortProcessor shortprocessor = new ShortProcessor(width, height);
short[] sp = (short[]) shortprocessor.getPixels();
i = 0;
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
sp[i] = is[h][w][sz];
w++;
i++;
}
i = ++h * width;
}
imagestack.addSlice("", shortprocessor);
}
imp = new ImagePlusExtended(title, imagestack);
} else if (object instanceof int[][][]) {
int[][][] is = (int[][][]) object;
int height = is.length;
int width = is[0].length;
int stackSize = is[0][0].length;
ImageStack imagestack = new ImageStack(width, height);
for (int sz = 0; sz < stackSize; sz++) {
ShortProcessor shortprocessor = new ShortProcessor(width, height);
short[] sp = (short[]) shortprocessor.getPixels();
i = 0;
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
sp[i] = (short) is[h][w][sz];
w++;
i++;
}
i = ++h * width;
}
if (sz == 0) shortprocessor.resetMinAndMax();
imagestack.addSlice("", shortprocessor);
}
imp = new ImagePlusExtended(title, imagestack);
} else if (object instanceof float[][][]) {
float[][][] fs = (float[][][]) object;
int height = fs.length;
int width = fs[0].length;
int stackSize = fs[0][0].length;
ImageStack imagestack = new ImageStack(width, height);
for (int sz = 0; sz < stackSize; sz++) {
FloatProcessor floatprocessor = new FloatProcessor(width, height);
float[] fp = (float[]) floatprocessor.getPixels();
i = 0;
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
fp[i] = fs[h][w][sz];
w++;
i++;
}
i = ++h * width;
}
if (sz == 0) floatprocessor.resetMinAndMax();
imagestack.addSlice("", floatprocessor);
}
imp = new ImagePlusExtended(title, imagestack);
} else if (object instanceof double[][][]) {
double[][][] ds = (double[][][]) object;
int height = ds.length;
int width = ds[0].length;
int stackSize = ds[0][0].length;
ImageStack imagestack = new ImageStack(width, height);
for (int sz = 0; sz < stackSize; sz++) {
FloatProcessor floatprocessor = new FloatProcessor(width, height);
float[] fp = (float[]) floatprocessor.getPixels();
i = 0;
int h = 0;
while (h < height) {
int w = 0;
while (w < width) {
fp[i] = (float) ds[h][w][sz];
w++;
i++;
}
i = ++h * width;
}
if (sz == 0) floatprocessor.resetMinAndMax();
imagestack.addSlice("", floatprocessor);
}
imp = new ImagePlusExtended(title, imagestack);
} else {
System.out.println("MIJ Error message: Unknow type of images or volumes.");
return null;
}
if (showImage) {
imp.show();
imp.updateAndDraw();
}
return imp;
}