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BioinformaticDataCompression
BigDataViewer_Core_Extension
Commits
eb9bde3f
Commit
eb9bde3f
authored
8 years ago
by
Tobias Pietzsch
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remove deprecated WriteSequenceToHdf5 methods
parent
ce4c39d9
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1 changed file
src/main/java/bdv/export/WriteSequenceToHdf5.java
+10
-90
10 additions, 90 deletions
src/main/java/bdv/export/WriteSequenceToHdf5.java
with
10 additions
and
90 deletions
src/main/java/bdv/export/WriteSequenceToHdf5.java
+
10
−
90
View file @
eb9bde3f
...
...
@@ -6,13 +6,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
...
...
@@ -37,6 +37,14 @@ import java.util.Map;
import
java.util.Map.Entry
;
import
java.util.concurrent.CountDownLatch
;
import
bdv.img.hdf5.Hdf5ImageLoader
;
import
bdv.img.hdf5.Partition
;
import
bdv.img.hdf5.Util
;
import
bdv.spimdata.SequenceDescriptionMinimal
;
import
ch.systemsx.cisd.hdf5.HDF5Factory
;
import
ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures
;
import
ch.systemsx.cisd.hdf5.IHDF5Reader
;
import
ch.systemsx.cisd.hdf5.IHDF5Writer
;
import
mpicbg.spim.data.XmlHelpers
;
import
mpicbg.spim.data.generic.sequence.AbstractSequenceDescription
;
import
mpicbg.spim.data.generic.sequence.BasicImgLoader
;
...
...
@@ -58,14 +66,6 @@ import net.imglib2.iterator.LocalizingIntervalIterator;
import
net.imglib2.type.numeric.RealType
;
import
net.imglib2.type.numeric.integer.UnsignedShortType
;
import
net.imglib2.view.Views
;
import
bdv.img.hdf5.Hdf5ImageLoader
;
import
bdv.img.hdf5.Partition
;
import
bdv.img.hdf5.Util
;
import
bdv.spimdata.SequenceDescriptionMinimal
;
import
ch.systemsx.cisd.hdf5.HDF5Factory
;
import
ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures
;
import
ch.systemsx.cisd.hdf5.IHDF5Reader
;
import
ch.systemsx.cisd.hdf5.IHDF5Writer
;
/**
* Create a hdf5 files containing image data from all views and all timepoints
...
...
@@ -962,84 +962,4 @@ public class WriteSequenceToHdf5
for
(
int
j
=
0
;
j
<
numBlockPixels
;
++
j
)
out
.
next
().
setReal
(
accumulator
[
j
]
*
scale
);
}
/**
* DEPRECATED. Use
* {@link #writeHdf5File(AbstractSequenceDescription, Map, boolean, File, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter)}
* instead.
*/
@Deprecated
public
static
void
writeHdf5File
(
final
AbstractSequenceDescription
<
?,
?,
?
>
seq
,
final
Map
<
Integer
,
ExportMipmapInfo
>
perSetupMipmapInfo
,
final
boolean
deflate
,
final
File
hdf5File
,
final
LoopbackHeuristic
loopbackHeuristic
,
final
AfterEachPlane
afterEachPlane
,
final
ProgressWriter
progressWriter
)
{
final
int
numThreads
=
Math
.
max
(
1
,
Runtime
.
getRuntime
().
availableProcessors
()
-
2
);
writeHdf5File
(
seq
,
perSetupMipmapInfo
,
deflate
,
hdf5File
,
loopbackHeuristic
,
afterEachPlane
,
numThreads
,
progressWriter
);
}
/**
* DEPRECATED. Use
* {@link #writeHdf5File(AbstractSequenceDescription, int[][], int[][], boolean, File, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter)}
* instead.
*/
@Deprecated
public
static
void
writeHdf5File
(
final
AbstractSequenceDescription
<
?,
?,
?
>
seq
,
final
int
[][]
resolutions
,
final
int
[][]
subdivisions
,
final
boolean
deflate
,
final
File
hdf5File
,
final
LoopbackHeuristic
loopbackHeuristic
,
final
AfterEachPlane
afterEachPlane
,
final
ProgressWriter
progressWriter
)
{
final
int
numThreads
=
Math
.
max
(
1
,
Runtime
.
getRuntime
().
availableProcessors
()
-
2
);
writeHdf5File
(
seq
,
resolutions
,
subdivisions
,
deflate
,
hdf5File
,
loopbackHeuristic
,
afterEachPlane
,
numThreads
,
progressWriter
);
}
/**
* DEPRECATED. Use
* {@link #writeHdf5PartitionFile(AbstractSequenceDescription, Map, boolean, Partition, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter)}
* instead.
*/
@Deprecated
public
static
void
writeHdf5PartitionFile
(
final
AbstractSequenceDescription
<
?,
?,
?
>
seq
,
final
Map
<
Integer
,
ExportMipmapInfo
>
perSetupMipmapInfo
,
final
boolean
deflate
,
final
Partition
partition
,
final
LoopbackHeuristic
loopbackHeuristic
,
final
AfterEachPlane
afterEachPlane
,
final
ProgressWriter
progressWriter
)
{
final
int
numThreads
=
Math
.
max
(
1
,
Runtime
.
getRuntime
().
availableProcessors
()
-
2
);
writeHdf5PartitionFile
(
seq
,
perSetupMipmapInfo
,
deflate
,
partition
,
loopbackHeuristic
,
afterEachPlane
,
numThreads
,
progressWriter
);
}
/**
* DEPRECATED. Use
* {@link #writeViewToHdf5PartitionFile(RandomAccessibleInterval, Partition, int, int, ExportMipmapInfo, boolean, boolean, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter)}
* instead.
*/
@Deprecated
public
static
void
writeViewToHdf5PartitionFile
(
final
RandomAccessibleInterval
<
UnsignedShortType
>
img
,
final
Partition
partition
,
final
int
timepointIdPartition
,
final
int
setupIdPartition
,
final
ExportMipmapInfo
mipmapInfo
,
final
boolean
writeMipmapInfo
,
final
boolean
deflate
,
final
LoopbackHeuristic
loopbackHeuristic
,
final
AfterEachPlane
afterEachPlane
,
final
ProgressWriter
progressWriter
)
{
final
int
numThreads
=
Math
.
max
(
1
,
Runtime
.
getRuntime
().
availableProcessors
()
-
2
);
writeViewToHdf5PartitionFile
(
img
,
partition
,
timepointIdPartition
,
setupIdPartition
,
mipmapInfo
,
writeMipmapInfo
,
deflate
,
loopbackHeuristic
,
afterEachPlane
,
numThreads
,
progressWriter
);
}
}
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