diff --git a/src/main/java/azgracompress/cache/CacheFileHeader.java b/src/main/java/azgracompress/cache/CacheFileHeader.java
index 0e6b5c1d1e02e582f69cd06a3cd8d527e9909751..d55ef41e79a6d208c05f31013548e16dc9cc4464 100644
--- a/src/main/java/azgracompress/cache/CacheFileHeader.java
+++ b/src/main/java/azgracompress/cache/CacheFileHeader.java
@@ -3,6 +3,7 @@ package azgracompress.cache;
import azgracompress.data.V2i;
import azgracompress.data.V3i;
import azgracompress.fileformat.QuantizationType;
+import azgracompress.utilities.Utils;
import java.io.DataInputStream;
import java.io.DataOutputStream;
@@ -22,29 +23,29 @@ public class CacheFileHeader {
private int vectorSizeY;
private int vectorSizeZ;
- public void setQuantizationType(QuantizationType quantizationType) {
+ public void setQuantizationType(final QuantizationType quantizationType) {
this.quantizationType = quantizationType;
}
- public void setCodebookSize(int codebookSize) {
+ public void setCodebookSize(final int codebookSize) {
this.codebookSize = codebookSize;
}
- public void setTrainFileName(String trainFileName) {
+ public void setTrainFileName(final String trainFileName) {
this.trainFileName = trainFileName;
this.trainFileNameSize = this.trainFileName.length();
}
- public void setVectorSizeX(int vectorSizeX) {
+ public void setVectorSizeX(final int vectorSizeX) {
this.vectorSizeX = vectorSizeX;
}
- public void setVectorSizeY(int vectorSizeY) {
+ public void setVectorSizeY(final int vectorSizeY) {
this.vectorSizeY = vectorSizeY;
}
- public void setVectorSizeZ(int vectorSizeZ) {
+ public void setVectorSizeZ(final int vectorSizeZ) {
this.vectorSizeZ = vectorSizeZ;
}
@@ -56,6 +57,10 @@ public class CacheFileHeader {
return codebookSize;
}
+ public int getBitsPerCodebookIndex() {
+ return (int) Utils.log2(codebookSize);
+ }
+
public int getTrainFileNameSize() {
return trainFileNameSize;
}
@@ -86,7 +91,7 @@ public class CacheFileHeader {
* @param outputStream Data output stream.
* @throws IOException when fails to write the header to stream.
*/
- public void writeToStream(DataOutputStream outputStream) throws IOException {
+ public void writeToStream(final DataOutputStream outputStream) throws IOException {
outputStream.writeBytes(QCMP_CACHE_MAGIC_VALUE);
outputStream.writeByte(quantizationType.getValue());
outputStream.writeShort(codebookSize);
@@ -122,18 +127,23 @@ public class CacheFileHeader {
*
* @param inputStream Data input stream.
*/
- public void readFromStream(DataInputStream inputStream) throws IOException {
+ public void readFromStream(final DataInputStream inputStream) throws IOException {
final int MIN_AVAIL = 9;
if (inputStream.available() < MIN_AVAIL) {
throw new IOException("Invalid file. File too small.");
}
- byte[] magicBuffer = new byte[QCMP_CACHE_MAGIC_VALUE.length()];
+ final byte[] magicBuffer = new byte[QCMP_CACHE_MAGIC_VALUE.length()];
- final int readFromMagic = inputStream.read(magicBuffer, 0, QCMP_CACHE_MAGIC_VALUE.length());
- if (readFromMagic != QCMP_CACHE_MAGIC_VALUE.length()) {
- throw new IOException("Invalid file type. Unable to read magic value");
+ int toRead = QCMP_CACHE_MAGIC_VALUE.length();
+ while (toRead > 0) {
+ final int read = inputStream.read(magicBuffer, QCMP_CACHE_MAGIC_VALUE.length() - toRead, toRead);
+ if (read < 0) {
+ throw new IOException("Invalid file type. Unable to read magic value");
+ }
+ toRead -= read;
}
+
magicValue = new String(magicBuffer);
if (!magicValue.equals(QCMP_CACHE_MAGIC_VALUE)) {
throw new IOException("Invalid file type. Wrong magic value.");
@@ -142,8 +152,15 @@ public class CacheFileHeader {
codebookSize = inputStream.readUnsignedShort();
trainFileNameSize = inputStream.readUnsignedShort();
- byte[] fileNameBuffer = new byte[trainFileNameSize];
- final int readBytes = inputStream.read(fileNameBuffer, 0, trainFileNameSize);
+ final byte[] fileNameBuffer = new byte[trainFileNameSize];
+
+
+ toRead = trainFileNameSize;
+ while (toRead > 0) {
+ toRead -= inputStream.read(fileNameBuffer, trainFileNameSize - toRead, toRead);
+ }
+
+
trainFileName = new String(fileNameBuffer);
vectorSizeX = inputStream.readUnsignedShort();
diff --git a/src/main/java/azgracompress/compression/ImageCompressor.java b/src/main/java/azgracompress/compression/ImageCompressor.java
index 4c23d1db16774067e1a9f1ddca6f1a1af8919056..2ace74cb14d8e7b01135d26f64df0b715e1ed568 100644
--- a/src/main/java/azgracompress/compression/ImageCompressor.java
+++ b/src/main/java/azgracompress/compression/ImageCompressor.java
@@ -15,7 +15,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
private final IImageCompressor imageCompressor;
- public ImageCompressor(CompressionOptions options) {
+ public ImageCompressor(final CompressionOptions options) {
super(options);
imageCompressor = getImageCompressor();
}
@@ -25,6 +25,10 @@ public class ImageCompressor extends CompressorDecompressorBase {
imageCompressor.preloadGlobalCodebook(codebookCacheFile);
}
+ public int getBitsPerCodebookIndex() {
+ return this.options.getBitsPerCodebookIndex();
+ }
+
/**
* Set InputData object for compressor.
*
@@ -43,7 +47,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
* @return Correct implementation of image compressor or null if configuration is not valid.
*/
private IImageCompressor getImageCompressor() {
- IImageCompressor compressor;
+ final IImageCompressor compressor;
switch (options.getQuantizationType()) {
case Scalar:
compressor = new SQImageCompressor(options);
@@ -80,7 +84,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
}
try {
imageCompressor.trainAndSaveCodebook();
- } catch (ImageCompressionException e) {
+ } catch (final ImageCompressionException e) {
System.err.println(e.getMessage());
e.printStackTrace();
return false;
@@ -91,7 +95,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
public int streamCompressChunk(final OutputStream outputStream, final InputData inputData) {
assert (imageCompressor != null);
- try (DataOutputStream compressStream = new DataOutputStream(new BufferedOutputStream(outputStream, 8192))) {
+ try (final DataOutputStream compressStream = new DataOutputStream(new BufferedOutputStream(outputStream, 8192))) {
final long[] chunkSizes = imageCompressor.compressStreamChunk(compressStream, inputData);
for (final long chunkSize : chunkSizes) {
assert (chunkSize < U16.Max);
@@ -99,11 +103,11 @@ public class ImageCompressor extends CompressorDecompressorBase {
}
return (4 * 2) + ((int) Arrays.stream(chunkSizes).sum()) + (chunkSizes.length * 2);
- } catch (ImageCompressionException ice) {
+ } catch (final ImageCompressionException ice) {
System.err.println(ice.getMessage());
return -1;
- } catch (Exception e) {
+ } catch (final Exception e) {
System.err.println(e.getMessage());
e.printStackTrace();
return -1;
@@ -118,8 +122,8 @@ public class ImageCompressor extends CompressorDecompressorBase {
long[] planeDataSizes = null;
- try (FileOutputStream fos = new FileOutputStream(options.getOutputFilePath(), false);
- DataOutputStream compressStream = new DataOutputStream(new BufferedOutputStream(fos, 8192))) {
+ try (final FileOutputStream fos = new FileOutputStream(options.getOutputFilePath(), false);
+ final DataOutputStream compressStream = new DataOutputStream(new BufferedOutputStream(fos, 8192))) {
final QCMPFileHeader header = createHeader();
header.writeHeader(compressStream);
@@ -129,10 +133,10 @@ public class ImageCompressor extends CompressorDecompressorBase {
if (options.isVerbose()) {
reportCompressionRatio(header, compressStream.size());
}
- } catch (ImageCompressionException ex) {
+ } catch (final ImageCompressionException ex) {
System.err.println(ex.getMessage());
return false;
- } catch (Exception e) {
+ } catch (final Exception e) {
e.printStackTrace();
return false;
}
@@ -142,10 +146,10 @@ public class ImageCompressor extends CompressorDecompressorBase {
return false;
}
- try (RandomAccessFile raf = new RandomAccessFile(options.getOutputFilePath(), "rw")) {
+ try (final RandomAccessFile raf = new RandomAccessFile(options.getOutputFilePath(), "rw")) {
raf.seek(PLANE_DATA_SIZES_OFFSET);
writePlaneDataSizes(raf, planeDataSizes);
- } catch (IOException ex) {
+ } catch (final IOException ex) {
ex.printStackTrace();
return false;
}
@@ -160,7 +164,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
* @param planeDataSizes Written compressed plane sizes.
* @throws IOException when fails to write plane data size.
*/
- private void writePlaneDataSizes(RandomAccessFile outStream, final long[] planeDataSizes) throws IOException {
+ private void writePlaneDataSizes(final RandomAccessFile outStream, final long[] planeDataSizes) throws IOException {
for (final long planeDataSize : planeDataSizes) {
outStream.writeInt((int) planeDataSize);
}
@@ -189,7 +193,7 @@ public class ImageCompressor extends CompressorDecompressorBase {
* @return Valid QCMPFile header for compressed file.
*/
private QCMPFileHeader createHeader() {
- QCMPFileHeader header = new QCMPFileHeader();
+ final QCMPFileHeader header = new QCMPFileHeader();
header.setQuantizationType(options.getQuantizationType());
diff --git a/src/main/java/azgracompress/fileformat/QCMPFileHeader.java b/src/main/java/azgracompress/fileformat/QCMPFileHeader.java
index 0a0755a411ced5afb2f0ee1ac8d6784221f83084..7f8ffd75af3a6d73f2dff5bf04b1e9827ae4c26a 100644
--- a/src/main/java/azgracompress/fileformat/QCMPFileHeader.java
+++ b/src/main/java/azgracompress/fileformat/QCMPFileHeader.java
@@ -65,12 +65,12 @@ public class QCMPFileHeader implements Cloneable {
public QCMPFileHeader copyOf() {
try {
return (QCMPFileHeader) this.clone();
- } catch (CloneNotSupportedException e) {
+ } catch (final CloneNotSupportedException e) {
return null;
}
}
- public void writeHeader(DataOutputStream outputStream) throws IOException {
+ public void writeHeader(final DataOutputStream outputStream) throws IOException {
outputStream.writeBytes(QCMP_MAGIC_VALUE);
outputStream.writeByte(quantizationType.getValue());
@@ -95,16 +95,21 @@ public class QCMPFileHeader implements Cloneable {
}
}
- public boolean readHeader(DataInputStream inputStream) throws IOException {
+ public boolean readHeader(final DataInputStream inputStream) throws IOException {
if (inputStream.available() < BASE_QCMP_HEADER_SIZE) {
return false;
}
- byte[] magicBuffer = new byte[QCMP_MAGIC_VALUE.length()];
- final int readFromMagic = inputStream.read(magicBuffer, 0, QCMP_MAGIC_VALUE.length());
- if (readFromMagic != QCMP_MAGIC_VALUE.length()) {
- // Invalid magic value.
- return false;
+ final byte[] magicBuffer = new byte[QCMP_MAGIC_VALUE.length()];
+
+ int toRead = QCMP_MAGIC_VALUE.length();
+ while (toRead > 0) {
+ final int read = inputStream.read(magicBuffer, QCMP_MAGIC_VALUE.length() - toRead, toRead);
+ if (read < 0) {
+ // Invalid magic value.
+ return false;
+ }
+ toRead -= read;
}
magicValue = new String(magicBuffer);
@@ -142,7 +147,7 @@ public class QCMPFileHeader implements Cloneable {
return quantizationType;
}
- public void setQuantizationType(QuantizationType quantizationType) {
+ public void setQuantizationType(final QuantizationType quantizationType) {
this.quantizationType = quantizationType;
}
@@ -150,7 +155,7 @@ public class QCMPFileHeader implements Cloneable {
return bitsPerCodebookIndex;
}
- public void setBitsPerCodebookIndex(byte bitsPerCodebookIndex) {
+ public void setBitsPerCodebookIndex(final byte bitsPerCodebookIndex) {
this.bitsPerCodebookIndex = bitsPerCodebookIndex;
}
@@ -158,7 +163,7 @@ public class QCMPFileHeader implements Cloneable {
return codebookPerPlane;
}
- public void setCodebookPerPlane(boolean codebookPerPlane) {
+ public void setCodebookPerPlane(final boolean codebookPerPlane) {
this.codebookPerPlane = codebookPerPlane;
}
@@ -166,7 +171,7 @@ public class QCMPFileHeader implements Cloneable {
return imageSizeX;
}
- public void setImageSizeX(int imageSizeX) {
+ public void setImageSizeX(final int imageSizeX) {
this.imageSizeX = imageSizeX;
}
@@ -174,7 +179,7 @@ public class QCMPFileHeader implements Cloneable {
return imageSizeY;
}
- public void setImageSizeY(int imageSizeY) {
+ public void setImageSizeY(final int imageSizeY) {
this.imageSizeY = imageSizeY;
}
@@ -186,7 +191,7 @@ public class QCMPFileHeader implements Cloneable {
return new V3i(imageSizeX, imageSizeY, imageSizeZ);
}
- public void setImageSizeZ(int imageSizeZ) {
+ public void setImageSizeZ(final int imageSizeZ) {
this.imageSizeZ = imageSizeZ;
}
@@ -194,7 +199,7 @@ public class QCMPFileHeader implements Cloneable {
return vectorSizeX;
}
- public void setVectorSizeX(int vectorSizeX) {
+ public void setVectorSizeX(final int vectorSizeX) {
this.vectorSizeX = vectorSizeX;
}
@@ -202,7 +207,7 @@ public class QCMPFileHeader implements Cloneable {
return vectorSizeY;
}
- public void setVectorSizeY(int vectorSizeY) {
+ public void setVectorSizeY(final int vectorSizeY) {
this.vectorSizeY = vectorSizeY;
}
@@ -210,7 +215,7 @@ public class QCMPFileHeader implements Cloneable {
return vectorSizeZ;
}
- public void setVectorSizeZ(int vectorSizeZ) {
+ public void setVectorSizeZ(final int vectorSizeZ) {
this.vectorSizeZ = vectorSizeZ;
}
diff --git a/src/main/java/azgracompress/io/InBitStream.java b/src/main/java/azgracompress/io/InBitStream.java
index 7945e4e5fc4595a141cfdd4ab868f517c96555dd..9293c4b5e28dbddfc8f6fb1a0c8d991baa4f36f5 100644
--- a/src/main/java/azgracompress/io/InBitStream.java
+++ b/src/main/java/azgracompress/io/InBitStream.java
@@ -5,8 +5,8 @@ import java.io.InputStream;
public class InBitStream implements AutoCloseable {
- private InputStream inputStream;
- private byte[] buffer;
+ private final InputStream inputStream;
+ private final byte[] buffer;
private int bufferPosition;
private int bytesAvailable;
@@ -17,7 +17,7 @@ public class InBitStream implements AutoCloseable {
private boolean allowReadFromUnderlyingStream = true;
- public InBitStream(InputStream inputStream, final int bitsPerValue, final int bufferSize) {
+ public InBitStream(final InputStream inputStream, final int bitsPerValue, final int bufferSize) {
this.inputStream = inputStream;
this.bitsPerValue = bitsPerValue;
@@ -29,8 +29,17 @@ public class InBitStream implements AutoCloseable {
bitBufferSize = 0;
}
+ /**
+ * Read whole buffer from input stream.
+ *
+ * @throws IOException when unable to read from input stream.
+ */
public void readToBuffer() throws IOException {
- bytesAvailable = inputStream.read(buffer, 0, buffer.length);
+ int toRead = buffer.length;
+ while (toRead > 0) {
+ toRead -= inputStream.read(buffer, buffer.length - toRead, toRead);
+ }
+ bytesAvailable = buffer.length;
bufferPosition = 0;
}
@@ -62,7 +71,7 @@ public class InBitStream implements AutoCloseable {
readByteToBitBuffer();
}
--bitBufferSize;
- int bit = bitBuffer & (1 << bitBufferSize);
+ final int bit = bitBuffer & (1 << bitBufferSize);
return (bit > 0 ? 1 : 0);
}
@@ -79,7 +88,7 @@ public class InBitStream implements AutoCloseable {
}
public int[] readNValues(final int n) throws IOException {
- int[] values = new int[n];
+ final int[] values = new int[n];
for (int i = 0; i < n; i++) {
values[i] = readValue();
}
diff --git a/src/main/java/azgracompress/io/loader/RawDataLoader.java b/src/main/java/azgracompress/io/loader/RawDataLoader.java
index 385f17f8d66343b53f0b9d91c09d40ed9b7275c6..7dc0e781c5c54ef09b654788c5c04f2cd889fc33 100644
--- a/src/main/java/azgracompress/io/loader/RawDataLoader.java
+++ b/src/main/java/azgracompress/io/loader/RawDataLoader.java
@@ -22,9 +22,9 @@ public final class RawDataLoader extends BasicLoader implements IPlaneLoader {
@Override
public int[] loadPlaneData(final int plane) throws IOException {
- byte[] buffer;
+ final byte[] buffer;
- try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath())) {
+ try (final FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath())) {
final long planeSize = (long) dims.getX() * (long) dims.getY() * 2;
final long expectedFileSize = planeSize * dims.getZ();
final long fileSize = fileStream.getChannel().size();
@@ -41,15 +41,21 @@ public final class RawDataLoader extends BasicLoader implements IPlaneLoader {
if (fileStream.skip(planeOffset) != planeOffset) {
throw new IOException("Failed to skip.");
}
- if (fileStream.read(buffer, 0, (int) planeSize) != planeSize) {
- throw new IOException("Read wrong number of bytes.");
+
+ int toRead = (int) planeSize;
+ while (toRead > 0) {
+ final int read = fileStream.read(buffer, (int) planeSize - toRead, toRead);
+ if (read < 0) {
+ throw new IOException("Read wrong number of bytes.");
+ }
+ toRead -= read;
}
}
return TypeConverter.unsignedShortBytesToIntArray(buffer);
}
@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) {
@@ -65,12 +71,12 @@ public final class RawDataLoader 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);
- try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
- DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
+ try (final FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
+ final DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
int lastIndex = 0;
int valIndex = 0;
@@ -104,10 +110,10 @@ public final class RawDataLoader extends BasicLoader implements IPlaneLoader {
throw new IOException("RawFile size is too big.");
}
- int[] values = new int[(int) dataSize];
+ final int[] values = new int[(int) dataSize];
- try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
- DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
+ try (final FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
+ final DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
for (int i = 0; i < (int) dataSize; i++) {
values[i] = dis.readUnsignedShort();
@@ -123,7 +129,7 @@ public final class RawDataLoader 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);
}