/**
* Retrieve byte data of 8 bits image
*
* @param imp : image to analyze
* @return byte array with data for each pixel
*/
public static byte[] getByteData(ImagePlus imp) {
byte[] imagebyte = null;
for (int i = 0; i < imp.getStackSize(); i++) {
ByteProcessor fp = (ByteProcessor) imp.getImageStack().getProcessor(i + 1).duplicate();
if (i == 0) imagebyte = (byte[]) fp.getPixels();
else
imagebyte =
concatByte(imagebyte, (byte[]) fp.getPixels()); // (byte[]) ArrayUtils.addAll(imagebyte,
// (byte[])fp.getPixels());
System.out.println("slice : " + (i + 1) + "/" + imp.getStackSize());
}
return imagebyte;
}
protected static final FloatProcessor scaleByte(final ByteProcessor bp) {
final FloatProcessor fp = new FloatProcessor(bp.getWidth(), bp.getHeight());
final byte[] bytes = (byte[]) bp.getPixels();
final float[] floats = (float[]) fp.getPixels();
for (int i = 0; i < bytes.length; ++i) floats[i] = (bytes[i] & 0xff) / 255.0f;
return fp;
}
/**
* 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;
}