diff --git a/src/main/java/azgracompress/compression/VQImageCompressor.java b/src/main/java/azgracompress/compression/VQImageCompressor.java
index 714857e30d6a5463d6d18ab01a16315becbb29a1..6292c15702129daba0064f278bb67965f285e03e 100644
--- a/src/main/java/azgracompress/compression/VQImageCompressor.java
+++ b/src/main/java/azgracompress/compression/VQImageCompressor.java
@@ -1,6 +1,7 @@
package azgracompress.compression;
import azgracompress.cache.QuantizationCacheManager;
+import azgracompress.data.Chunk3D;
import azgracompress.fileformat.QuantizationType;
import azgracompress.io.InputData;
import azgracompress.compression.exception.ImageCompressionException;
@@ -236,11 +237,7 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
planeIndex), e);
}
- System.arraycopy(planeVectors,
- 0,
- trainData,
- (planeCounter * chunkCountPerPlane),
- chunkCountPerPlane);
+ System.arraycopy(planeVectors, 0, trainData, (planeCounter * chunkCountPerPlane), chunkCountPerPlane);
++planeCounter;
}
}
@@ -273,8 +270,19 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
reportStatusToListeners("Operation completed.");
}
+
public long[] compressVoxels(DataOutputStream compressStream) throws ImageCompressionException {
-
+ int[][] voxels;
+ try {
+ IPlaneLoader loader = PlaneLoaderFactory.getPlaneLoaderForInputFile(options.getInputDataInfo());
+ final int[] data = loader.loadAllPlanesU16Data();
+ Chunk3D bigVoxel = new Chunk3D(options.getInputDataInfo().getDimensions(), data);
+ voxels = bigVoxel.divideInto3DVectors(options.getQuantizationVector());
+ } catch (Exception e) {
+ throw new ImageCompressionException("Unable to create data loader or load image data.", e);
+ }
+ return null;
+
}
}
diff --git a/src/main/java/azgracompress/data/Chunk2D.java b/src/main/java/azgracompress/data/Chunk2D.java
index e562d437d6798ce225d61cc651eef3d77e824a2f..51d6a480366baf352d1a10df50cab729d6304ad3 100644
--- a/src/main/java/azgracompress/data/Chunk2D.java
+++ b/src/main/java/azgracompress/data/Chunk2D.java
@@ -47,8 +47,8 @@ public class Chunk2D {
* @return Index inside chunk dimension data array.
*/
private int index(final int x, final int y, final V2i chunkDims) {
- assert (x >= 0 && x < dims.getX()) : "Index X out of bounds.";
- assert (y >= 0 && y < dims.getY()) : "Index Y out of bounds.";
+ assert (x >= 0 && x < chunkDims.getX()) : "Index X out of bounds.";
+ assert (y >= 0 && y < chunkDims.getY()) : "Index Y out of bounds.";
return (y * chunkDims.getX()) + x;
}
diff --git a/src/main/java/azgracompress/data/Chunk3D.java b/src/main/java/azgracompress/data/Chunk3D.java
index a3539dc5c9bea8e46a85929921d789f7b12320a4..7b90b37af8424eb48fb57264b13df3dd61a04dbc 100644
--- a/src/main/java/azgracompress/data/Chunk3D.java
+++ b/src/main/java/azgracompress/data/Chunk3D.java
@@ -1,7 +1,5 @@
package azgracompress.data;
-import java.util.Arrays;
-
public class Chunk3D {
private final int FILL_VALUE = 0;
private final int[] data;
@@ -40,9 +38,9 @@ public class Chunk3D {
* @return Index inside chunk dimension data array.
*/
private int index(final int x, final int y, final int z, final V3i chunkDims) {
- assert (x >= 0 && x < dims.getX()) : "Index X out of bounds.";
- assert (y >= 0 && y < dims.getY()) : "Index Y out of bounds.";
- assert (z >= 0 && z < dims.getZ()) : "Index Z out of bounds.";
+ assert (x >= 0 && x < chunkDims.getX()) : "Index X out of bounds.";
+ assert (y >= 0 && y < chunkDims.getY()) : "Index Y out of bounds.";
+ assert (z >= 0 && z < chunkDims.getZ()) : "Index Z out of bounds.";
// NOTE(Moravec): Description of the following calculation
// plane index * plane pixel count
@@ -60,7 +58,7 @@ public class Chunk3D {
// V
// colOffset = x;
- return (chunkDims.getZ() * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x;
+ return (z * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x;
}
@@ -163,8 +161,4 @@ public class Chunk3D {
public int[] getData() {
return data;
}
-
- public void zeroData() {
- Arrays.fill(data, 0);
- }
}
diff --git a/src/main/java/azgracompress/io/loader/IPlaneLoader.java b/src/main/java/azgracompress/io/loader/IPlaneLoader.java
index b629191af7641a4743ddf35e0ac3d0712d9b52c4..6e3ff5f9b9e8a3373077c188b47ed89a994e970f 100644
--- a/src/main/java/azgracompress/io/loader/IPlaneLoader.java
+++ b/src/main/java/azgracompress/io/loader/IPlaneLoader.java
@@ -1,6 +1,7 @@
package azgracompress.io.loader;
import azgracompress.data.ImageU16;
+import azgracompress.data.V3i;
import java.io.IOException;
@@ -10,4 +11,8 @@ public interface IPlaneLoader {
int[] loadPlanesU16Data(int[] planes) throws IOException;
int[] loadAllPlanesU16Data() throws IOException;
+
+ default int[][] loadVoxels(final V3i voxelDim) throws IOException {
+ throw new IOException("NOT IMPLEMENTED");
+ }
}
diff --git a/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java b/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
index 6f6b42a187ea4dda5eca466e7486432010c30724..b9e70a22e393f8c171e6f92398d8ae0e0f04c733 100644
--- a/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
+++ b/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
@@ -1,5 +1,6 @@
package azgracompress.io.loader;
+import azgracompress.data.Chunk3D;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import azgracompress.io.BufferInputData;
@@ -39,8 +40,8 @@ public class ImageJBufferLoader implements IPlaneLoader {
final int planePixelCount = bufferInputData.getDimensions().getX() * bufferInputData.getDimensions().getY();
final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(plane);
return new ImageU16(bufferInputData.getDimensions().getX(),
- bufferInputData.getDimensions().getY(),
- copyShortArray(srcBuffer, planePixelCount));
+ bufferInputData.getDimensions().getY(),
+ copyShortArray(srcBuffer, planePixelCount));
}
default:
throw new IOException("Unable to load unsupported pixel type.");
@@ -106,4 +107,133 @@ public class ImageJBufferLoader implements IPlaneLoader {
throw new IOException("Unable to load unsupported pixel type.");
}
}
+
+ @Override
+ public int[][] loadVoxels(V3i voxelDim) throws IOException {
+
+ switch (bufferInputData.getPixelType()) {
+ case Gray16: {
+ final V3i dims = bufferInputData.getDimensions();
+ final int voxelSize = (int) voxelDim.multiplyTogether();
+ final int voxelCount = Chunk3D.calculateRequiredChunkCount(bufferInputData.getDimensions(), voxelDim);
+
+ int[][] voxels = new int[voxelCount][voxelSize];
+ int voxelIndex = 0;
+
+ for (int chunkZOffset = 0; chunkZOffset < dims.getZ(); chunkZOffset += voxelDim.getZ()) {
+ for (int chunkYOffset = 0; chunkYOffset < dims.getY(); chunkYOffset += voxelDim.getY()) {
+ for (int chunkXOffset = 0; chunkXOffset < dims.getX(); chunkXOffset += voxelDim.getX()) {
+ copyDataToVector(voxels[voxelIndex++], voxelDim, chunkXOffset, chunkYOffset, chunkZOffset);
+ }
+ }
+ }
+ return voxels;
+ }
+ default:
+ throw new IOException("Unable to load unsupported pixel type.");
+ }
+ }
+
+ private int readDataAt(final int x, final int y, final int z) {
+
+ final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(z);
+ return srcBuffer[(y * bufferInputData.getDimensions().getX()) + x];
+ }
+
+ /**
+ * Copy this chunk data to chunk vector.
+ *
+ * @param vector Chunk vector.
+ * @param qVectorDims Dimensions of the vector.
+ * @param chunkXOffset Chunk X offset
+ * @param chunkYOffset Chunk Y offset.
+ * @param chunkZOffset Chunk Z offset.
+ */
+ private void copyDataToVector(int[] vector,
+ final V3i qVectorDims,
+ final int chunkXOffset,
+ final int chunkYOffset,
+ final int chunkZOffset) {
+ int srcZ;
+ for (int z = 0; z < qVectorDims.getZ(); z++) {
+ srcZ = chunkZOffset + z;
+ fillVoxelFromPlane(vector, qVectorDims, srcZ, z, chunkXOffset, chunkYOffset);
+ }
+ }
+
+ private void fillVoxelFromPlane(int[] vector,
+ final V3i qVectorDims,
+ final int srcZ,
+ final int z,
+ final int chunkXOffset,
+ final int chunkYOffset) {
+
+ if (srcZ >= bufferInputData.getDimensions().getZ())
+ return;
+
+ final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(srcZ);
+ final int width = bufferInputData.getDimensions().getX();
+
+ int srcX, srcY;
+ for (int y = 0; y < qVectorDims.getY(); y++) {
+ srcY = chunkYOffset + y;
+ for (int x = 0; x < qVectorDims.getX(); x++) {
+ srcX = chunkXOffset + x;
+ final int dstIndex = index(x, y, z, qVectorDims);
+ vector[dstIndex] = isInside(srcX, srcY, srcZ) ? srcBuffer[(srcY * width) + srcX] : 0;
+ }
+ }
+ }
+
+ private boolean isInside(final int x, final int y, final int z) {
+ return (((x >= 0) && (x < bufferInputData.getDimensions().getX())) && (y >= 0) &&
+ (y < bufferInputData.getDimensions().getY()) && (z >= 0) &&
+ (z < bufferInputData.getDimensions().getZ()));
+ }
+
+ /**
+ * Calculate the index inside data array.
+ *
+ * @param x Zero based x coordinate.
+ * @param y Zero based y coordinate.
+ * @param z Zero based z coordinate.
+ * @return Index inside data array.
+ */
+ private int index(final int x, final int y, final int z) {
+ return index(x, y, z, bufferInputData.getDimensions());
+ }
+
+ /**
+ * Calculate the index inside array of dimensions specified by chunkDims.
+ *
+ * @param x Zero based x coordinate.
+ * @param y Zero based y coordinate.
+ * @param z Zero based z coordinate.
+ * @param chunkDims Chunk dimensions.
+ * @return Index inside chunk dimension data array.
+ */
+ private int index(final int x, final int y, final int z, final V3i chunkDims) {
+ assert (x >= 0 && x < chunkDims.getX()) : "Index X out of bounds.";
+ assert (y >= 0 && y < chunkDims.getY()) : "Index Y out of bounds.";
+ assert (z >= 0 && z < chunkDims.getZ()) : "Index Z out of bounds.";
+
+ // NOTE(Moravec): Description of the following calculation
+ // plane index * plane pixel count
+ // | |
+ // V V
+ // planeOffset = chunkDims.getZ() * (chunkDims.getX() * chunkDims.getY())
+
+ // row * pixels in row
+ // | |
+ // V V
+ // rowOffset = y * chunkDims.getX();
+
+ // column
+ // |
+ // V
+ // colOffset = x;
+
+ return (z * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x;
+ }
}
+