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BioinformaticDataCompression
BigDataViewer_Server_Extension
Commits
0a170f6b
Commit
0a170f6b
authored
9 years ago
by
Tobias Pietzsch
Browse files
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Plain Diff
fix wrt spim-data 2.0.0 API changes
parent
b2d4e0df
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2 changed files
src/main/java/bdv/server/CellHandler.java
+35
-26
35 additions, 26 deletions
src/main/java/bdv/server/CellHandler.java
src/main/java/bdv/util/ThumbnailGenerator.java
+2
-1
2 additions, 1 deletion
src/main/java/bdv/util/ThumbnailGenerator.java
with
37 additions
and
27 deletions
src/main/java/bdv/server/CellHandler.java
+
35
−
26
View file @
0a170f6b
package
bdv.server
;
import
bdv.BigDataViewer
;
import
bdv.img.cache.CacheHints
;
import
bdv.img.cache.LoadingStrategy
;
import
bdv.img.cache.VolatileCell
;
import
bdv.img.cache.VolatileGlobalCellCache
;
import
bdv.img.hdf5.Hdf5ImageLoader
;
import
bdv.img.remote.AffineTransform3DJsonSerializer
;
import
bdv.img.remote.RemoteImageLoader
;
import
bdv.img.remote.RemoteImageLoaderMetaData
;
import
bdv.spimdata.SequenceDescriptionMinimal
;
import
bdv.spimdata.SpimDataMinimal
;
import
bdv.spimdata.XmlIoSpimDataMinimal
;
import
bdv.util.ThumbnailGenerator
;
import
java.awt.image.BufferedImage
;
import
java.io.File
;
import
java.io.IOException
;
import
java.io.OutputStream
;
import
java.io.PrintWriter
;
import
java.io.StringWriter
;
import
java.nio.file.Files
;
import
java.nio.file.Path
;
import
java.nio.file.Paths
;
import
com.google.gson.GsonBuilder
;
import
javax.imageio.ImageIO
;
import
javax.servlet.http.HttpServletRequest
;
import
javax.servlet.http.HttpServletResponse
;
import
mpicbg.spim.data.SpimDataException
;
import
net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray
;
...
...
@@ -29,21 +27,30 @@ import org.jdom2.input.SAXBuilder;
import
org.jdom2.output.Format
;
import
org.jdom2.output.XMLOutputter
;
import
javax.imageio.ImageIO
;
import
javax.servlet.http.HttpServletRequest
;
import
javax.servlet.http.HttpServletResponse
;
import
bdv.BigDataViewer
;
import
bdv.img.cache.CacheHints
;
import
bdv.img.cache.LoadingStrategy
;
import
bdv.img.cache.VolatileCell
;
import
bdv.img.cache.VolatileGlobalCellCache
;
import
bdv.img.hdf5.Hdf5ImageLoader
;
import
bdv.img.hdf5.Hdf5VolatileShortArrayLoader
;
import
bdv.img.remote.AffineTransform3DJsonSerializer
;
import
bdv.img.remote.RemoteImageLoader
;
import
bdv.img.remote.RemoteImageLoaderMetaData
;
import
bdv.spimdata.SequenceDescriptionMinimal
;
import
bdv.spimdata.SpimDataMinimal
;
import
bdv.spimdata.XmlIoSpimDataMinimal
;
import
bdv.util.ThumbnailGenerator
;
import
java.awt.image.BufferedImage
;
import
java.io.*
;
import
java.nio.file.Files
;
import
java.nio.file.Path
;
import
java.nio.file.Paths
;
import
com.google.gson.GsonBuilder
;
public
class
CellHandler
extends
ContextHandler
{
private
static
final
org
.
eclipse
.
jetty
.
util
.
log
.
Logger
LOG
=
Log
.
getLogger
(
CellHandler
.
class
);
private
final
VolatileGlobalCellCache
<
VolatileShortArray
>
cache
;
private
final
VolatileGlobalCellCache
cache
;
private
final
Hdf5VolatileShortArrayLoader
loader
;
private
final
CacheHints
cacheHints
;
...
...
@@ -91,6 +98,7 @@ public class CellHandler extends ContextHandler
final
Hdf5ImageLoader
imgLoader
=
(
Hdf5ImageLoader
)
seq
.
getImgLoader
();
cache
=
imgLoader
.
getCache
();
loader
=
imgLoader
.
getShortArrayLoader
();
cacheHints
=
new
CacheHints
(
LoadingStrategy
.
BLOCKING
,
0
,
false
);
// dataSetURL property is used for providing the XML file by replace
...
...
@@ -136,7 +144,7 @@ public class CellHandler extends ContextHandler
final
int
timepoint
=
Integer
.
parseInt
(
parts
[
2
]
);
final
int
setup
=
Integer
.
parseInt
(
parts
[
3
]
);
final
int
level
=
Integer
.
parseInt
(
parts
[
4
]
);
VolatileCell
<
VolatileShortArray
>
cell
=
cache
.
getGlobalIfCached
(
timepoint
,
setup
,
level
,
index
,
cacheHints
);
VolatileCell
<
?
>
cell
=
cache
.
getGlobalIfCached
(
timepoint
,
setup
,
level
,
index
,
cacheHints
);
if
(
cell
==
null
)
{
final
int
[]
cellDims
=
new
int
[]
{
...
...
@@ -147,10 +155,11 @@ public class CellHandler extends ContextHandler
Long
.
parseLong
(
parts
[
8
]
),
Long
.
parseLong
(
parts
[
9
]
),
Long
.
parseLong
(
parts
[
10
]
)
};
cell
=
cache
.
createGlobal
(
cellDims
,
cellMin
,
timepoint
,
setup
,
level
,
index
,
cacheHints
);
cell
=
cache
.
createGlobal
(
cellDims
,
cellMin
,
timepoint
,
setup
,
level
,
index
,
cacheHints
,
loader
);
}
final
short
[]
data
=
cell
.
getData
().
getCurrentStorageArray
();
@SuppressWarnings
(
"unchecked"
)
final
short
[]
data
=
(
(
VolatileCell
<
VolatileShortArray
>
)
cell
).
getData
().
getCurrentStorageArray
();
final
byte
[]
buf
=
new
byte
[
2
*
data
.
length
];
for
(
int
i
=
0
,
j
=
0
;
i
<
data
.
length
;
i
++
)
{
...
...
This diff is collapsed.
Click to expand it.
src/main/java/bdv/util/ThumbnailGenerator.java
+
2
−
1
View file @
0a170f6b
...
...
@@ -26,6 +26,7 @@ import bdv.tools.transformation.TransformedSource;
import
bdv.tools.transformation.XmlIoTransformedSources
;
import
bdv.viewer.Source
;
import
bdv.viewer.SourceAndConverter
;
import
bdv.viewer.render.AccumulateProjectorARGB
;
import
bdv.viewer.render.MultiResolutionRenderer
;
import
bdv.viewer.state.SourceGroup
;
import
bdv.viewer.state.SourceState
;
...
...
@@ -93,7 +94,7 @@ public class ThumbnailGenerator
}
}
final
ThumbnailTarget
renderTarget
=
new
ThumbnailTarget
();
new
MultiResolutionRenderer
(
renderTarget
,
new
PainterThread
(
null
),
new
double
[]
{
1
},
0
,
false
,
1
,
null
,
false
,
new
Cache
.
Dummy
()
).
paint
(
state
);
new
MultiResolutionRenderer
(
renderTarget
,
new
PainterThread
(
null
),
new
double
[]
{
1
},
0
,
false
,
1
,
null
,
false
,
AccumulateProjectorARGB
.
factory
,
new
Cache
.
Dummy
()
).
paint
(
state
);
return
renderTarget
.
bi
;
}
...
...
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