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Merge pull request #1 from bigdataviewer/michael_heyde_masterarbeit 

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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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− 0
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Copyright (c) 2012 - 2015, Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch,
Jean-Yves Tinevez, HongKee Moon, Johannes Schindelin, Curtis Rueden
All rights reserved.
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
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
pom.xml
+ 38
− 5
View file @ 1ff7ef57
......@@ -6,11 +6,13 @@
<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-bigdataviewer</artifactId>
<version>2.1.4</version>
<version>2.2.0</version>
</parent>
<artifactId>bigdataviewer-core</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>2.0.1-SNAPSHOT</version>
<url>http://github.com/bigdataviewer/bigdataviewer-core</url>
<inceptionYear>2012</inceptionYear>
<name>BigDataViewer Core</name>
<description>BigDataViewer core classes with minimal dependencies</description>
......@@ -91,9 +93,40 @@
</repositories>
<scm>
<connection>scm:git:git://github.com/tpietzsch/bigdataviewer-core</connection>
<developerConnection>scm:git:git@github.com:tpietzsch/bigdataviewer-core</developerConnection>
<connection>scm:git:git://github.com/bigdataviewer/bigdataviewer-core</connection>
<developerConnection>scm:git:git@github.com:bigdataviewer/bigdataviewer-core</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/tpietzsch/bigdataviewer-core</url>
<url>https://github.com/bigdataviewer/bigdataviewer-core</url>
</scm>
<ciManagement>
<system>Jenkins</system>
<url>http://jenkins.imagej.net/job/BigDataViewer-Core/</url>
</ciManagement>
<licenses>
<license>
<name>BSD 2-Clause License</name>
<url>http://opensource.org/licenses/BSD-2-Clause</url>
<distribution>repo</distribution>
</license>
</licenses>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<configuration>
<licenseName>bsd_2</licenseName>
<copyrightOwners>Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch,
Jean-Yves Tinevez, HongKee Moon, Johannes Schindelin, Curtis Rueden</copyrightOwners>
<organizationName>BigDataViewer authors</organizationName>
<projectName>BigDataViewer core classes with minimal dependencies</projectName>
<roots>
<root>src/main/java</root>
<root>src/test/java</root>
</roots>
</configuration>
</plugin>
</plugins>
</build>
</project>
src/main/java/bdv/AbstractSpimSource.java
+ 31
− 3
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import java.util.HashSet;
......@@ -67,7 +95,7 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
? new HashSet< ViewId >()
: seq.getMissingViews().getMissingViews();
voxelDimensions = seq.getViewSetups().get( setupId ).getVoxelSize();
numMipmapLevels = ( ( ViewerImgLoader< ?, ? > ) seq.getImgLoader() ).numMipmapLevels( setupId );
numMipmapLevels = ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setupId ).numMipmapLevels();
currentSources = new RandomAccessibleInterval[ numMipmapLevels ];
currentInterpolatedSources = new RealRandomAccessible[ numMipmapLevels ][ numInterpolationMethods ];
currentSourceTransforms = new AffineTransform3D[ numMipmapLevels ];
......@@ -93,7 +121,7 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
final AffineTransform3D mipmapTransform = getMipmapTransforms()[ level ];
currentSourceTransforms[ level ].set( reg );
currentSourceTransforms[ level ].concatenate( mipmapTransform );
currentSources[ level ] = getImage( viewId, level );
currentSources[ level ] = getImage( timepointId, level );
for ( int method = 0; method < numInterpolationMethods; ++method )
currentInterpolatedSources[ level ][ method ] = Views.interpolate( Views.extendValue( currentSources[ level ], zero ), interpolatorFactories[ method ] );
}
......@@ -112,7 +140,7 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
protected abstract AffineTransform3D[] getMipmapTransforms();
protected abstract RandomAccessibleInterval< T > getImage( final ViewId viewId, final int level );
protected abstract RandomAccessibleInterval< T > getImage( final int timepointId, final int level );
@Override
public boolean isPresent( final int t )
......
src/main/java/bdv/AbstractViewerImgLoader.java deleted 100644 → 0
+ 0
− 36
View file @ 453d132d
package bdv;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
public abstract class AbstractViewerImgLoader< T, V extends Volatile< T > > implements ViewerImgLoader< T, V >
{
protected final T type;
protected final V volatileType;
public AbstractViewerImgLoader( final T type, final V volatileType )
{
this.type = type;
this.volatileType = volatileType;
}
@Override
public T getImageType()
{
return type;
}
@Override
public V getVolatileImageType()
{
return volatileType;
}
@Override
public RandomAccessibleInterval< T > getImage( final ViewId view )
{
return getImage( view, 0 );
}
}
src/main/java/bdv/AbstractViewerSetupImgLoader.java 0 → 100644
+ 64
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
public abstract class AbstractViewerSetupImgLoader< T, V extends Volatile< T > > implements ViewerSetupImgLoader< T, V >
{
protected final T type;
protected final V volatileType;
public AbstractViewerSetupImgLoader( final T type, final V volatileType )
{
this.type = type;
this.volatileType = volatileType;
}
@Override
public T getImageType()
{
return type;
}
@Override
public V getVolatileImageType()
{
return volatileType;
}
@Override
public RandomAccessibleInterval< T > getImage( final int timepointId, final ImgLoaderHint... hints )
{
return getImage( timepointId, 0, hints );
}
}
src/main/java/bdv/BigDataViewer.java
+ 133
− 119
View file @ 1ff7ef57
This diff is collapsed.
src/main/java/bdv/BigDataViewerActions.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import java.awt.event.ActionEvent;
......
src/main/java/bdv/SpimSource.java
+ 33
− 6
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.NumericType;
public class SpimSource< T extends NumericType< T > > extends AbstractSpimSource< T >
{
protected final ViewerImgLoader< T, ? > imgLoader;
protected final ViewerSetupImgLoader< T, ? > imgLoader;
@SuppressWarnings( "unchecked" )
public SpimSource( final AbstractSpimData< ? > spimData, final int setup, final String name )
{
super( spimData, setup, name );
final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
imgLoader = ( ViewerImgLoader< T, ? > ) seq.getImgLoader();
imgLoader = ( ViewerSetupImgLoader< T, ? > ) ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setup );
loadTimepoint( 0 );
}
......@@ -27,14 +54,14 @@ public class SpimSource< T extends NumericType< T > > extends AbstractSpimSource
}
@Override
protected RandomAccessibleInterval< T > getImage( final ViewId viewId, final int level )
protected RandomAccessibleInterval< T > getImage( final int timepointId, final int level )
{
return imgLoader.getImage( viewId, level );
return imgLoader.getImage( timepointId, level );
}
@Override
protected AffineTransform3D[] getMipmapTransforms()
{
return imgLoader.getMipmapTransforms( setupId );
return imgLoader.getMipmapTransforms();
}
}
src/main/java/bdv/ViewerImgLoader.java
+ 32
− 17
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D;
import mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader;
import bdv.img.cache.Cache;
public interface ViewerImgLoader< T, V extends Volatile< T > > extends BasicImgLoader< T >
public interface ViewerImgLoader extends BasicMultiResolutionImgLoader
{
public RandomAccessibleInterval< T > getImage( final ViewId view, final int level );
public RandomAccessibleInterval< V > getVolatileImage( final ViewId view, final int level );
public V getVolatileImageType();
public double[][] getMipmapResolutions( final int setupId );
public AffineTransform3D[] getMipmapTransforms( final int setupId );
public int numMipmapLevels( final int setupId );
@Override
public ViewerSetupImgLoader< ?, ? > getSetupImgLoader( final int setupId );
public Cache getCache();
}
src/main/java/bdv/ViewerSetupImgLoader.java 0 → 100644
+ 41
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
public interface ViewerSetupImgLoader< T, V extends Volatile< T > > extends BasicMultiResolutionSetupImgLoader< T >
{
public RandomAccessibleInterval< V > getVolatileImage( final int timepointId, final int level, ImgLoaderHint... hints );
public V getVolatileImageType();
}
src/main/java/bdv/VolatileSpimSource.java
+ 33
− 6
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv;
import mpicbg.spim.data.generic.AbstractSpimData;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D;
......@@ -19,7 +46,7 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile<
{
protected final SpimSource< T > nonVolatileSource;
protected final ViewerImgLoader< ?, V > imgLoader;
protected final ViewerSetupImgLoader< ?, V > imgLoader;
protected final MipmapOrdering mipmapOrdering;
......@@ -29,7 +56,7 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile<
super( spimData, setup, name );
nonVolatileSource = new SpimSource< T >( spimData, setup, name );
final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
imgLoader = ( ViewerImgLoader< ?, V > ) seq.getImgLoader();
imgLoader = ( ViewerSetupImgLoader< ?, V > ) ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setup );
if ( MipmapOrdering.class.isInstance( imgLoader ) )
mipmapOrdering = ( ( MipmapOrdering ) imgLoader );
else
......@@ -49,15 +76,15 @@ public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile<
}
@Override
protected RandomAccessibleInterval< V > getImage( final ViewId viewId, final int level )
protected RandomAccessibleInterval< V > getImage( final int timepointId, final int level )
{
return imgLoader.getVolatileImage( viewId, level );
return imgLoader.getVolatileImage( timepointId, level );
}
@Override
protected AffineTransform3D[] getMipmapTransforms()
{
return imgLoader.getMipmapTransforms( setupId );
return imgLoader.getMipmapTransforms();
}
@Override
......
src/main/java/bdv/export/Downsample.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import net.imglib2.Cursor;
......
src/main/java/bdv/export/ExportMipmapInfo.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import bdv.img.hdf5.MipmapInfo;
......
src/main/java/bdv/export/HDF5Access.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import static bdv.img.hdf5.Util.reorder;
......
src/main/java/bdv/export/HDF5AccessHack.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import static bdv.img.hdf5.Util.reorder;
......
src/main/java/bdv/export/Hdf5BlockWriterThread.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import java.io.File;
......
src/main/java/bdv/export/IHDF5Access.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures;
......
src/main/java/bdv/export/ProgressWriter.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import java.io.PrintStream;
......
src/main/java/bdv/export/ProgressWriterConsole.java
+ 28
− 0
View file @ 1ff7ef57
/*
* #%L
* BigDataViewer core classes with minimal dependencies
* %%
* Copyright (C) 2012 - 2015 BigDataViewer authors
* %%
* 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
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package bdv.export;
import java.io.PrintStream;
......
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