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Commit 0b976466 authored by Vojtěch Moravec's avatar Vojtěch Moravec
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Code revision in Chunk3D, still need work.

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src/main/java/azgracompress/data/Chunk3D.java
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− 111
View file @ 0b976466
package azgracompress.data; package azgracompress.data;
import azgracompress.utilities.TypeConverter; import java.util.Arrays;
public class Chunk3D { public class Chunk3D {
private final int FILL_VALUE = 0;
private final int[] data; private final int[] data;
private final V3i dims; private final V3i dims;
private final V3l offset;
public Chunk3D(final V3i dims, final V3l offset, final int[] data) { public Chunk3D(final V3i dims, final int[] data) {
this.dims = dims; this.dims = dims;
this.data = data; this.data = data;
this.offset = offset;
assert (data.length == (dims.getX() * dims.getY() * dims.getZ())) : "Wrong box data."; assert (data.length == (dims.getX() * dims.getY() * dims.getZ())) : "Wrong box data.";
} }
public Chunk3D(final V3i chunkDdims, final V3l offset) { public Chunk3D(final V3i chunkDims) {
this(chunkDdims, offset, new int[chunkDdims.getX() * chunkDdims.getY() * chunkDdims.getZ()]); this(chunkDims, new int[(int) chunkDims.multiplyTogether()]);
} }
/** /**
...@@ -28,24 +27,7 @@ public class Chunk3D { ...@@ -28,24 +27,7 @@ public class Chunk3D {
* @return Index inside data array. * @return Index inside data array.
*/ */
private int index(final int x, final int y, final int z) { private int index(final int x, final int y, final int z) {
assert (x >= 0 && x < dims.getX()) : "Index X out of bounds."; return index(x, y, z, dims);
assert (y >= 0 && y < dims.getY()) : "Index Y out of bounds.";
assert (z >= 0 && z < dims.getZ()) : "Index Z out of bounds.";
/// NOTE In higher dimensions, the last dimension specified is the fastest changing on disk.
// So if we have a four dimensional dataset A, then the first element on disk would be A[0][0][0][0],
// the second A[0][0][0][1], the third A[0][0][0][2], and so on.
// SOURCE: https://support.hdfgroup.org/HDF5/doc/Advanced/Chunking/index.html
/*
0 1 2 3 4 5 6 7
A[0][0][0] A[0][0][1] A[0][1][0] A[0][1][1] A[1][0][0] A[1][0][1] A[1][1][0] A[1][1][1]
*/
// TODO(Moravec): Test which version is correct!
//final int index = (x * (dims.getY() * dims.getZ())) + (y * dims.getZ()) + z;
final int index = (z * (dims.getX() * dims.getY())) + (y * dims.getX()) + x;
assert (index < data.length) : "Index calculation is wrong";
return index;
} }
/** /**
...@@ -58,14 +40,27 @@ public class Chunk3D { ...@@ -58,14 +40,27 @@ public class Chunk3D {
* @return Index inside chunk dimension data array. * @return Index inside chunk dimension data array.
*/ */
private int index(final int x, final int y, final int z, final V3i chunkDims) { private int index(final int x, final int y, final int z, final V3i chunkDims) {
if (((x < 0) || (x >= chunkDims.getX())) || (y < 0) || (y >= chunkDims.getY()) || (z < 0) || (z >= chunkDims.getZ())) { assert (x >= 0 && x < dims.getX()) : "Index X out of bounds.";
throw new IndexOutOfBoundsException("One of index x,y,z is out of bounds of the 3D box"); assert (y >= 0 && y < dims.getY()) : "Index Y out of bounds.";
} assert (z >= 0 && z < dims.getZ()) : "Index Z out of bounds.";
// TODO(Moravec): Test which version is correct! // NOTE(Moravec): Description of the following calculation
//final int index = (x * (chunkDims.getY() * chunkDims.getZ())) + (y * chunkDims.getZ()) + z; // plane index * plane pixel count
final int index = (z * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x; // | |
return index; // V V
// planeOffset = chunkDims.getZ() * (chunkDims.getX() * chunkDims.getY())
// row * pixels in row
// | |
// V V
// rowOffset = y * chunkDims.getX();
// column
// |
// V
// colOffset = x;
return (chunkDims.getZ() * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x;
} }
...@@ -81,105 +76,69 @@ public class Chunk3D { ...@@ -81,105 +76,69 @@ public class Chunk3D {
return dims; return dims;
} }
public V3l getOffset() {
return offset;
}
@Override @Override
public String toString() { public String toString() {
return String.format("3D box %s %d values", dims.toString(), data.length); return String.format("3D box %s %d values", dims.toString(), data.length);
} }
public Chunk3D[] divideIntoChunks(final V3i chunkDims) { public int[][] divideInto3DVectors(final V3i qVectorDims) {
final int chunkSize = qVectorDims.getX() * qVectorDims.getY() * qVectorDims.getZ();
final int chunkCount = calculateRequiredChunkCount(qVectorDims);
final int xSize = dims.getX(); int[][] vectors = new int[chunkCount][chunkSize];
final int ySize = dims.getY(); int vecIndex = 0;
final int zSize = dims.getZ();
final int chunkCount = getRequiredChunkCount(chunkDims); for (int chunkZOffset = 0; chunkZOffset < dims.getZ(); chunkZOffset += qVectorDims.getZ()) {
for (int chunkYOffset = 0; chunkYOffset < dims.getY(); chunkYOffset += qVectorDims.getY()) {
Chunk3D[] chunks = new Chunk3D[chunkCount]; for (int chunkXOffset = 0; chunkXOffset < dims.getX(); chunkXOffset += qVectorDims.getX()) {
int chunkIndex = 0; copyDataToVector(vectors[vecIndex++], qVectorDims, chunkXOffset, chunkYOffset, chunkZOffset);
for (int chunkZOffset = 0; chunkZOffset < zSize; chunkZOffset += chunkDims.getZ()) {
for (int chunkYOffset = 0; chunkYOffset < ySize; chunkYOffset += chunkDims.getY()) {
for (int chunkXOffset = 0; chunkXOffset < xSize; chunkXOffset += chunkDims.getX()) {
chunks[chunkIndex++] = copyToChunk(chunkDims, new V3i(chunkXOffset, chunkYOffset, chunkZOffset));
} }
} }
} }
return chunks; return vectors;
} }
private int getRequiredChunkCount(final V3i chunkDims) { private int calculateRequiredChunkCount(final V3i chunkDims) {
final int xChunkCount = (int) Math.ceil(dims.getX() / (double) chunkDims.getX()); return calculateRequiredChunkCount(dims, chunkDims);
final int yChunkCount = (int) Math.ceil(dims.getY() / (double) chunkDims.getY());
final int zChunkCount = (int) Math.ceil(dims.getZ() / (double) chunkDims.getZ());
final int expectedChunkCount = xChunkCount * yChunkCount * zChunkCount;
return expectedChunkCount;
} }
public void reconstructFromChunks(final Chunk3D[] chunks) { public static int calculateRequiredChunkCount(final V3i imageDims, final V3i chunkDims) {
assert (chunks.length > 0) : "No chunks in reconstruct"; final int xChunkCount = (int) Math.ceil((double) imageDims.getX() / (double) chunkDims.getX());
final V3i chunkDims = chunks[0].getDims(); final int yChunkCount = (int) Math.ceil((double) imageDims.getY() / (double) chunkDims.getY());
final int zChunkCount = (int) Math.ceil((double) imageDims.getZ() / (double) chunkDims.getZ());
assert (getRequiredChunkCount(chunkDims) == chunks.length) : "Wrong chunk count in reconstruct"; return (xChunkCount * yChunkCount * zChunkCount);
for (final Chunk3D chunk : chunks) {
copyFromChunk(chunk);
}
} }
private boolean isInside(final int x, final int y, final int z) { private boolean isInside(final int x, final int y, final int z) {
return (((x >= 0) && (x < dims.getX())) && (y >= 0) && (y < dims.getY()) && (z >= 0) && (z < dims.getZ())); return (((x >= 0) && (x < dims.getX())) && (y >= 0) && (y < dims.getY()) && (z >= 0) && (z < dims.getZ()));
} }
private void copyFromChunk(final Chunk3D chunk) { /**
* Copy this chunk data to chunk vector.
final V3i chunkDims = chunk.getDims(); *
final V3l localOffset = chunk.getOffset(); * @param vector Chunk vector.
int dstX, dstY, dstZ; * @param qVectorDims Dimensions of the vector.
* @param chunkXOffset Chunk X offset
for (int chunkZ = 0; chunkZ < chunkDims.getZ(); chunkZ++) { * @param chunkYOffset Chunk Y offset.
dstZ = (int) localOffset.getZ() + chunkZ; * @param chunkZOffset Chunk Z offset.
for (int chunkY = 0; chunkY < chunkDims.getY(); chunkY++) { */
dstY = (int) localOffset.getY() + chunkY; private void copyDataToVector(int[] vector,
for (int chunkX = 0; chunkX < chunkDims.getX(); chunkX++) { final V3i qVectorDims,
dstX = (int) localOffset.getX() + chunkX; final int chunkXOffset,
final int chunkYOffset,
// NOTE(Moravec): Negating this expression! final int chunkZOffset) {
// If dst coordinates are NOT outside bounds, copy the value.
if (!(dstX >= dims.getX() || dstY >= dims.getY() || dstZ >= dims.getZ())) {
setValueAt(dstX, dstY, dstZ, chunk.getValueAt(chunkX, chunkY, chunkZ));
}
}
}
}
}
private Chunk3D copyToChunk(final V3i chunkDims, final V3i chunkOffset) {
int[] chunkData = new int[(int) (chunkDims.getX() * chunkDims.getY() * chunkDims.getZ())];
final int FILL_VALUE = 0;
int srcX, srcY, srcZ; int srcX, srcY, srcZ;
for (int z = 0; z < qVectorDims.getZ(); z++) {
for (int z = 0; z < chunkDims.getZ(); z++) { srcZ = chunkZOffset + z;
srcZ = chunkOffset.getZ() + z; for (int y = 0; y < qVectorDims.getY(); y++) {
for (int y = 0; y < chunkDims.getY(); y++) { srcY = chunkYOffset + y;
srcY = chunkOffset.getY() + y; for (int x = 0; x < qVectorDims.getX(); x++) {
for (int x = 0; x < chunkDims.getX(); x++) { srcX = chunkXOffset + x;
srcX = chunkOffset.getX() + x; final int dstIndex = index(x, y, z, qVectorDims);
chunkData[index(x, y, z, chunkDims)] = isInside(srcX, srcY, srcZ) ? vector[dstIndex] = isInside(srcX, srcY, srcZ) ? data[index(srcX, srcY, srcZ)] : FILL_VALUE;
data[index(srcX, srcY, srcZ)] :
FILL_VALUE;
} }
} }
} }
// NOTE(Moravec): We will save only local offset inside current box, which will be used
// to reconstruct the original box.
final Chunk3D chunk = new Chunk3D(chunkDims, chunkOffset.toV3l(), chunkData);
return chunk;
} }
@Override @Override
...@@ -188,8 +147,6 @@ public class Chunk3D { ...@@ -188,8 +147,6 @@ public class Chunk3D {
final Chunk3D otherChunk = (Chunk3D) obj; final Chunk3D otherChunk = (Chunk3D) obj;
if (data.length != otherChunk.data.length) { if (data.length != otherChunk.data.length) {
return false; return false;
} else if (!(offset.equals(otherChunk.offset))) {
return false;
} else { } else {
for (int i = 0; i < data.length; i++) { for (int i = 0; i < data.length; i++) {
if (data[i] != otherChunk.data[i]) { if (data[i] != otherChunk.data[i]) {
...@@ -208,8 +165,6 @@ public class Chunk3D { ...@@ -208,8 +165,6 @@ public class Chunk3D {
} }
public void zeroData() { public void zeroData() {
for (int i = 0; i < data.length; i++) { Arrays.fill(data, 0);
data[i] = 0;
}
} }
} }
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