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BioinformaticDataCompression
QcmpCompressionLibrary
Commits
17ca80e1
Commit
17ca80e1
authored
4 years ago
by
Vojtech Moravec
Browse files
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Plain Diff
Fix stream decompression.
parent
b6806878
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Changes
1
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1 changed file
src/main/java/azgracompress/compression/ImageDecompressor.java
+11
-7
11 additions, 7 deletions
...ain/java/azgracompress/compression/ImageDecompressor.java
with
11 additions
and
7 deletions
src/main/java/azgracompress/compression/ImageDecompressor.java
+
11
−
7
View file @
17ca80e1
...
@@ -10,6 +10,7 @@ import azgracompress.utilities.Utils;
...
@@ -10,6 +10,7 @@ import azgracompress.utilities.Utils;
import
org.jetbrains.annotations.Nullable
;
import
org.jetbrains.annotations.Nullable
;
import
java.io.*
;
import
java.io.*
;
import
java.util.Arrays
;
import
java.util.Optional
;
import
java.util.Optional
;
...
@@ -293,9 +294,12 @@ public class ImageDecompressor extends CompressorDecompressorBase {
...
@@ -293,9 +294,12 @@ public class ImageDecompressor extends CompressorDecompressorBase {
try
(
DataInputStream
dis
=
new
DataInputStream
(
new
BufferedInputStream
(
compressedStream
)))
{
try
(
DataInputStream
dis
=
new
DataInputStream
(
new
BufferedInputStream
(
compressedStream
)))
{
assert
(
dis
.
markSupported
());
assert
(
dis
.
markSupported
());
cachedHeader
.
setImageSizeX
(
dis
.
readUnsignedShort
());
final
QCMPFileHeader
header
=
cachedHeader
.
copyOf
();
cachedHeader
.
setImageSizeY
(
dis
.
readUnsignedShort
());
cachedHeader
.
setImageSizeZ
(
dis
.
readUnsignedShort
());
header
.
setImageSizeX
(
dis
.
readUnsignedShort
());
header
.
setImageSizeY
(
dis
.
readUnsignedShort
());
header
.
setImageSizeZ
(
dis
.
readUnsignedShort
());
final
int
chunkCount
=
dis
.
readUnsignedShort
();
final
int
chunkCount
=
dis
.
readUnsignedShort
();
final
long
[]
chunkSizes
=
new
long
[
chunkCount
];
final
long
[]
chunkSizes
=
new
long
[
chunkCount
];
...
@@ -303,7 +307,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
...
@@ -303,7 +307,7 @@ public class ImageDecompressor extends CompressorDecompressorBase {
dis
.
mark
(
contentLength
);
dis
.
mark
(
contentLength
);
{
{
int
toSkip
=
contentLength
-
(
4
*
2
);
int
toSkip
=
contentLength
-
(
(
4
*
2
)
+
(
chunkCount
*
2
))
;
while
(
toSkip
>
0
)
{
while
(
toSkip
>
0
)
{
int
skipped
=
dis
.
skipBytes
(
toSkip
);
int
skipped
=
dis
.
skipBytes
(
toSkip
);
assert
(
skipped
>
0
);
assert
(
skipped
>
0
);
...
@@ -311,16 +315,16 @@ public class ImageDecompressor extends CompressorDecompressorBase {
...
@@ -311,16 +315,16 @@ public class ImageDecompressor extends CompressorDecompressorBase {
}
}
assert
(
toSkip
==
0
);
assert
(
toSkip
==
0
);
for
(
int
i
=
0
;
i
<
chunkCount
;
i
++)
{
for
(
int
i
=
0
;
i
<
chunkCount
;
i
++)
{
chunkSizes
[
i
]
=
dis
.
read
In
t
();
chunkSizes
[
i
]
=
dis
.
read
UnsignedShor
t
();
}
}
}
}
dis
.
reset
();
dis
.
reset
();
cachedH
eader
.
setPlaneDataSizes
(
chunkSizes
);
h
eader
.
setPlaneDataSizes
(
chunkSizes
);
return
cachedDecompressor
.
decompressStreamMode
(
dis
,
cachedH
eader
);
return
cachedDecompressor
.
decompressStreamMode
(
dis
,
h
eader
);
}
catch
(
IOException
e
)
{
}
catch
(
IOException
e
)
{
throw
new
ImageDecompressionException
(
"Unable to decompress chunk of image from stream."
,
e
);
throw
new
ImageDecompressionException
(
"Unable to decompress chunk of image from stream."
,
e
);
}
}
...
...
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