OpenCL compression of binary data - java
I'd like to ask for your help if you're experience in OpenCL.
The task is so trivial, it's a shame I can't see what's wrong, but I couldn't solve this for 2 days now.
We have a binary 3D volume data stored in 2D slices. On the CPU side in Java, each slice is compressed into a bit array, that is, each slice's size is calculated as:
sliceSize = (width*height+31)/32;
The Java code for compressing slices from 1 byte/voxel to 1 int/32 voxels is:
hostUncompressed = new byte[depth * height * width];
hostCompressed = new int[depth * sliceSize];
deviceUncompressed = new byte[depth * height * width];
deviceCompressed = new int[depth * sliceSize];
int numOnes = 0;
int k = 0;
for (int i = 0; i < depth; ++i) {
for (int y = 0; y < height; ++y) {
for (int x = 0; x < width; ++x) {
hostUncompressed[k++] = (byte) (((int) (Math.random() * 1000)) % 2);
numOnes += (hostUncompressed[k - 1] == 1) ? 1 : 0;
}
}
}
for (int i = 0; i < depth; ++i) {
int start = i * sliceSize;
int index = start;
int targetIndex = 0;
int mask = 1;
int buffer = 0;
for (int y = 0; y < height; ++y) {
for (int x = 0; x < width; ++x) {
if (hostUncompressed[index] > 0) {
buffer |= mask;
}
++index;
if ((index & 31) == 0) {
hostCompressed[start + targetIndex++] = buffer;
buffer = 0;
mask = 1;
} else {
mask <<= 1;
}
}
}
}
My OpenCL port of it looks like this:
public void compress(cl_mem vol, int[] size3, int[] voxels) {
int totalCompressedSize = voxels.length;
cl_mem devCompressed = CL.clCreateBuffer(cl.getContext(),
CL.CL_MEM_WRITE_ONLY, Sizeof.cl_int * totalCompressedSize,
null, null);
int[] sliceSizeInts = new int[]{(size3[0] * size3[1] + 31) / 32};
int[] dimensions = new int[]{size3[0], size3[1], size3[2], 0};
long[] localWorkSize = new long[]{1, 1, 1};
long[] globalWorkSize = new long[]{sliceSizeInts[0], size3[2], 1};
cl.calcLocalWorkSize(globalWorkSize, localWorkSize);
CLUtils.round_size(localWorkSize, globalWorkSize);
int k = 0;
CL.clSetKernelArg(kernels[1], k++, Sizeof.cl_mem,
Pointer.to(devCompressed));
CL.clSetKernelArg(kernels[1], k++, Sizeof.cl_mem, Pointer.to(vol));
CL.clSetKernelArg(kernels[1], k++, Sizeof.cl_int4,
Pointer.to(dimensions));
CL.clEnqueueNDRangeKernel(cl.getCommandQueue(), kernels[1], 2, null,
globalWorkSize, localWorkSize, 0, null, null);
CL.clEnqueueReadBuffer(cl.getCommandQueue(), devCompressed, CL.CL_TRUE,
0, Sizeof.cl_int * totalCompressedSize, Pointer.to(voxels), 0,
null, null);
CL.clReleaseMemObject(devCompressed);
CL.clFinish(cl.getCommandQueue());
}
kernel void roiVolume_dataCompress(
global int* compressed,
global char* raw,
int4 dimensions) {
int comprSubId = get_global_id(0);
int sliceIndex = get_global_id(1);
int rawSliceSize = dimensions.y * dimensions.x;
int comprSliceSize = (rawSliceSize + 31)/32;
if ( sliceIndex < 0 || sliceIndex >= dimensions.z ||
comprSubId < 0 || comprSubId >= comprSliceSize )
return;
int rawIndex;
int rawSubIndex;
int value = 0;
for (int i = 0; i < 32; ++i)
{
rawSubIndex = comprSubId*32+i;
if ( rawSubIndex < rawSliceSize)
{
rawIndex = sliceIndex * rawSliceSize + rawSubIndex;
if (raw[rawIndex] != 0)
value |= (1 << i);
}
}
int comprIndex = sliceIndex * comprSliceSize + comprSubId;
compressed[comprIndex] = value;
}
It works if depth=1, so if executed only on one slice, but from the second slice it gets wrong and I can't see any pattern in the array that could help.
Any help would really be appreciated.
Thank you.
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Is there some empirical mode decomposition library in java? [closed]
Closed. This question does not meet Stack Overflow guidelines. It is not currently accepting answers. We don’t allow questions seeking recommendations for books, tools, software libraries, and more. You can edit the question so it can be answered with facts and citations. Closed 6 years ago. Improve this question I would like to ask you about any empirical mode decomposition library written in java. I cannot find any. Best if it is open source. Thank you
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So please note that this code snipped is not Java styled code, it is just Java code that compiles and runs. /* * To change this template, choose Tools | Templates * and open the template in the editor. */ package tryout.emd; /** * * #author Krusty */ public class Emd { private void emdSetup(EmdData emd, int order, int iterations, int locality) { emd.iterations = iterations; emd.order = order; emd.locality = locality; emd.size = 0; emd.imfs = null; emd.residue = null; emd.minPoints = null; emd.maxPoints = null; emd.min = null; emd.max = null; } private void emdResize(EmdData emd, int size) { int i; // emdClear(emd); emd.size = size; emd.imfs = new double[emd.order][]; // cnew(double*, emd->order); for(i = 0; i < emd.order; i++) emd.imfs[i] = new double[size]; // cnew(double, size); emd.residue = new double[size]; // cnew(double, size); emd.minPoints = new int[size / 2]; // cnew(int, size / 2); emd.maxPoints = new int[size/2]; //cnew(int, size / 2); emd.min = new double[size]; // cnew(double, size); emd.max = new double[size]; // cnew(double, size); } private void emdCreate(EmdData emd, int size, int order, int iterations, int locality) { emdSetup(emd, order, iterations, locality); emdResize(emd, size); } private void emdDecompose(EmdData emd, double[] signal) { int i, j; System.arraycopy(signal, 0, emd.imfs[0], 0, emd.size); // memcpy(emd->imfs[0], signal, emd->size * sizeof(double)); System.arraycopy(signal, 0, emd.residue, 0, emd.size); // memcpy(emd->residue, signal, emd->size * sizeof(double)); for(i = 0; i < emd.order - 1; i++) { double[] curImf = emd.imfs[i]; // double* curImf = emd->imfs[i]; for(j = 0; j < emd.iterations; j++) { emdMakeExtrema(emd, curImf); if(emd.minSize < 4 || emd.maxSize < 4) break; // can't fit splines emdInterpolate(emd, curImf, emd.min, emd.minPoints, emd.minSize); emdInterpolate(emd, curImf, emd.max, emd.maxPoints, emd.maxSize); emdUpdateImf(emd, curImf); } emdMakeResidue(emd, curImf); System.arraycopy(emd.residue, 0, emd.imfs[i+1], 0, emd.size); // memcpy(emd->imfs[i + 1], emd->residue, emd->size * sizeof(double)); } } // Currently, extrema within (locality) of the boundaries are not allowed. // A better algorithm might be to collect all the extrema, and then assume // that extrema near the boundaries are valid, working toward the center. private void emdMakeExtrema(EmdData emd, double[] curImf) { int i, lastMin = 0, lastMax = 0; emd.minSize = 0; emd.maxSize = 0; for(i = 1; i < emd.size - 1; i++) { if(curImf[i - 1] < curImf[i]) { if(curImf[i] > curImf[i + 1] && (i - lastMax) > emd.locality) { emd.maxPoints[emd.maxSize++] = i; lastMax = i; } } else { if(curImf[i] < curImf[i + 1] && (i - lastMin) > emd.locality) { emd.minPoints[emd.minSize++] = i; lastMin = i; } } } } private void emdInterpolate(EmdData emd, double[] in, double[] out, int[] points, int pointsSize) { int size = emd.size; int i, j, i0, i1, i2, i3, start, end; double a0, a1, a2, a3; double y0, y1, y2, y3, muScale, mu; for(i = -1; i < pointsSize; i++) { i0 = points[mirrorIndex(i - 1, pointsSize)]; i1 = points[mirrorIndex(i, pointsSize)]; i2 = points[mirrorIndex(i + 1, pointsSize)]; i3 = points[mirrorIndex(i + 2, pointsSize)]; y0 = in[i0]; y1 = in[i1]; y2 = in[i2]; y3 = in[i3]; a0 = y3 - y2 - y0 + y1; a1 = y0 - y1 - a0; a2 = y2 - y0; a3 = y1; // left boundary if(i == -1) { start = 0; i1 = -i1; } else start = i1; // right boundary if(i == pointsSize - 1) { end = size; i2 = size + size - i2; } else end = i2; muScale = 1.f / (i2 - i1); for(j = start; j < end; j++) { mu = (j - i1) * muScale; out[j] = ((a0 * mu + a1) * mu + a2) * mu + a3; } } } private void emdUpdateImf(EmdData emd, double[] imf) { int i; for(i = 0; i < emd.size; i++) imf[i] -= (emd.min[i] + emd.max[i]) * .5f; } private void emdMakeResidue(EmdData emd, double[] cur) { int i; for(i = 0; i < emd.size; i++) emd.residue[i] -= cur[i]; } private int mirrorIndex(int i, int size) { if(i < size) { if(i < 0) return -i - 1; return i; } return (size - 1) + (size - i); } public static void main(String[] args) { /* This code implements empirical mode decomposition in C. Required paramters include: - order: the number of IMFs to return - iterations: the number of iterations per IMF - locality: in samples, the nearest two extrema may be If it is not specified, there is no limit (locality = 0). Typical use consists of calling emdCreate(), followed by emdDecompose(), and then using the struct's "imfs" field to retrieve the data. Call emdClear() to deallocate memory inside the struct. */ double[] data = new double[]{229.49,231.94,232.97,234,233.36,235.15,235.64,235.78,238.95,242.09,240.61,240.29,237.88,252.11,259.16,263.4,262.1,254.85,254.42,261.27,253.92,259.04,251.58,248.96,239.49,229.39,247.02,249.48,254.9,251.27,246.85,245.43,241.52,231.23,235.67,239.99,238.49,237.41,246.4,249.83,253.67,256.71,255.9,248.93,244.05,242.49,236.52,243.63,246.55,247.3,252.56,259.91,264.41,266.55,262.75,266.33,263.53,261.62,259.38,260.94,249.14,244.63,241.66,240.16,241.81,251.57,251.01,252.49,250.23,244.89,245.79,244.55,243.04,238.84,244.98,247.26,251.91,252.81,252.16,256.83,253.8,251.03,250.19,254.66,254.74,255.76,254.52,252.95,254.57,252.29,243.32,244.88,242.26,240.84,245.05,246.12,243.02,242.79,239.05,233.34,236.22,233.69,234.99,235.84,236.43,243.46,245.25,251.67,250.73,255.7,255.85,256.18,259.71,260.7,262.8,268.98,267.81,275.46,275.98,279.85,280.99,284.3,283.17,278.99,279.48,275.96,274.77,270.99,281.01,281.25,281.28,286,287.25,290.35,291.9,294.01,306.1,309.27,301,302.01,301.02,299.03,300.36,299.59,299.38,296.86,292.72,295.83,300.87,304.21,309.53,308.43,309.87,307.4,309.3,307.96,299.58,298.61,293.31,292.25,299.96,298.31,304.76,300.26,306.16,306.35,308.17,302.61,307.72,309.42,308.73,311.36,309.48,312.2,310.98,311.76,312.84,311.5,311.57,312.43,311.81,313.37,315.3,316.24,314.72,315.77,316.54,316.36,314.78,313.71,320.52,322.2,324.83,324.57,326.89,333.05,332.26,334.97,336.19,338.92,331.3,329.54,323.55,317.75,328.19,332.03,334.41,333.79,326.88,330.01,335.56,334.87,334.01,336.99,342.22,345.45,348.33,344.81,347.06,349.32,350.02,353.16,348.47,340.94,329.32,333.22,333.47,338.6,343.52,339.72,342.46,349.69,350.12,345.61,346,342.8,337.15,342.33,343.86,335.95,320.95,325.46,321.59,329.99,331.84,329.88,335.5,341.89,340.82,341.33,339.06,338.94,335.1,331.83,329.59,328.76,328.8,325.86,321.72,323.28,326.9,323.3,318.47,322.74,328.59,333.01,341.07,343.32,340.8,340.54,337.23,340.52,336.78,338.64,339.98,337.23,337.15,338.06,339.86,337.7,337.06,331.15,324.15,326.91,330.54,331.18,326.02,325.22,323.07,327.54,325.81,328.15,338.28,336.03,336.6,334.01,328.76,322.93,323.12,322.39,316.96,317.64,323.32,317.78,316.24,311.47,306.67,316.37,313.76,322.14,317.39,322.93,326.06,324.87,326.46,333.84,339.84,342.11,347.4,349.84,344.28,344.04,348.19,347.95,354.9,363.54,366.51,376.28,376.66,382.51,387.56,392.34,381.81,381.07,379.76,385.86,378.24,381.8,367.01,363.37,343.52,363.74,353.71,363.44,366.64,372.89,370.04,370,356,346.26,346.66,363.35,365.85,363.46,373.05,379.27,379.29,374.27,370.57,363.78,369.32,373.39,373.6,367.12,369.51,374.06,378.61,382.17,389.51,400.33,402.1,400.83,390.79,393.2,392.1,388.3,386.11,379.85,370.85,364.32,362.28,367.87,367.01,359.65,378.14,389.3,391.15,397.22,410.42,408.46,410.65,387.68,384.46,382.09,394.63,386.85,389.6,393.58,393.84,393.67,385.63,386.5,392.01,389.25,388.76,395.08,384.43,374.65,374.06,368.85,378.16,374.21,367.05,364.65,358.88,366.18,356.92,353.59,365.8,362.96,371.71,377.28,379,382.22,380.22,378.41,379.94,382.82,381.09,378.14,369.75,368.54,370.56,371.72,385.08,385.57,387.61,392.26,395.37,391.59,394,393.88,399.94,402.09,406.56,410.81,410.15,411.62,410.95,409.82,408.29,413.04,417.33,416.01,408.76,415.68,408.87,434.4,432.43,435,440.58,443.95,443.67,442.63,447.06,451.24,455.96,463.6,479.63,479.88,488.81,495.48,484.01,488.43,488.34,500.72,498.96,502.22,508.07,511.33,520.71,527.55,529.53,530.22,518.53,515.71,516.12,527.11,530.21,536.85,552.51,573.4,569.49,569.5,584.6,589.33,585.96,582.89,579.69,590.32,597.61,600.67,593.12,583.09,601.65,612.05,607.17,616.29,618.77,611.19,609.01,605.68,588.62,564.21,592.97,591.64,571.32,557.25,556.01,544.9,593.26,591.02,586.45,567.95,566.15,569.9,565.85,549.74,553.85,552.59,553.56,554.86,551.16,542.9,537.99,531.09,515.57,515.82,545.87,541.68,554.9,549.8,546.86,556.56,563.27,561.87,545.59,548.8,547.38,555.78,556.03,564.39,555.49,560.35,556.46,555.84,558.37,569.7,571.29,569.66,561.81,566.12,555.1,556.33,558.73,553.43,567.97,576.26,582.96,593.2,589.25,597.04,591.52,587.84,582.46,588.37,590.25,590.28,589.62,597.46,587.71,587.26,584.43,559.19,559.1,569.1}; Emd emd = new Emd(); EmdData emdData = new EmdData(); int order = 4; emd.emdCreate(emdData, data.length, order, 20, 0); emd.emdDecompose(emdData, data); for (int i=0;i<data.length;i++) { System.out.print(data[i]+";"); for (int j=0;j<order; j++) System.out.print(emdData.imfs[j][i] + ";"); System.out.println(); } } private static class EmdData { protected int iterations, order, locality; protected int[] minPoints, maxPoints; protected double[] min, max, residue; protected double[][] imfs; protected int size, minSize, maxSize; } }