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Commit 1e9706d6 authored by Vojtech Moravec's avatar Vojtech Moravec
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Iplement voxel loading from specified planes. 

Support voxel loading from specified plane range of the dataset.
This allows us to compress dataset in multiple passes.
parent c63da526
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src/main/java/azgracompress/io/loader/BasicLoader.java
+ 48
− 39
View file @ 1e9706d6
package azgracompress.io.loader;
import azgracompress.data.Range;
import azgracompress.data.V3i;
import azgracompress.data.Voxel;
import java.io.IOException;
import java.util.Arrays;
public abstract class BasicLoader {
protected final V3i dims;
......@@ -25,22 +27,25 @@ public abstract class BasicLoader {
/**
* Load dataset into voxel data.
* Load specified planes from dataset to voxel of specified dimensions.
* This overload uses the loadPlaneData function to read src data.
*
* @param voxelDim Single voxel dimensions.
* @param voxelDim Single voxel dimensions.
* @param planeRange Range of planes to load voxels from.
* @return Voxel data arranged in arrays.
*/
protected int[][] loadVoxelsImplByLoadPlaneData(final V3i voxelDim) {
final Voxel voxel = new Voxel(voxelDim);
protected int[][] loadVoxelsImplByLoadPlaneData(final V3i voxelDim, final Range<Integer> planeRange) {
final Voxel dstVoxel = new Voxel(voxelDim);
final int rangeSize = planeRange.getTo() - planeRange.getFrom();
final V3i srcVoxel = new V3i(dims.getX(), dims.getY(), rangeSize);
final int xVoxelCount = (int) Math.ceil((double) dims.getX() / (double) voxelDim.getX());
final int yVoxelCount = (int) Math.ceil((double) dims.getY() / (double) voxelDim.getY());
int[][] voxels = new int[Voxel.calculateRequiredVoxelCount(dims, voxelDim)][(int) voxelDim.multiplyTogether()];
int[][] voxels = new int[Voxel.calculateRequiredVoxelCount(srcVoxel, voxelDim)][(int) voxelDim.multiplyTogether()];
final int dimX = dims.getX();
final int dimY = dims.getY();
final int dimZ = dims.getZ();
final int dimZ = planeRange.getTo();
final int voxelDimX = voxelDim.getX();
final int voxelDimY = voxelDim.getY();
final int voxelDimZ = voxelDim.getZ();
......@@ -48,13 +53,12 @@ public abstract class BasicLoader {
int dstZ, dstY, dstX, voxelX, voxelY, voxelZ, voxelIndex;
int[] planeData;
for (int srcZ = 0; srcZ < dimZ; srcZ++) {
for (int srcZ = planeRange.getFrom(); srcZ < dimZ; srcZ++) {
try {
planeData = loadPlaneData(srcZ);
} catch (IOException e) {
e.printStackTrace();
break;
return null;
}
dstZ = srcZ / voxelDimZ;
voxelZ = srcZ - (dstZ * voxelDimZ);
......@@ -69,7 +73,7 @@ public abstract class BasicLoader {
voxelX = srcX - (dstX * voxelDimX);
voxelIndex = (dstZ * (xVoxelCount * yVoxelCount)) + (dstY * xVoxelCount) + dstX;
voxels[voxelIndex][voxel.dataIndex(voxelX, voxelY, voxelZ, voxelDim)] = planeData[(srcY * dimX) + srcX];
voxels[voxelIndex][dstVoxel.dataIndex(voxelX, voxelY, voxelZ, voxelDim)] = planeData[(srcY * dimX) + srcX];
}
}
}
......@@ -78,40 +82,44 @@ public abstract class BasicLoader {
}
/**
* Load dataset into voxel data.
* Load specified planes from dataset to voxel of specified dimensions.
* This overload uses the valueAt function to read src data.
*
* @param voxelDim Single voxel dimensions.
* @param voxelDim Single voxel dimensions.
* @param planeRange Range of planes to load voxels from.
* @param threadCount Number of threads used for loading.
* @return Voxel data arranged in arrays.
* @throws IOException When fails to load plane data.
*/
protected int[][] loadVoxelsImplByValueAt(final V3i voxelDim) throws IOException {
final Voxel voxel = new Voxel(voxelDim);
protected int[][] loadVoxelsImplByValueAt(final V3i voxelDim, final Range<Integer> planeRange, final int threadCount) {
// TODO(Moravec): Improve performance of loading.
final Voxel dstVoxel = new Voxel(voxelDim);
final int rangeSize = planeRange.getTo() - planeRange.getFrom();
final V3i srcVoxel = new V3i(dims.getX(), dims.getY(), rangeSize);
final int xVoxelCount = (int) Math.ceil((double) dims.getX() / (double) voxelDim.getX());
final int yVoxelCount = (int) Math.ceil((double) dims.getY() / (double) voxelDim.getY());
int[][] voxels = new int[Voxel.calculateRequiredVoxelCount(srcVoxel, voxelDim)][(int) voxelDim.multiplyTogether()];
int[][] voxels = new int[Voxel.calculateRequiredVoxelCount(dims, voxelDim)][(int) voxelDim.multiplyTogether()];
final int workSize = rangeSize / threadCount;
Thread[] threads = new Thread[threadCount];
final int workerCount = 4;
final int workSize = dims.getZ() / workerCount;
Thread[] workers = new Thread[workerCount];
final int dimX = dims.getX();
final int dimY = dims.getY();
final int voxelDimX = voxelDim.getX();
final int voxelDimY = voxelDim.getY();
final int voxelDimZ = voxelDim.getZ();
// TODO(Moravec): Try to simplify the math inside, which is slowing the process.
for (int wId = 0; wId < workerCount; wId++) {
for (int wId = 0; wId < threadCount; wId++) {
final int fromZ = wId * workSize;
final int toZ = (wId == workerCount - 1) ? dims.getZ() : (workSize + (wId * workSize));
// System.out.printf("%d-%d\n", fromZ, toZ);
workers[wId] = new Thread(() -> {
int dstZ, dstY, dstX, voxelX, voxelY, voxelZ, voxelIndex;
for (int srcZ = fromZ; srcZ < toZ; srcZ++) {
final int toZ = (wId == threadCount - 1) ? rangeSize : (workSize + (wId * workSize));
threads[wId] = new Thread(() -> {
final int dimX = dims.getX();
final int dimY = dims.getY();
final int zBase = planeRange.getFrom();
final int voxelDimX = voxelDim.getX();
final int voxelDimY = voxelDim.getY();
final int voxelDimZ = voxelDim.getZ();
int srcZ, dstZ, dstY, dstX, voxelX, voxelY, voxelZ, voxelIndex;
for (int zOffset = fromZ; zOffset < toZ; zOffset++) {
srcZ = zBase + zOffset;
dstZ = srcZ / voxelDimZ;
voxelZ = srcZ - (dstZ * voxelDimZ);
......@@ -124,20 +132,21 @@ public abstract class BasicLoader {
voxelX = srcX - (dstX * voxelDimX);
voxelIndex = (dstZ * (xVoxelCount * yVoxelCount)) + (dstY * xVoxelCount) + dstX;
voxels[voxelIndex][voxel.dataIndex(voxelX, voxelY, voxelZ, voxelDim)] = valueAt(srcZ, (srcY * dimX) + srcX);
voxels[voxelIndex][dstVoxel.dataIndex(voxelX, voxelY, voxelZ, voxelDim)] = valueAt(srcZ, (srcY * dimX) + srcX);
}
}
}
});
workers[wId].start();
threads[wId].start();
}
try {
for (int wId = 0; wId < workerCount; wId++) {
workers[wId].join();
for (int wId = 0; wId < threadCount; wId++) {
threads[wId].join();
}
} catch (InterruptedException e) {
e.printStackTrace();
return null;
}
return voxels;
}
......
src/main/java/azgracompress/io/loader/IPlaneLoader.java
+ 12
− 0
View file @ 1e9706d6
package azgracompress.io.loader;
import azgracompress.data.Range;
import azgracompress.data.V3i;
import java.io.IOException;
......@@ -43,4 +44,15 @@ public interface IPlaneLoader {
* @throws IOException when fails to load plane data.
*/
int[][] loadVoxels(final V3i voxelDim) throws IOException;
/**
* Load voxels from specified plane range in the datasIet.
* Plane range should be divisible by `voxelDim.getZ()`
*
* @param voxelDim Voxel dimensions.
* @param planeRange Source voxel dimensions.
* @return Voxel data from the entire dataset.
* @throws IOException when fails to load plane data.
*/
int[][] loadVoxels(final V3i voxelDim, final Range<Integer> planeRange) throws IOException;
}
src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
+ 10
− 3
View file @ 1e9706d6
package azgracompress.io.loader;
import azgracompress.data.Range;
import azgracompress.data.V3i;
import azgracompress.io.BufferInputData;
import azgracompress.io.InputData;
......@@ -34,7 +35,7 @@ public final class ImageJBufferLoader extends BasicLoader implements IPlaneLoade
protected int valueAt(int plane, int offset) {
final short value = ((short[]) bufferInputData.getPixelBuffer(plane))[offset];
return TypeConverter.shortToInt(value);
// return ((value & 0xFF00) | (value & 0x00FF));
// return ((value & 0xFF00) | (value & 0x00FF));
}
@Override
......@@ -87,8 +88,14 @@ public final class ImageJBufferLoader extends BasicLoader implements IPlaneLoade
}
@Override
public int[][] loadVoxels(final V3i voxelDim) throws IOException {
return loadVoxelsImplByValueAt(voxelDim);
public int[][] loadVoxels(final V3i voxelDim) {
return loadVoxels(voxelDim, new Range<>(0, bufferInputData.getDimensions().getZ()));
}
@Override
public int[][] loadVoxels(final V3i voxelDim, final Range<Integer> planeRange) {
// TODO(Moravec): Thread count, now 4, should be configurable.
return loadVoxelsImplByValueAt(voxelDim, planeRange, 4);
}
}
src/main/java/azgracompress/io/loader/RawDataLoader.java
+ 8
− 2
View file @ 1e9706d6
package azgracompress.io.loader;
import azgracompress.data.Range;
import azgracompress.data.V3i;
import azgracompress.io.FileInputData;
import azgracompress.utilities.TypeConverter;
......@@ -122,7 +123,12 @@ public final class RawDataLoader extends BasicLoader implements IPlaneLoader {
}
@Override
public int[][] loadVoxels(V3i voxelDim) throws IOException {
return loadVoxelsImplByLoadPlaneData(voxelDim);
public int[][] loadVoxels(final V3i voxelDim) {
return loadVoxels(voxelDim, new Range<>(0, inputDataInfo.getDimensions().getZ()));
}
@Override
public int[][] loadVoxels(final V3i voxelDim, final Range<Integer> planeRange) {
return loadVoxelsImplByLoadPlaneData(voxelDim, planeRange);
}
}
src/main/java/azgracompress/io/loader/SCIFIOLoader.java
+ 7
− 3
View file @ 1e9706d6
package azgracompress.io.loader;
import azgracompress.ScifioWrapper;
import azgracompress.data.Range;
import azgracompress.data.V3i;
import azgracompress.io.FileInputData;
import azgracompress.utilities.TypeConverter;
......@@ -111,9 +112,12 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
}
@Override
public int[][] loadVoxels(final V3i voxelDim) throws IOException {
return loadVoxelsImplByLoadPlaneData(voxelDim);
public int[][] loadVoxels(final V3i voxelDim) {
return loadVoxels(voxelDim, new Range<>(0, inputDataInfo.getDimensions().getZ()));
}
@Override
public int[][] loadVoxels(final V3i voxelDim, final Range<Integer> planeRange) {
return loadVoxelsImplByLoadPlaneData(voxelDim, planeRange);
}
}
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