From 2c6d978179e6a4a5a9c41bcadbe38e82955b131b Mon Sep 17 00:00:00 2001
From: Vojtech Moravec <vojtech.moravec.st@vsb.cz>
Date: Tue, 6 Oct 2020 13:44:51 +0200
Subject: [PATCH] Rename package azgracompress -> cz.it4i.qcmp
---
.gitignore | 1 +
.../benchmark/CompressionBenchmark.java | 28 -----
src/main/java/azgracompress/io/RawDataIO.java | 34 ------
.../it4i/qcmp}/DataCompressor.java | 20 +--
.../it4i/qcmp}/ScifioWrapper.java | 4 +-
.../{azgracompress => cz/it4i/qcmp}/U16.java | 2 +-
.../it4i/qcmp}/benchmark/Benchmark.java | 62 +++++-----
.../it4i/qcmp}/benchmark/BenchmarkBase.java | 42 +++----
.../qcmp/benchmark/CompressionBenchmark.java | 28 +++++
.../it4i/qcmp}/benchmark/SQBenchmark.java | 54 ++++-----
.../it4i/qcmp}/benchmark/VQBenchmark.java | 14 +--
.../it4i/qcmp}/cache/CacheFileHeader.java | 10 +-
.../it4i/qcmp}/cache/ICacheFile.java | 2 +-
.../qcmp}/cache/QuantizationCacheManager.java | 12 +-
.../it4i/qcmp}/cache/SQCacheFile.java | 4 +-
.../it4i/qcmp}/cache/VQCacheFile.java | 4 +-
.../it4i/qcmp}/cli/CliConstants.java | 4 +-
.../cli/CompressionOptionsCLIParser.java | 61 +++++-----
.../it4i/qcmp}/cli/CustomFunctionBase.java | 6 +-
.../it4i/qcmp}/cli/ParseUtils.java | 10 +-
.../it4i/qcmp}/cli/ProgramMethod.java | 2 +-
.../cli/functions/EntropyCalculation.java | 20 +--
.../functions/MeasurePlaneErrorFunction.java | 34 +++---
.../it4i/qcmp}/cli/functions/PlaneError.java | 4 +-
.../qcmp}/compression/CompressionOptions.java | 10 +-
.../CompressorDecompressorBase.java | 16 +--
.../qcmp}/compression/IImageCompressor.java | 9 +-
.../qcmp}/compression/IImageDecompressor.java | 8 +-
.../it4i/qcmp}/compression/IListenable.java | 6 +-
.../qcmp}/compression/ImageCompressor.java | 16 +--
.../qcmp}/compression/ImageDecompressor.java | 67 +++++-----
.../qcmp}/compression/SQImageCompressor.java | 85 +++++++------
.../compression/SQImageDecompressor.java | 77 ++++++------
.../qcmp}/compression/VQImageCompressor.java | 36 +++---
.../compression/VQImageDecompressor.java | 28 ++---
.../exception/ImageCompressionException.java | 2 +-
.../ImageDecompressionException.java | 2 +-
.../listeners/IProgressListener.java | 2 +-
.../listeners/IStatusListener.java | 2 +-
.../it4i/qcmp}/data/Block.java | 10 +-
.../it4i/qcmp}/data/ImageU16.java | 38 +++---
.../it4i/qcmp}/data/ImageU16Dataset.java | 4 +-
.../it4i/qcmp}/data/Range.java | 4 +-
.../it4i/qcmp}/data/V2.java | 4 +-
.../it4i/qcmp}/data/V2i.java | 2 +-
.../it4i/qcmp}/data/V3.java | 4 +-
.../it4i/qcmp}/data/V3i.java | 2 +-
.../it4i/qcmp}/data/Voxel.java | 3 +-
.../it4i/qcmp}/fileformat/FileExtensions.java | 2 +-
.../it4i/qcmp}/fileformat/QCMPFileHeader.java | 8 +-
.../qcmp}/fileformat/QuantizationType.java | 4 +-
.../it4i/qcmp}/huffman/Huffman.java | 26 ++--
.../it4i/qcmp}/huffman/HuffmanNode.java | 8 +-
.../it4i/qcmp}/io/BufferInputData.java | 4 +-
.../it4i/qcmp}/io/FileInputData.java | 4 +-
.../it4i/qcmp}/io/FlatBufferInputData.java | 4 +-
.../it4i/qcmp}/io/InBitStream.java | 2 +-
.../it4i/qcmp}/io/InputData.java | 14 +--
.../it4i/qcmp}/io/MemoryOutputStream.java | 2 +-
.../it4i/qcmp}/io/OutBitStream.java | 8 +-
src/main/java/cz/it4i/qcmp/io/RawDataIO.java | 34 ++++++
.../it4i/qcmp}/io/loader/BasicLoader.java | 4 +-
.../qcmp}/io/loader/DataWrappingStrategy.java | 2 +-
.../qcmp}/io/loader/FlatBufferLoader.java | 12 +-
.../it4i/qcmp}/io/loader/IPlaneLoader.java | 14 +--
.../qcmp}/io/loader/ImageJBufferLoader.java | 16 +--
.../qcmp}/io/loader/PlaneLoaderFactory.java | 10 +-
.../it4i/qcmp}/io/loader/RawDataLoader.java | 12 +-
.../it4i/qcmp}/io/loader/SCIFIOLoader.java | 32 ++---
.../it4i/qcmp}/kdtree/KDNode.java | 2 +-
.../it4i/qcmp}/kdtree/KDTree.java | 12 +-
.../it4i/qcmp}/kdtree/KDTreeBuilder.java | 8 +-
.../it4i/qcmp}/kdtree/TerminalKDNode.java | 4 +-
.../qcmp}/quantization/QTrainIteration.java | 4 +-
.../scalar/LloydMaxU16ScalarQuantization.java | 36 +++---
.../scalar/RunnableLloydMseCalc.java | 4 +-
.../qcmp}/quantization/scalar/SQCodebook.java | 2 +-
.../quantization/scalar/ScalarQuantizer.java | 20 +--
.../qcmp}/quantization/vector/EntryInfo.java | 8 +-
.../qcmp}/quantization/vector/LBGResult.java | 4 +-
.../vector/LBGVectorQuantizer.java | 114 +++++++++---------
.../vector/LearningCodebookEntry.java | 4 +-
.../quantization/vector/TrainingVector.java | 4 +-
.../qcmp}/quantization/vector/VQCodebook.java | 6 +-
.../vector/VectorDistanceMetric.java | 2 +-
.../quantization/vector/VectorQuantizer.java | 8 +-
.../it4i/qcmp}/utilities/ColorConsole.java | 2 +-
.../it4i/qcmp}/utilities/Means.java | 12 +-
.../it4i/qcmp}/utilities/MinMaxResult.java | 4 +-
.../it4i/qcmp}/utilities/Stopwatch.java | 10 +-
.../it4i/qcmp}/utilities/TypeConverter.java | 16 +--
.../it4i/qcmp}/utilities/Utils.java | 20 +--
92 files changed, 714 insertions(+), 713 deletions(-)
delete mode 100644 src/main/java/azgracompress/benchmark/CompressionBenchmark.java
delete mode 100644 src/main/java/azgracompress/io/RawDataIO.java
rename src/main/java/{azgracompress => cz/it4i/qcmp}/DataCompressor.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/ScifioWrapper.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/U16.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/benchmark/Benchmark.java (62%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/benchmark/BenchmarkBase.java (84%)
create mode 100644 src/main/java/cz/it4i/qcmp/benchmark/CompressionBenchmark.java
rename src/main/java/{azgracompress => cz/it4i/qcmp}/benchmark/SQBenchmark.java (76%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/benchmark/VQBenchmark.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cache/CacheFileHeader.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cache/ICacheFile.java (94%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cache/QuantizationCacheManager.java (98%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cache/SQCacheFile.java (96%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cache/VQCacheFile.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/CliConstants.java (98%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/CompressionOptionsCLIParser.java (91%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/CustomFunctionBase.java (76%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/ParseUtils.java (94%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/ProgramMethod.java (84%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/functions/EntropyCalculation.java (70%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/functions/MeasurePlaneErrorFunction.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/cli/functions/PlaneError.java (78%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/CompressionOptions.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/CompressorDecompressorBase.java (94%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/IImageCompressor.java (87%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/IImageDecompressor.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/IListenable.java (77%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/ImageCompressor.java (96%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/ImageDecompressor.java (83%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/SQImageCompressor.java (79%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/SQImageDecompressor.java (74%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/VQImageCompressor.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/VQImageDecompressor.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/exception/ImageCompressionException.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/exception/ImageDecompressionException.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/listeners/IProgressListener.java (73%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/compression/listeners/IStatusListener.java (64%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/Block.java (96%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/ImageU16.java (63%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/ImageU16Dataset.java (81%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/Range.java (92%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/V2.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/V2i.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/V3.java (94%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/V3i.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/data/Voxel.java (99%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/fileformat/FileExtensions.java (84%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/fileformat/QCMPFileHeader.java (98%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/fileformat/QuantizationType.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/huffman/Huffman.java (77%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/huffman/HuffmanNode.java (87%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/BufferInputData.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/FileInputData.java (87%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/FlatBufferInputData.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/InBitStream.java (99%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/InputData.java (84%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/MemoryOutputStream.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/OutBitStream.java (92%)
create mode 100644 src/main/java/cz/it4i/qcmp/io/RawDataIO.java
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/BasicLoader.java (99%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/DataWrappingStrategy.java (92%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/FlatBufferLoader.java (94%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/IPlaneLoader.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/ImageJBufferLoader.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/PlaneLoaderFactory.java (83%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/RawDataLoader.java (95%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/io/loader/SCIFIOLoader.java (84%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/kdtree/KDNode.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/kdtree/KDTree.java (91%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/kdtree/KDTreeBuilder.java (96%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/kdtree/TerminalKDNode.java (92%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/QTrainIteration.java (76%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/scalar/LloydMaxU16ScalarQuantization.java (88%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/scalar/RunnableLloydMseCalc.java (87%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/scalar/SQCodebook.java (96%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/scalar/ScalarQuantizer.java (85%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/EntryInfo.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/LBGResult.java (92%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/LBGVectorQuantizer.java (89%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/LearningCodebookEntry.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/TrainingVector.java (93%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/VQCodebook.java (92%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/VectorDistanceMetric.java (65%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/quantization/vector/VectorQuantizer.java (97%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/ColorConsole.java (98%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/Means.java (76%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/MinMaxResult.java (75%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/Stopwatch.java (90%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/TypeConverter.java (89%)
rename src/main/java/{azgracompress => cz/it4i/qcmp}/utilities/Utils.java (88%)
diff --git a/.gitignore b/.gitignore
index b076730..e197e72 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,5 @@ out/
*.raw
*.qcmp
*.QCMP
+*.MF
dc.bat
diff --git a/src/main/java/azgracompress/benchmark/CompressionBenchmark.java b/src/main/java/azgracompress/benchmark/CompressionBenchmark.java
deleted file mode 100644
index bc29bea..0000000
--- a/src/main/java/azgracompress/benchmark/CompressionBenchmark.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package azgracompress.benchmark;
-
-import azgracompress.cli.CompressionOptionsCLIParser;
-
-public class CompressionBenchmark {
- public static void runBenchmark(final CompressionOptionsCLIParser options) {
- Benchmark benchmark = new Benchmark(options);
- benchmark.startBenchmark();
-// switch (options.getQuantizationType()) {
-// case Scalar: {
-// SQBenchmark sqBenchmark = new SQBenchmark(options);
-// sqBenchmark.startBenchmark();
-// }
-// break;
-// case Vector1D:
-// case Vector2D: {
-// VQBenchmark vqBenchmark = new VQBenchmark(options);
-// vqBenchmark.startBenchmark(options.getVectorDimension());
-// }
-// break;
-// case Vector3D:
-// case Invalid: {
-// System.err.println("Unsupported benchmark type.");
-// }
-// break;
-// }
- }
-}
diff --git a/src/main/java/azgracompress/io/RawDataIO.java b/src/main/java/azgracompress/io/RawDataIO.java
deleted file mode 100644
index ee7500c..0000000
--- a/src/main/java/azgracompress/io/RawDataIO.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package azgracompress.io;
-
-import azgracompress.data.ImageU16;
-import azgracompress.utilities.TypeConverter;
-
-import java.io.FileOutputStream;
-import java.io.IOException;
-
-public class RawDataIO {
-
- public static void writeImageU16(final String rawFile,
- final ImageU16 image,
- final boolean littleEndian) throws IOException {
- byte[] buffer = TypeConverter.unsignedShortArrayToByteArray(image.getData(), littleEndian);
- writeBytesToFile(rawFile, buffer);
- }
-
- public static void writeDataI32(String rawFile,
- int[] differenceData,
- final boolean littleEndian) throws IOException {
- byte[] buffer = TypeConverter.intArrayToByteArray(differenceData, littleEndian);
- writeBytesToFile(rawFile, buffer);
- }
-
- public static void writeBytesToFile(String rawFile,
- byte[] buffer) throws IOException {
- FileOutputStream fileStream = new FileOutputStream(rawFile, false);
- fileStream.write(buffer, 0, buffer.length);
- fileStream.flush();
- fileStream.close();
- }
-
-
-}
diff --git a/src/main/java/azgracompress/DataCompressor.java b/src/main/java/cz/it4i/qcmp/DataCompressor.java
similarity index 90%
rename from src/main/java/azgracompress/DataCompressor.java
rename to src/main/java/cz/it4i/qcmp/DataCompressor.java
index 7cecf19..4b12ea3 100644
--- a/src/main/java/azgracompress/DataCompressor.java
+++ b/src/main/java/cz/it4i/qcmp/DataCompressor.java
@@ -1,14 +1,14 @@
-package azgracompress;
+package cz.it4i.qcmp;
-import azgracompress.benchmark.CompressionBenchmark;
-import azgracompress.cache.QuantizationCacheManager;
-import azgracompress.cli.CliConstants;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.cli.CustomFunctionBase;
-import azgracompress.cli.functions.EntropyCalculation;
-import azgracompress.compression.ImageCompressor;
-import azgracompress.compression.ImageDecompressor;
-import azgracompress.fileformat.FileExtensions;
+import cz.it4i.qcmp.benchmark.CompressionBenchmark;
+import cz.it4i.qcmp.cache.QuantizationCacheManager;
+import cz.it4i.qcmp.cli.CliConstants;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.cli.CustomFunctionBase;
+import cz.it4i.qcmp.cli.functions.EntropyCalculation;
+import cz.it4i.qcmp.compression.ImageCompressor;
+import cz.it4i.qcmp.compression.ImageDecompressor;
+import cz.it4i.qcmp.fileformat.FileExtensions;
import org.apache.commons.cli.*;
import java.io.IOException;
diff --git a/src/main/java/azgracompress/ScifioWrapper.java b/src/main/java/cz/it4i/qcmp/ScifioWrapper.java
similarity index 95%
rename from src/main/java/azgracompress/ScifioWrapper.java
rename to src/main/java/cz/it4i/qcmp/ScifioWrapper.java
index b6e7d15..37bc9c8 100644
--- a/src/main/java/azgracompress/ScifioWrapper.java
+++ b/src/main/java/cz/it4i/qcmp/ScifioWrapper.java
@@ -1,4 +1,4 @@
-package azgracompress;
+package cz.it4i.qcmp;
import io.scif.FormatException;
import io.scif.Reader;
@@ -36,7 +36,7 @@ public class ScifioWrapper {
* @throws FormatException
*/
public static Reader getReader(final String path) throws IOException, FormatException {
- SCIFIO scifio = getScifio();
+ final SCIFIO scifio = getScifio();
// return scifio.initializer().initializeReader(new FileLocation(path));
return scifio.initializer().initializeReader(path);
}
diff --git a/src/main/java/azgracompress/U16.java b/src/main/java/cz/it4i/qcmp/U16.java
similarity index 93%
rename from src/main/java/azgracompress/U16.java
rename to src/main/java/cz/it4i/qcmp/U16.java
index 4f79d22..b85d7ce 100644
--- a/src/main/java/azgracompress/U16.java
+++ b/src/main/java/cz/it4i/qcmp/U16.java
@@ -1,4 +1,4 @@
-package azgracompress;
+package cz.it4i.qcmp;
public class U16 {
public static final int Min = 0x0;
diff --git a/src/main/java/azgracompress/benchmark/Benchmark.java b/src/main/java/cz/it4i/qcmp/benchmark/Benchmark.java
similarity index 62%
rename from src/main/java/azgracompress/benchmark/Benchmark.java
rename to src/main/java/cz/it4i/qcmp/benchmark/Benchmark.java
index 91fb4fd..117259d 100644
--- a/src/main/java/azgracompress/benchmark/Benchmark.java
+++ b/src/main/java/cz/it4i/qcmp/benchmark/Benchmark.java
@@ -1,16 +1,16 @@
-package azgracompress.benchmark;
-
-import azgracompress.U16;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.compression.ImageCompressor;
-import azgracompress.compression.ImageDecompressor;
-import azgracompress.data.ImageU16Dataset;
-import azgracompress.io.FileInputData;
-import azgracompress.io.RawDataIO;
-import azgracompress.io.loader.IPlaneLoader;
-import azgracompress.io.loader.PlaneLoaderFactory;
-import azgracompress.utilities.TypeConverter;
-import azgracompress.utilities.Utils;
+package cz.it4i.qcmp.benchmark;
+
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.compression.ImageCompressor;
+import cz.it4i.qcmp.compression.ImageDecompressor;
+import cz.it4i.qcmp.data.ImageU16Dataset;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.io.RawDataIO;
+import cz.it4i.qcmp.io.loader.IPlaneLoader;
+import cz.it4i.qcmp.io.loader.PlaneLoaderFactory;
+import cz.it4i.qcmp.utilities.TypeConverter;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.File;
import java.io.IOException;
@@ -19,33 +19,33 @@ import java.util.Optional;
public class Benchmark extends BenchmarkBase {
- protected Benchmark(CompressionOptionsCLIParser options) {
+ protected Benchmark(final CompressionOptionsCLIParser options) {
super(options);
}
@Override
public void startBenchmark() {
assert (options.getInputDataInfo().isPlaneIndexSet());
- CompressionOptionsCLIParser compressOps;
- CompressionOptionsCLIParser decompressOps;
+ final CompressionOptionsCLIParser compressOps;
+ final CompressionOptionsCLIParser decompressOps;
try {
// NOTE: This works, right?
compressOps = (CompressionOptionsCLIParser) options.clone();
decompressOps = (CompressionOptionsCLIParser) options.clone();
- } catch (CloneNotSupportedException e) {
+ } catch (final CloneNotSupportedException e) {
System.err.println(e.getMessage());
e.printStackTrace();
return;
}
// dirCreated is ignored.
- boolean dirCreated = new File(options.getOutputFilePath()).mkdirs();
+ final boolean dirCreated = new File(options.getOutputFilePath()).mkdirs();
final String qcmpFilePath = getFileNamePathIntoOutDir(String.format(COMPRESSED_FILE_TEMPLATE,
- options.getInputDataInfo().getPlaneIndex(),
- codebookSize));
+ options.getInputDataInfo().getPlaneIndex(),
+ codebookSize));
compressOps.setOutputFilePath(qcmpFilePath);
- ImageCompressor compressor = new ImageCompressor(compressOps);
+ final ImageCompressor compressor = new ImageCompressor(compressOps);
if (!compressor.compress()) {
System.err.println("Errors occurred during compression.");
return;
@@ -54,11 +54,11 @@ public class Benchmark extends BenchmarkBase {
decompressOps.setInputDataInfo(new FileInputData(qcmpFilePath));
final String decompressedFile = getFileNamePathIntoOutDir(String.format(QUANTIZED_FILE_TEMPLATE,
- options.getInputDataInfo().getPlaneIndex(),
- codebookSize));
+ options.getInputDataInfo().getPlaneIndex(),
+ codebookSize));
decompressOps.setOutputFilePath(decompressedFile);
- ImageDecompressor decompressor = new ImageDecompressor(decompressOps);
+ final ImageDecompressor decompressor = new ImageDecompressor(decompressOps);
final Optional<ImageU16Dataset> maybeDataset = decompressor.decompressInMemory();
if (!maybeDataset.isPresent()) {
@@ -66,11 +66,11 @@ public class Benchmark extends BenchmarkBase {
return;
}
- int[] originalData;
+ final int[] originalData;
try {
final IPlaneLoader loader = PlaneLoaderFactory.getPlaneLoaderForInputFile(options.getInputDataInfo());
originalData = loader.loadPlaneData(options.getInputDataInfo().getPlaneIndex());
- } catch (Exception e) {
+ } catch (final Exception e) {
System.err.println("Failed to get plane loader. " + e.getMessage());
e.printStackTrace();
return;
@@ -86,12 +86,12 @@ public class Benchmark extends BenchmarkBase {
final int[] absDifferenceData = Utils.asAbsoluteValues(diffArray);
final String diffFilePath = getFileNamePathIntoOutDir(String.format(DIFFERENCE_FILE_TEMPLATE,
- options.getInputDataInfo().getPlaneIndex(),
- codebookSize));
+ options.getInputDataInfo().getPlaneIndex(),
+ codebookSize));
final String absDiffFilePath = getFileNamePathIntoOutDir(String.format(ABSOLUTE_DIFFERENCE_FILE_TEMPLATE,
- options.getInputDataInfo().getPlaneIndex(),
- codebookSize));
+ options.getInputDataInfo().getPlaneIndex(),
+ codebookSize));
try {
// NOTE(Moravec): Use little endian so that gnuplot can read the array.
@@ -100,7 +100,7 @@ public class Benchmark extends BenchmarkBase {
RawDataIO.writeDataI32(diffFilePath, diffArray, true);
System.out.println("Saved difference to: " + absDiffFilePath);
- } catch (IOException e) {
+ } catch (final IOException e) {
System.err.println("Failed to save difference.");
e.printStackTrace();
}
diff --git a/src/main/java/azgracompress/benchmark/BenchmarkBase.java b/src/main/java/cz/it4i/qcmp/benchmark/BenchmarkBase.java
similarity index 84%
rename from src/main/java/azgracompress/benchmark/BenchmarkBase.java
rename to src/main/java/cz/it4i/qcmp/benchmark/BenchmarkBase.java
index 43c1e2f..2e7cf83 100644
--- a/src/main/java/azgracompress/benchmark/BenchmarkBase.java
+++ b/src/main/java/cz/it4i/qcmp/benchmark/BenchmarkBase.java
@@ -1,13 +1,13 @@
-package azgracompress.benchmark;
+package cz.it4i.qcmp.benchmark;
-import azgracompress.compression.CompressionOptions;
-import azgracompress.io.InputData;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.data.ImageU16;
-import azgracompress.data.V3i;
-import azgracompress.io.RawDataIO;
-import azgracompress.quantization.QTrainIteration;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.compression.CompressionOptions;
+import cz.it4i.qcmp.data.ImageU16;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.io.RawDataIO;
+import cz.it4i.qcmp.quantization.QTrainIteration;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.File;
import java.io.FileOutputStream;
@@ -118,12 +118,12 @@ abstract class BenchmarkBase {
* @return True if file was saved.
*/
protected boolean saveQuantizedPlaneData(final int[] data, final String filename) {
- ImageU16 img = new ImageU16(rawImageDims.getX(), rawImageDims.getY(), data);
+ final ImageU16 img = new ImageU16(rawImageDims.getX(), rawImageDims.getY(), data);
try {
// NOTE(Moravec): Use big endian so that FIJI can read the image.
RawDataIO.writeImageU16(getFileNamePathIntoOutDir(filename), img, false);
System.out.println(String.format("Saved %s", filename));
- } catch (Exception e) {
+ } catch (final Exception e) {
e.printStackTrace();
return false;
}
@@ -146,9 +146,9 @@ abstract class BenchmarkBase {
final String diffFilePath = getFileNamePathIntoOutDir(diffFile);
final String absDiffFilePath = getFileNamePathIntoOutDir(absDiffFile);
- ImageU16 img = new ImageU16(rawImageDims.getX(),
- rawImageDims.getY(),
- absDifferenceData);
+ final ImageU16 img = new ImageU16(rawImageDims.getX(),
+ rawImageDims.getY(),
+ absDifferenceData);
try {
// NOTE(Moravec): Use little endian so that gnuplot can read the array.
RawDataIO.writeImageU16(absDiffFilePath, img, true);
@@ -156,7 +156,7 @@ abstract class BenchmarkBase {
RawDataIO.writeDataI32(diffFilePath, differenceData, true);
System.out.println("Saved difference to: " + absDiffFilePath);
- } catch (Exception e) {
+ } catch (final Exception e) {
e.printStackTrace();
System.err.println("Failed to save difference.");
return false;
@@ -174,21 +174,21 @@ abstract class BenchmarkBase {
protected void saveQTrainLog(final String filename, final QTrainIteration[] trainingLog) {
final String CSV_HEADER = "It;MSE;PSNR\n";
try {
- FileOutputStream fileStream = new FileOutputStream(getFileNamePathIntoOutDir(filename));
- OutputStreamWriter writer = new OutputStreamWriter(fileStream);
+ final FileOutputStream fileStream = new FileOutputStream(getFileNamePathIntoOutDir(filename));
+ final OutputStreamWriter writer = new OutputStreamWriter(fileStream);
writer.write(CSV_HEADER);
for (final QTrainIteration it : trainingLog) {
writer.write(String.format("%d;%.5f;%.5f\n",
- it.getIteration(),
- it.getMse(),
- it.getPSNR()));
+ it.getIteration(),
+ it.getMse(),
+ it.getPSNR()));
}
writer.flush();
fileStream.flush();
fileStream.close();
- } catch (IOException ioE) {
+ } catch (final IOException ioE) {
ioE.printStackTrace();
System.err.println("Failed to save QTtrain log.");
}
diff --git a/src/main/java/cz/it4i/qcmp/benchmark/CompressionBenchmark.java b/src/main/java/cz/it4i/qcmp/benchmark/CompressionBenchmark.java
new file mode 100644
index 0000000..5370c35
--- /dev/null
+++ b/src/main/java/cz/it4i/qcmp/benchmark/CompressionBenchmark.java
@@ -0,0 +1,28 @@
+package cz.it4i.qcmp.benchmark;
+
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+
+public class CompressionBenchmark {
+ public static void runBenchmark(final CompressionOptionsCLIParser options) {
+ final Benchmark benchmark = new Benchmark(options);
+ benchmark.startBenchmark();
+ // switch (options.getQuantizationType()) {
+ // case Scalar: {
+ // SQBenchmark sqBenchmark = new SQBenchmark(options);
+ // sqBenchmark.startBenchmark();
+ // }
+ // break;
+ // case Vector1D:
+ // case Vector2D: {
+ // VQBenchmark vqBenchmark = new VQBenchmark(options);
+ // vqBenchmark.startBenchmark(options.getVectorDimension());
+ // }
+ // break;
+ // case Vector3D:
+ // case Invalid: {
+ // System.err.println("Unsupported benchmark type.");
+ // }
+ // break;
+ // }
+ }
+}
diff --git a/src/main/java/azgracompress/benchmark/SQBenchmark.java b/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
similarity index 76%
rename from src/main/java/azgracompress/benchmark/SQBenchmark.java
rename to src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
index f423cc5..a90c39d 100644
--- a/src/main/java/azgracompress/benchmark/SQBenchmark.java
+++ b/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
@@ -1,16 +1,16 @@
-package azgracompress.benchmark;
-
-import azgracompress.U16;
-import azgracompress.cache.QuantizationCacheManager;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.compression.CompressionOptions;
-import azgracompress.io.loader.IPlaneLoader;
-import azgracompress.io.loader.PlaneLoaderFactory;
-import azgracompress.quantization.QTrainIteration;
-import azgracompress.quantization.scalar.LloydMaxU16ScalarQuantization;
-import azgracompress.quantization.scalar.SQCodebook;
-import azgracompress.quantization.scalar.ScalarQuantizer;
-import azgracompress.utilities.Utils;
+package cz.it4i.qcmp.benchmark;
+
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.cache.QuantizationCacheManager;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.compression.CompressionOptions;
+import cz.it4i.qcmp.io.loader.IPlaneLoader;
+import cz.it4i.qcmp.io.loader.PlaneLoaderFactory;
+import cz.it4i.qcmp.quantization.QTrainIteration;
+import cz.it4i.qcmp.quantization.scalar.LloydMaxU16ScalarQuantization;
+import cz.it4i.qcmp.quantization.scalar.SQCodebook;
+import cz.it4i.qcmp.quantization.scalar.ScalarQuantizer;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.File;
import java.io.FileOutputStream;
@@ -25,10 +25,10 @@ public class SQBenchmark extends BenchmarkBase {
@Override
public void startBenchmark() {
- IPlaneLoader planeLoader;
+ final IPlaneLoader planeLoader;
try {
planeLoader = PlaneLoaderFactory.getPlaneLoaderForInputFile(options.getInputDataInfo());
- } catch (Exception e) {
+ } catch (final Exception e) {
e.printStackTrace();
System.err.println("Unable to create SCIFIO reader.");
return;
@@ -37,13 +37,13 @@ public class SQBenchmark extends BenchmarkBase {
if (planes.length < 1) {
return;
}
- boolean dirCreated = new File(this.outputDirectory).mkdirs();
+ final boolean dirCreated = new File(this.outputDirectory).mkdirs();
System.out.println(String.format("|CODEBOOK| = %d", codebookSize));
ScalarQuantizer quantizer = null;
if (options.getCodebookType() == CompressionOptions.CodebookType.Global) {
System.out.println("Loading codebook from cache");
- QuantizationCacheManager cacheManager = new QuantizationCacheManager(cacheFolder);
+ final QuantizationCacheManager cacheManager = new QuantizationCacheManager(cacheFolder);
final SQCodebook codebook = cacheManager.loadSQCodebook(inputFile, codebookSize);
if (codebook == null) {
@@ -59,7 +59,7 @@ public class SQBenchmark extends BenchmarkBase {
final int[] middlePlaneData;
try {
middlePlaneData = planeLoader.loadPlaneData(middlePlaneIndex);
- } catch (IOException e) {
+ } catch (final IOException e) {
e.printStackTrace();
System.err.println("Failed to load middle plane data.");
return;
@@ -74,7 +74,7 @@ public class SQBenchmark extends BenchmarkBase {
final int[] planeData;
try {
planeData = planeLoader.loadPlaneData(planeIndex);
- } catch (IOException e) {
+ } catch (final IOException e) {
e.printStackTrace();
System.err.println("Failed to load plane data.");
return;
@@ -87,8 +87,8 @@ public class SQBenchmark extends BenchmarkBase {
final String quantizedFile = String.format(QUANTIZED_FILE_TEMPLATE, planeIndex, codebookSize);
final String diffFile = String.format(DIFFERENCE_FILE_TEMPLATE, planeIndex, codebookSize);
final String absoluteDiffFile = String.format(ABSOLUTE_DIFFERENCE_FILE_TEMPLATE,
- planeIndex,
- codebookSize);
+ planeIndex,
+ codebookSize);
final String trainLogFile = String.format(TRAIN_FILE_TEMPLATE, planeIndex, codebookSize);
if (options.getCodebookType() == CompressionOptions.CodebookType.Individual) {
@@ -121,10 +121,10 @@ public class SQBenchmark extends BenchmarkBase {
private void saveCentroids(final int[] centroids, final String centroidsFile) {
final String outFile = getFileNamePathIntoOutDir(centroidsFile);
try {
- FileOutputStream fileStream = new FileOutputStream(outFile);
- OutputStreamWriter writer = new OutputStreamWriter(fileStream);
+ final FileOutputStream fileStream = new FileOutputStream(outFile);
+ final OutputStreamWriter writer = new OutputStreamWriter(fileStream);
- StringBuilder sb = new StringBuilder();
+ final StringBuilder sb = new StringBuilder();
for (final int entry : centroids) {
@@ -137,7 +137,7 @@ public class SQBenchmark extends BenchmarkBase {
writer.flush();
fileStream.flush();
fileStream.close();
- } catch (IOException ioE) {
+ } catch (final IOException ioE) {
ioE.printStackTrace();
System.err.println("Failed to save codebook vectors.");
}
@@ -146,8 +146,8 @@ public class SQBenchmark extends BenchmarkBase {
private ScalarQuantizer trainLloydMaxQuantizer(final int[] data,
final int codebookSize,
final String trainLogFile) {
- LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(data, codebookSize, workerCount);
- QTrainIteration[] trainingReport = lloydMax.train();
+ final LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(data, codebookSize, workerCount);
+ final QTrainIteration[] trainingReport = lloydMax.train();
if (trainLogFile != null) {
saveQTrainLog(trainLogFile, trainingReport);
System.out.println("Saved the train log file to: " + trainLogFile);
diff --git a/src/main/java/azgracompress/benchmark/VQBenchmark.java b/src/main/java/cz/it4i/qcmp/benchmark/VQBenchmark.java
similarity index 95%
rename from src/main/java/azgracompress/benchmark/VQBenchmark.java
rename to src/main/java/cz/it4i/qcmp/benchmark/VQBenchmark.java
index 5c9257c..33e0a36 100644
--- a/src/main/java/azgracompress/benchmark/VQBenchmark.java
+++ b/src/main/java/cz/it4i/qcmp/benchmark/VQBenchmark.java
@@ -1,10 +1,10 @@
-package azgracompress.benchmark;
+package cz.it4i.qcmp.benchmark;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.data.Block;
-import azgracompress.data.ImageU16;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.data.Block;
+import cz.it4i.qcmp.data.ImageU16;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
public class VQBenchmark extends BenchmarkBase {
@@ -19,7 +19,7 @@ public class VQBenchmark extends BenchmarkBase {
private ImageU16 reconstructImageFromQuantizedVectors(final int[][] vectors,
final V2i qVector) {
- Block reconstructedChunk = new Block(new V2i(rawImageDims.getX(), rawImageDims.getY()));
+ final Block reconstructedChunk = new Block(new V2i(rawImageDims.getX(), rawImageDims.getY()));
if (qVector.getY() > 1) {
reconstructedChunk.reconstructFrom2DVectors(vectors, qVector);
} else {
diff --git a/src/main/java/azgracompress/cache/CacheFileHeader.java b/src/main/java/cz/it4i/qcmp/cache/CacheFileHeader.java
similarity index 97%
rename from src/main/java/azgracompress/cache/CacheFileHeader.java
rename to src/main/java/cz/it4i/qcmp/cache/CacheFileHeader.java
index d55ef41..888c0c2 100644
--- a/src/main/java/azgracompress/cache/CacheFileHeader.java
+++ b/src/main/java/cz/it4i/qcmp/cache/CacheFileHeader.java
@@ -1,9 +1,9 @@
-package azgracompress.cache;
+package cz.it4i.qcmp.cache;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/cache/ICacheFile.java b/src/main/java/cz/it4i/qcmp/cache/ICacheFile.java
similarity index 94%
rename from src/main/java/azgracompress/cache/ICacheFile.java
rename to src/main/java/cz/it4i/qcmp/cache/ICacheFile.java
index e1e5191..88a441f 100644
--- a/src/main/java/azgracompress/cache/ICacheFile.java
+++ b/src/main/java/cz/it4i/qcmp/cache/ICacheFile.java
@@ -1,4 +1,4 @@
-package azgracompress.cache;
+package cz.it4i.qcmp.cache;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/cache/QuantizationCacheManager.java b/src/main/java/cz/it4i/qcmp/cache/QuantizationCacheManager.java
similarity index 98%
rename from src/main/java/azgracompress/cache/QuantizationCacheManager.java
rename to src/main/java/cz/it4i/qcmp/cache/QuantizationCacheManager.java
index 0224eb7..52c6fee 100644
--- a/src/main/java/azgracompress/cache/QuantizationCacheManager.java
+++ b/src/main/java/cz/it4i/qcmp/cache/QuantizationCacheManager.java
@@ -1,10 +1,10 @@
-package azgracompress.cache;
+package cz.it4i.qcmp.cache;
-import azgracompress.compression.CompressionOptions;
-import azgracompress.data.V3i;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.quantization.scalar.SQCodebook;
-import azgracompress.quantization.vector.VQCodebook;
+import cz.it4i.qcmp.compression.CompressionOptions;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.quantization.scalar.SQCodebook;
+import cz.it4i.qcmp.quantization.vector.VQCodebook;
import java.io.*;
import java.util.ArrayList;
diff --git a/src/main/java/azgracompress/cache/SQCacheFile.java b/src/main/java/cz/it4i/qcmp/cache/SQCacheFile.java
similarity index 96%
rename from src/main/java/azgracompress/cache/SQCacheFile.java
rename to src/main/java/cz/it4i/qcmp/cache/SQCacheFile.java
index 99b78c3..5277bba 100644
--- a/src/main/java/azgracompress/cache/SQCacheFile.java
+++ b/src/main/java/cz/it4i/qcmp/cache/SQCacheFile.java
@@ -1,6 +1,6 @@
-package azgracompress.cache;
+package cz.it4i.qcmp.cache;
-import azgracompress.quantization.scalar.SQCodebook;
+import cz.it4i.qcmp.quantization.scalar.SQCodebook;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/cache/VQCacheFile.java b/src/main/java/cz/it4i/qcmp/cache/VQCacheFile.java
similarity index 97%
rename from src/main/java/azgracompress/cache/VQCacheFile.java
rename to src/main/java/cz/it4i/qcmp/cache/VQCacheFile.java
index feb842f..de10952 100644
--- a/src/main/java/azgracompress/cache/VQCacheFile.java
+++ b/src/main/java/cz/it4i/qcmp/cache/VQCacheFile.java
@@ -1,6 +1,6 @@
-package azgracompress.cache;
+package cz.it4i.qcmp.cache;
-import azgracompress.quantization.vector.VQCodebook;
+import cz.it4i.qcmp.quantization.vector.VQCodebook;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/cli/CliConstants.java b/src/main/java/cz/it4i/qcmp/cli/CliConstants.java
similarity index 98%
rename from src/main/java/azgracompress/cli/CliConstants.java
rename to src/main/java/cz/it4i/qcmp/cli/CliConstants.java
index 586737b..9d32749 100644
--- a/src/main/java/azgracompress/cli/CliConstants.java
+++ b/src/main/java/cz/it4i/qcmp/cli/CliConstants.java
@@ -1,4 +1,4 @@
-package azgracompress.cli;
+package cz.it4i.qcmp.cli;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionGroup;
@@ -7,7 +7,7 @@ import org.jetbrains.annotations.NotNull;
public class CliConstants {
- public static final String MAIN_HELP = "azgracompress.DataCompressor [options] input";
+ public static final String MAIN_HELP = "DataCompressor [options] input";
public static final String HELP_SHORT = "h";
public static final String HELP_LONG = "help";
diff --git a/src/main/java/azgracompress/cli/CompressionOptionsCLIParser.java b/src/main/java/cz/it4i/qcmp/cli/CompressionOptionsCLIParser.java
similarity index 91%
rename from src/main/java/azgracompress/cli/CompressionOptionsCLIParser.java
rename to src/main/java/cz/it4i/qcmp/cli/CompressionOptionsCLIParser.java
index 9737e72..c36aef2 100644
--- a/src/main/java/azgracompress/cli/CompressionOptionsCLIParser.java
+++ b/src/main/java/cz/it4i/qcmp/cli/CompressionOptionsCLIParser.java
@@ -1,15 +1,15 @@
-package azgracompress.cli;
-
-import azgracompress.ScifioWrapper;
-import azgracompress.compression.CompressionOptions;
-import azgracompress.compression.CompressorDecompressorBase;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.fileformat.FileExtensions;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.io.FileInputData;
-import azgracompress.io.InputData;
+package cz.it4i.qcmp.cli;
+
+import cz.it4i.qcmp.ScifioWrapper;
+import cz.it4i.qcmp.compression.CompressionOptions;
+import cz.it4i.qcmp.compression.CompressorDecompressorBase;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.fileformat.FileExtensions;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.io.InputData;
import io.scif.FormatException;
import io.scif.Plane;
import io.scif.Reader;
@@ -44,7 +44,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
*
* @param cmdInput Command line arguments.
*/
- public CompressionOptionsCLIParser(CommandLine cmdInput) {
+ public CompressionOptionsCLIParser(final CommandLine cmdInput) {
parseCLI(cmdInput);
}
@@ -110,7 +110,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param cmd Provided command line arguments.
*/
private void parseCLI(final CommandLine cmd) {
- StringBuilder errorBuilder = new StringBuilder("Errors:\n");
+ final StringBuilder errorBuilder = new StringBuilder("Errors:\n");
parseErrorOccurred = false;
parseProgramMethod(cmd, errorBuilder);
@@ -140,7 +140,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
if (cmd.hasOption(CliConstants.WORKER_COUNT_LONG)) {
final String wcString = cmd.getOptionValue(CliConstants.WORKER_COUNT_LONG);
- Optional<Integer> pr = ParseUtils.tryParseInt(wcString);
+ final Optional<Integer> pr = ParseUtils.tryParseInt(wcString);
if (pr.isPresent()) {
setWorkerCount(pr.get());
} else {
@@ -170,7 +170,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param inputFileArguments Input file info strings.
*/
- private void parseInputFilePart(StringBuilder errorBuilder, final String[] inputFileArguments) {
+ private void parseInputFilePart(final StringBuilder errorBuilder, final String[] inputFileArguments) {
if (inputFileArguments.length < 1) {
parseErrorOccurred = true;
@@ -203,12 +203,12 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
}
- private void parseSCIFIOFileArguments(StringBuilder errorBuilder, final String[] inputFileArguments) {
+ private void parseSCIFIOFileArguments(final StringBuilder errorBuilder, final String[] inputFileArguments) {
getInputDataInfo().setDataLoaderType(InputData.DataLoaderType.SCIFIOLoader);
- Reader reader;
+ final Reader reader;
try {
reader = ScifioWrapper.getReader(getInputDataInfo().getFilePath());
- } catch (IOException | FormatException e) {
+ } catch (final IOException | FormatException e) {
parseErrorOccurred = true;
errorBuilder.append("Failed to get SCIFIO reader for file.\n");
errorBuilder.append(e.getMessage());
@@ -228,9 +228,10 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
errorBuilder.append("Too many planes.\n");
}
- long planeWidth, planeHeight;
+ final long planeWidth;
+ final long planeHeight;
try {
- Plane plane = reader.openPlane(0, 0);
+ final Plane plane = reader.openPlane(0, 0);
planeWidth = plane.getLengths()[0];
planeHeight = plane.getLengths()[1];
@@ -243,7 +244,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
}
- } catch (FormatException | IOException e) {
+ } catch (final FormatException | IOException e) {
parseErrorOccurred = true;
errorBuilder.append("Unable to open first plane of the first image.\n")
.append(e.getMessage());
@@ -261,7 +262,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
}
}
- private void parseRawFileArguments(StringBuilder errorBuilder, String[] inputFileArguments) {
+ private void parseRawFileArguments(final StringBuilder errorBuilder, final String[] inputFileArguments) {
// We require the file path and dimensions, like input.raw 1920x1080x5
// First argument is input file name.
if (inputFileArguments.length < 2) {
@@ -296,13 +297,13 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param inputFileArguments Input file arguments.
* @param inputFileArgumentsOffset Offset of the plane argument.
*/
- private void parseInputFilePlaneOptions(StringBuilder errorBuilder,
+ private void parseInputFilePlaneOptions(final StringBuilder errorBuilder,
final String[] inputFileArguments,
final int inputFileArgumentsOffset) {
- int rangeSeparatorIndex = inputFileArguments[inputFileArgumentsOffset].indexOf("-");
+ final int rangeSeparatorIndex = inputFileArguments[inputFileArgumentsOffset].indexOf("-");
if (rangeSeparatorIndex != -1) {
- Optional<Range<Integer>> parsedRange =
+ final Optional<Range<Integer>> parsedRange =
ParseUtils.tryParseRange(inputFileArguments[inputFileArgumentsOffset], '-');
if (!parsedRange.isPresent()) {
@@ -332,7 +333,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param cmd Command line arguments.
* @param errorBuilder String error builder.
*/
- private void parseBitsPerPixel(CommandLine cmd, StringBuilder errorBuilder) {
+ private void parseBitsPerPixel(final CommandLine cmd, final StringBuilder errorBuilder) {
if (cmd.hasOption(CliConstants.BITS_LONG)) {
final String bitsString = cmd.getOptionValue(CliConstants.BITS_LONG);
final Optional<Integer> parseResult = ParseUtils.tryParseInt(bitsString);
@@ -365,7 +366,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param cmd Command line arguments.
* @param errorBuilder String error builder.
*/
- private void parseCompressionType(CommandLine cmd, StringBuilder errorBuilder) {
+ private void parseCompressionType(final CommandLine cmd, final StringBuilder errorBuilder) {
if (hasQuantizationType(method)) {
if (cmd.hasOption(CliConstants.SCALAR_QUANTIZATION_LONG)) {
setQuantizationType(QuantizationType.Scalar);
@@ -418,7 +419,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
* @param cmd Command line arguments.
* @param errorBuilder String error builder.
*/
- private void parseProgramMethod(CommandLine cmd, StringBuilder errorBuilder) {
+ private void parseProgramMethod(final CommandLine cmd, final StringBuilder errorBuilder) {
if (cmd.hasOption(CliConstants.HELP_LONG)) {
method = ProgramMethod.PrintHelp;
} else if (cmd.hasOption(CliConstants.COMPRESS_LONG)) {
@@ -453,7 +454,7 @@ public class CompressionOptionsCLIParser extends CompressionOptions implements C
}
public String report() {
- StringBuilder sb = new StringBuilder();
+ final StringBuilder sb = new StringBuilder();
sb.append("Method: ");
switch (method) {
diff --git a/src/main/java/azgracompress/cli/CustomFunctionBase.java b/src/main/java/cz/it4i/qcmp/cli/CustomFunctionBase.java
similarity index 76%
rename from src/main/java/azgracompress/cli/CustomFunctionBase.java
rename to src/main/java/cz/it4i/qcmp/cli/CustomFunctionBase.java
index 8af8992..e5f143b 100644
--- a/src/main/java/azgracompress/cli/CustomFunctionBase.java
+++ b/src/main/java/cz/it4i/qcmp/cli/CustomFunctionBase.java
@@ -1,18 +1,20 @@
-package azgracompress.cli;
+package cz.it4i.qcmp.cli;
public abstract class CustomFunctionBase {
protected final CompressionOptionsCLIParser options;
/**
* Base constructor with parsed CLI options.
+ *
* @param options Parsed cli options.
*/
- public CustomFunctionBase(CompressionOptionsCLIParser options) {
+ public CustomFunctionBase(final CompressionOptionsCLIParser options) {
this.options = options;
}
/**
* Run custom function.
+ *
* @return True if no errors occurred.
*/
public abstract boolean run();
diff --git a/src/main/java/azgracompress/cli/ParseUtils.java b/src/main/java/cz/it4i/qcmp/cli/ParseUtils.java
similarity index 94%
rename from src/main/java/azgracompress/cli/ParseUtils.java
rename to src/main/java/cz/it4i/qcmp/cli/ParseUtils.java
index 7ebf967..5aa279b 100644
--- a/src/main/java/azgracompress/cli/ParseUtils.java
+++ b/src/main/java/cz/it4i/qcmp/cli/ParseUtils.java
@@ -1,8 +1,8 @@
-package azgracompress.cli;
+package cz.it4i.qcmp.cli;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
import java.util.Optional;
@@ -21,7 +21,7 @@ public abstract class ParseUtils {
public static Optional<Integer> tryParseInt(final String string) {
try {
return Optional.of(Integer.parseInt(string));
- } catch (NumberFormatException ignored) {
+ } catch (final NumberFormatException ignored) {
return Optional.empty();
}
}
diff --git a/src/main/java/azgracompress/cli/ProgramMethod.java b/src/main/java/cz/it4i/qcmp/cli/ProgramMethod.java
similarity index 84%
rename from src/main/java/azgracompress/cli/ProgramMethod.java
rename to src/main/java/cz/it4i/qcmp/cli/ProgramMethod.java
index ba97c0f..73d3abd 100644
--- a/src/main/java/azgracompress/cli/ProgramMethod.java
+++ b/src/main/java/cz/it4i/qcmp/cli/ProgramMethod.java
@@ -1,4 +1,4 @@
-package azgracompress.cli;
+package cz.it4i.qcmp.cli;
public enum ProgramMethod {
Compress,
diff --git a/src/main/java/azgracompress/cli/functions/EntropyCalculation.java b/src/main/java/cz/it4i/qcmp/cli/functions/EntropyCalculation.java
similarity index 70%
rename from src/main/java/azgracompress/cli/functions/EntropyCalculation.java
rename to src/main/java/cz/it4i/qcmp/cli/functions/EntropyCalculation.java
index 1110002..d99e1b3 100644
--- a/src/main/java/azgracompress/cli/functions/EntropyCalculation.java
+++ b/src/main/java/cz/it4i/qcmp/cli/functions/EntropyCalculation.java
@@ -1,10 +1,10 @@
-package azgracompress.cli.functions;
+package cz.it4i.qcmp.cli.functions;
-import azgracompress.cli.CustomFunctionBase;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.io.loader.IPlaneLoader;
-import azgracompress.io.loader.PlaneLoaderFactory;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.cli.CustomFunctionBase;
+import cz.it4i.qcmp.io.loader.IPlaneLoader;
+import cz.it4i.qcmp.io.loader.PlaneLoaderFactory;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.IOException;
@@ -14,16 +14,16 @@ public class EntropyCalculation extends CustomFunctionBase {
*
* @param options Parsed cli options.
*/
- public EntropyCalculation(CompressionOptionsCLIParser options) {
+ public EntropyCalculation(final CompressionOptionsCLIParser options) {
super(options);
}
@Override
public boolean run() {
- IPlaneLoader loader;
+ final IPlaneLoader loader;
try {
loader = PlaneLoaderFactory.getPlaneLoaderForInputFile(options.getInputDataInfo());
- } catch (Exception ex) {
+ } catch (final Exception ex) {
System.err.println("EntropyCalculation::run() - Unable to get plane loader. " + ex.getMessage());
return false;
}
@@ -32,7 +32,7 @@ public class EntropyCalculation extends CustomFunctionBase {
final int[] planeData;
try {
planeData = loader.loadPlaneData(planeIndex);
- } catch (IOException e) {
+ } catch (final IOException e) {
System.err.printf("Failed to load plane %d data. %s", planeIndex, e.getMessage());
return false;
}
diff --git a/src/main/java/azgracompress/cli/functions/MeasurePlaneErrorFunction.java b/src/main/java/cz/it4i/qcmp/cli/functions/MeasurePlaneErrorFunction.java
similarity index 90%
rename from src/main/java/azgracompress/cli/functions/MeasurePlaneErrorFunction.java
rename to src/main/java/cz/it4i/qcmp/cli/functions/MeasurePlaneErrorFunction.java
index 161bc15..17fee7f 100644
--- a/src/main/java/azgracompress/cli/functions/MeasurePlaneErrorFunction.java
+++ b/src/main/java/cz/it4i/qcmp/cli/functions/MeasurePlaneErrorFunction.java
@@ -1,11 +1,11 @@
-package azgracompress.cli.functions;
+package cz.it4i.qcmp.cli.functions;
-import azgracompress.cli.CustomFunctionBase;
-import azgracompress.cli.CompressionOptionsCLIParser;
-import azgracompress.data.V3i;
-import azgracompress.io.FileInputData;
-import azgracompress.io.loader.RawDataLoader;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.cli.CompressionOptionsCLIParser;
+import cz.it4i.qcmp.cli.CustomFunctionBase;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.io.loader.RawDataLoader;
+import cz.it4i.qcmp.utilities.Utils;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -13,7 +13,7 @@ import java.io.OutputStreamWriter;
import java.util.Arrays;
public class MeasurePlaneErrorFunction extends CustomFunctionBase {
- public MeasurePlaneErrorFunction(CompressionOptionsCLIParser options) {
+ public MeasurePlaneErrorFunction(final CompressionOptionsCLIParser options) {
super(options);
}
@@ -122,17 +122,17 @@ public class MeasurePlaneErrorFunction extends CustomFunctionBase {
final V3i dims = new V3i(1041, 996, 946);
final int planePixelCount = dims.getX() * dims.getY();
- PlaneError[] planeErrors = new PlaneError[dims.getZ()];
+ final PlaneError[] planeErrors = new PlaneError[dims.getZ()];
- FileInputData refFileInfo = new FileInputData(compFile);
+ final FileInputData refFileInfo = new FileInputData(compFile);
refFileInfo.setDimension(dims);
- FileInputData compFileInfo = new FileInputData(compressedFile);
+ final FileInputData compFileInfo = new FileInputData(compressedFile);
compFileInfo.setDimension(dims);
final RawDataLoader refPlaneloader = new RawDataLoader(refFileInfo);
final RawDataLoader compPlaneloader = new RawDataLoader(compFileInfo);
- Thread[] workers = new Thread[workerCount];
+ final Thread[] workers = new Thread[workerCount];
final int workSize = dims.getZ() / workerCount;
for (int wId = 0; wId < workerCount; wId++) {
@@ -147,7 +147,7 @@ public class MeasurePlaneErrorFunction extends CustomFunctionBase {
try {
originalPlaneData = refPlaneloader.loadPlaneData(planeIndex);
compressedPlaneData = compPlaneloader.loadPlaneData(planeIndex);
- } catch (IOException e) {
+ } catch (final IOException e) {
e.printStackTrace();
break;
}
@@ -169,12 +169,12 @@ public class MeasurePlaneErrorFunction extends CustomFunctionBase {
for (int wId = 0; wId < workerCount; wId++) {
workers[wId].join();
}
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
e.printStackTrace();
}
- try (FileOutputStream fos = new FileOutputStream(reportFile, false);
- OutputStreamWriter writer = new OutputStreamWriter(fos)) {
+ try (final FileOutputStream fos = new FileOutputStream(reportFile, false);
+ final OutputStreamWriter writer = new OutputStreamWriter(fos)) {
writer.write("PlaneIndex\tErrorSum\tMeanError\n");
@@ -185,7 +185,7 @@ public class MeasurePlaneErrorFunction extends CustomFunctionBase {
planeError.getMeanAbsoluteError()));
}
- } catch (IOException e) {
+ } catch (final IOException e) {
e.printStackTrace();
}
System.out.println("Finished reportPlaneDifference");
diff --git a/src/main/java/azgracompress/cli/functions/PlaneError.java b/src/main/java/cz/it4i/qcmp/cli/functions/PlaneError.java
similarity index 78%
rename from src/main/java/azgracompress/cli/functions/PlaneError.java
rename to src/main/java/cz/it4i/qcmp/cli/functions/PlaneError.java
index 6b858bf..45031c9 100644
--- a/src/main/java/azgracompress/cli/functions/PlaneError.java
+++ b/src/main/java/cz/it4i/qcmp/cli/functions/PlaneError.java
@@ -1,11 +1,11 @@
-package azgracompress.cli.functions;
+package cz.it4i.qcmp.cli.functions;
public class PlaneError {
private final int planeIndex;
private final double absoluteError;
private final double meanAbsoluteError;
- public PlaneError(int planeIndex, double absoluteError, double meanAbsoluteError) {
+ public PlaneError(final int planeIndex, final double absoluteError, final double meanAbsoluteError) {
this.planeIndex = planeIndex;
this.absoluteError = absoluteError;
this.meanAbsoluteError = meanAbsoluteError;
diff --git a/src/main/java/azgracompress/compression/CompressionOptions.java b/src/main/java/cz/it4i/qcmp/compression/CompressionOptions.java
similarity index 95%
rename from src/main/java/azgracompress/compression/CompressionOptions.java
rename to src/main/java/cz/it4i/qcmp/compression/CompressionOptions.java
index e32af40..e974e6a 100644
--- a/src/main/java/azgracompress/compression/CompressionOptions.java
+++ b/src/main/java/cz/it4i/qcmp/compression/CompressionOptions.java
@@ -1,9 +1,9 @@
-package azgracompress.compression;
+package cz.it4i.qcmp.compression;
-import azgracompress.cache.ICacheFile;
-import azgracompress.data.V3i;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.io.InputData;
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.io.InputData;
/**
* Options for the compressor/decompressor.
diff --git a/src/main/java/azgracompress/compression/CompressorDecompressorBase.java b/src/main/java/cz/it4i/qcmp/compression/CompressorDecompressorBase.java
similarity index 94%
rename from src/main/java/azgracompress/compression/CompressorDecompressorBase.java
rename to src/main/java/cz/it4i/qcmp/compression/CompressorDecompressorBase.java
index 469f7b3..2df7a95 100644
--- a/src/main/java/azgracompress/compression/CompressorDecompressorBase.java
+++ b/src/main/java/cz/it4i/qcmp/compression/CompressorDecompressorBase.java
@@ -1,11 +1,11 @@
-package azgracompress.compression;
-
-import azgracompress.compression.exception.ImageCompressionException;
-import azgracompress.compression.listeners.IProgressListener;
-import azgracompress.compression.listeners.IStatusListener;
-import azgracompress.huffman.Huffman;
-import azgracompress.io.InputData;
-import azgracompress.io.OutBitStream;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.compression.listeners.IProgressListener;
+import cz.it4i.qcmp.compression.listeners.IStatusListener;
+import cz.it4i.qcmp.huffman.Huffman;
+import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.io.OutBitStream;
import java.io.DataOutputStream;
import java.util.ArrayList;
diff --git a/src/main/java/azgracompress/compression/IImageCompressor.java b/src/main/java/cz/it4i/qcmp/compression/IImageCompressor.java
similarity index 87%
rename from src/main/java/azgracompress/compression/IImageCompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/IImageCompressor.java
index a7610fa..8d8ae98 100644
--- a/src/main/java/azgracompress/compression/IImageCompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/IImageCompressor.java
@@ -1,9 +1,8 @@
-package azgracompress.compression;
+package cz.it4i.qcmp.compression;
-import azgracompress.cache.ICacheFile;
-import azgracompress.compression.exception.ImageCompressionException;
-import azgracompress.data.V3i;
-import azgracompress.io.InputData;
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.io.InputData;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/compression/IImageDecompressor.java b/src/main/java/cz/it4i/qcmp/compression/IImageDecompressor.java
similarity index 90%
rename from src/main/java/azgracompress/compression/IImageDecompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/IImageDecompressor.java
index 8037521..175d9e5 100644
--- a/src/main/java/azgracompress/compression/IImageDecompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/IImageDecompressor.java
@@ -1,8 +1,8 @@
-package azgracompress.compression;
+package cz.it4i.qcmp.compression;
-import azgracompress.cache.ICacheFile;
-import azgracompress.compression.exception.ImageDecompressionException;
-import azgracompress.fileformat.QCMPFileHeader;
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.compression.exception.ImageDecompressionException;
+import cz.it4i.qcmp.fileformat.QCMPFileHeader;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/compression/IListenable.java b/src/main/java/cz/it4i/qcmp/compression/IListenable.java
similarity index 77%
rename from src/main/java/azgracompress/compression/IListenable.java
rename to src/main/java/cz/it4i/qcmp/compression/IListenable.java
index 6a1f066..72b6661 100644
--- a/src/main/java/azgracompress/compression/IListenable.java
+++ b/src/main/java/cz/it4i/qcmp/compression/IListenable.java
@@ -1,7 +1,7 @@
-package azgracompress.compression;
+package cz.it4i.qcmp.compression;
-import azgracompress.compression.listeners.IProgressListener;
-import azgracompress.compression.listeners.IStatusListener;
+import cz.it4i.qcmp.compression.listeners.IProgressListener;
+import cz.it4i.qcmp.compression.listeners.IStatusListener;
public interface IListenable {
/**
diff --git a/src/main/java/azgracompress/compression/ImageCompressor.java b/src/main/java/cz/it4i/qcmp/compression/ImageCompressor.java
similarity index 96%
rename from src/main/java/azgracompress/compression/ImageCompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/ImageCompressor.java
index 2e0d000..23f5792 100644
--- a/src/main/java/azgracompress/compression/ImageCompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/ImageCompressor.java
@@ -1,11 +1,11 @@
-package azgracompress.compression;
-
-import azgracompress.U16;
-import azgracompress.cache.ICacheFile;
-import azgracompress.compression.exception.ImageCompressionException;
-import azgracompress.data.Range;
-import azgracompress.fileformat.QCMPFileHeader;
-import azgracompress.io.InputData;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.fileformat.QCMPFileHeader;
+import cz.it4i.qcmp.io.InputData;
import java.io.*;
import java.util.Arrays;
diff --git a/src/main/java/azgracompress/compression/ImageDecompressor.java b/src/main/java/cz/it4i/qcmp/compression/ImageDecompressor.java
similarity index 83%
rename from src/main/java/azgracompress/compression/ImageDecompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/ImageDecompressor.java
index b8ab49d..23503fa 100644
--- a/src/main/java/azgracompress/compression/ImageDecompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/ImageDecompressor.java
@@ -1,16 +1,15 @@
-package azgracompress.compression;
-
-import azgracompress.cache.ICacheFile;
-import azgracompress.compression.exception.ImageDecompressionException;
-import azgracompress.data.ImageU16Dataset;
-import azgracompress.fileformat.QCMPFileHeader;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.Utils;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.compression.exception.ImageDecompressionException;
+import cz.it4i.qcmp.data.ImageU16Dataset;
+import cz.it4i.qcmp.fileformat.QCMPFileHeader;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.Utils;
import org.jetbrains.annotations.Nullable;
import java.io.*;
-import java.util.Arrays;
import java.util.Optional;
@@ -44,8 +43,8 @@ public class ImageDecompressor extends CompressorDecompressorBase {
* @return Decompressed file header.
* @throws IOException when failed to read header.
*/
- private QCMPFileHeader readQCMPFileHeader(DataInputStream inputStream) throws IOException {
- QCMPFileHeader header = new QCMPFileHeader();
+ private QCMPFileHeader readQCMPFileHeader(final DataInputStream inputStream) throws IOException {
+ final QCMPFileHeader header = new QCMPFileHeader();
if (!header.readHeader(inputStream)) {
// Invalid QCMPFile header.
return null;
@@ -59,7 +58,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
* @return Correct implementation of image decompressor.
*/
private IImageDecompressor getImageDecompressor(final QuantizationType quantizationType) {
- IImageDecompressor decompressor;
+ final IImageDecompressor decompressor;
switch (quantizationType) {
case Scalar:
decompressor = new SQImageDecompressor(options);
@@ -90,14 +89,14 @@ public class ImageDecompressor extends CompressorDecompressorBase {
* @throws IOException When fails to read the header.
*/
public String inspectCompressedFile() throws IOException {
- StringBuilder logBuilder = new StringBuilder();
+ final StringBuilder logBuilder = new StringBuilder();
boolean validFile = true;
- QCMPFileHeader header;
- try (FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
- DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
+ final QCMPFileHeader header;
+ try (final FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
+ final DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
header = readQCMPFileHeader(dataInputStream);
- } catch (IOException ioEx) {
+ } catch (final IOException ioEx) {
ioEx.printStackTrace();
return "";
}
@@ -199,8 +198,8 @@ public class ImageDecompressor extends CompressorDecompressorBase {
public boolean decompressToFile() {
final Stopwatch decompressionStopwatch = Stopwatch.startNew();
final long decompressedFileSize;
- try (FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
- DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
+ try (final FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
+ final DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
final QCMPFileHeader header = decompressQcmpHeader(dataInputStream);
if (header == null)
@@ -218,17 +217,17 @@ public class ImageDecompressor extends CompressorDecompressorBase {
return false;
}
- try (FileOutputStream fos = new FileOutputStream(options.getOutputFilePath(), false);
- DataOutputStream decompressStream = new DataOutputStream(fos)) {
+ try (final FileOutputStream fos = new FileOutputStream(options.getOutputFilePath(), false);
+ final DataOutputStream decompressStream = new DataOutputStream(fos)) {
imageDecompressor.decompress(dataInputStream, decompressStream, header);
- } catch (ImageDecompressionException ex) {
+ } catch (final ImageDecompressionException ex) {
System.err.println(ex.getMessage());
return false;
}
- } catch (IOException ioEx) {
+ } catch (final IOException ioEx) {
ioEx.printStackTrace();
return false;
}
@@ -241,7 +240,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
return true;
}
- private boolean checkInputFileSize(QCMPFileHeader header, IImageDecompressor imageDecompressor) {
+ private boolean checkInputFileSize(final QCMPFileHeader header, final IImageDecompressor imageDecompressor) {
final long fileSize = new File(options.getInputDataInfo().getFilePath()).length();
final long dataSize = fileSize - header.getHeaderSize();
final long expectedDataSize = imageDecompressor.getExpectedDataSize(header);
@@ -253,14 +252,14 @@ public class ImageDecompressor extends CompressorDecompressorBase {
}
public Optional<ImageU16Dataset> decompressInMemory() {
- try (FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
- DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
+ try (final FileInputStream fileInputStream = new FileInputStream(options.getInputDataInfo().getFilePath());
+ final DataInputStream dataInputStream = new DataInputStream(fileInputStream)) {
final QCMPFileHeader header = decompressQcmpHeader(dataInputStream);
if (header == null)
return Optional.empty();
- IImageDecompressor imageDecompressor = getImageDecompressor(header.getQuantizationType());
+ final IImageDecompressor imageDecompressor = getImageDecompressor(header.getQuantizationType());
if (imageDecompressor == null) {
System.err.println("Unable to create correct decompressor.");
return Optional.empty();
@@ -276,14 +275,14 @@ public class ImageDecompressor extends CompressorDecompressorBase {
try {
imageDecompressor.decompressToBuffer(dataInputStream, decompressedData, header);
- } catch (ImageDecompressionException ex) {
+ } catch (final ImageDecompressionException ex) {
System.err.println(ex.getMessage());
return Optional.empty();
}
return Optional.of(new ImageU16Dataset(header.getImageDims().toV2i(), header.getImageSizeZ(), decompressedData));
- } catch (IOException ioEx) {
+ } catch (final IOException ioEx) {
ioEx.printStackTrace();
return Optional.empty();
}
@@ -291,7 +290,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
public short[] decompressStream(final InputStream compressedStream, final int contentLength) throws ImageDecompressionException {
- try (DataInputStream dis = new DataInputStream(new BufferedInputStream(compressedStream))) {
+ try (final DataInputStream dis = new DataInputStream(new BufferedInputStream(compressedStream))) {
assert (dis.markSupported());
final QCMPFileHeader header = cachedHeader.copyOf();
@@ -309,7 +308,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
{
int toSkip = contentLength - ((4 * 2) + (chunkCount * 2));
while (toSkip > 0) {
- int skipped = dis.skipBytes(toSkip);
+ final int skipped = dis.skipBytes(toSkip);
assert (skipped > 0);
toSkip -= skipped;
}
@@ -325,13 +324,13 @@ public class ImageDecompressor extends CompressorDecompressorBase {
return cachedDecompressor.decompressStreamMode(dis, header);
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageDecompressionException("Unable to decompress chunk of image from stream.", e);
}
}
@Nullable
- private QCMPFileHeader decompressQcmpHeader(DataInputStream dataInputStream) throws IOException {
+ private QCMPFileHeader decompressQcmpHeader(final DataInputStream dataInputStream) throws IOException {
final QCMPFileHeader header = readQCMPFileHeader(dataInputStream);
if (header == null) {
System.err.println("Failed to read QCMPFile header");
diff --git a/src/main/java/azgracompress/compression/SQImageCompressor.java b/src/main/java/cz/it4i/qcmp/compression/SQImageCompressor.java
similarity index 79%
rename from src/main/java/azgracompress/compression/SQImageCompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/SQImageCompressor.java
index 31fd8d6..22a8dd9 100644
--- a/src/main/java/azgracompress/compression/SQImageCompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/SQImageCompressor.java
@@ -1,19 +1,18 @@
-package azgracompress.compression;
-
-import azgracompress.U16;
-import azgracompress.cache.ICacheFile;
-import azgracompress.cache.QuantizationCacheManager;
-import azgracompress.cache.SQCacheFile;
-import azgracompress.compression.exception.ImageCompressionException;
-import azgracompress.data.V3i;
-import azgracompress.huffman.Huffman;
-import azgracompress.io.InputData;
-import azgracompress.io.loader.IPlaneLoader;
-import azgracompress.io.loader.PlaneLoaderFactory;
-import azgracompress.quantization.scalar.LloydMaxU16ScalarQuantization;
-import azgracompress.quantization.scalar.SQCodebook;
-import azgracompress.quantization.scalar.ScalarQuantizer;
-import azgracompress.utilities.Stopwatch;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.cache.QuantizationCacheManager;
+import cz.it4i.qcmp.cache.SQCacheFile;
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.huffman.Huffman;
+import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.io.loader.IPlaneLoader;
+import cz.it4i.qcmp.io.loader.PlaneLoaderFactory;
+import cz.it4i.qcmp.quantization.scalar.LloydMaxU16ScalarQuantization;
+import cz.it4i.qcmp.quantization.scalar.SQCodebook;
+import cz.it4i.qcmp.quantization.scalar.ScalarQuantizer;
+import cz.it4i.qcmp.utilities.Stopwatch;
import java.io.DataOutputStream;
import java.io.IOException;
@@ -23,7 +22,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
private ScalarQuantizer cachedQuantizer;
private Huffman cachedHuffman;
- public SQImageCompressor(CompressionOptions options) {
+ public SQImageCompressor(final CompressionOptions options) {
super(options);
}
@@ -35,15 +34,15 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
*/
private ScalarQuantizer trainScalarQuantizerFromData(final int[] planeData) {
- LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(planeData,
- getCodebookSize(),
- options.getWorkerCount());
+ final LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(planeData,
+ getCodebookSize(),
+ options.getWorkerCount());
lloydMax.train();
return new ScalarQuantizer(U16.Min, U16.Max, lloydMax.getCodebook());
}
@Override
- public void preloadGlobalCodebook(ICacheFile codebookCacheFile) {
+ public void preloadGlobalCodebook(final ICacheFile codebookCacheFile) {
final SQCodebook cachedCodebook = ((SQCacheFile) codebookCacheFile).getCodebook();
cachedQuantizer = new ScalarQuantizer(cachedCodebook);
cachedHuffman = createHuffmanCoder(createHuffmanSymbols(cachedCodebook.getCodebookSize()), cachedCodebook.getSymbolFrequencies());
@@ -57,7 +56,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
* @throws ImageCompressionException when writing to the stream fails.
*/
private void writeCodebookToOutputStream(final ScalarQuantizer quantizer,
- DataOutputStream compressStream) throws ImageCompressionException {
+ final DataOutputStream compressStream) throws ImageCompressionException {
final SQCodebook codebook = quantizer.getCodebook();
final int[] centroids = codebook.getCentroids();
final long[] frequencies = codebook.getSymbolFrequencies();
@@ -68,7 +67,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
for (final long symbolFrequency : frequencies) {
compressStream.writeLong(symbolFrequency);
}
- } catch (IOException ioEx) {
+ } catch (final IOException ioEx) {
throw new ImageCompressionException("Unable to write codebook to compress stream.", ioEx);
}
if (options.isVerbose()) {
@@ -83,7 +82,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
* @throws ImageCompressionException when fails to read cached codebook.
*/
private ScalarQuantizer loadQuantizerFromCache() throws ImageCompressionException {
- QuantizationCacheManager cacheManager = new QuantizationCacheManager(options.getCodebookCacheFolder());
+ final QuantizationCacheManager cacheManager = new QuantizationCacheManager(options.getCodebookCacheFolder());
if (!cacheManager.doesSQCacheExists(options.getInputDataInfo().getCacheFileName(), getCodebookSize())) {
trainAndSaveCodebook();
@@ -104,15 +103,15 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
* @throws ImageCompressionException When compress process fails.
*/
@Override
- public long[] compress(DataOutputStream compressStream) throws ImageCompressionException {
+ public long[] compress(final DataOutputStream compressStream) throws ImageCompressionException {
final InputData inputDataInfo = options.getInputDataInfo();
- Stopwatch stopwatch = new Stopwatch();
+ final Stopwatch stopwatch = new Stopwatch();
final boolean hasGeneralQuantizer = options.getCodebookType() != CompressionOptions.CodebookType.Individual;
final IPlaneLoader planeLoader;
try {
planeLoader = PlaneLoaderFactory.getPlaneLoaderForInputFile(inputDataInfo);
- } catch (Exception e) {
+ } catch (final Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
@@ -129,11 +128,11 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
writeCodebookToOutputStream(quantizer, compressStream);
} else if (options.getCodebookType() == CompressionOptions.CodebookType.MiddlePlane) {
stopwatch.restart();
- int[] middlePlaneData;
+ final int[] middlePlaneData;
final int middlePlaneIndex = getMiddlePlaneIndex();
try {
middlePlaneData = planeLoader.loadPlaneData(middlePlaneIndex);
- } catch (IOException ex) {
+ } catch (final IOException ex) {
throw new ImageCompressionException("Unable to load middle plane data.", ex);
}
@@ -147,15 +146,15 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
}
final int[] planeIndices = getPlaneIndicesForCompression(options.getInputDataInfo());
- long[] planeDataSizes = new long[planeIndices.length];
+ final long[] planeDataSizes = new long[planeIndices.length];
int planeCounter = 0;
for (final int planeIndex : planeIndices) {
stopwatch.restart();
- int[] planeData;
+ final int[] planeData;
try {
planeData = planeLoader.loadPlaneData(planeIndex);
- } catch (IOException ex) {
+ } catch (final IOException ex) {
throw new ImageCompressionException("Unable to load plane data.", ex);
}
@@ -187,7 +186,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
final IPlaneLoader planeLoader;
try {
planeLoader = PlaneLoaderFactory.getPlaneLoaderForInputFile(inputDataInfo);
- } catch (Exception e) {
+ } catch (final Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
int[] trainData = null;
@@ -196,7 +195,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
try {
reportStatusToListeners("Loading single plane data.");
trainData = planeLoader.loadPlaneData(inputDataInfo.getPlaneIndex());
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageCompressionException("Failed to load plane data.", e);
}
} else if (inputDataInfo.isPlaneRangeSet()) {
@@ -204,7 +203,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
final int[] planes = getPlaneIndicesForCompression(options.getInputDataInfo());
try {
trainData = planeLoader.loadPlanesU16Data(planes);
- } catch (IOException e) {
+ } catch (final IOException e) {
e.printStackTrace();
throw new ImageCompressionException("Failed to load plane range data.", e);
}
@@ -212,7 +211,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
reportStatusToListeners("Loading all planes data.");
try {
trainData = planeLoader.loadAllPlanesU16Data();
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageCompressionException("Failed to load all planes data.", e);
}
}
@@ -221,11 +220,11 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
@Override
public void trainAndSaveCodebook() throws ImageCompressionException {
- int[] trainData = loadConfiguredPlanesData();
+ final int[] trainData = loadConfiguredPlanesData();
- LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(trainData,
- getCodebookSize(),
- options.getWorkerCount());
+ final LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(trainData,
+ getCodebookSize(),
+ options.getWorkerCount());
reportStatusToListeners("Starting LloydMax training.");
lloydMax.setStatusListener(this::reportStatusToListeners);
@@ -233,18 +232,18 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
final SQCodebook codebook = lloydMax.getCodebook();
reportStatusToListeners("Finished LloydMax training.");
- QuantizationCacheManager cacheManager = new QuantizationCacheManager(options.getCodebookCacheFolder());
+ final QuantizationCacheManager cacheManager = new QuantizationCacheManager(options.getCodebookCacheFolder());
try {
final String cacheFilePath = cacheManager.saveCodebook(options.getInputDataInfo().getCacheFileName(), codebook);
reportStatusToListeners(String.format("Saved cache file to %s", cacheFilePath));
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageCompressionException("Unable to write cache.", e);
}
reportStatusToListeners("Operation completed.");
}
@Override
- public long[] compressStreamChunk(DataOutputStream compressStream, InputData inputData) throws ImageCompressionException {
+ public long[] compressStreamChunk(final DataOutputStream compressStream, final InputData inputData) throws ImageCompressionException {
throw new ImageCompressionException("Not implemented yet");
}
}
diff --git a/src/main/java/azgracompress/compression/SQImageDecompressor.java b/src/main/java/cz/it4i/qcmp/compression/SQImageDecompressor.java
similarity index 74%
rename from src/main/java/azgracompress/compression/SQImageDecompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/SQImageDecompressor.java
index 49ae127..66f8d3a 100644
--- a/src/main/java/azgracompress/compression/SQImageDecompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/SQImageDecompressor.java
@@ -1,16 +1,15 @@
-package azgracompress.compression;
-
-import azgracompress.cache.ICacheFile;
-import azgracompress.cache.SQCacheFile;
-import azgracompress.cache.VQCacheFile;
-import azgracompress.compression.exception.ImageDecompressionException;
-import azgracompress.fileformat.QCMPFileHeader;
-import azgracompress.huffman.Huffman;
-import azgracompress.huffman.HuffmanNode;
-import azgracompress.io.InBitStream;
-import azgracompress.quantization.scalar.SQCodebook;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.TypeConverter;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.cache.SQCacheFile;
+import cz.it4i.qcmp.compression.exception.ImageDecompressionException;
+import cz.it4i.qcmp.fileformat.QCMPFileHeader;
+import cz.it4i.qcmp.huffman.Huffman;
+import cz.it4i.qcmp.huffman.HuffmanNode;
+import cz.it4i.qcmp.io.InBitStream;
+import cz.it4i.qcmp.quantization.scalar.SQCodebook;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.TypeConverter;
import java.io.DataInputStream;
import java.io.DataOutputStream;
@@ -20,14 +19,14 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
private SQCodebook cachedCodebook = null;
private Huffman cachedHuffman = null;
- public SQImageDecompressor(CompressionOptions options) {
+ public SQImageDecompressor(final CompressionOptions options) {
super(options);
}
- private SQCodebook readScalarQuantizationValues(DataInputStream compressedStream,
+ private SQCodebook readScalarQuantizationValues(final DataInputStream compressedStream,
final int codebookSize) throws ImageDecompressionException {
- int[] quantizationValues = new int[codebookSize];
- long[] symbolFrequencies = new long[codebookSize];
+ final int[] quantizationValues = new int[codebookSize];
+ final long[] symbolFrequencies = new long[codebookSize];
try {
for (int i = 0; i < codebookSize; i++) {
quantizationValues[i] = compressedStream.readUnsignedShort();
@@ -35,23 +34,23 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
for (int i = 0; i < codebookSize; i++) {
symbolFrequencies[i] = compressedStream.readLong();
}
- } catch (IOException ioEx) {
+ } catch (final IOException ioEx) {
throw new ImageDecompressionException("Unable to read quantization values from compressed stream.", ioEx);
}
return new SQCodebook(quantizationValues, symbolFrequencies);
}
@Override
- public long getExpectedDataSize(QCMPFileHeader header) {
+ public long getExpectedDataSize(final QCMPFileHeader header) {
// Quantization value count.
final int codebookSize = (int) Math.pow(2, header.getBitsPerCodebookIndex());
// Total codebook size in bytes. Also symbol frequencies for Huffman.
- long codebookDataSize = ((2 * codebookSize) + (LONG_BYTES * codebookSize)) *
+ final long codebookDataSize = ((2 * codebookSize) + (LONG_BYTES * codebookSize)) *
(header.isCodebookPerPlane() ? header.getImageSizeZ() : 1);
// Indices are encoded using huffman. Plane data size is written in the header.
- long[] planeDataSizes = header.getPlaneDataSizes();
+ final long[] planeDataSizes = header.getPlaneDataSizes();
long totalPlaneDataSize = 0;
for (final long planeDataSize : planeDataSizes) {
totalPlaneDataSize += planeDataSize;
@@ -61,9 +60,9 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
}
@Override
- public void decompress(DataInputStream compressedStream,
- DataOutputStream decompressStream,
- QCMPFileHeader header) throws ImageDecompressionException {
+ public void decompress(final DataInputStream compressedStream,
+ final DataOutputStream decompressStream,
+ final QCMPFileHeader header) throws ImageDecompressionException {
final int codebookSize = (int) Math.pow(2, header.getBitsPerCodebookIndex());
final int[] huffmanSymbols = createHuffmanSymbols(codebookSize);
@@ -80,7 +79,7 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
huffman = createHuffmanCoder(huffmanSymbols, codebook.getSymbolFrequencies());
}
- Stopwatch stopwatch = new Stopwatch();
+ final Stopwatch stopwatch = new Stopwatch();
for (int planeIndex = 0; planeIndex < planeCountForDecompression; planeIndex++) {
stopwatch.restart();
if (header.isCodebookPerPlane()) {
@@ -93,13 +92,13 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
reportStatusToListeners(String.format("Decompressing plane %d...", planeIndex));
byte[] decompressedPlaneData = null;
final int planeDataSize = (int) header.getPlaneDataSizes()[planeIndex];
- try (InBitStream inBitStream = new InBitStream(compressedStream,
- header.getBitsPerCodebookIndex(),
- planeDataSize)) {
+ try (final InBitStream inBitStream = new InBitStream(compressedStream,
+ header.getBitsPerCodebookIndex(),
+ planeDataSize)) {
inBitStream.readToBuffer();
inBitStream.setAllowReadFromUnderlyingStream(false);
- int[] decompressedValues = new int[planePixelCount];
+ final int[] decompressedValues = new int[planePixelCount];
final int[] quantizationValues = codebook.getCentroids();
for (int pixel = 0; pixel < planePixelCount; pixel++) {
HuffmanNode currentHuffmanNode = huffman.getRoot();
@@ -115,12 +114,12 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
TypeConverter.unsignedShortArrayToByteArray(decompressedValues, false);
- } catch (Exception ex) {
+ } catch (final Exception ex) {
throw new ImageDecompressionException("SQImageDecompressor::decompress() - Unable to read indices from InBitStream.", ex);
}
try {
decompressStream.write(decompressedPlaneData);
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageDecompressionException("Unable to write decompressed data to decompress stream.", e);
}
@@ -133,16 +132,16 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
public void preloadGlobalCodebook(final ICacheFile codebookCacheFile) {
assert (codebookCacheFile instanceof SQCacheFile) : "Incorrect codebook cache file type for SQImageDecompressor";
- SQCacheFile codebookCache = (SQCacheFile) codebookCacheFile;
+ final SQCacheFile codebookCache = (SQCacheFile) codebookCacheFile;
cachedCodebook = codebookCache.getCodebook();
cachedHuffman = createHuffmanCoder(createHuffmanSymbols(cachedCodebook.getCodebookSize()), cachedCodebook.getSymbolFrequencies());
}
@Override
- public void decompressToBuffer(DataInputStream compressedStream,
- short[][] buffer,
- QCMPFileHeader header) throws ImageDecompressionException {
+ public void decompressToBuffer(final DataInputStream compressedStream,
+ final short[][] buffer,
+ final QCMPFileHeader header) throws ImageDecompressionException {
final int codebookSize = (int) Math.pow(2, header.getBitsPerCodebookIndex());
final int[] huffmanSymbols = createHuffmanSymbols(codebookSize);
final int planeCountForDecompression = header.getImageSizeZ();
@@ -166,11 +165,11 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
assert (codebook != null && huffman != null);
final int planeDataSize = (int) header.getPlaneDataSizes()[planeIndex];
- try (InBitStream inBitStream = new InBitStream(compressedStream, header.getBitsPerCodebookIndex(), planeDataSize)) {
+ try (final InBitStream inBitStream = new InBitStream(compressedStream, header.getBitsPerCodebookIndex(), planeDataSize)) {
inBitStream.readToBuffer();
inBitStream.setAllowReadFromUnderlyingStream(false);
- int[] decompressedValues = new int[planePixelCount];
+ final int[] decompressedValues = new int[planePixelCount];
final int[] quantizationValues = codebook.getCentroids();
for (int pixel = 0; pixel < planePixelCount; pixel++) {
HuffmanNode currentHuffmanNode = huffman.getRoot();
@@ -183,7 +182,7 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
}
buffer[planeIndex] = TypeConverter.intArrayToShortArray(decompressedValues);
- } catch (Exception ex) {
+ } catch (final Exception ex) {
throw new ImageDecompressionException("SQImageDecompressor::decompressToBuffer() - Unable to read indices from " +
"InBitStream.",
ex);
@@ -192,7 +191,7 @@ public class SQImageDecompressor extends CompressorDecompressorBase implements I
}
@Override
- public short[] decompressStreamMode(DataInputStream compressedStream, QCMPFileHeader header) throws ImageDecompressionException {
+ public short[] decompressStreamMode(final DataInputStream compressedStream, final QCMPFileHeader header) throws ImageDecompressionException {
throw new ImageDecompressionException("Not implemented yet.");
}
}
diff --git a/src/main/java/azgracompress/compression/VQImageCompressor.java b/src/main/java/cz/it4i/qcmp/compression/VQImageCompressor.java
similarity index 95%
rename from src/main/java/azgracompress/compression/VQImageCompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/VQImageCompressor.java
index 4652ee9..2165311 100644
--- a/src/main/java/azgracompress/compression/VQImageCompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/VQImageCompressor.java
@@ -1,21 +1,21 @@
-package azgracompress.compression;
-
-import azgracompress.cache.ICacheFile;
-import azgracompress.cache.QuantizationCacheManager;
-import azgracompress.cache.VQCacheFile;
-import azgracompress.compression.exception.ImageCompressionException;
-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.LBGResult;
-import azgracompress.quantization.vector.LBGVectorQuantizer;
-import azgracompress.quantization.vector.VQCodebook;
-import azgracompress.quantization.vector.VectorQuantizer;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.Utils;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.cache.QuantizationCacheManager;
+import cz.it4i.qcmp.cache.VQCacheFile;
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.huffman.Huffman;
+import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.io.loader.IPlaneLoader;
+import cz.it4i.qcmp.io.loader.PlaneLoaderFactory;
+import cz.it4i.qcmp.quantization.vector.LBGResult;
+import cz.it4i.qcmp.quantization.vector.LBGVectorQuantizer;
+import cz.it4i.qcmp.quantization.vector.VQCodebook;
+import cz.it4i.qcmp.quantization.vector.VectorQuantizer;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.Utils;
import org.jetbrains.annotations.NotNull;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/compression/VQImageDecompressor.java b/src/main/java/cz/it4i/qcmp/compression/VQImageDecompressor.java
similarity index 97%
rename from src/main/java/azgracompress/compression/VQImageDecompressor.java
rename to src/main/java/cz/it4i/qcmp/compression/VQImageDecompressor.java
index 323b82c..31920ff 100644
--- a/src/main/java/azgracompress/compression/VQImageDecompressor.java
+++ b/src/main/java/cz/it4i/qcmp/compression/VQImageDecompressor.java
@@ -1,17 +1,17 @@
-package azgracompress.compression;
-
-import azgracompress.cache.ICacheFile;
-import azgracompress.cache.VQCacheFile;
-import azgracompress.compression.exception.ImageDecompressionException;
-import azgracompress.data.*;
-import azgracompress.fileformat.QCMPFileHeader;
-import azgracompress.fileformat.QuantizationType;
-import azgracompress.huffman.Huffman;
-import azgracompress.huffman.HuffmanNode;
-import azgracompress.io.InBitStream;
-import azgracompress.quantization.vector.VQCodebook;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.TypeConverter;
+package cz.it4i.qcmp.compression;
+
+import cz.it4i.qcmp.cache.ICacheFile;
+import cz.it4i.qcmp.cache.VQCacheFile;
+import cz.it4i.qcmp.compression.exception.ImageDecompressionException;
+import cz.it4i.qcmp.data.*;
+import cz.it4i.qcmp.fileformat.QCMPFileHeader;
+import cz.it4i.qcmp.fileformat.QuantizationType;
+import cz.it4i.qcmp.huffman.Huffman;
+import cz.it4i.qcmp.huffman.HuffmanNode;
+import cz.it4i.qcmp.io.InBitStream;
+import cz.it4i.qcmp.quantization.vector.VQCodebook;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.TypeConverter;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/compression/exception/ImageCompressionException.java b/src/main/java/cz/it4i/qcmp/compression/exception/ImageCompressionException.java
similarity index 93%
rename from src/main/java/azgracompress/compression/exception/ImageCompressionException.java
rename to src/main/java/cz/it4i/qcmp/compression/exception/ImageCompressionException.java
index 6ccb78f..65c7e0a 100644
--- a/src/main/java/azgracompress/compression/exception/ImageCompressionException.java
+++ b/src/main/java/cz/it4i/qcmp/compression/exception/ImageCompressionException.java
@@ -1,4 +1,4 @@
-package azgracompress.compression.exception;
+package cz.it4i.qcmp.compression.exception;
public class ImageCompressionException extends Exception {
private final Exception innerException;
diff --git a/src/main/java/azgracompress/compression/exception/ImageDecompressionException.java b/src/main/java/cz/it4i/qcmp/compression/exception/ImageDecompressionException.java
similarity index 93%
rename from src/main/java/azgracompress/compression/exception/ImageDecompressionException.java
rename to src/main/java/cz/it4i/qcmp/compression/exception/ImageDecompressionException.java
index 4ddeaa3..6093386 100644
--- a/src/main/java/azgracompress/compression/exception/ImageDecompressionException.java
+++ b/src/main/java/cz/it4i/qcmp/compression/exception/ImageDecompressionException.java
@@ -1,4 +1,4 @@
-package azgracompress.compression.exception;
+package cz.it4i.qcmp.compression.exception;
public class ImageDecompressionException extends Exception {
private final Exception innerException;
diff --git a/src/main/java/azgracompress/compression/listeners/IProgressListener.java b/src/main/java/cz/it4i/qcmp/compression/listeners/IProgressListener.java
similarity index 73%
rename from src/main/java/azgracompress/compression/listeners/IProgressListener.java
rename to src/main/java/cz/it4i/qcmp/compression/listeners/IProgressListener.java
index 3c9c688..c3fcca5 100644
--- a/src/main/java/azgracompress/compression/listeners/IProgressListener.java
+++ b/src/main/java/cz/it4i/qcmp/compression/listeners/IProgressListener.java
@@ -1,4 +1,4 @@
-package azgracompress.compression.listeners;
+package cz.it4i.qcmp.compression.listeners;
public interface IProgressListener {
void sendProgress(final String message, final int index, final int finalIndex);
diff --git a/src/main/java/azgracompress/compression/listeners/IStatusListener.java b/src/main/java/cz/it4i/qcmp/compression/listeners/IStatusListener.java
similarity index 64%
rename from src/main/java/azgracompress/compression/listeners/IStatusListener.java
rename to src/main/java/cz/it4i/qcmp/compression/listeners/IStatusListener.java
index bd549e4..e28370f 100644
--- a/src/main/java/azgracompress/compression/listeners/IStatusListener.java
+++ b/src/main/java/cz/it4i/qcmp/compression/listeners/IStatusListener.java
@@ -1,4 +1,4 @@
-package azgracompress.compression.listeners;
+package cz.it4i.qcmp.compression.listeners;
public interface IStatusListener {
void sendMessage(final String message);
diff --git a/src/main/java/azgracompress/data/Block.java b/src/main/java/cz/it4i/qcmp/data/Block.java
similarity index 96%
rename from src/main/java/azgracompress/data/Block.java
rename to src/main/java/cz/it4i/qcmp/data/Block.java
index cf4a42f..5165fd0 100644
--- a/src/main/java/azgracompress/data/Block.java
+++ b/src/main/java/cz/it4i/qcmp/data/Block.java
@@ -1,8 +1,8 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public class Block {
private final int FILL_VALUE = 0;
- private int[] data;
+ private final int[] data;
private final V2i dims;
@@ -75,7 +75,7 @@ public class Block {
*
* @param vectors Array of 1D row vectors.
*/
- public void reconstructFromVectors(int[][] vectors) {
+ public void reconstructFromVectors(final int[][] vectors) {
if (vectors.length == 0) {
return;
}
@@ -155,7 +155,7 @@ public class Block {
* @param chunkXOffset Chunk X offset.
* @param chunkYOffset Chunk Y offset.
*/
- private void copyDataFromVector(int[] vector,
+ private void copyDataFromVector(final int[] vector,
final V2i qVectorDims,
final int chunkXOffset,
final int chunkYOffset) {
@@ -182,7 +182,7 @@ public class Block {
* @return True if same.
*/
@Override
- public boolean equals(Object obj) {
+ public boolean equals(final Object obj) {
if (obj instanceof Block) {
final Block otherChunk = (Block) obj;
if (data.length != otherChunk.data.length) {
diff --git a/src/main/java/azgracompress/data/ImageU16.java b/src/main/java/cz/it4i/qcmp/data/ImageU16.java
similarity index 63%
rename from src/main/java/azgracompress/data/ImageU16.java
rename to src/main/java/cz/it4i/qcmp/data/ImageU16.java
index c2787c2..8326f60 100644
--- a/src/main/java/azgracompress/data/ImageU16.java
+++ b/src/main/java/cz/it4i/qcmp/data/ImageU16.java
@@ -1,12 +1,12 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.utilities.Utils;
public class ImageU16 {
private final int width;
private final int height;
- private int[] data;
+ private final int[] data;
public ImageU16(final int width, final int height, final int[] data) {
assert ((width * height) == data.length) : "Wrong data size in ImageU16 constructor.";
@@ -54,20 +54,20 @@ public class ImageU16 {
return height;
}
-// /**
-// * Chunk the image data into quantization vectors of requested dimension.
-// *
-// * @param qVectorDims Quantization vector dimension.
-// * @return Array of quantization vectors.
-// */
-// public int[][] toQuantizationVectors(final V2i qVectorDims) {
-// if (qVectorDims.getY() == 1) {
-// // 1D row vectors.
-// return as2dChunk().divideInto1DVectors(qVectorDims.getX());
-// } else {
-// // 2D matrix vectors.
-// return as2dChunk().divideInto2DVectors(qVectorDims);
-// //return Chunk2D.chunksAsImageVectors(as2dChunk().divideIntoChunks(qVectorDims));
-// }
-// }
+ // /**
+ // * Chunk the image data into quantization vectors of requested dimension.
+ // *
+ // * @param qVectorDims Quantization vector dimension.
+ // * @return Array of quantization vectors.
+ // */
+ // public int[][] toQuantizationVectors(final V2i qVectorDims) {
+ // if (qVectorDims.getY() == 1) {
+ // // 1D row vectors.
+ // return as2dChunk().divideInto1DVectors(qVectorDims.getX());
+ // } else {
+ // // 2D matrix vectors.
+ // return as2dChunk().divideInto2DVectors(qVectorDims);
+ // //return Chunk2D.chunksAsImageVectors(as2dChunk().divideIntoChunks(qVectorDims));
+ // }
+ // }
}
diff --git a/src/main/java/azgracompress/data/ImageU16Dataset.java b/src/main/java/cz/it4i/qcmp/data/ImageU16Dataset.java
similarity index 81%
rename from src/main/java/azgracompress/data/ImageU16Dataset.java
rename to src/main/java/cz/it4i/qcmp/data/ImageU16Dataset.java
index 0e4d42c..da3cb46 100644
--- a/src/main/java/azgracompress/data/ImageU16Dataset.java
+++ b/src/main/java/cz/it4i/qcmp/data/ImageU16Dataset.java
@@ -1,11 +1,11 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public class ImageU16Dataset {
private final V2i planeDimensions;
private final int planeCount;
private final short[][] data;
- public ImageU16Dataset(V2i planeDimensions, int planeCount, short[][] planeData) {
+ public ImageU16Dataset(final V2i planeDimensions, final int planeCount, final short[][] planeData) {
this.planeDimensions = planeDimensions;
this.planeCount = planeCount;
this.data = planeData;
diff --git a/src/main/java/azgracompress/data/Range.java b/src/main/java/cz/it4i/qcmp/data/Range.java
similarity index 92%
rename from src/main/java/azgracompress/data/Range.java
rename to src/main/java/cz/it4i/qcmp/data/Range.java
index a30f7a8..c309cd4 100644
--- a/src/main/java/azgracompress/data/Range.java
+++ b/src/main/java/cz/it4i/qcmp/data/Range.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public final class Range<T extends Comparable<T>> {
/**
@@ -17,7 +17,7 @@ public final class Range<T extends Comparable<T>> {
* @param from Start of the interval,
* @param to Inclusive end of the interval.
*/
- public Range(T from, T to) {
+ public Range(final T from, final T to) {
this.from = from;
this.to = to;
}
diff --git a/src/main/java/azgracompress/data/V2.java b/src/main/java/cz/it4i/qcmp/data/V2.java
similarity index 95%
rename from src/main/java/azgracompress/data/V2.java
rename to src/main/java/cz/it4i/qcmp/data/V2.java
index b8968af..50dd462 100644
--- a/src/main/java/azgracompress/data/V2.java
+++ b/src/main/java/cz/it4i/qcmp/data/V2.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
/**
* Template for vector with two values.
@@ -71,7 +71,7 @@ public class V2<T> {
* @return True if both objects are equal.
*/
@Override
- public boolean equals(Object obj) {
+ public boolean equals(final Object obj) {
if (obj instanceof V2<?>) {
final V2<?> other = (V2<?>) obj;
return ((x == other.x) && (y == other.y));
diff --git a/src/main/java/azgracompress/data/V2i.java b/src/main/java/cz/it4i/qcmp/data/V2i.java
similarity index 95%
rename from src/main/java/azgracompress/data/V2i.java
rename to src/main/java/cz/it4i/qcmp/data/V2i.java
index ee00c8b..aca7fe5 100644
--- a/src/main/java/azgracompress/data/V2i.java
+++ b/src/main/java/cz/it4i/qcmp/data/V2i.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public final class V2i extends V2<Integer> {
public V2i(final int x, final int y) {
diff --git a/src/main/java/azgracompress/data/V3.java b/src/main/java/cz/it4i/qcmp/data/V3.java
similarity index 94%
rename from src/main/java/azgracompress/data/V3.java
rename to src/main/java/cz/it4i/qcmp/data/V3.java
index c9ae9c7..973bd9d 100644
--- a/src/main/java/azgracompress/data/V3.java
+++ b/src/main/java/cz/it4i/qcmp/data/V3.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
/**
* Template for vector with three values.
@@ -49,7 +49,7 @@ public class V3<T> extends V2<T> {
* @return True if both objects are equal.
*/
@Override
- public boolean equals(Object obj) {
+ public boolean equals(final Object obj) {
if (obj instanceof V3<?>) {
final V3<?> other = (V3<?>) obj;
return ((getX() == other.getX()) && (getY() == other.getY()) && (z == other.z));
diff --git a/src/main/java/azgracompress/data/V3i.java b/src/main/java/cz/it4i/qcmp/data/V3i.java
similarity index 97%
rename from src/main/java/azgracompress/data/V3i.java
rename to src/main/java/cz/it4i/qcmp/data/V3i.java
index b8c730e..b757672 100644
--- a/src/main/java/azgracompress/data/V3i.java
+++ b/src/main/java/cz/it4i/qcmp/data/V3i.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public final class V3i extends V3<Integer> {
diff --git a/src/main/java/azgracompress/data/Voxel.java b/src/main/java/cz/it4i/qcmp/data/Voxel.java
similarity index 99%
rename from src/main/java/azgracompress/data/Voxel.java
rename to src/main/java/cz/it4i/qcmp/data/Voxel.java
index 582a065..b41fd31 100644
--- a/src/main/java/azgracompress/data/Voxel.java
+++ b/src/main/java/cz/it4i/qcmp/data/Voxel.java
@@ -1,4 +1,4 @@
-package azgracompress.data;
+package cz.it4i.qcmp.data;
public final class Voxel {
/**
@@ -128,6 +128,7 @@ public final class Voxel {
reconstructFromVoxels(voxelDims, voxelData, reconstructedData, 0);
return new ImageU16Dataset(dims.toV2i(), dims.getZ(), reconstructedData);
}
+
/*
public short[] reconstructFromVoxelsToVoxelArray(final V3i voxelDims, final int[][] voxelData) {
final short[] reconstructedVoxel = new short[(int) dims.multiplyTogether()];
diff --git a/src/main/java/azgracompress/fileformat/FileExtensions.java b/src/main/java/cz/it4i/qcmp/fileformat/FileExtensions.java
similarity index 84%
rename from src/main/java/azgracompress/fileformat/FileExtensions.java
rename to src/main/java/cz/it4i/qcmp/fileformat/FileExtensions.java
index f0f9a6c..cb8675d 100644
--- a/src/main/java/azgracompress/fileformat/FileExtensions.java
+++ b/src/main/java/cz/it4i/qcmp/fileformat/FileExtensions.java
@@ -1,4 +1,4 @@
-package azgracompress.fileformat;
+package cz.it4i.qcmp.fileformat;
public class FileExtensions {
public static final String RAW = "raw";
diff --git a/src/main/java/azgracompress/fileformat/QCMPFileHeader.java b/src/main/java/cz/it4i/qcmp/fileformat/QCMPFileHeader.java
similarity index 98%
rename from src/main/java/azgracompress/fileformat/QCMPFileHeader.java
rename to src/main/java/cz/it4i/qcmp/fileformat/QCMPFileHeader.java
index 7f8ffd7..f613977 100644
--- a/src/main/java/azgracompress/fileformat/QCMPFileHeader.java
+++ b/src/main/java/cz/it4i/qcmp/fileformat/QCMPFileHeader.java
@@ -1,8 +1,8 @@
-package azgracompress.fileformat;
+package cz.it4i.qcmp.fileformat;
-import azgracompress.U16;
-import azgracompress.compression.VQImageCompressor;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.compression.VQImageCompressor;
+import cz.it4i.qcmp.data.V3i;
import java.io.DataInputStream;
import java.io.DataOutputStream;
diff --git a/src/main/java/azgracompress/fileformat/QuantizationType.java b/src/main/java/cz/it4i/qcmp/fileformat/QuantizationType.java
similarity index 90%
rename from src/main/java/azgracompress/fileformat/QuantizationType.java
rename to src/main/java/cz/it4i/qcmp/fileformat/QuantizationType.java
index 649b926..3acce0a 100644
--- a/src/main/java/azgracompress/fileformat/QuantizationType.java
+++ b/src/main/java/cz/it4i/qcmp/fileformat/QuantizationType.java
@@ -1,4 +1,4 @@
-package azgracompress.fileformat;
+package cz.it4i.qcmp.fileformat;
public enum QuantizationType {
Scalar(0),
@@ -9,7 +9,7 @@ public enum QuantizationType {
private final int value;
- QuantizationType(int enumValue) {
+ QuantizationType(final int enumValue) {
value = enumValue;
}
diff --git a/src/main/java/azgracompress/huffman/Huffman.java b/src/main/java/cz/it4i/qcmp/huffman/Huffman.java
similarity index 77%
rename from src/main/java/azgracompress/huffman/Huffman.java
rename to src/main/java/cz/it4i/qcmp/huffman/Huffman.java
index 771efbc..624fbf9 100644
--- a/src/main/java/azgracompress/huffman/Huffman.java
+++ b/src/main/java/cz/it4i/qcmp/huffman/Huffman.java
@@ -1,4 +1,4 @@
-package azgracompress.huffman;
+package cz.it4i.qcmp.huffman;
import java.util.*;
@@ -9,14 +9,14 @@ public class Huffman {
private final int[] symbols;
private final long[] symbolFrequencies;
- public Huffman(int[] symbols, long[] symbolFrequencies) {
+ public Huffman(final int[] symbols, final long[] symbolFrequencies) {
assert (symbols.length == symbolFrequencies.length) : "Array lengths mismatch";
this.symbols = symbols;
this.symbolFrequencies = symbolFrequencies;
}
public void buildHuffmanTree() {
- PriorityQueue<HuffmanNode> queue = buildPriorityQueue();
+ final PriorityQueue<HuffmanNode> queue = buildPriorityQueue();
while (queue.size() != 1) {
@@ -46,7 +46,7 @@ public class Huffman {
traverseSymbolCodes(root, new ArrayList<Boolean>());
}
- private void traverseSymbolCodes(HuffmanNode currentNode, ArrayList<Boolean> currentCode) {
+ private void traverseSymbolCodes(final HuffmanNode currentNode, final ArrayList<Boolean> currentCode) {
boolean inLeaf = true;
final int bit = currentNode.getBit();
if (bit != -1) {
@@ -54,12 +54,12 @@ public class Huffman {
}
if (currentNode.subNodeA != null) {
- ArrayList<Boolean> codeCopy = new ArrayList<Boolean>(currentCode);
+ final ArrayList<Boolean> codeCopy = new ArrayList<Boolean>(currentCode);
traverseSymbolCodes(currentNode.subNodeA, codeCopy);
inLeaf = false;
}
if (currentNode.subNodeB != null) {
- ArrayList<Boolean> codeCopy = new ArrayList<Boolean>(currentCode);
+ final ArrayList<Boolean> codeCopy = new ArrayList<Boolean>(currentCode);
traverseSymbolCodes(currentNode.subNodeB, codeCopy);
inLeaf = false;
}
@@ -68,7 +68,7 @@ public class Huffman {
assert (currentNode.isLeaf());
//currentNode.setIsLeaf(true);
- boolean[] finalSymbolCode = new boolean[currentCode.size()];
+ final boolean[] finalSymbolCode = new boolean[currentCode.size()];
for (int i = 0; i < finalSymbolCode.length; i++) {
finalSymbolCode[i] = currentCode.get(i);
}
@@ -84,7 +84,7 @@ public class Huffman {
totalFrequency += symbolFrequency;
}
- PriorityQueue<HuffmanNode> queue = new PriorityQueue<>(symbols.length);
+ final PriorityQueue<HuffmanNode> queue = new PriorityQueue<>(symbols.length);
for (int sIndex = 0; sIndex < symbols.length; sIndex++) {
final double symbolProbability = (double) symbolFrequencies[sIndex] / totalFrequency;
@@ -108,18 +108,18 @@ public class Huffman {
return createSortedHashMap(symbolProbabilityMap);
}
- private HashMap<Integer, Double> createSortedHashMap(HashMap<Integer, Double> map) {
- List<Map.Entry<Integer, Double>> list = new LinkedList<Map.Entry<Integer, Double>>(map.entrySet());
+ private HashMap<Integer, Double> createSortedHashMap(final HashMap<Integer, Double> map) {
+ final List<Map.Entry<Integer, Double>> list = new LinkedList<Map.Entry<Integer, Double>>(map.entrySet());
//Custom Comparator
list.sort(new Comparator<Map.Entry<Integer, Double>>() {
@Override
- public int compare(Map.Entry<Integer, Double> t0, Map.Entry<Integer, Double> t1) {
+ public int compare(final Map.Entry<Integer, Double> t0, final Map.Entry<Integer, Double> t1) {
return -(t0.getValue().compareTo(t1.getValue()));
}
});
//copying the sorted list in HashMap to preserve the iteration order
- HashMap<Integer,Double> sortedHashMap = new LinkedHashMap<Integer,Double>();
- for (Map.Entry<Integer, Double> entry : list) {
+ final HashMap<Integer, Double> sortedHashMap = new LinkedHashMap<Integer, Double>();
+ for (final Map.Entry<Integer, Double> entry : list) {
sortedHashMap.put(entry.getKey(), entry.getValue());
}
return sortedHashMap;
diff --git a/src/main/java/azgracompress/huffman/HuffmanNode.java b/src/main/java/cz/it4i/qcmp/huffman/HuffmanNode.java
similarity index 87%
rename from src/main/java/azgracompress/huffman/HuffmanNode.java
rename to src/main/java/cz/it4i/qcmp/huffman/HuffmanNode.java
index 4b0ea72..34d16cc 100644
--- a/src/main/java/azgracompress/huffman/HuffmanNode.java
+++ b/src/main/java/cz/it4i/qcmp/huffman/HuffmanNode.java
@@ -1,4 +1,4 @@
-package azgracompress.huffman;
+package cz.it4i.qcmp.huffman;
import org.jetbrains.annotations.NotNull;
@@ -22,7 +22,7 @@ public class HuffmanNode implements Comparable<HuffmanNode> {
this.leaf = true;
}
- public HuffmanNode(final double probability, HuffmanNode parentA, HuffmanNode parentB) {
+ public HuffmanNode(final double probability, final HuffmanNode parentA, final HuffmanNode parentB) {
this.probability = probability;
this.subNodeA = parentA;
this.subNodeB = parentB;
@@ -39,11 +39,11 @@ public class HuffmanNode implements Comparable<HuffmanNode> {
}
@Override
- public int compareTo(@NotNull HuffmanNode otherNode) {
+ public int compareTo(@NotNull final HuffmanNode otherNode) {
return Double.compare(probability, otherNode.probability);
}
- public void setBit(int bit) {
+ public void setBit(final int bit) {
this.bit = bit;
}
diff --git a/src/main/java/azgracompress/io/BufferInputData.java b/src/main/java/cz/it4i/qcmp/io/BufferInputData.java
similarity index 95%
rename from src/main/java/azgracompress/io/BufferInputData.java
rename to src/main/java/cz/it4i/qcmp/io/BufferInputData.java
index f46dd05..3b263a2 100644
--- a/src/main/java/azgracompress/io/BufferInputData.java
+++ b/src/main/java/cz/it4i/qcmp/io/BufferInputData.java
@@ -1,6 +1,6 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.V3i;
/**
* Input data backed by the buffer object.
diff --git a/src/main/java/azgracompress/io/FileInputData.java b/src/main/java/cz/it4i/qcmp/io/FileInputData.java
similarity index 87%
rename from src/main/java/azgracompress/io/FileInputData.java
rename to src/main/java/cz/it4i/qcmp/io/FileInputData.java
index 968fbd6..fccce4c 100644
--- a/src/main/java/azgracompress/io/FileInputData.java
+++ b/src/main/java/cz/it4i/qcmp/io/FileInputData.java
@@ -1,4 +1,4 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
/**
* Input data backed by the file.
@@ -15,7 +15,7 @@ public class FileInputData extends InputData {
*
* @param filePath
*/
- public FileInputData(String filePath) {
+ public FileInputData(final String filePath) {
this.filePath = filePath;
}
diff --git a/src/main/java/azgracompress/io/FlatBufferInputData.java b/src/main/java/cz/it4i/qcmp/io/FlatBufferInputData.java
similarity index 95%
rename from src/main/java/azgracompress/io/FlatBufferInputData.java
rename to src/main/java/cz/it4i/qcmp/io/FlatBufferInputData.java
index 5e5629b..3cad98b 100644
--- a/src/main/java/azgracompress/io/FlatBufferInputData.java
+++ b/src/main/java/cz/it4i/qcmp/io/FlatBufferInputData.java
@@ -1,6 +1,6 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.V3i;
/**
* Input data backed by the single buffer object.
diff --git a/src/main/java/azgracompress/io/InBitStream.java b/src/main/java/cz/it4i/qcmp/io/InBitStream.java
similarity index 99%
rename from src/main/java/azgracompress/io/InBitStream.java
rename to src/main/java/cz/it4i/qcmp/io/InBitStream.java
index 9293c4b..c7c5827 100644
--- a/src/main/java/azgracompress/io/InBitStream.java
+++ b/src/main/java/cz/it4i/qcmp/io/InBitStream.java
@@ -1,4 +1,4 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
import java.io.IOException;
import java.io.InputStream;
diff --git a/src/main/java/azgracompress/io/InputData.java b/src/main/java/cz/it4i/qcmp/io/InputData.java
similarity index 84%
rename from src/main/java/azgracompress/io/InputData.java
rename to src/main/java/cz/it4i/qcmp/io/InputData.java
index 0a384d2..d6a3fe3 100644
--- a/src/main/java/azgracompress/io/InputData.java
+++ b/src/main/java/cz/it4i/qcmp/io/InputData.java
@@ -1,7 +1,7 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
-import azgracompress.data.Range;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V3i;
/**
* Information about the input file.
@@ -67,7 +67,7 @@ public abstract class InputData {
return planeIndex;
}
- public void setPlaneIndex(Integer planeIndex) {
+ public void setPlaneIndex(final Integer planeIndex) {
this.planeIndex = planeIndex;
}
@@ -75,7 +75,7 @@ public abstract class InputData {
return planeRange;
}
- public void setPlaneRange(Range<Integer> planeRange) {
+ public void setPlaneRange(final Range<Integer> planeRange) {
this.planeRange = planeRange;
}
@@ -83,7 +83,7 @@ public abstract class InputData {
return dataLoaderType;
}
- public void setDataLoaderType(DataLoaderType dataLoaderType) {
+ public void setDataLoaderType(final DataLoaderType dataLoaderType) {
this.dataLoaderType = dataLoaderType;
}
@@ -91,7 +91,7 @@ public abstract class InputData {
return pixelType;
}
- public void setPixelType(PixelType pixelType) {
+ public void setPixelType(final PixelType pixelType) {
this.pixelType = pixelType;
}
diff --git a/src/main/java/azgracompress/io/MemoryOutputStream.java b/src/main/java/cz/it4i/qcmp/io/MemoryOutputStream.java
similarity index 93%
rename from src/main/java/azgracompress/io/MemoryOutputStream.java
rename to src/main/java/cz/it4i/qcmp/io/MemoryOutputStream.java
index f23a80c..48309eb 100644
--- a/src/main/java/azgracompress/io/MemoryOutputStream.java
+++ b/src/main/java/cz/it4i/qcmp/io/MemoryOutputStream.java
@@ -1,4 +1,4 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
import java.io.ByteArrayOutputStream;
diff --git a/src/main/java/azgracompress/io/OutBitStream.java b/src/main/java/cz/it4i/qcmp/io/OutBitStream.java
similarity index 92%
rename from src/main/java/azgracompress/io/OutBitStream.java
rename to src/main/java/cz/it4i/qcmp/io/OutBitStream.java
index 2d3b886..344f033 100644
--- a/src/main/java/azgracompress/io/OutBitStream.java
+++ b/src/main/java/cz/it4i/qcmp/io/OutBitStream.java
@@ -1,12 +1,12 @@
-package azgracompress.io;
+package cz.it4i.qcmp.io;
import java.io.IOException;
import java.io.OutputStream;
public class OutBitStream implements AutoCloseable {
- private OutputStream outStream;
+ private final OutputStream outStream;
- private byte[] buffer;
+ private final byte[] buffer;
private int bufferPosition;
private byte bitBuffer = 0x00;
@@ -16,7 +16,7 @@ public class OutBitStream implements AutoCloseable {
private long bytesWritten = 0;
- public OutBitStream(OutputStream outputStream, final int bitsPerValue, final int bufferSize) {
+ public OutBitStream(final OutputStream outputStream, final int bitsPerValue, final int bufferSize) {
outStream = outputStream;
this.bitsPerValue = bitsPerValue;
diff --git a/src/main/java/cz/it4i/qcmp/io/RawDataIO.java b/src/main/java/cz/it4i/qcmp/io/RawDataIO.java
new file mode 100644
index 0000000..fade99a
--- /dev/null
+++ b/src/main/java/cz/it4i/qcmp/io/RawDataIO.java
@@ -0,0 +1,34 @@
+package cz.it4i.qcmp.io;
+
+import cz.it4i.qcmp.data.ImageU16;
+import cz.it4i.qcmp.utilities.TypeConverter;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+
+public class RawDataIO {
+
+ public static void writeImageU16(final String rawFile,
+ final ImageU16 image,
+ final boolean littleEndian) throws IOException {
+ final byte[] buffer = TypeConverter.unsignedShortArrayToByteArray(image.getData(), littleEndian);
+ writeBytesToFile(rawFile, buffer);
+ }
+
+ public static void writeDataI32(final String rawFile,
+ final int[] differenceData,
+ final boolean littleEndian) throws IOException {
+ final byte[] buffer = TypeConverter.intArrayToByteArray(differenceData, littleEndian);
+ writeBytesToFile(rawFile, buffer);
+ }
+
+ public static void writeBytesToFile(final String rawFile,
+ final byte[] buffer) throws IOException {
+ final FileOutputStream fileStream = new FileOutputStream(rawFile, false);
+ fileStream.write(buffer, 0, buffer.length);
+ fileStream.flush();
+ fileStream.close();
+ }
+
+
+}
diff --git a/src/main/java/azgracompress/io/loader/BasicLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/BasicLoader.java
similarity index 99%
rename from src/main/java/azgracompress/io/loader/BasicLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/BasicLoader.java
index f3b7867..1ef3ccd 100644
--- a/src/main/java/azgracompress/io/loader/BasicLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/BasicLoader.java
@@ -1,6 +1,6 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
-import azgracompress.data.*;
+import cz.it4i.qcmp.data.*;
import java.io.IOException;
diff --git a/src/main/java/azgracompress/io/loader/DataWrappingStrategy.java b/src/main/java/cz/it4i/qcmp/io/loader/DataWrappingStrategy.java
similarity index 92%
rename from src/main/java/azgracompress/io/loader/DataWrappingStrategy.java
rename to src/main/java/cz/it4i/qcmp/io/loader/DataWrappingStrategy.java
index fc2015e..2f9faaf 100644
--- a/src/main/java/azgracompress/io/loader/DataWrappingStrategy.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/DataWrappingStrategy.java
@@ -1,4 +1,4 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
/**
* What to do when blocks or voxels extend outside the source image. These parameters are based on OpenGL texture wrapping options.
diff --git a/src/main/java/azgracompress/io/loader/FlatBufferLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/FlatBufferLoader.java
similarity index 94%
rename from src/main/java/azgracompress/io/loader/FlatBufferLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/FlatBufferLoader.java
index 58c145d..023c76d 100644
--- a/src/main/java/azgracompress/io/loader/FlatBufferLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/FlatBufferLoader.java
@@ -1,10 +1,10 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.io.FlatBufferInputData;
-import azgracompress.utilities.TypeConverter;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.FlatBufferInputData;
+import cz.it4i.qcmp.utilities.TypeConverter;
import java.io.IOException;
import java.util.Arrays;
diff --git a/src/main/java/azgracompress/io/loader/IPlaneLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/IPlaneLoader.java
similarity index 95%
rename from src/main/java/azgracompress/io/loader/IPlaneLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/IPlaneLoader.java
index 5db29c5..9352e1f 100644
--- a/src/main/java/azgracompress/io/loader/IPlaneLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/IPlaneLoader.java
@@ -1,10 +1,10 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
-import azgracompress.compression.CompressionOptions;
-import azgracompress.compression.exception.ImageCompressionException;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.compression.CompressionOptions;
+import cz.it4i.qcmp.compression.exception.ImageCompressionException;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
import java.io.IOException;
@@ -165,7 +165,7 @@ public interface IPlaneLoader {
throw new ImageCompressionException("Invalid QuantizationType '" + options.getQuantizationType().toString() + "'");
}
}
- } catch (IOException e) {
+ } catch (final IOException e) {
throw new ImageCompressionException("Unable to load vectors QuantizationType=" + options.getQuantizationType(), e);
}
}
diff --git a/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/ImageJBufferLoader.java
similarity index 93%
rename from src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/ImageJBufferLoader.java
index 25c1d4e..259964b 100644
--- a/src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/ImageJBufferLoader.java
@@ -1,11 +1,11 @@
-package azgracompress.io.loader;
-
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.io.BufferInputData;
-import azgracompress.io.InputData;
-import azgracompress.utilities.TypeConverter;
+package cz.it4i.qcmp.io.loader;
+
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.BufferInputData;
+import cz.it4i.qcmp.io.InputData;
+import cz.it4i.qcmp.utilities.TypeConverter;
import java.io.IOException;
import java.util.Arrays;
diff --git a/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java b/src/main/java/cz/it4i/qcmp/io/loader/PlaneLoaderFactory.java
similarity index 83%
rename from src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java
rename to src/main/java/cz/it4i/qcmp/io/loader/PlaneLoaderFactory.java
index b34f67e..e35ff32 100644
--- a/src/main/java/azgracompress/io/loader/PlaneLoaderFactory.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/PlaneLoaderFactory.java
@@ -1,9 +1,9 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
-import azgracompress.io.BufferInputData;
-import azgracompress.io.FileInputData;
-import azgracompress.io.FlatBufferInputData;
-import azgracompress.io.InputData;
+import cz.it4i.qcmp.io.BufferInputData;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.io.FlatBufferInputData;
+import cz.it4i.qcmp.io.InputData;
public final class PlaneLoaderFactory {
diff --git a/src/main/java/azgracompress/io/loader/RawDataLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/RawDataLoader.java
similarity index 95%
rename from src/main/java/azgracompress/io/loader/RawDataLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/RawDataLoader.java
index 7dc0e78..b699e3a 100644
--- a/src/main/java/azgracompress/io/loader/RawDataLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/RawDataLoader.java
@@ -1,10 +1,10 @@
-package azgracompress.io.loader;
+package cz.it4i.qcmp.io.loader;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.io.FileInputData;
-import azgracompress.utilities.TypeConverter;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.utilities.TypeConverter;
import java.io.BufferedInputStream;
import java.io.DataInputStream;
diff --git a/src/main/java/azgracompress/io/loader/SCIFIOLoader.java b/src/main/java/cz/it4i/qcmp/io/loader/SCIFIOLoader.java
similarity index 84%
rename from src/main/java/azgracompress/io/loader/SCIFIOLoader.java
rename to src/main/java/cz/it4i/qcmp/io/loader/SCIFIOLoader.java
index 7b4d012..aaf7e86 100644
--- a/src/main/java/azgracompress/io/loader/SCIFIOLoader.java
+++ b/src/main/java/cz/it4i/qcmp/io/loader/SCIFIOLoader.java
@@ -1,11 +1,11 @@
-package azgracompress.io.loader;
-
-import azgracompress.ScifioWrapper;
-import azgracompress.data.Range;
-import azgracompress.data.V2i;
-import azgracompress.data.V3i;
-import azgracompress.io.FileInputData;
-import azgracompress.utilities.TypeConverter;
+package cz.it4i.qcmp.io.loader;
+
+import cz.it4i.qcmp.ScifioWrapper;
+import cz.it4i.qcmp.data.Range;
+import cz.it4i.qcmp.data.V2i;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.io.FileInputData;
+import cz.it4i.qcmp.utilities.TypeConverter;
import io.scif.FormatException;
import io.scif.Reader;
@@ -31,17 +31,17 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
@Override
public int[] loadPlaneData(final int plane) throws IOException {
- byte[] planeBytes;
+ final byte[] planeBytes;
try {
planeBytes = reader.openPlane(0, plane).getBytes();
- } catch (FormatException e) {
+ } catch (final FormatException e) {
throw new IOException("Unable to open plane with the reader. " + e.getMessage());
}
return TypeConverter.unsignedShortBytesToIntArray(planeBytes);
}
@Override
- public int[] loadPlanesU16Data(int[] planes) throws IOException {
+ public int[] loadPlanesU16Data(final int[] planes) throws IOException {
if (planes.length < 1) {
return new int[0];
} else if (planes.length == 1) {
@@ -57,7 +57,7 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
throw new IOException("Integer count is too big.");
}
- int[] values = new int[(int) totalValueCount];
+ final int[] values = new int[(int) totalValueCount];
Arrays.sort(planes);
byte[] planeBytes;
@@ -66,7 +66,7 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
try {
planeBytes = reader.openPlane(0, plane).getBytes();
- } catch (FormatException e) {
+ } catch (final FormatException e) {
throw new IOException("Unable to open plane.");
}
if (planeBytes.length != planeDataSize) {
@@ -88,12 +88,12 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
throw new IOException("FileSize is too big.");
}
- int[] values = new int[(int) dataSize];
+ final int[] values = new int[(int) dataSize];
byte[] planeBytes;
for (int plane = 0; plane < imageDims.getZ(); plane++) {
try {
planeBytes = reader.openPlane(0, plane).getBytes();
- } catch (FormatException e) {
+ } catch (final FormatException e) {
throw new IOException("Unable to open plane.");
}
if (planeBytes.length != 2 * planePixelCount) {
@@ -111,7 +111,7 @@ public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
}
@Override
- public int[][] loadBlocks(V2i blockDim, Range<Integer> planeRange) throws IOException {
+ public int[][] loadBlocks(final V2i blockDim, final Range<Integer> planeRange) throws IOException {
return loadBlocksImplByLoadPlaneData(blockDim, planeRange);
}
diff --git a/src/main/java/azgracompress/kdtree/KDNode.java b/src/main/java/cz/it4i/qcmp/kdtree/KDNode.java
similarity index 97%
rename from src/main/java/azgracompress/kdtree/KDNode.java
rename to src/main/java/cz/it4i/qcmp/kdtree/KDNode.java
index 026ca06..9f07543 100644
--- a/src/main/java/azgracompress/kdtree/KDNode.java
+++ b/src/main/java/cz/it4i/qcmp/kdtree/KDNode.java
@@ -1,4 +1,4 @@
-package azgracompress.kdtree;
+package cz.it4i.qcmp.kdtree;
public class KDNode {
private final int discriminator;
diff --git a/src/main/java/azgracompress/kdtree/KDTree.java b/src/main/java/cz/it4i/qcmp/kdtree/KDTree.java
similarity index 91%
rename from src/main/java/azgracompress/kdtree/KDTree.java
rename to src/main/java/cz/it4i/qcmp/kdtree/KDTree.java
index 4c286de..3f1ee40 100644
--- a/src/main/java/azgracompress/kdtree/KDTree.java
+++ b/src/main/java/cz/it4i/qcmp/kdtree/KDTree.java
@@ -1,4 +1,4 @@
-package azgracompress.kdtree;
+package cz.it4i.qcmp.kdtree;
import org.jetbrains.annotations.NotNull;
@@ -53,7 +53,7 @@ public class KDTree {
private final KDNode node;
private final double distance;
- private NodeWithDistance(KDNode node, double distance) {
+ private NodeWithDistance(final KDNode node, final double distance) {
this.node = node;
this.distance = distance;
}
@@ -67,7 +67,7 @@ public class KDTree {
}
@Override
- public int compareTo(@NotNull KDTree.NodeWithDistance o) {
+ public int compareTo(@NotNull final KDTree.NodeWithDistance o) {
return Double.compare(distance, o.distance);
}
}
@@ -87,14 +87,14 @@ public class KDTree {
public int findNearestBBF(final int[] queryVector, final int maxE) {
- PriorityQueue<NodeWithDistance> priorityQueue = new PriorityQueue<>();
+ final PriorityQueue<NodeWithDistance> priorityQueue = new PriorityQueue<>();
priorityQueue.add(new NodeWithDistance(root, 0.0));
- BBFSearchInfo searchInfo = new BBFSearchInfo(featureVectors);
+ final BBFSearchInfo searchInfo = new BBFSearchInfo(featureVectors);
int tryIndex = 0;
int partition, discriminator;
while (!priorityQueue.isEmpty() && tryIndex < maxE) {
- NodeWithDistance current = priorityQueue.remove();
+ final NodeWithDistance current = priorityQueue.remove();
if (current.getNode().isTerminal()) {
((TerminalKDNode) current.getNode()).findNearestNeighborInBucket(queryVector, searchInfo);
++tryIndex;
diff --git a/src/main/java/azgracompress/kdtree/KDTreeBuilder.java b/src/main/java/cz/it4i/qcmp/kdtree/KDTreeBuilder.java
similarity index 96%
rename from src/main/java/azgracompress/kdtree/KDTreeBuilder.java
rename to src/main/java/cz/it4i/qcmp/kdtree/KDTreeBuilder.java
index ace1fee..e14b883 100644
--- a/src/main/java/azgracompress/kdtree/KDTreeBuilder.java
+++ b/src/main/java/cz/it4i/qcmp/kdtree/KDTreeBuilder.java
@@ -1,4 +1,4 @@
-package azgracompress.kdtree;
+package cz.it4i.qcmp.kdtree;
import java.util.ArrayList;
import java.util.Arrays;
@@ -69,7 +69,7 @@ public class KDTreeBuilder {
return makeTerminalNode(indices);
}
- int dimensionIndex = findDimensionWithGreatestVariance(indices);
+ final int dimensionIndex = findDimensionWithGreatestVariance(indices);
final int median = calculateKeyMedian(indices, dimensionIndex);
// Divide records in one method to hi and lo.
@@ -87,8 +87,8 @@ public class KDTreeBuilder {
* @return Divided vectors.
*/
private DividedRecords divideRecords(final int[] indices, final int median, final int dimension) {
- ArrayList<Integer> loIndices = new ArrayList<>();
- ArrayList<Integer> hiIndices = new ArrayList<>();
+ final ArrayList<Integer> loIndices = new ArrayList<>();
+ final ArrayList<Integer> hiIndices = new ArrayList<>();
for (final int fVecIndex : indices) {
if (featureVectors[fVecIndex][dimension] <= median) {
diff --git a/src/main/java/azgracompress/kdtree/TerminalKDNode.java b/src/main/java/cz/it4i/qcmp/kdtree/TerminalKDNode.java
similarity index 92%
rename from src/main/java/azgracompress/kdtree/TerminalKDNode.java
rename to src/main/java/cz/it4i/qcmp/kdtree/TerminalKDNode.java
index 0dac9c4..8ec2f0f 100644
--- a/src/main/java/azgracompress/kdtree/TerminalKDNode.java
+++ b/src/main/java/cz/it4i/qcmp/kdtree/TerminalKDNode.java
@@ -1,6 +1,6 @@
-package azgracompress.kdtree;
+package cz.it4i.qcmp.kdtree;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.utilities.Utils;
public class TerminalKDNode extends KDNode {
diff --git a/src/main/java/azgracompress/quantization/QTrainIteration.java b/src/main/java/cz/it4i/qcmp/quantization/QTrainIteration.java
similarity index 76%
rename from src/main/java/azgracompress/quantization/QTrainIteration.java
rename to src/main/java/cz/it4i/qcmp/quantization/QTrainIteration.java
index 0f6d444..2fd613f 100644
--- a/src/main/java/azgracompress/quantization/QTrainIteration.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/QTrainIteration.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization;
+package cz.it4i.qcmp.quantization;
public class QTrainIteration {
private final int iteration;
@@ -6,7 +6,7 @@ public class QTrainIteration {
private final double PSNR;
- public QTrainIteration(int iteration, double mse, double psnr) {
+ public QTrainIteration(final int iteration, final double mse, final double psnr) {
this.iteration = iteration;
this.mse = mse;
this.PSNR = psnr;
diff --git a/src/main/java/azgracompress/quantization/scalar/LloydMaxU16ScalarQuantization.java b/src/main/java/cz/it4i/qcmp/quantization/scalar/LloydMaxU16ScalarQuantization.java
similarity index 88%
rename from src/main/java/azgracompress/quantization/scalar/LloydMaxU16ScalarQuantization.java
rename to src/main/java/cz/it4i/qcmp/quantization/scalar/LloydMaxU16ScalarQuantization.java
index 0ace21c..0dc3f31 100644
--- a/src/main/java/azgracompress/quantization/scalar/LloydMaxU16ScalarQuantization.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/scalar/LloydMaxU16ScalarQuantization.java
@@ -1,11 +1,11 @@
-package azgracompress.quantization.scalar;
+package cz.it4i.qcmp.quantization.scalar;
-import azgracompress.U16;
-import azgracompress.compression.listeners.IStatusListener;
-import azgracompress.quantization.QTrainIteration;
-import azgracompress.utilities.MinMaxResult;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.compression.listeners.IStatusListener;
+import cz.it4i.qcmp.quantization.QTrainIteration;
+import cz.it4i.qcmp.utilities.MinMaxResult;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.Utils;
import java.util.ArrayList;
import java.util.Arrays;
@@ -13,7 +13,7 @@ import java.util.Arrays;
public class LloydMaxU16ScalarQuantization {
private final int[] trainingData;
- private int codebookSize;
+ private final int codebookSize;
private int dataMin;
private int dataMax;
@@ -48,7 +48,7 @@ public class LloydMaxU16ScalarQuantization {
boundaryPoints = new int[codebookSize + 1];
- MinMaxResult<Integer> minMax = Utils.getMinAndMax(trainingData);
+ final MinMaxResult<Integer> minMax = Utils.getMinAndMax(trainingData);
dataMin = minMax.getMin();
dataMax = minMax.getMax();
final int dataSpan = dataMax - dataMin;
@@ -56,7 +56,7 @@ public class LloydMaxU16ScalarQuantization {
boundaryPoints[0] = dataMin;
boundaryPoints[codebookSize] = dataMax;
- double intervalSize = (double) (dataSpan) / (double) codebookSize;
+ final double intervalSize = (double) (dataSpan) / (double) codebookSize;
for (int i = 0; i < codebookSize; i++) {
centroids[i] = (int) Math.floor(((double) i + 0.5) * intervalSize);
}
@@ -87,7 +87,7 @@ public class LloydMaxU16ScalarQuantization {
private void initializeCentroids() {
int lowerBound, upperBound;
- double[] centroidPdf = new double[codebookSize];
+ final double[] centroidPdf = new double[codebookSize];
for (int centroidIndex = 0; centroidIndex < codebookSize; centroidIndex++) {
lowerBound = boundaryPoints[centroidIndex];
upperBound = boundaryPoints[centroidIndex + 1];
@@ -150,8 +150,8 @@ public class LloydMaxU16ScalarQuantization {
if (workerCount > 1) {
final int workSize = trainingData.length / workerCount;
- RunnableLloydMseCalc[] runnables = new RunnableLloydMseCalc[workerCount];
- Thread[] workers = new Thread[workerCount];
+ final RunnableLloydMseCalc[] runnables = new RunnableLloydMseCalc[workerCount];
+ final Thread[] workers = new Thread[workerCount];
for (int wId = 0; wId < workerCount; wId++) {
final int fromIndex = wId * workSize;
final int toIndex = (wId == workerCount - 1) ? trainingData.length : (workSize + (wId * workSize));
@@ -172,12 +172,12 @@ public class LloydMaxU16ScalarQuantization {
addWorkerFrequencies(runnables[wId].getFrequencies());
mse += runnables[wId].getMse();
}
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
e.printStackTrace();
}
} else {
for (final int trainingDatum : trainingData) {
- int quantizedValue = quantize(trainingDatum);
+ final int quantizedValue = quantize(trainingDatum);
mse += Math.pow((double) trainingDatum - (double) quantizedValue, 2);
}
}
@@ -206,12 +206,12 @@ public class LloydMaxU16ScalarQuantization {
initializeProbabilityDensityFunction();
- double currMAE = 1.0;
+ final double currMAE = 1.0;
double prevMse = 1.0;
double currentMse = 1.0;
double psnr;
- ArrayList<QTrainIteration> solutionHistory = new ArrayList<>();
+ final ArrayList<QTrainIteration> solutionHistory = new ArrayList<>();
recalculateBoundaryPoints();
initializeCentroids();
@@ -225,7 +225,7 @@ public class LloydMaxU16ScalarQuantization {
double mseImprovement = 1;
int iteration = 0;
- Stopwatch stopwatch = new Stopwatch();
+ final Stopwatch stopwatch = new Stopwatch();
do {
stopwatch.restart();
for (int i = 0; i < RECALCULATE_N_TIMES; i++) {
diff --git a/src/main/java/azgracompress/quantization/scalar/RunnableLloydMseCalc.java b/src/main/java/cz/it4i/qcmp/quantization/scalar/RunnableLloydMseCalc.java
similarity index 87%
rename from src/main/java/azgracompress/quantization/scalar/RunnableLloydMseCalc.java
rename to src/main/java/cz/it4i/qcmp/quantization/scalar/RunnableLloydMseCalc.java
index d4bdc58..f3ead20 100644
--- a/src/main/java/azgracompress/quantization/scalar/RunnableLloydMseCalc.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/scalar/RunnableLloydMseCalc.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization.scalar;
+package cz.it4i.qcmp.quantization.scalar;
public class RunnableLloydMseCalc implements Runnable {
final int[] trainingData;
@@ -10,7 +10,7 @@ public class RunnableLloydMseCalc implements Runnable {
double mse = 0.0;
final long[] frequencies;
- public RunnableLloydMseCalc(int[] trainingData, int fromIndex, int toIndex, int[] centroids, int[] boundaryPoints,
+ public RunnableLloydMseCalc(final int[] trainingData, final int fromIndex, final int toIndex, final int[] centroids, final int[] boundaryPoints,
final int codebookSize) {
this.trainingData = trainingData;
this.fromIndex = fromIndex;
diff --git a/src/main/java/azgracompress/quantization/scalar/SQCodebook.java b/src/main/java/cz/it4i/qcmp/quantization/scalar/SQCodebook.java
similarity index 96%
rename from src/main/java/azgracompress/quantization/scalar/SQCodebook.java
rename to src/main/java/cz/it4i/qcmp/quantization/scalar/SQCodebook.java
index f55749e..ff06d5d 100644
--- a/src/main/java/azgracompress/quantization/scalar/SQCodebook.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/scalar/SQCodebook.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization.scalar;
+package cz.it4i.qcmp.quantization.scalar;
/**
diff --git a/src/main/java/azgracompress/quantization/scalar/ScalarQuantizer.java b/src/main/java/cz/it4i/qcmp/quantization/scalar/ScalarQuantizer.java
similarity index 85%
rename from src/main/java/azgracompress/quantization/scalar/ScalarQuantizer.java
rename to src/main/java/cz/it4i/qcmp/quantization/scalar/ScalarQuantizer.java
index 480b3d9..a8133f7 100644
--- a/src/main/java/azgracompress/quantization/scalar/ScalarQuantizer.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/scalar/ScalarQuantizer.java
@@ -1,12 +1,12 @@
-package azgracompress.quantization.scalar;
+package cz.it4i.qcmp.quantization.scalar;
-import azgracompress.U16;
+import cz.it4i.qcmp.U16;
public class ScalarQuantizer {
private final int min;
private final int max;
private final SQCodebook codebook;
- private int[] boundaryPoints;
+ private final int[] boundaryPoints;
public ScalarQuantizer(final int min, final int max, final SQCodebook codebook) {
this.codebook = codebook;
@@ -21,16 +21,16 @@ public class ScalarQuantizer {
this(U16.Min, U16.Max, codebook);
}
- public int[] quantize(int[] data) {
- int[] result = new int[data.length];
+ public int[] quantize(final int[] data) {
+ final int[] result = new int[data.length];
for (int i = 0; i < data.length; i++) {
result[i] = quantize(data[i]);
}
return result;
}
- public int[] quantizeIntoIndices(int[] data, final int maxWorkerCount) {
- int[] indices = new int[data.length];
+ public int[] quantizeIntoIndices(final int[] data, final int maxWorkerCount) {
+ final int[] indices = new int[data.length];
// Speedup?
if (maxWorkerCount == 1) {
for (int i = 0; i < data.length; i++) {
@@ -40,7 +40,7 @@ public class ScalarQuantizer {
} else {
// NOTE(Moravec): This function is fast enough single thread. So we use max 2 threads.
final int workerCount = Math.min(maxWorkerCount, 2);
- Thread[] workers = new Thread[workerCount];
+ final Thread[] workers = new Thread[workerCount];
final int workSize = data.length / workerCount;
for (int wId = 0; wId < workerCount; wId++) {
@@ -59,7 +59,7 @@ public class ScalarQuantizer {
for (int wId = 0; wId < workerCount; wId++) {
workers[wId].join();
}
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
e.printStackTrace();
}
}
@@ -92,7 +92,7 @@ public class ScalarQuantizer {
public double getMse(final int[] data) {
double mse = 0.0;
for (int i = 0; i < data.length; i++) {
- int quantizedValue = quantize(data[i]);
+ final int quantizedValue = quantize(data[i]);
mse += Math.pow(((double) data[i] - (double) quantizedValue), 2);
}
mse /= (double) data.length;
diff --git a/src/main/java/azgracompress/quantization/vector/EntryInfo.java b/src/main/java/cz/it4i/qcmp/quantization/vector/EntryInfo.java
similarity index 90%
rename from src/main/java/azgracompress/quantization/vector/EntryInfo.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/EntryInfo.java
index 1292179..c43f7fc 100644
--- a/src/main/java/azgracompress/quantization/vector/EntryInfo.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/EntryInfo.java
@@ -1,6 +1,6 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
-import azgracompress.U16;
+import cz.it4i.qcmp.U16;
import java.util.Arrays;
@@ -41,7 +41,7 @@ public class EntryInfo {
* @return Centroid of the vectors.
*/
public int[] calculateCentroid() {
- int[] centroid = new int[vectorSize];
+ final int[] centroid = new int[vectorSize];
for (int dim = 0; dim < vectorSize; dim++) {
centroid[dim] = (int) Math.round(dimensionSum[dim] / (double) vectorCount);
}
@@ -54,7 +54,7 @@ public class EntryInfo {
* @return Perturbation vector of the vectors.
*/
public double[] calculatePRTVector() {
- double[] prtV = new double[vectorSize];
+ final double[] prtV = new double[vectorSize];
for (int dim = 0; dim < vectorSize; dim++) {
prtV[dim] = ((double) max[dim] - (double) min[dim]) / LBGVectorQuantizer.PRT_VECTOR_DIVIDER;
}
diff --git a/src/main/java/azgracompress/quantization/vector/LBGResult.java b/src/main/java/cz/it4i/qcmp/quantization/vector/LBGResult.java
similarity index 92%
rename from src/main/java/azgracompress/quantization/vector/LBGResult.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/LBGResult.java
index 4b72a79..2bb63af 100644
--- a/src/main/java/azgracompress/quantization/vector/LBGResult.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/LBGResult.java
@@ -1,6 +1,6 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.V3i;
public class LBGResult {
diff --git a/src/main/java/azgracompress/quantization/vector/LBGVectorQuantizer.java b/src/main/java/cz/it4i/qcmp/quantization/vector/LBGVectorQuantizer.java
similarity index 89%
rename from src/main/java/azgracompress/quantization/vector/LBGVectorQuantizer.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/LBGVectorQuantizer.java
index 0ad49cf..6577004 100644
--- a/src/main/java/azgracompress/quantization/vector/LBGVectorQuantizer.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/LBGVectorQuantizer.java
@@ -1,10 +1,10 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
-import azgracompress.U16;
-import azgracompress.compression.listeners.IStatusListener;
-import azgracompress.data.V3i;
-import azgracompress.utilities.Stopwatch;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.compression.listeners.IStatusListener;
+import cz.it4i.qcmp.data.V3i;
+import cz.it4i.qcmp.utilities.Stopwatch;
+import cz.it4i.qcmp.utilities.Utils;
import java.util.ArrayList;
import java.util.Arrays;
@@ -23,7 +23,7 @@ public class LBGVectorQuantizer {
private final TrainingVector[] trainingVectors;
private final VectorDistanceMetric metric = VectorDistanceMetric.Euclidean;
- private long[] frequencies;
+ private final long[] frequencies;
private IStatusListener statusListener = null;
private double _mse = 0.0;
@@ -93,7 +93,7 @@ public class LBGVectorQuantizer {
reportStatus("There is only %d unique vectors. Creating codebook from unique vectors...",
uniqueTrainingVectors.size());
final int[][] codebook = new int[codebookSize][vectorSize];
- int[] zeroEntry = new int[vectorSize];
+ final int[] zeroEntry = new int[vectorSize];
Arrays.fill(zeroEntry, 0);
for (int i = 0; i < codebookSize; i++) {
if (i < uniqueVectorCount) {
@@ -114,13 +114,13 @@ public class LBGVectorQuantizer {
* @return Result of the search.
*/
public LBGResult findOptimalCodebook() {
- Stopwatch stopwatch = Stopwatch.startNew("LBG::findOptimalCodebook()");
+ final Stopwatch stopwatch = Stopwatch.startNew("LBG::findOptimalCodebook()");
if (uniqueVectorCount < codebookSize) {
return createCodebookFromUniqueVectors();
}
- LearningCodebookEntry[] codebook = initializeCodebook();
+ final LearningCodebookEntry[] codebook = initializeCodebook();
reportStatus("LBG::findOptimalCodebook() - Got initial codebook. Improving it...");
LBG(codebook, EPSILON * 0.1);
@@ -183,17 +183,17 @@ public class LBGVectorQuantizer {
if (workerCount > 1) {
// Reset the global mse
_mse = 0.0;
- Thread[] workers = new Thread[workerCount];
+ final Thread[] workers = new Thread[workerCount];
final int workSize = trainingVectors.length / workerCount;
for (int wId = 0; wId < workerCount; wId++) {
final int fromIndex = wId * workSize;
final int toIndex = (wId == workerCount - 1) ? trainingVectors.length : (workSize + (wId * workSize));
workers[wId] = new Thread(() -> {
- long[] workerFrequencies = new long[codebook.length];
- VectorQuantizer quantizer = new VectorQuantizer(new VQCodebook(vectorDimensions,
- codebook,
- frequencies));
+ final long[] workerFrequencies = new long[codebook.length];
+ final VectorQuantizer quantizer = new VectorQuantizer(new VQCodebook(vectorDimensions,
+ codebook,
+ frequencies));
double threadMse = 0.0;
int[] vector;
@@ -224,14 +224,14 @@ public class LBGVectorQuantizer {
for (int wId = 0; wId < workerCount; wId++) {
workers[wId].join();
}
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
e.printStackTrace();
}
mse = _mse / (double) workerCount;
} else {
- VectorQuantizer quantizer = new VectorQuantizer(new VQCodebook(vectorDimensions,
- codebook,
- frequencies));
+ final VectorQuantizer quantizer = new VectorQuantizer(new VQCodebook(vectorDimensions,
+ codebook,
+ frequencies));
int qIndex;
int[] qVector;
for (final TrainingVector trV : trainingVectors) {
@@ -256,9 +256,9 @@ public class LBGVectorQuantizer {
private double[] getPerturbationVector(final TrainingVector[] vectors) {
// Max is initialized to zero that is ok.
- int[] max = new int[vectorSize];
+ final int[] max = new int[vectorSize];
// We have to initialize min to Max values.
- int[] min = new int[vectorSize];
+ final int[] min = new int[vectorSize];
Arrays.fill(min, U16.Max);
for (final TrainingVector v : vectors) {
@@ -272,7 +272,7 @@ public class LBGVectorQuantizer {
}
}
- double[] perturbationVector = new double[vectorSize];
+ final double[] perturbationVector = new double[vectorSize];
for (int i = 0; i < vectorSize; i++) {
perturbationVector[i] = ((double) max[i] - (double) min[i]) / PRT_VECTOR_DIVIDER;
}
@@ -285,14 +285,14 @@ public class LBGVectorQuantizer {
* @return Initial codebook entry.
*/
private LearningCodebookEntry createInitialEntry() {
- double[] vectorSum = new double[vectorSize];
+ final double[] vectorSum = new double[vectorSize];
for (final TrainingVector trainingVector : trainingVectors) {
for (int i = 0; i < vectorSize; i++) {
vectorSum[i] += (double) trainingVector.getVector()[i];
}
}
- int[] result = new int[vectorSize];
+ final int[] result = new int[vectorSize];
for (int i = 0; i < vectorSize; i++) {
result[i] = (int) Math.round(vectorSum[i] / (double) trainingVectors.length);
}
@@ -311,11 +311,11 @@ public class LBGVectorQuantizer {
while (currentCodebookSize != codebookSize) {
int cbIndex = 0;
- LearningCodebookEntry[] newCodebook = new LearningCodebookEntry[currentCodebookSize * 2];
+ final LearningCodebookEntry[] newCodebook = new LearningCodebookEntry[currentCodebookSize * 2];
// Split each entry in codebook with fixed perturbation vector.
for (final LearningCodebookEntry entryToSplit : codebook) {
- double[] prtV;
+ final double[] prtV;
if (codebook.length == 1) {
assert (trainingVectors.length > 0) :
"There are no vectors from which to create perturbation " + "vector";
@@ -339,7 +339,7 @@ public class LBGVectorQuantizer {
newCodebook[cbIndex++] = entryToSplit;
// Create another codebook entry from perturbation vector.
- int[] entryFromPrtVecValues = new int[prtV.length];
+ final int[] entryFromPrtVecValues = new int[prtV.length];
for (int i = 0; i < prtV.length; i++) {
final int value = (int) Math.floor(prtV[i]);
// assert (value >= 0) : "value is too low!";
@@ -360,8 +360,8 @@ public class LBGVectorQuantizer {
newCodebook[cbIndex++] = entryToSplit;
newCodebook[cbIndex++] = new LearningCodebookEntry(randomEntryValues);
} else {
- int[] left = new int[prtV.length];
- int[] right = new int[prtV.length];
+ final int[] left = new int[prtV.length];
+ final int[] right = new int[prtV.length];
for (int i = 0; i < prtV.length; i++) {
final int lVal = (int) ((double) entryToSplit.getVector()[i] - prtV[i]);
final int rVal = (int) ((double) entryToSplit.getVector()[i] + prtV[i]);
@@ -399,8 +399,8 @@ public class LBGVectorQuantizer {
* @return Generated random vector.
*/
private int[] generateRandomVector() {
- int[] randomVector = new int[vectorSize];
- Random rnd = new Random();
+ final int[] randomVector = new int[vectorSize];
+ final Random rnd = new Random();
for (int i = 0; i < vectorSize; i++) {
randomVector[i] = rnd.nextInt(U16.Max + 1);
}
@@ -408,8 +408,8 @@ public class LBGVectorQuantizer {
}
private double[] generateRandomVectorDouble() {
- double[] randomVector = new double[vectorSize];
- Random rnd = new Random();
+ final double[] randomVector = new double[vectorSize];
+ final Random rnd = new Random();
for (int i = 0; i < vectorSize; i++) {
randomVector[i] = rnd.nextInt(U16.Max + 1);
}
@@ -422,7 +422,7 @@ public class LBGVectorQuantizer {
*
* @param codebook Codebook to improve.
*/
- private void LBG(LearningCodebookEntry[] codebook) {
+ private void LBG(final LearningCodebookEntry[] codebook) {
LBG(codebook, EPSILON);
}
@@ -432,7 +432,7 @@ public class LBGVectorQuantizer {
* @param codebook Codebook to improve.
* @param epsilon Epsilon value.
*/
- private void LBG(LearningCodebookEntry[] codebook, final double epsilon) {
+ private void LBG(final LearningCodebookEntry[] codebook, final double epsilon) {
//this.verbose = true;
double previousDistortion = Double.POSITIVE_INFINITY;
int iteration = 1;
@@ -446,13 +446,13 @@ public class LBGVectorQuantizer {
// Calculate average distortion of the codebook.
double avgDistortion = 0;
- for (LearningCodebookEntry entry : codebook) {
+ for (final LearningCodebookEntry entry : codebook) {
avgDistortion += entry.getAverageDistortion();
}
avgDistortion /= codebook.length;
// Calculate distortion
- double distortion = (previousDistortion - avgDistortion) / avgDistortion;
+ final double distortion = (previousDistortion - avgDistortion) / avgDistortion;
reportStatus("LBG::LBG() - Iteration: %d Distortion: %.5f", iteration++, distortion);
@@ -481,7 +481,7 @@ public class LBGVectorQuantizer {
*
* @param codebook Vector codebook.
*/
- private void assignVectorsToClosestEntry(LearningCodebookEntry[] codebook) {
+ private void assignVectorsToClosestEntry(final LearningCodebookEntry[] codebook) {
// Stopwatch stopwatch = Stopwatch.startNew("assignVectorsToClosestEntry");
if (workerCount > 1) {
parallelAssignVectors(codebook);
@@ -503,18 +503,18 @@ public class LBGVectorQuantizer {
*
* @param codebook Vector codebook.
*/
- private void defaultAssignVectors(LearningCodebookEntry[] codebook) {
+ private void defaultAssignVectors(final LearningCodebookEntry[] codebook) {
double minDist;
int closestEntryIndex;
- for (TrainingVector trainingVector : trainingVectors) {
+ for (final TrainingVector trainingVector : trainingVectors) {
minDist = Double.POSITIVE_INFINITY;
closestEntryIndex = -1;
for (int entryIndex = 0; entryIndex < codebook.length; entryIndex++) {
- double entryDistance = VectorQuantizer.distanceBetweenVectors(codebook[entryIndex].getVector(),
- trainingVector.getVector(),
- metric);
+ final double entryDistance = VectorQuantizer.distanceBetweenVectors(codebook[entryIndex].getVector(),
+ trainingVector.getVector(),
+ metric);
if (entryDistance < minDist) {
minDist = entryDistance;
@@ -537,10 +537,10 @@ public class LBGVectorQuantizer {
*
* @param codebook Vector codebook.
*/
- private void parallelAssignVectors(LearningCodebookEntry[] codebook) {
- Thread[] workers = new Thread[workerCount];
+ private void parallelAssignVectors(final LearningCodebookEntry[] codebook) {
+ final Thread[] workers = new Thread[workerCount];
final int workSize = trainingVectors.length / workerCount;
- EntryInfo[][] threadEntryInfos = new EntryInfo[workerCount][codebook.length];
+ final EntryInfo[][] threadEntryInfos = new EntryInfo[workerCount][codebook.length];
for (int wId = 0; wId < workerCount; wId++) {
@@ -603,13 +603,13 @@ public class LBGVectorQuantizer {
for (int wId = 0; wId < workerCount; wId++) {
workers[wId].join();
}
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
e.printStackTrace();
assert (false) : "Failed parallel join";
}
// Combine all thread entry infos to final array distributed to the entries.
- EntryInfo[] entryInfos = new EntryInfo[codebook.length];
+ final EntryInfo[] entryInfos = new EntryInfo[codebook.length];
// Assign first thread infos and we can skip it later.
System.arraycopy(threadEntryInfos[0], 0, entryInfos, 0, codebook.length);
@@ -624,7 +624,7 @@ public class LBGVectorQuantizer {
}
}
- private void combine(EntryInfo finalEntryInfo, final EntryInfo threadEntryInfo) {
+ private void combine(final EntryInfo finalEntryInfo, final EntryInfo threadEntryInfo) {
finalEntryInfo.vectorCount += threadEntryInfo.vectorCount;
finalEntryInfo.distanceSum += threadEntryInfo.distanceSum;
@@ -646,10 +646,10 @@ public class LBGVectorQuantizer {
*
* @param codebook Vector codebook.
*/
- private void calculateEntryProperties(LearningCodebookEntry[] codebook) {
+ private void calculateEntryProperties(final LearningCodebookEntry[] codebook) {
int value;
- EntryInfo[] entryInfos = new EntryInfo[codebook.length];
+ final EntryInfo[] entryInfos = new EntryInfo[codebook.length];
for (int i = 0; i < entryInfos.length; i++) {
entryInfos[i] = new EntryInfo(vectorSize);
}
@@ -685,7 +685,7 @@ public class LBGVectorQuantizer {
*
* @param codebook Vector codebook.
*/
- private void fixEmptyEntries(LearningCodebookEntry[] codebook) {
+ private void fixEmptyEntries(final LearningCodebookEntry[] codebook) {
int emptyEntryIndex = -1;
for (int i = 0; i < codebook.length; i++) {
if (codebook[i].getVectorCount() < 2) {
@@ -720,7 +720,7 @@ public class LBGVectorQuantizer {
* @param codebook Vector codebook.
* @param emptyEntryIndex Index of the empty entry.
*/
- private boolean fixSingleEmptyEntry(LearningCodebookEntry[] codebook, final int emptyEntryIndex) {
+ private boolean fixSingleEmptyEntry(final LearningCodebookEntry[] codebook, final int emptyEntryIndex) {
// Find biggest partition.
int largestEntryIndex = emptyEntryIndex;
int largestEntrySize = codebook[emptyEntryIndex].getVectorCount();
@@ -745,7 +745,7 @@ public class LBGVectorQuantizer {
codebook[largestEntryIndex].getVectorCount());
// Choose random trainingVector from biggest partition and set it as new entry.
- int randomIndex = new Random().nextInt(largestPartitionVectors.length);
+ final int randomIndex = new Random().nextInt(largestPartitionVectors.length);
// Plane the new entry on the index of the empty entry.
codebook[emptyEntryIndex] = new LearningCodebookEntry(largestPartitionVectors[randomIndex].getVector());
@@ -753,8 +753,8 @@ public class LBGVectorQuantizer {
// Speedup - speed the look for closest entry.
- EntryInfo oldEntryInfo = new EntryInfo(vectorSize);
- EntryInfo newEntryInfo = new EntryInfo(vectorSize);
+ final EntryInfo oldEntryInfo = new EntryInfo(vectorSize);
+ final EntryInfo newEntryInfo = new EntryInfo(vectorSize);
int value, entryIndex;
double oldDistance, newDistance, distance;
@@ -828,7 +828,7 @@ public class LBGVectorQuantizer {
++count;
}
}
- TrainingVector[] vectors = new TrainingVector[count];
+ final TrainingVector[] vectors = new TrainingVector[count];
for (final TrainingVector trainingVector : trainingVectors) {
if (trainingVector.getEntryIndex() == entryIndex) {
diff --git a/src/main/java/azgracompress/quantization/vector/LearningCodebookEntry.java b/src/main/java/cz/it4i/qcmp/quantization/vector/LearningCodebookEntry.java
similarity index 93%
rename from src/main/java/azgracompress/quantization/vector/LearningCodebookEntry.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/LearningCodebookEntry.java
index 4492e4c..cc13c66 100644
--- a/src/main/java/azgracompress/quantization/vector/LearningCodebookEntry.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/LearningCodebookEntry.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
public class LearningCodebookEntry {
@@ -7,7 +7,7 @@ public class LearningCodebookEntry {
private double averageDistortion = -1.0f;
private double[] perturbationVector;
- public LearningCodebookEntry(int[] codebookVector) {
+ public LearningCodebookEntry(final int[] codebookVector) {
this.codebookVector = codebookVector;
}
diff --git a/src/main/java/azgracompress/quantization/vector/TrainingVector.java b/src/main/java/cz/it4i/qcmp/quantization/vector/TrainingVector.java
similarity index 93%
rename from src/main/java/azgracompress/quantization/vector/TrainingVector.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/TrainingVector.java
index 8746cdd..95df967 100644
--- a/src/main/java/azgracompress/quantization/vector/TrainingVector.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/TrainingVector.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
import java.util.Arrays;
@@ -11,7 +11,7 @@ public class TrainingVector {
private int entryIndex = -1;
private double entryDistance = Double.POSITIVE_INFINITY;
- public TrainingVector(int[] vector) {
+ public TrainingVector(final int[] vector) {
this.vector = vector;
}
diff --git a/src/main/java/azgracompress/quantization/vector/VQCodebook.java b/src/main/java/cz/it4i/qcmp/quantization/vector/VQCodebook.java
similarity index 92%
rename from src/main/java/azgracompress/quantization/vector/VQCodebook.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/VQCodebook.java
index d56fc6b..a000184 100644
--- a/src/main/java/azgracompress/quantization/vector/VQCodebook.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/VQCodebook.java
@@ -1,6 +1,6 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
-import azgracompress.data.V3i;
+import cz.it4i.qcmp.data.V3i;
/**
* Codebook for vector quantizer.
@@ -14,7 +14,7 @@ public class VQCodebook {
/**
* Absolute frequencies of quantization vectors.
*/
- private long[] vectorFrequencies;
+ private final long[] vectorFrequencies;
/**
* Size of the codebook.
diff --git a/src/main/java/azgracompress/quantization/vector/VectorDistanceMetric.java b/src/main/java/cz/it4i/qcmp/quantization/vector/VectorDistanceMetric.java
similarity index 65%
rename from src/main/java/azgracompress/quantization/vector/VectorDistanceMetric.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/VectorDistanceMetric.java
index 565fb93..ae2ce1b 100644
--- a/src/main/java/azgracompress/quantization/vector/VectorDistanceMetric.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/VectorDistanceMetric.java
@@ -1,4 +1,4 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
public enum VectorDistanceMetric {
Manhattan,
diff --git a/src/main/java/azgracompress/quantization/vector/VectorQuantizer.java b/src/main/java/cz/it4i/qcmp/quantization/vector/VectorQuantizer.java
similarity index 97%
rename from src/main/java/azgracompress/quantization/vector/VectorQuantizer.java
rename to src/main/java/cz/it4i/qcmp/quantization/vector/VectorQuantizer.java
index 8806b18..6f987d8 100644
--- a/src/main/java/azgracompress/quantization/vector/VectorQuantizer.java
+++ b/src/main/java/cz/it4i/qcmp/quantization/vector/VectorQuantizer.java
@@ -1,8 +1,8 @@
-package azgracompress.quantization.vector;
+package cz.it4i.qcmp.quantization.vector;
-import azgracompress.kdtree.KDTree;
-import azgracompress.kdtree.KDTreeBuilder;
-import azgracompress.utilities.Utils;
+import cz.it4i.qcmp.kdtree.KDTree;
+import cz.it4i.qcmp.kdtree.KDTreeBuilder;
+import cz.it4i.qcmp.utilities.Utils;
public class VectorQuantizer {
diff --git a/src/main/java/azgracompress/utilities/ColorConsole.java b/src/main/java/cz/it4i/qcmp/utilities/ColorConsole.java
similarity index 98%
rename from src/main/java/azgracompress/utilities/ColorConsole.java
rename to src/main/java/cz/it4i/qcmp/utilities/ColorConsole.java
index 2117887..d41b659 100644
--- a/src/main/java/azgracompress/utilities/ColorConsole.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/ColorConsole.java
@@ -1,4 +1,4 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
public final class ColorConsole {
private static final String ANSI_RESET = "\u001B[0m";
diff --git a/src/main/java/azgracompress/utilities/Means.java b/src/main/java/cz/it4i/qcmp/utilities/Means.java
similarity index 76%
rename from src/main/java/azgracompress/utilities/Means.java
rename to src/main/java/cz/it4i/qcmp/utilities/Means.java
index fc96e0d..616872e 100644
--- a/src/main/java/azgracompress/utilities/Means.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/Means.java
@@ -1,15 +1,15 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
import java.util.ArrayList;
public class Means {
public static double arithmeticMean(final ArrayList<Double> values) {
double sum = 0.0;
- for (double val : values) {
+ for (final double val : values) {
sum += val;
}
- double result = sum / (double) values.size();
+ final double result = sum / (double) values.size();
return result;
}
@@ -17,12 +17,12 @@ public class Means {
double numerator = 0.0;
double denominator = 0.0;
- for (double val : values) {
+ for (final double val : values) {
numerator += Math.pow(val, 2);
denominator += val;
}
- double result = numerator / denominator;
+ final double result = numerator / denominator;
return result;
}
@@ -38,7 +38,7 @@ public class Means {
denominator += (weights[i] * values.get(i));
}
- double result = numerator / denominator;
+ final double result = numerator / denominator;
return result;
}
}
diff --git a/src/main/java/azgracompress/utilities/MinMaxResult.java b/src/main/java/cz/it4i/qcmp/utilities/MinMaxResult.java
similarity index 75%
rename from src/main/java/azgracompress/utilities/MinMaxResult.java
rename to src/main/java/cz/it4i/qcmp/utilities/MinMaxResult.java
index 5a37e75..5181632 100644
--- a/src/main/java/azgracompress/utilities/MinMaxResult.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/MinMaxResult.java
@@ -1,10 +1,10 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
public class MinMaxResult<T> {
private final T min;
private final T max;
- MinMaxResult(T min, T max) {
+ MinMaxResult(final T min, final T max) {
this.min = min;
this.max = max;
}
diff --git a/src/main/java/azgracompress/utilities/Stopwatch.java b/src/main/java/cz/it4i/qcmp/utilities/Stopwatch.java
similarity index 90%
rename from src/main/java/azgracompress/utilities/Stopwatch.java
rename to src/main/java/cz/it4i/qcmp/utilities/Stopwatch.java
index c7088b6..e09e195 100644
--- a/src/main/java/azgracompress/utilities/Stopwatch.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/Stopwatch.java
@@ -1,4 +1,4 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
import org.jetbrains.annotations.NotNull;
@@ -13,7 +13,7 @@ public class Stopwatch {
@NotNull
public static Stopwatch startNew(final String name) {
- Stopwatch stopwatch = new Stopwatch(name);
+ final Stopwatch stopwatch = new Stopwatch(name);
stopwatch.start();
return stopwatch;
}
@@ -67,15 +67,15 @@ public class Stopwatch {
double H = 0;
S = MS / 1000.0;
- double fS = Math.floor(S);
+ final double fS = Math.floor(S);
MS = (S - fS) * 1000.0;
M = fS / 60.0;
- double fM = Math.floor(M);
+ final double fM = Math.floor(M);
S = (M - fM) * 60.0;
H = fM / 60.0;
- double fH = Math.floor(H);
+ final double fH = Math.floor(H);
M = (H - fH) * 60.0;
H = fH;
diff --git a/src/main/java/azgracompress/utilities/TypeConverter.java b/src/main/java/cz/it4i/qcmp/utilities/TypeConverter.java
similarity index 89%
rename from src/main/java/azgracompress/utilities/TypeConverter.java
rename to src/main/java/cz/it4i/qcmp/utilities/TypeConverter.java
index 3437885..daa4b3f 100644
--- a/src/main/java/azgracompress/utilities/TypeConverter.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/TypeConverter.java
@@ -1,6 +1,6 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
-import azgracompress.U16;
+import cz.it4i.qcmp.U16;
public class TypeConverter {
@@ -10,7 +10,7 @@ public class TypeConverter {
public static int[] unsignedShortBytesToIntArray(final byte[] bytes) {
assert (bytes.length % 2 == 0);
- int[] values = new int[bytes.length / 2];
+ final int[] values = new int[bytes.length / 2];
int index = 0;
for (int i = 0; i < bytes.length; i += 2) {
@@ -21,7 +21,7 @@ public class TypeConverter {
}
public static int[] shortArrayToIntArray(final short[] src) {
- int[] result = new int[src.length];
+ final int[] result = new int[src.length];
for (int i = 0; i < src.length; i++) {
// Hopefully call to shortToInt gets inlined by JVM.
result[i] = shortToInt(src[i]);
@@ -30,7 +30,7 @@ public class TypeConverter {
}
public static short[] intArrayToShortArray(final int[] src) {
- short[] result = new short[src.length];
+ final short[] result = new short[src.length];
for (int i = 0; i < src.length; i++) {
if (src[i] < 0 || src[i] > U16.Max) {
@@ -42,7 +42,7 @@ public class TypeConverter {
}
public static byte[] unsignedShortArrayToByteArray(final int[] data, final boolean littleEndian) {
- byte[] buffer = new byte[data.length * 2];
+ final byte[] buffer = new byte[data.length * 2];
int j = 0;
for (final int v : data) {
@@ -58,7 +58,7 @@ public class TypeConverter {
}
public static byte[] unsignedShortArrayToByteArray(final short[] data, final boolean littleEndian) {
- byte[] buffer = new byte[data.length * 2];
+ final byte[] buffer = new byte[data.length * 2];
int j = 0;
for (final short v : data) {
@@ -74,7 +74,7 @@ public class TypeConverter {
}
public static byte[] intArrayToByteArray(final int[] data, final boolean littleEndian) {
- byte[] buffer = new byte[data.length * 4];
+ final byte[] buffer = new byte[data.length * 4];
int j = 0;
for (final int v : data) {
diff --git a/src/main/java/azgracompress/utilities/Utils.java b/src/main/java/cz/it4i/qcmp/utilities/Utils.java
similarity index 88%
rename from src/main/java/azgracompress/utilities/Utils.java
rename to src/main/java/cz/it4i/qcmp/utilities/Utils.java
index 7ec9b1e..5c00075 100644
--- a/src/main/java/azgracompress/utilities/Utils.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/Utils.java
@@ -1,7 +1,7 @@
-package azgracompress.utilities;
+package cz.it4i.qcmp.utilities;
-import azgracompress.U16;
-import azgracompress.data.Range;
+import cz.it4i.qcmp.U16;
+import cz.it4i.qcmp.data.Range;
import java.util.ArrayList;
@@ -13,7 +13,7 @@ public class Utils {
}
public static double calculatePsnr(final double mse, final int signalMax) {
- double psnr = 10.0 * Math.log10((Math.pow(signalMax, 2) / mse));
+ final double psnr = 10.0 * Math.log10((Math.pow(signalMax, 2) / mse));
return psnr;
}
@@ -56,22 +56,22 @@ public class Utils {
public static int[] getDifference(final int[] original, final int[] transformed) {
assert (original.length == transformed.length) : "Array lengths doesn't match";
- int[] difference = new int[original.length];
+ final int[] difference = new int[original.length];
for (int i = 0; i < original.length; i++) {
difference[i] = (original[i] - transformed[i]);
}
return difference;
}
- public static int[] asAbsoluteValues(int[] values) {
- int[] absValues = new int[values.length];
+ public static int[] asAbsoluteValues(final int[] values) {
+ final int[] absValues = new int[values.length];
for (int i = 0; i < values.length; i++) {
absValues[i] = Math.abs(values[i]);
}
return absValues;
}
- public static void applyAbsFunction(int[] values) {
+ public static void applyAbsFunction(final int[] values) {
for (int i = 0; i < values.length; i++) {
values[i] = Math.abs(values[i]);
}
@@ -101,7 +101,7 @@ public class Utils {
* @return Pixel value frequencies.
*/
public static double[] calculatePixelFrequencies(final int[] data) {
- double[] frequencies = new double[U16.Max + 1];
+ final double[] frequencies = new double[U16.Max + 1];
for (final int pixelValue : data) {
++frequencies[pixelValue];
}
@@ -123,7 +123,7 @@ public class Utils {
double entropy = 0.0;
- for (double pixelProbability : pixelProbabilities) {
+ for (final double pixelProbability : pixelProbabilities) {
if (pixelProbability > 0.0) {
entropy += pixelProbability * log2(pixelProbability);
}
--
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