@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(); }