@SuppressWarnings("unchecked")
@Override
public Region<E> erode(Region<E> reg) {
try {
CubeHistogram<E> ch = new CubeHistogram<E>((PixelCube<E, BaseIndex>) reg);
Erosion<E> er = new Erosion<E>((StructureElement<E>) se);
er.initFunction(ch);
reg.setIterationPattern(IP_DEFAULT);
reg.setIndexing(BASE_INDEXING);
reg.setElementFnct(er);
setLimboErosion(reg, ch);
Region<E> out = new Region<E>((PixelCube<E, ?>) reg.clone(), (StructureElement<E>) se);
// out.setIterationPattern(IP_DEFAULT);
// out.setIndexing(BASE_INDEXING);
final ZonalProcessor zp = reg.getProcessor();
VectorCube<E> ve = reg.getVectorCube();
// System.out.println(ve);
BoundaryCondition<int[]> bc = reg.getBoundaryCondition();
// System.out.println(bc);
if (useIter) {
ArrayIterator<E> iter = (ArrayIterator<E>) reg.iterator();
ArrayIterator<E> iterout = (ArrayIterator<E>) out.iterator();
while (iter.hasNext() && iterout.hasNext()) {
int idx = iter.index();
// System.out.print(idx+" ");
// final E elem=zp.elementTransform(ve, er, idx);
final E elem = zp.elementTransformCond(ve, er, bc, idx);
iter.inc();
iterout.put(elem);
}
} else {
Access<E> accessOut = out.getAccess();
final int n = accessOut.size()[0];
for (int idx = 0; idx < n; idx++) {
// System.out.print(" i="+i+",");
// final E elem=zp.elementTransform(ve, er, idx);
final E elem = zp.elementTransformCond(ve, er, bc, idx);
accessOut.putE(idx, elem);
}
}
return out;
} catch (UnsupportedTypeException e) {
e.printStackTrace();
}
return null;
}
@SuppressWarnings("unchecked")
@Override
public Region<E> close(Region<E> reg) {
// return erode(dilate(reg));
try {
CubeHistogram<E> ch = new CubeHistogram<E>((PixelCube<E, BaseIndex>) reg);
Erosion<E> er = new Erosion<E>((StructureElement<E>) se);
er.initFunction(ch);
Dilation<E> dil = new Dilation<E>((StructureElement<E>) se);
dil.initFunction(ch);
reg.setIterationPattern(IP_DEFAULT);
reg.setIndexing(BASE_INDEXING);
Region<E> out = new Region<E>((PixelCube<E, ?>) reg.clone(), (StructureElement<E>) se);
// out.setIterationPattern(IP_DEFAULT);
// out.setIndexing(BASE_INDEXING);
final ZonalProcessor zp = reg.getProcessor();
final VectorCube<E> ve = reg.getVectorCube();
// System.out.println(ve);
// final double limbodil=0;s
// Pair<Number,Number> p= (Pair<Number, Number>) ch.getMinMax();
// final double limboer=p.second.doubleValue();
Access<E> accessOut = out.getAccess();
BoundaryCondition<int[]> bc = reg.getBoundaryCondition();
final int n = (int) accessOut.length();
int offset = Util.cumprod(se.getDimensions()) + 1; // (int)ve.size();
System.out.println("offset: " + offset);
for (int i = 0; i < n + offset; i++) {
if (i < n) {
final E elem = zp.elementTransformCond(ve, dil, bc, i);
accessOut.putE(i, elem);
}
if (i >= offset) {
final int z = i - offset;
// System.out.println("z: "+ z);
final E elem = zp.elementTransformCond(ve, er, bc, z);
accessOut.putE(z, elem);
}
}
// } // end if
return out;
} catch (UnsupportedTypeException e) {
e.printStackTrace();
}
return null;
}
public Region<E> rankMin(Region<E> reg) {
CubeHistogram<E> ch;
try {
ch = new CubeHistogram<E>((PixelCube<E, BaseIndex>) reg);
int ndim = reg.getNDimensions();
final int[] center = new int[ndim];
RankMin<E> dil = new RankMin<E>((StructureElement<E>) se);
dil.initFunction(ch);
reg.setIterationPattern(IP_DEFAULT);
reg.setIndexing(BASE_INDEXING);
reg.setElementFnct(dil);
// setLimboDilation(reg, ch);
setLimboErosion(reg, ch);
Region<E> out = new Region<E>((PixelCube<E, ?>) reg.clone(), (StructureElement<E>) se);
out.setIterationPattern(IP_DEFAULT);
out.setIndexing(BASE_INDEXING);
if (useIter) {
ArrayIterator<E> iter = (ArrayIterator<E>) reg.iterator();
ArrayIterator<E> iterout = (ArrayIterator<E>) out.iterator();
while (iter.hasNext() && iterout.hasNext()) {
final int idx = iter.index();
// System.out.print(idx+" ");
final E elem = reg.elementTransform(idx, center);
iter.inc();
if (elem.intValue() == 0) iterout.putInt(0);
else iterout.inc();
}
} else {
Access<E> accessOut = out.getAccess();
final int n = accessOut.size()[0];
for (int i = 0; i < n; i++) {
final E elem = reg.elementTransform(i, center); // we return a masking element
if (elem.intValue() == 0) {
// System.out.print(elem.intValue()+"+");
accessOut.putInt(i, 0);
}
}
}
return out;
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
/*
* tensor product
*/
public <N, V> void tPoduct(N arr1, V arr2) {
try {
Access<?> access1 = Access.rawAccess(arr1, null);
Access<?> access2 = Access.rawAccess(arr2, null);
for (int i = 0; i < access1.size()[0]; i++) {
final float f = access1.elementFloat(i) * access2.elementFloat(i);
access1.putFloat(i, f);
}
} catch (UnsupportedTypeException e) {
e.printStackTrace();
}
}
// TODO
@SuppressWarnings("unchecked")
@Override
public N join() {
PixelCube<E, BaseIndex> pc = new PixelCube<E, BaseIndex>(dim, dummy);
pc.setIndexing(BASE_INDEXING);
pc.one();
pc.setIterationPattern(IP_SINGLE + IP_DIR + IP_FWD);
pc.setDir(new int[] {0, 1});
PixelDirForwardIterator<E> iter = (PixelDirForwardIterator<E>) pc.iterator();
PixelDirForwardIterator<E> iter2 = (PixelDirForwardIterator<E>) pc.iterator();
for (int i = 0; i < nKernels; i++) {
System.out.println("iter: " + i);
for (int u = 0; u < ndim; u++) {
int[] dir = {0, u + 1}; // direction
if (u == ndim - 1) dir = new int[] {1, 0};
iter.setDirection(dir);
iter2.setDirection(dir);
int p = 0;
Access<?> kaccess;
try {
kaccess = Access.rawAccess(kernels[i], null);
final int len = kaccess.size()[0];
System.out.println(dim[u] + ",");
while (iter.hasNext()) {
float elem = iter.next().floatValue();
elem *= kaccess.elementFloat(p);
System.out.print(elem + ",");
iter2.putFloat(elem);
iter2.inc();
p++;
p = p % len;
}
iter.reset();
iter2.reset();
System.out.println();
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
} // end catch
} // end for
} // end for
// System.out.println(pc);
return (N) pc.getAccess().getArray();
} //
/*
* dot product
*/
public <N, V> float dotPoduct(N arr1, V arr2) {
float sum = 0;
try {
Access<?> access1 = Access.rawAccess(arr1, null);
Access<?> access2 = Access.rawAccess(arr2, null);
for (int i = 0; i < access1.size()[0]; i++) {
final float f = access1.elementFloat(i) * access2.elementFloat(i);
sum += f;
}
} catch (UnsupportedTypeException e) {
e.printStackTrace();
}
return sum;
}
public static void main(String[] args) {
// n_cpus=1;
new MtreadingTest();
System.out.println("CPUs " + n_cpus + "");
int[] dims = {2000, 2000};
final int size = Util.cumprod(dims);
byte[] byte_pixels = Util.rampByte(size, 100);
final Thread[] threads = new Thread[n_cpus];
int csize = size / n_cpus;
System.out.println("size " + size + " csize " + csize + "");
final int overlap = 10;
try {
final Access<Byte> accesin = Access.rawAccess(byte_pixels, null);
for (int ithread = 0; ithread < threads.length; ithread++) {
final int offset = ithread * csize;
int climit = offset + csize + overlap;
if (ithread == threads.length - 1) climit = size;
final int limit = climit;
// System.out.println("offset "+offset+" limit "+limit);
final int u = ithread;
threads[ithread] =
new Thread() {
int _id = u;
boolean _debug = debug;
{
setPriority(Thread.NORM_PRIORITY);
}
// task specific code goes here
public void run() {
for (int i = offset; i < limit; i++) {
int p = accesin.elementInt(i) + 1;
accesin.putInt(i, p);
}
if (_debug) System.out.println("finishing " + limit + " " + _id);
} // end run
}; // end thread
// Concurrently run in as many threads as CPUs
} // end for
long time = -System.currentTimeMillis();
startAndJoin(threads);
time += System.currentTimeMillis();
System.out.println("run time " + time + " ");
PixelCube<Byte, BaseIndex> pci = new PixelCube<Byte, BaseIndex>(dims, byte_pixels);
new ImageJ();
PixLib plib = new PixLib();
ImagePlus imp1 = null;
try {
imp1 = plib.imageFrom("test", pci);
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
imp1.show();
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/** @param args */
public static void main(String[] args) {
final int[] dims = {50, 30};
final int n = 1500;
final short[] short_pixels = Util.rampShort(n, 0);
// final int[] int_pixels=Util.rampInt(n,0);
final float[] float_pixels = Util.rampFloat(n, 0);
final short[] labels = {0, 1, 2};
final int[] borders = {0, 10, 200, 1000};
final float[] flabels = {0, 1, 2};
final float[] fborders = {0.0f, 10, 200, 1000};
PixelCube<Short, BaseIndex> pci = new PixelCube<Short, BaseIndex>(dims, short_pixels);
pci.setIterationPattern(IP_FWD + IP_SINGLE);
pci.setIndexing(BASE_INDEXING);
PixelCube<Short, BaseIndex> outc = (PixelCube<Short, BaseIndex>) pci.clone();
RasterForwardIterator<Short> in = (RasterForwardIterator<Short>) pci.iterator();
RasterForwardIterator<Short> out = (RasterForwardIterator<Short>) outc.iterator();
Labeling<Short> labeling = new Labeling<Short>(labels, borders);
labeling.setIO(in, out);
labeling.run();
new ImageJ();
PixLib plib = new PixLib();
ImagePlus imp1 = null;
try {
imp1 = plib.imageFrom("test", pci);
} catch (UnsupportedTypeException e2) {
// TODO Auto-generated catch block
e2.printStackTrace();
}
imp1.show();
ImagePlus imp2 = null;
try {
imp2 = plib.imageFrom("thresholded", outc);
} catch (UnsupportedTypeException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
imp2.show();
PixelCube<Float, BaseIndex> pcif = new PixelCube<Float, BaseIndex>(dims, float_pixels);
pcif.setIterationPattern(IP_FWD + IP_SINGLE);
pcif.setIndexing(BASE_INDEXING);
PixelCube<Float, BaseIndex> outcf = (PixelCube<Float, BaseIndex>) pcif.clone();
RasterForwardIterator<Float> inf = (RasterForwardIterator<Float>) pcif.iterator();
RasterForwardIterator<Float> outf = (RasterForwardIterator<Float>) outcf.iterator();
Labeling<Float> labelingf = new Labeling<Float>(flabels, fborders);
labelingf.setIO(inf, outf);
Float elem = Float.valueOf(3.0f);
System.out.println(labelingf.mapFloat(elem).getClass());
labelingf.run();
// PixLib plibf=new PixLib();
ImagePlus imp3 = null;
try {
imp3 = plib.imageFrom("test", pcif);
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
imp3.show();
ImagePlus imp4 = null;
try {
imp4 = plib.imageFrom("thresholded", outcf);
} catch (UnsupportedTypeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
imp4.show();
}