diff --git a/src/main/java/azgracompress/compression/ImageDecompressor.java b/src/main/java/azgracompress/compression/ImageDecompressor.java
index 6a552ea1beb2daabb70453464f4c137c8f9bd38a..38f28ec0144c10b56750e8ead5b5e3ee19f52ab8 100644
--- a/src/main/java/azgracompress/compression/ImageDecompressor.java
+++ b/src/main/java/azgracompress/compression/ImageDecompressor.java
@@ -1,8 +1,6 @@
package azgracompress.compression;
import azgracompress.compression.exception.ImageDecompressionException;
-import azgracompress.compression.listeners.IProgressListener;
-import azgracompress.compression.listeners.IStatusListener;
import azgracompress.data.ImageU16Dataset;
import azgracompress.fileformat.QCMPFileHeader;
import azgracompress.utilities.Stopwatch;
@@ -47,9 +45,9 @@ public class ImageDecompressor extends CompressorDecompressorBase {
break;
case Vector1D:
case Vector2D:
+ case Vector3D:
decompressor = new VQImageDecompressor(options);
break;
- case Vector3D:
case Invalid:
default:
return null;
@@ -70,7 +68,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
StringBuilder logBuilder = new StringBuilder();
boolean validFile = true;
- QCMPFileHeader header = null;
+ QCMPFileHeader header;
try (FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
header = readQCMPFileHeader(dataInputStream);
diff --git a/src/main/java/azgracompress/compression/VQImageCompressor.java b/src/main/java/azgracompress/compression/VQImageCompressor.java
index 68d8b49e8a187c3a59d430365605f64b0170a513..a68bf572a5677d35460b1a0798339aa6a8f46318 100644
--- a/src/main/java/azgracompress/compression/VQImageCompressor.java
+++ b/src/main/java/azgracompress/compression/VQImageCompressor.java
@@ -1,16 +1,18 @@
package azgracompress.compression;
import azgracompress.cache.QuantizationCacheManager;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.io.InputData;
import azgracompress.compression.exception.ImageCompressionException;
import azgracompress.data.Chunk2D;
import azgracompress.data.ImageU16;
+import azgracompress.data.Range;
+import azgracompress.fileformat.QuantizationType;
import azgracompress.huffman.Huffman;
+import azgracompress.io.InputData;
import azgracompress.io.loader.IPlaneLoader;
import azgracompress.io.loader.PlaneLoaderFactory;
import azgracompress.quantization.vector.*;
import azgracompress.utilities.Stopwatch;
+import org.jetbrains.annotations.NotNull;
import java.io.DataOutputStream;
import java.io.IOException;
@@ -104,7 +106,11 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
return compressVoxels(compressStream);
}
assert (options.getQuantizationVector().getZ() == 1);
+ return compress1D2DVectors(compressStream);
+ }
+ @NotNull
+ private long[] compress1D2DVectors(DataOutputStream compressStream) throws ImageCompressionException {
final InputData inputDataInfo = options.getInputDataInfo();
Stopwatch stopwatch = new Stopwatch();
final boolean hasGeneralQuantizer = options.getCodebookType() != CompressionOptions.CodebookType.Individual;
@@ -113,7 +119,7 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
try {
planeLoader = PlaneLoaderFactory.getPlaneLoaderForInputFile(inputDataInfo);
} catch (Exception e) {
- throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
+ throw new ImageCompressionException("Unable to create plane reader. " + e.getMessage());
}
VectorQuantizer quantizer = null;
Huffman huffman = null;
@@ -285,19 +291,67 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
reportStatusToListeners("Operation completed.");
}
+ /**
+ * Calculate the number of voxel layers needed for dataset of plane count.
+ *
+ * @param datasetPlaneCount Dataset plane count
+ * @param voxelDepth Z dimension of voxel.
+ * @return Number of voxel layers.
+ */
+ public static int calculateVoxelLayerCount(final int datasetPlaneCount, final int voxelDepth) {
+ return (datasetPlaneCount / voxelDepth);
+ }
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;
+ assert (options.getCodebookType() == CompressionOptions.CodebookType.Global);
+ final IPlaneLoader planeLoader;
+ final int[] huffmanSymbols = createHuffmanSymbols(getCodebookSize());
+ try {
+ planeLoader = PlaneLoaderFactory.getPlaneLoaderForInputFile(options.getInputDataInfo());
+ } catch (Exception e) {
+ throw new ImageCompressionException("Unable to create plane reader. " + e.getMessage());
+ }
+
+ final int voxelLayerDepth = options.getQuantizationVector().getZ();
+ final int voxelLayerCount = calculateVoxelLayerCount(options.getInputDataInfo().getDimensions().getZ(), voxelLayerDepth);
+ long[] voxelLayersSizes = new long[voxelLayerCount];
+
+ final VectorQuantizer quantizer = loadQuantizerFromCache();
+ final Huffman huffman = createHuffmanCoder(huffmanSymbols, quantizer.getFrequencies());
+ writeQuantizerToCompressStream(quantizer, compressStream);
+
+ int[][] voxelData;
+ Stopwatch stopwatch = new Stopwatch();
+ for (int voxelLayerIndex = 0; voxelLayerIndex < voxelLayerCount; voxelLayerIndex++) {
+ stopwatch.restart();
+ final int fromZ = (voxelLayerIndex * voxelLayerDepth);
+
+ // TODO(Moravec): There is a problem!
+ // If dataset.Z is not divisible by voxel.Z we end up creating a lot stupid voxels.
+ // Those stupid voxels have only one or two layers of actual data and the rest are zeros.
+ // This ends up increasing the file size because they have quite long Huffman codes.
+ final int toZ = (voxelLayerIndex == voxelLayerCount - 1)
+ ? options.getInputDataInfo().getDimensions().getZ()
+ : (voxelLayerDepth + (voxelLayerIndex * voxelLayerDepth));
+
+ final Range<Integer> voxelLayerRange = new Range<>(fromZ, toZ);
+
+ try {
+ voxelData = planeLoader.loadVoxels(options.getQuantizationVector(), voxelLayerRange);
+ System.out.println("voxelData.length=" + voxelData.length);
+ } catch (IOException e) {
+ throw new ImageCompressionException("Unable to load voxels from voxel layer " + voxelLayerRange, e);
+ }
+
+ final int[] indices = quantizer.quantizeIntoIndices(voxelData, options.getWorkerCount());
+ voxelLayersSizes[voxelLayerIndex] = writeHuffmanEncodedIndices(compressStream, huffman, indices);
+ stopwatch.stop();
+ reportProgressToListeners(voxelLayerIndex, voxelLayerCount,
+ "%d/%d Finished voxel layer %s compression pass in %s",
+ voxelLayerIndex, voxelLayerCount, voxelLayerRange.toString(), stopwatch.getElapsedTimeString());
+ }
+ return voxelLayersSizes;
}
}
diff --git a/src/main/java/azgracompress/compression/VQImageDecompressor.java b/src/main/java/azgracompress/compression/VQImageDecompressor.java
index 3f5d5784e3f5584832c4f619d3354ccb6769713d..a1c1e50e6ef46eef6db86ccd6d92252ec9bc064d 100644
--- a/src/main/java/azgracompress/compression/VQImageDecompressor.java
+++ b/src/main/java/azgracompress/compression/VQImageDecompressor.java
@@ -76,14 +76,16 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
public long getExpectedDataSize(QCMPFileHeader header) {
// Vector count in codebook
final int codebookSize = (int) Math.pow(2, header.getBitsPerCodebookIndex());
+ System.out.println("codebookSize=" + codebookSize);
// Single vector size in bytes.
- assert (header.getVectorSizeZ() == 1);
final int vectorDataSize = 2 * header.getVectorSizeX() * header.getVectorSizeY() * header.getVectorSizeZ();
+ System.out.println("vectorDataSize=" + vectorDataSize);
// Total codebook size in bytes.
final long codebookDataSize = ((codebookSize * vectorDataSize) + (codebookSize * LONG_BYTES)) *
(header.isCodebookPerPlane() ? header.getImageSizeZ() : 1);
+ System.out.println("codebookDataSize=" + codebookDataSize);
// Indices are encoded using huffman. Plane data size is written in the header.
long[] planeDataSizes = header.getPlaneDataSizes();
@@ -91,6 +93,8 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
for (final long planeDataSize : planeDataSizes) {
totalPlaneDataSize += planeDataSize;
}
+ System.out.println("totalPlaneDataSize=" + totalPlaneDataSize);
+ System.out.println("TOTAL=" + (codebookDataSize + totalPlaneDataSize));
return (codebookDataSize + totalPlaneDataSize);
}
@@ -132,8 +136,8 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
final int planeDataSize = (int) header.getPlaneDataSizes()[planeIndex];
try (InBitStream inBitStream = new InBitStream(compressedStream,
- header.getBitsPerCodebookIndex(),
- planeDataSize)) {
+ header.getBitsPerCodebookIndex(),
+ planeDataSize)) {
inBitStream.readToBuffer();
inBitStream.setAllowReadFromUnderlyingStream(false);
@@ -146,16 +150,16 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
currentHuffmanNode = currentHuffmanNode.traverse(bit);
}
System.arraycopy(codebook.getVectors()[currentHuffmanNode.getSymbol()].getVector(),
- 0,
- decompressedVectors[vecIndex],
- 0,
- vectorSize);
+ 0,
+ decompressedVectors[vecIndex],
+ 0,
+ vectorSize);
}
final ImageU16 decompressedPlane = reconstructImageFromQuantizedVectors(decompressedVectors,
- qVector,
- header.getImageDims());
+ qVector,
+ header.getImageDims());
decompressedPlaneData =
TypeConverter.unsignedShortArrayToByteArray(decompressedPlane.getData(), false);
} catch (Exception ex) {
@@ -171,12 +175,14 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
stopwatch.stop();
reportProgressToListeners(planeIndex, planeCountForDecompression,
- "Decompressed plane %d in %s", planeIndex, stopwatch.getElapsedTimeString());
+ "Decompressed plane %d in %s", planeIndex, stopwatch.getElapsedTimeString());
}
}
@Override
- public void decompressToBuffer(DataInputStream compressedStream, short[][] buffer, QCMPFileHeader header) throws ImageDecompressionException {
+ public void decompressToBuffer(DataInputStream compressedStream,
+ short[][] buffer,
+ QCMPFileHeader header) throws ImageDecompressionException {
// TODO: Think how to remove the duplicate code.
final int codebookSize = (int) Math.pow(2, header.getBitsPerCodebookIndex());
assert (header.getVectorSizeZ() == 1);
@@ -205,8 +211,8 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
final int planeDataSize = (int) header.getPlaneDataSizes()[planeIndex];
try (InBitStream inBitStream = new InBitStream(compressedStream,
- header.getBitsPerCodebookIndex(),
- planeDataSize)) {
+ header.getBitsPerCodebookIndex(),
+ planeDataSize)) {
inBitStream.readToBuffer();
inBitStream.setAllowReadFromUnderlyingStream(false);
@@ -219,23 +225,23 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
currentHuffmanNode = currentHuffmanNode.traverse(bit);
}
System.arraycopy(codebook.getVectors()[currentHuffmanNode.getSymbol()].getVector(),
- 0,
- decompressedVectors[vecIndex],
- 0,
- vectorSize);
+ 0,
+ decompressedVectors[vecIndex],
+ 0,
+ vectorSize);
}
final ImageU16 decompressedPlane = reconstructImageFromQuantizedVectors(decompressedVectors,
- qVector,
- header.getImageDims());
+ qVector,
+ header.getImageDims());
buffer[planeIndex] = TypeConverter.intArrayToShortArray(decompressedPlane.getData());
} catch (Exception ex) {
throw new ImageDecompressionException("Unable to read indices from InBitStream.", ex);
}
reportProgressToListeners(planeIndex, planeCountForDecompression,
- "Decompressed plane %d.", planeIndex);
+ "Decompressed plane %d.", planeIndex);
}
}
}