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BioinformaticDataCompression
QcmpCompressionLibrary
Commits
68ad75ef
Commit
68ad75ef
authored
4 years ago
by
Vojtěch Moravec
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Prepare Voxel decompression in memory.
parent
7662a4e6
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src/main/java/azgracompress/compression/VQImageDecompressor.java
+84
-76
84 additions, 76 deletions
...n/java/azgracompress/compression/VQImageDecompressor.java
with
84 additions
and
76 deletions
src/main/java/azgracompress/compression/VQImageDecompressor.java
+
84
−
76
View file @
68ad75ef
...
...
@@ -11,12 +11,12 @@ import azgracompress.quantization.vector.CodebookEntry;
import
azgracompress.quantization.vector.VQCodebook
;
import
azgracompress.utilities.Stopwatch
;
import
azgracompress.utilities.TypeConverter
;
import
org.jetbrains.annotations.NotNull
;
import
java.io.DataInputStream
;
import
java.io.DataOutputStream
;
import
java.io.IOException
;
@SuppressWarnings
(
"DuplicatedCode"
)
public
class
VQImageDecompressor
extends
CompressorDecompressorBase
implements
IImageDecompressor
{
public
VQImageDecompressor
(
CompressionOptions
options
)
{
super
(
options
);
...
...
@@ -136,8 +136,8 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
final
int
planeDataSize
=
(
int
)
header
.
getPlaneDataSizes
()[
planeIndex
];
try
(
InBitStream
inBitStream
=
new
InBitStream
(
compressedStream
,
header
.
getBitsPerCodebookIndex
(),
planeDataSize
))
{
header
.
getBitsPerCodebookIndex
(),
planeDataSize
))
{
inBitStream
.
readToBuffer
();
inBitStream
.
setAllowReadFromUnderlyingStream
(
false
);
...
...
@@ -145,13 +145,13 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
for
(
int
vecIndex
=
0
;
vecIndex
<
planeVectorCount
;
vecIndex
++)
{
final
int
huffmanSymbol
=
decodeHuffmanSymbol
(
huffman
,
inBitStream
);
System
.
arraycopy
(
codebook
.
getVectors
()[
huffmanSymbol
].
getVector
(),
0
,
decompressedVectors
[
vecIndex
],
0
,
vectorSize
);
0
,
decompressedVectors
[
vecIndex
],
0
,
vectorSize
);
}
final
ImageU16
decompressedPlane
=
reconstructImageFromQuantizedVectors
(
decompressedVectors
,
qVector
,
header
.
getImageDims
());
qVector
,
header
.
getImageDims
());
decompressedPlaneData
=
TypeConverter
.
unsignedShortArrayToByteArray
(
decompressedPlane
.
getData
(),
false
);
}
catch
(
Exception
ex
)
{
...
...
@@ -167,10 +167,84 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
stopwatch
.
stop
();
reportProgressToListeners
(
planeIndex
,
planeCountForDecompression
,
"Decompressed plane %d in %s"
,
planeIndex
,
stopwatch
.
getElapsedTimeString
());
"Decompressed plane %d in %s"
,
planeIndex
,
stopwatch
.
getElapsedTimeString
());
}
}
@Override
public
void
decompressToBuffer
(
DataInputStream
compressedStream
,
short
[][]
buffer
,
QCMPFileHeader
header
)
throws
ImageDecompressionException
{
if
(
header
.
getQuantizationType
()
==
QuantizationType
.
Vector3D
)
{
decompressVoxelsToBuffer
(
compressedStream
,
buffer
,
header
);
return
;
}
// NOTE(Moravec): Think how to remove the duplicate code.
final
int
codebookSize
=
(
int
)
Math
.
pow
(
2
,
header
.
getBitsPerCodebookIndex
());
assert
(
header
.
getVectorSizeZ
()
==
1
);
final
int
vectorSize
=
header
.
getVectorSizeX
()
*
header
.
getVectorSizeY
()
*
header
.
getVectorSizeZ
();
final
int
planeCountForDecompression
=
header
.
getImageSizeZ
();
final
long
planeVectorCount
=
calculatePlaneVectorCount
(
header
);
final
V2i
qVector
=
new
V2i
(
header
.
getVectorSizeX
(),
header
.
getVectorSizeY
());
final
int
[]
huffmanSymbols
=
createHuffmanSymbols
(
codebookSize
);
VQCodebook
codebook
=
null
;
Huffman
huffman
=
null
;
if
(!
header
.
isCodebookPerPlane
())
{
// There is only one codebook.
codebook
=
readCodebook
(
compressedStream
,
codebookSize
,
vectorSize
);
huffman
=
createHuffmanCoder
(
huffmanSymbols
,
codebook
.
getVectorFrequencies
());
}
for
(
int
planeIndex
=
0
;
planeIndex
<
planeCountForDecompression
;
planeIndex
++)
{
if
(
header
.
isCodebookPerPlane
())
{
codebook
=
readCodebook
(
compressedStream
,
codebookSize
,
vectorSize
);
huffman
=
createHuffmanCoder
(
huffmanSymbols
,
codebook
.
getVectorFrequencies
());
}
assert
(
codebook
!=
null
&&
huffman
!=
null
);
final
int
planeDataSize
=
(
int
)
header
.
getPlaneDataSizes
()[
planeIndex
];
try
(
InBitStream
inBitStream
=
new
InBitStream
(
compressedStream
,
header
.
getBitsPerCodebookIndex
(),
planeDataSize
))
{
inBitStream
.
readToBuffer
();
inBitStream
.
setAllowReadFromUnderlyingStream
(
false
);
int
[][]
decompressedVectors
=
new
int
[(
int
)
planeVectorCount
][
vectorSize
];
for
(
int
vecIndex
=
0
;
vecIndex
<
planeVectorCount
;
vecIndex
++)
{
HuffmanNode
currentHuffmanNode
=
huffman
.
getRoot
();
boolean
bit
;
while
(!
currentHuffmanNode
.
isLeaf
())
{
bit
=
inBitStream
.
readBit
();
currentHuffmanNode
=
currentHuffmanNode
.
traverse
(
bit
);
}
System
.
arraycopy
(
codebook
.
getVectors
()[
currentHuffmanNode
.
getSymbol
()].
getVector
(),
0
,
decompressedVectors
[
vecIndex
],
0
,
vectorSize
);
}
final
ImageU16
decompressedPlane
=
reconstructImageFromQuantizedVectors
(
decompressedVectors
,
qVector
,
header
.
getImageDims
());
buffer
[
planeIndex
]
=
TypeConverter
.
intArrayToShortArray
(
decompressedPlane
.
getData
());
}
catch
(
Exception
ex
)
{
throw
new
ImageDecompressionException
(
"VQImageDecompressor::decompressToBuffer() - Unable to read indices from InBitStream."
,
ex
);
}
reportProgressToListeners
(
planeIndex
,
planeCountForDecompression
,
"Decompressed plane %d."
,
planeIndex
);
}
}
private
void
decompressVoxelsToBuffer
(
DataInputStream
compressedStream
,
short
[][]
buffer
,
QCMPFileHeader
header
)
throws
ImageDecompressionException
{
throw
new
ImageDecompressionException
(
"Implement this!!!"
);
}
private
void
decompressVoxels
(
DataInputStream
compressedStream
,
DataOutputStream
decompressStream
,
QCMPFileHeader
header
)
throws
ImageDecompressionException
{
...
...
@@ -209,7 +283,7 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
for
(
int
voxelIndex
=
0
;
voxelIndex
<
voxelLayerVoxelCount
;
voxelIndex
++)
{
final
int
huffmanSymbol
=
decodeHuffmanSymbol
(
huffman
,
inBitStream
);
System
.
arraycopy
(
codebook
.
getVectors
()[
huffmanSymbol
].
getVector
(),
0
,
decompressedVoxels
[
voxelIndex
],
0
,
vectorSize
);
0
,
decompressedVoxels
[
voxelIndex
],
0
,
vectorSize
);
}
final
Voxel
currentVoxel
=
new
Voxel
(
currentVoxelLayerDims
);
...
...
@@ -228,8 +302,8 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
stopwatch
.
stop
();
reportProgressToListeners
(
voxelLayerIndex
,
voxelLayerCount
,
"Decompressed voxel layer %d/%d in %s"
,
voxelLayerIndex
,
voxelLayerCount
,
stopwatch
.
getElapsedTimeString
());
"Decompressed voxel layer %d/%d in %s"
,
voxelLayerIndex
,
voxelLayerCount
,
stopwatch
.
getElapsedTimeString
());
}
}
...
...
@@ -240,70 +314,4 @@ public class VQImageDecompressor extends CompressorDecompressorBase implements I
}
return
currentHuffmanNode
.
getSymbol
();
}
@Override
public
void
decompressToBuffer
(
DataInputStream
compressedStream
,
short
[][]
buffer
,
QCMPFileHeader
header
)
throws
ImageDecompressionException
{
// TODO: Think how to remove the duplicate code.
final
int
codebookSize
=
(
int
)
Math
.
pow
(
2
,
header
.
getBitsPerCodebookIndex
());
assert
(
header
.
getVectorSizeZ
()
==
1
);
final
int
vectorSize
=
header
.
getVectorSizeX
()
*
header
.
getVectorSizeY
()
*
header
.
getVectorSizeZ
();
final
int
planeCountForDecompression
=
header
.
getImageSizeZ
();
final
long
planeVectorCount
=
calculatePlaneVectorCount
(
header
);
final
V2i
qVector
=
new
V2i
(
header
.
getVectorSizeX
(),
header
.
getVectorSizeY
());
final
int
[]
huffmanSymbols
=
createHuffmanSymbols
(
codebookSize
);
VQCodebook
codebook
=
null
;
Huffman
huffman
=
null
;
if
(!
header
.
isCodebookPerPlane
())
{
// There is only one codebook.
codebook
=
readCodebook
(
compressedStream
,
codebookSize
,
vectorSize
);
huffman
=
createHuffmanCoder
(
huffmanSymbols
,
codebook
.
getVectorFrequencies
());
}
for
(
int
planeIndex
=
0
;
planeIndex
<
planeCountForDecompression
;
planeIndex
++)
{
if
(
header
.
isCodebookPerPlane
())
{
codebook
=
readCodebook
(
compressedStream
,
codebookSize
,
vectorSize
);
huffman
=
createHuffmanCoder
(
huffmanSymbols
,
codebook
.
getVectorFrequencies
());
}
assert
(
codebook
!=
null
&&
huffman
!=
null
);
final
int
planeDataSize
=
(
int
)
header
.
getPlaneDataSizes
()[
planeIndex
];
try
(
InBitStream
inBitStream
=
new
InBitStream
(
compressedStream
,
header
.
getBitsPerCodebookIndex
(),
planeDataSize
))
{
inBitStream
.
readToBuffer
();
inBitStream
.
setAllowReadFromUnderlyingStream
(
false
);
int
[][]
decompressedVectors
=
new
int
[(
int
)
planeVectorCount
][
vectorSize
];
for
(
int
vecIndex
=
0
;
vecIndex
<
planeVectorCount
;
vecIndex
++)
{
HuffmanNode
currentHuffmanNode
=
huffman
.
getRoot
();
boolean
bit
;
while
(!
currentHuffmanNode
.
isLeaf
())
{
bit
=
inBitStream
.
readBit
();
currentHuffmanNode
=
currentHuffmanNode
.
traverse
(
bit
);
}
System
.
arraycopy
(
codebook
.
getVectors
()[
currentHuffmanNode
.
getSymbol
()].
getVector
(),
0
,
decompressedVectors
[
vecIndex
],
0
,
vectorSize
);
}
final
ImageU16
decompressedPlane
=
reconstructImageFromQuantizedVectors
(
decompressedVectors
,
qVector
,
header
.
getImageDims
());
buffer
[
planeIndex
]
=
TypeConverter
.
intArrayToShortArray
(
decompressedPlane
.
getData
());
}
catch
(
Exception
ex
)
{
throw
new
ImageDecompressionException
(
"VQImageDecompressor::decompressToBuffer() - Unable to read indices from InBitStream."
,
ex
);
}
reportProgressToListeners
(
planeIndex
,
planeCountForDecompression
,
"Decompressed plane %d."
,
planeIndex
);
}
}
}
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