diff --git a/src/main/java/bdv/AbstractSpimSource.java b/src/main/java/bdv/AbstractSpimSource.java
index 94b2af70d4671818f0711671d8695fa3f1f17057..ba8e1b93ed17032580371c1c890e55774753434e 100644
--- a/src/main/java/bdv/AbstractSpimSource.java
+++ b/src/main/java/bdv/AbstractSpimSource.java
@@ -28,8 +28,6 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
protected final SequenceViewsLoader sequenceViews;
- protected final ViewerImgLoader imgLoader;
-
protected final int numTimepoints;
protected final int numMipmapLevels;
@@ -49,9 +47,8 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
this.name = name;
this.sequenceViews = loader;
final SequenceDescription seq = loader.getSequenceDescription();
- imgLoader = ( ViewerImgLoader ) seq.imgLoader;
numTimepoints = seq.numTimepoints();
- numMipmapLevels = imgLoader.numMipmapLevels( setup );
+ numMipmapLevels = ( ( ViewerImgLoader< ?, ? > ) seq.imgLoader ).numMipmapLevels( setup );
currentSources = new RandomAccessibleInterval[ numMipmapLevels ];
currentInterpolatedSources = new RealRandomAccessible[ numMipmapLevels ][ numInterpolationMethods ];
currentSourceTransforms = new AffineTransform3D[ numMipmapLevels ];
@@ -60,7 +57,6 @@ public abstract class AbstractSpimSource< T extends NumericType< T > > implement
interpolatorFactories = new InterpolatorFactory[ numInterpolationMethods ];
interpolatorFactories[ iNearestNeighborMethod ] = new NearestNeighborInterpolatorFactory< T >();
interpolatorFactories[ iNLinearMethod ] = new NLinearInterpolatorFactory< T >();
- loadTimepoint( 0 );
}
protected abstract void loadTimepoint( final int timepoint );
diff --git a/src/main/java/bdv/BigDataViewer.java b/src/main/java/bdv/BigDataViewer.java
index 026c838cac2c9a907e2380396fe818ca48cb83bb..68ccc0dd00c5528e086c6562be43dfff4a55be32 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -13,10 +13,12 @@ import javax.swing.JMenuItem;
import javax.swing.filechooser.FileFilter;
import mpicbg.spim.data.SequenceDescription;
+import net.imglib2.Volatile;
+import net.imglib2.converter.TypeIdentity;
import net.imglib2.display.RealARGBColorConverter;
import net.imglib2.type.numeric.ARGBType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import net.imglib2.type.volatiles.VolatileUnsignedShortType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
import org.jdom2.Document;
import org.jdom2.Element;
@@ -78,35 +80,88 @@ public class BigDataViewer
manualTransformationEditor.toggle();
}
- private BigDataViewer( final String xmlFilename, final ProgressWriter progressWriter ) throws InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException, IOException
+ private static < T extends RealType< T >, V extends Volatile< T > & RealType< V > > void initSetupsRealType(
+ final SequenceViewsLoader loader,
+ final T type,
+ final ArrayList< ConverterSetup > converterSetups,
+ final ArrayList< SourceAndConverter< ? > > sources )
{
- final int width = 800;
- final int height = 600;
-
- final SequenceViewsLoader loader = new SequenceViewsLoader( xmlFilename );
+ final double typeMin = type.getMinValue();
+ final double typeMax = type.getMaxValue();
final SequenceDescription seq = loader.getSequenceDescription();
-
- final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
- final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
for ( int setup = 0; setup < seq.numViewSetups(); ++setup )
{
- final RealARGBColorConverter< VolatileUnsignedShortType > vconverter = new RealARGBColorConverter< VolatileUnsignedShortType >( 0, 65535 );
- vconverter.setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) );
- final RealARGBColorConverter< UnsignedShortType > converter = new RealARGBColorConverter< UnsignedShortType >( 0, 65535 );
- converter.setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) );
- final VolatileSpimSource vs = new VolatileSpimSource( loader, setup, "angle " + seq.setups.get( setup ).getAngle() );
- final SpimSource s = vs.nonVolatile();
+ final RealARGBColorConverter< V > vconverter = new RealARGBColorConverter< V >( typeMin, typeMax );
+ vconverter.setColor( new ARGBType( 0xffffffff ) );
+ final RealARGBColorConverter< T > converter = new RealARGBColorConverter< T >( typeMin, typeMax );
+ converter.setColor( new ARGBType( 0xffffffff ) );
+
+ final VolatileSpimSource< T, V > vs = new VolatileSpimSource< T, V >( loader, setup, "angle " + seq.setups.get( setup ).getAngle() );
+ final SpimSource< T > s = vs.nonVolatile();
// Decorate each source with an extra transformation, that can be edited manually in this viewer.
- final TransformedSource< VolatileUnsignedShortType > tvs = new TransformedSource< VolatileUnsignedShortType >( vs );
- final TransformedSource< UnsignedShortType > ts = new TransformedSource< UnsignedShortType >( s, tvs );
+ final TransformedSource< V > tvs = new TransformedSource< V >( vs );
+ final TransformedSource< T > ts = new TransformedSource< T >( s, tvs );
- final SourceAndConverter< VolatileUnsignedShortType > vsoc = new SourceAndConverter< VolatileUnsignedShortType >( tvs, vconverter );
- final SourceAndConverter< UnsignedShortType > soc = new SourceAndConverter< UnsignedShortType >( ts, converter, vsoc );
+ final SourceAndConverter< V > vsoc = new SourceAndConverter< V >( tvs, vconverter );
+ final SourceAndConverter< T > soc = new SourceAndConverter< T >( ts, converter, vsoc );
sources.add( soc );
converterSetups.add( new RealARGBColorConverterSetup( setup, converter, vconverter ) );
}
+ }
+
+ private static void initSetupsARGBType(
+ final SequenceViewsLoader loader,
+ final ARGBType type,
+ final ArrayList< ConverterSetup > converterSetups,
+ final ArrayList< SourceAndConverter< ? > > sources )
+ {
+ final SequenceDescription seq = loader.getSequenceDescription();
+ for ( int setup = 0; setup < seq.numViewSetups(); ++setup )
+ {
+ final TypeIdentity< ARGBType > vconverter = new TypeIdentity< ARGBType >();
+ final TypeIdentity< ARGBType > converter = new TypeIdentity< ARGBType >();
+
+// final VolatileSpimSource< ARGBType, VolatileARGBType > vs = new VolatileSpimSource< ARGBType, VolatileARGBType >( loader, setup, "angle " + seq.setups.get( setup ).getAngle() );
+// final SpimSource< ARGBType > s = vs.nonVolatile();
+//
+// // Decorate each source with an extra transformation, that can be edited manually in this viewer.
+// final TransformedSource< VolatileARGBType > tvs = new TransformedSource< VolatileARGBType >( vs );
+// final TransformedSource< ARGBType > ts = new TransformedSource< ARGBType >( s, tvs );
+//
+// final SourceAndConverter< VolatileARGBType > vsoc = new SourceAndConverter< VolatileARGBType >( tvs, vconverter );
+// final SourceAndConverter< ARGBType > soc = new SourceAndConverter< ARGBType >( ts, converter, vsoc );
+//
+// sources.add( soc );
+ }
+ }
+
+ @SuppressWarnings( { "unchecked", "rawtypes" } )
+ private static < T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > void initSetups(
+ final SequenceViewsLoader loader,
+ final ArrayList< ConverterSetup > converterSetups,
+ final ArrayList< SourceAndConverter< ? > > sources )
+ {
+ final T type = ( ( ViewerImgLoader< T, V > ) loader.getSequenceDescription().imgLoader ).getImageType();
+ if ( RealType.class.isInstance( type ) )
+ initSetupsRealType( loader, ( RealType ) type, converterSetups, sources );
+ else if ( ARGBType.class.isInstance( type ) )
+ initSetupsARGBType( loader, ( ARGBType ) type, converterSetups, sources );
+ else throw new IllegalArgumentException( "ImgLoader of type " + type.getClass() + " not supported." );
+ }
+
+ private BigDataViewer( final String xmlFilename, final ProgressWriter progressWriter ) throws InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException, IOException
+ {
+ final int width = 800;
+ final int height = 600;
+
+ final SequenceViewsLoader loader = new SequenceViewsLoader( xmlFilename );
+ final SequenceDescription seq = loader.getSequenceDescription();
+
+ final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
+ final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
+ initSetups( loader, converterSetups, sources );
viewerFrame = new ViewerFrame( width, height, sources, seq.numTimepoints(),
( ( CatmaidImageLoader ) seq.imgLoader ).getCache() );
diff --git a/src/main/java/bdv/SpimSource.java b/src/main/java/bdv/SpimSource.java
index 81925a62cbcfc95b4293087ee308e0646969161b..f5c8e6c89b8c1d1511367f7cdb9428cb0f90d89b 100644
--- a/src/main/java/bdv/SpimSource.java
+++ b/src/main/java/bdv/SpimSource.java
@@ -1,16 +1,22 @@
package bdv;
+import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.View;
import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import net.imglib2.type.volatiles.VolatileUnsignedShortType;
+import net.imglib2.type.numeric.NumericType;
import net.imglib2.view.Views;
-public class SpimSource extends AbstractSpimSource< UnsignedShortType >
+public class SpimSource< T extends NumericType< T > > extends AbstractSpimSource< T >
{
+ protected final ViewerImgLoader< T, ? > imgLoader;
+
+ @SuppressWarnings( "unchecked" )
public SpimSource( final SequenceViewsLoader loader, final int setup, final String name )
{
super( loader, setup, name );
+ final SequenceDescription seq = loader.getSequenceDescription();
+ imgLoader = ( ViewerImgLoader< T, ? > ) seq.imgLoader;
+ loadTimepoint( 0 );
}
@Override
@@ -19,7 +25,8 @@ public class SpimSource extends AbstractSpimSource< UnsignedShortType >
currentTimepoint = timepoint;
if ( isPresent( timepoint ) )
{
- final UnsignedShortType zero = new VolatileUnsignedShortType( 0 ).get();
+ final T zero = imgLoader.getImageType().createVariable();
+ zero.setZero();
final View view = sequenceViews.getView( timepoint, setup );
final AffineTransform3D reg = view.getModel();
final AffineTransform3D mipmapTransform = new AffineTransform3D();
@@ -33,7 +40,7 @@ public class SpimSource extends AbstractSpimSource< UnsignedShortType >
}
currentSourceTransforms[ level ].set( reg );
currentSourceTransforms[ level ].concatenate( mipmapTransform );
- currentSources[ level ] = imgLoader.getUnsignedShortImage( view, level );
+ currentSources[ level ] = imgLoader.getImage( view, level );
for ( int method = 0; method < numInterpolationMethods; ++method )
currentInterpolatedSources[ level ][ method ] = Views.interpolate( Views.extendValue( currentSources[ level ], zero ), interpolatorFactories[ method ] );
}
@@ -51,8 +58,8 @@ public class SpimSource extends AbstractSpimSource< UnsignedShortType >
}
@Override
- public UnsignedShortType getType()
+ public T getType()
{
- return new UnsignedShortType();
+ return imgLoader.getImageType();
}
}
diff --git a/src/main/java/bdv/ViewerImgLoader.java b/src/main/java/bdv/ViewerImgLoader.java
index 2355e3084b8a9544e2c193aeed3d2d9807f73a26..61634d081d28c38d0804f1f79df40875fba84537 100644
--- a/src/main/java/bdv/ViewerImgLoader.java
+++ b/src/main/java/bdv/ViewerImgLoader.java
@@ -3,14 +3,17 @@ package bdv;
import mpicbg.spim.data.ImgLoader;
import mpicbg.spim.data.View;
import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
-import net.imglib2.type.volatiles.VolatileUnsignedShortType;
+import net.imglib2.Volatile;
-public interface ViewerImgLoader extends ImgLoader
+public interface ViewerImgLoader< T, V extends Volatile< T > > extends ImgLoader< T >
{
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view, final int level );
+ public RandomAccessibleInterval< T > getImage( final View view, final int level );
- public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileUnsignedShortImage( final View view, final int level );
+ public T getImageType();
+
+ public RandomAccessibleInterval< V > getVolatileImage( final View view, final int level );
+
+ public V getVolatileImageType();
public double[][] getMipmapResolutions( final int setup );
diff --git a/src/main/java/bdv/VolatileSpimSource.java b/src/main/java/bdv/VolatileSpimSource.java
index 86d265891fd497a5fae65216eda380f554790bd7..7146faa469538e14443c057bd60f1e11bc153e11 100644
--- a/src/main/java/bdv/VolatileSpimSource.java
+++ b/src/main/java/bdv/VolatileSpimSource.java
@@ -1,18 +1,27 @@
package bdv;
+import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.View;
+import net.imglib2.Volatile;
import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.type.volatiles.VolatileUnsignedShortType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
-public class VolatileSpimSource extends AbstractSpimSource< VolatileUnsignedShortType >
+public class VolatileSpimSource< T extends NumericType< T >, V extends Volatile< T > & NumericType< V > > extends AbstractSpimSource< V >
{
- protected final SpimSource nonVolatileSource;
+ protected final SpimSource< T > nonVolatileSource;
+ protected final ViewerImgLoader< ?, V > imgLoader;
+
+ @SuppressWarnings( "unchecked" )
public VolatileSpimSource( final SequenceViewsLoader loader, final int setup, final String name )
{
super( loader, setup, name );
- nonVolatileSource = new SpimSource( loader, setup, name );
+ nonVolatileSource = new SpimSource< T >( loader, setup, name );
+ final SequenceDescription seq = loader.getSequenceDescription();
+ imgLoader = ( ViewerImgLoader< ?, V > ) seq.imgLoader;
+ loadTimepoint( 0 );
}
@Override
@@ -21,7 +30,9 @@ public class VolatileSpimSource extends AbstractSpimSource< VolatileUnsignedShor
currentTimepoint = timepoint;
if ( isPresent( timepoint ) )
{
- final VolatileUnsignedShortType zero = new VolatileUnsignedShortType( 128 );
+ final V zero = imgLoader.getVolatileImageType().createVariable();
+ // TODO: change to zero.setZero(); the following is just for debugging
+ ( ( RealType< ? > ) zero ).setReal( 128 );
final View view = sequenceViews.getView( timepoint, setup );
final AffineTransform3D reg = view.getModel();
final AffineTransform3D mipmapTransform = new AffineTransform3D();
@@ -35,7 +46,7 @@ public class VolatileSpimSource extends AbstractSpimSource< VolatileUnsignedShor
}
currentSourceTransforms[ level ].set( reg );
currentSourceTransforms[ level ].concatenate( mipmapTransform );
- currentSources[ level ] = imgLoader.getVolatileUnsignedShortImage( view, level );
+ currentSources[ level ] = imgLoader.getVolatileImage( view, level );
for ( int method = 0; method < numInterpolationMethods; ++method )
currentInterpolatedSources[ level ][ method ] = Views.interpolate( Views.extendValue( currentSources[ level ], zero ), interpolatorFactories[ method ] );
}
@@ -53,12 +64,12 @@ public class VolatileSpimSource extends AbstractSpimSource< VolatileUnsignedShor
}
@Override
- public VolatileUnsignedShortType getType()
+ public V getType()
{
- return new VolatileUnsignedShortType();
+ return imgLoader.getVolatileImageType();
}
- public SpimSource nonVolatile()
+ public SpimSource< T > nonVolatile()
{
return nonVolatileSource;
}
diff --git a/src/main/java/bdv/export/WriteSequenceToHdf5.java b/src/main/java/bdv/export/WriteSequenceToHdf5.java
index 6a9f2aaf6b4df2e804a64f0a70a0ef4e96b1065f..ffe67f628a3a3019d0ab86f247572fc9855a69d0 100644
--- a/src/main/java/bdv/export/WriteSequenceToHdf5.java
+++ b/src/main/java/bdv/export/WriteSequenceToHdf5.java
@@ -165,7 +165,8 @@ public class WriteSequenceToHdf5
final int setupOffsetSeq = partition.getSetupOffset() + partition.getSetupStart();
final int setupOffsetFile = partition.getSetupStart();
final int numSetups = partition.getSetupLength();
- final ImgLoader imgLoader = seq.imgLoader;
+ @SuppressWarnings( "unchecked" )
+ final ImgLoader< UnsignedShortType > imgLoader = ( ImgLoader< UnsignedShortType > ) seq.imgLoader;
// for progressWriter
// initial 1 is for writing resolutions etc.
@@ -231,7 +232,7 @@ public class WriteSequenceToHdf5
progressWriter.out().printf( "proccessing setup %d / %d\n", setup + 1, numSetups );
final View view = new View( seq, timepointSeq, setupSeq, null );
progressWriter.out().println( "loading image" );
- final RandomAccessibleInterval< UnsignedShortType > img = imgLoader.getUnsignedShortImage( view );
+ final RandomAccessibleInterval< UnsignedShortType > img = imgLoader.getImage( view );
progressWriter.setProgress( ( double ) numCompletedTasks++ / numTasks );
for ( int level = 0; level < numLevels; ++level )
diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
index 7667480d09231b42ef47ba1c8ff958e74b348d06..3773eaee37afbb7f9cc7cf5526197ced7b7dac60 100644
--- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
@@ -21,6 +21,7 @@ import mpicbg.spim.data.ViewRegistration;
import mpicbg.spim.data.ViewRegistrations;
import mpicbg.spim.data.ViewSetup;
import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
import bdv.export.ProgressWriter;
import bdv.export.SubTaskProgressWriter;
import bdv.export.WriteSequenceToHdf5;
@@ -78,7 +79,7 @@ public class ExportImagePlusPlugIn implements PlugIn
return;
// create ImgLoader wrapping the image
- final ImgLoader imgLoader;
+ final ImgLoader< UnsignedShortType > imgLoader;
switch ( imp.getType() )
{
case ImagePlus.GRAY8:
diff --git a/src/main/java/bdv/ij/ImportPlugIn.java b/src/main/java/bdv/ij/ImportPlugIn.java
index 9b8dd8c8d8a69e73ae2d191e9d20727b09961c27..cb76a1c65f444f5efad1e227057b74a35e4960dc 100644
--- a/src/main/java/bdv/ij/ImportPlugIn.java
+++ b/src/main/java/bdv/ij/ImportPlugIn.java
@@ -15,6 +15,7 @@ import java.awt.event.TextEvent;
import java.io.File;
import java.io.IOException;
+import mpicbg.spim.data.ImgLoader;
import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.View;
import net.imglib2.RandomAccessibleInterval;
@@ -134,7 +135,9 @@ public class ImportPlugIn implements PlugIn
final int numSetups = seq.numViewSetups();
timepoint = Math.max( Math.min( timepoint, numTimepoints - 1 ), 0 );
setup = Math.max( Math.min( setup, numSetups - 1 ), 0 );
- final RandomAccessibleInterval< UnsignedShortType > img = seq.imgLoader.getUnsignedShortImage( new View( seq, timepoint, setup, null ) );
+ @SuppressWarnings( "unchecked" )
+ final ImgLoader< UnsignedShortType > il = ( ImgLoader< UnsignedShortType > ) seq.imgLoader;
+ final RandomAccessibleInterval< UnsignedShortType > img = il.getImage( new View( seq, timepoint, setup, null ) );
final ImagePlus imp = net.imglib2.img.display.imagej.ImageJFunctions.wrap( img, "" ).duplicate();
imp.setTitle( new File( xmlFile ).getName() + " " + timepoint + " " + setup );
imp.show();
diff --git a/src/main/java/bdv/ij/export/FusionResult.java b/src/main/java/bdv/ij/export/FusionResult.java
index 8e5556416286272025cca765795b6914a544eeea..7a91803605ec03260d3b56ee7a53800b99957e90 100644
--- a/src/main/java/bdv/ij/export/FusionResult.java
+++ b/src/main/java/bdv/ij/export/FusionResult.java
@@ -4,14 +4,15 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import bdv.ij.export.imgloader.FusionImageLoader;
import mpicbg.spim.data.ImgLoader;
import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.ViewRegistration;
import mpicbg.spim.data.ViewRegistrations;
import mpicbg.spim.data.ViewSetup;
import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
+import bdv.ij.export.imgloader.FusionImageLoader;
public class FusionResult
{
@@ -32,7 +33,7 @@ public class FusionResult
public FusionResult( final String filepath, final String filepattern, final List< Integer > timepoints, final int referenceTimePoint, final int numSlices, final double sliceValueMin, final double sliceValueMax, final List< AffineTransform3D > fusionTransforms )
{
- final ImgLoader fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
+ final ImgLoader< UnsignedShortType > fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
desc = new SequenceDescription( Arrays.asList( new ViewSetup( 0, 0, 0, 0, 0, 0, numSlices, 1, 1, 1 ) ), timepoints, null, fusionLoader );
final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
for ( int timepoint = 0; timepoint < timepoints.size(); ++timepoint )
@@ -42,7 +43,7 @@ public class FusionResult
public FusionResult( final String filepath, final String filepattern, final List< Integer > channels, final List< Integer > timepoints, final int referenceTimePoint, final int numSlices, final double sliceValueMin, final double sliceValueMax, final List< AffineTransform3D > fusionTransforms )
{
- final ImgLoader fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
+ final ImgLoader< UnsignedShortType > fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
final ArrayList< ViewSetup > setups = new ArrayList< ViewSetup >();
for ( int id = 0; id < channels.size(); ++id )
setups.add( new ViewSetup( id, 0, 0, channels.get( id ), 0, 0, numSlices, 1, 1, 1 ) );
diff --git a/src/main/java/bdv/ij/export/SetupAggregator.java b/src/main/java/bdv/ij/export/SetupAggregator.java
index 23d750abea9d4b04b34cc28fbd35361f9ab489de..e0f40383772231946c937d285ad710c121847451 100644
--- a/src/main/java/bdv/ij/export/SetupAggregator.java
+++ b/src/main/java/bdv/ij/export/SetupAggregator.java
@@ -54,7 +54,7 @@ public class SetupAggregator
/**
* An {@link ImgLoader} that forwards to wrapped source sequences.
*/
- protected final ImgLoader imgLoader;
+ protected final ImgLoader< UnsignedShortType > imgLoader;
/**
* Create an empty aggregator.
@@ -67,7 +67,7 @@ public class SetupAggregator
setups = new ArrayList< ViewSetupWrapper >();
perSetupResolutions = new ArrayList< int[][] >();
perSetupSubdivisions = new ArrayList< int[][] >();
- imgLoader = new ImgLoader()
+ imgLoader = new ImgLoader< UnsignedShortType >()
{
@Override
public void init( final Element elem, final File basePath )
@@ -82,16 +82,18 @@ public class SetupAggregator
}
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
final ViewSetupWrapper w = ( ViewSetupWrapper ) view.getSetup();
- return w.getSourceSequence().imgLoader.getUnsignedShortImage( new View( w.getSourceSequence(), view.getTimepointIndex(), w.getSourceSetupIndex(), view.getModel() ) );
+ @SuppressWarnings( "unchecked" )
+ final ImgLoader< UnsignedShortType > il = ( ImgLoader< UnsignedShortType > ) w.getSourceSequence().imgLoader;
+ return il.getImage( new View( w.getSourceSequence(), view.getTimepointIndex(), w.getSourceSetupIndex(), view.getModel() ) );
}
};
}
diff --git a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
index 80b1c9ad2f0acfd0a5bada9c92b0ab8798a6455a..cd98eba5a8a13bb71c01c59c3144b4bd34e9ef5f 100644
--- a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
+++ b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
@@ -8,8 +8,6 @@ import java.util.List;
import javax.vecmath.Point3f;
-import bdv.ij.export.imgloader.HuiskenImageLoader;
-import bdv.ij.export.imgloader.StackImageLoader;
import mpicbg.spim.data.ImgLoader;
import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.ViewRegistration;
@@ -24,7 +22,10 @@ import mpicbg.spim.registration.bead.BeadRegistration;
import net.imglib2.FinalRealInterval;
import net.imglib2.RealInterval;
import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
import spimopener.SPIMExperiment;
+import bdv.ij.export.imgloader.HuiskenImageLoader;
+import bdv.ij.export.imgloader.StackImageLoader;
public class SpimRegistrationSequence
{
@@ -38,7 +39,7 @@ public class SpimRegistrationSequence
{
this.conf = conf;
final ArrayList< ViewSetup > setups = createViewSetups( conf );
- final ImgLoader imgLoader = createImageLoader( conf, setups );
+ final ImgLoader< UnsignedShortType > imgLoader = createImageLoader( conf, setups );
viewRegistrations = createViewRegistrations( conf, setups );
sequenceDescription = new SequenceDescription( setups, makeList( conf.timepoints ), new File( conf.inputdirectory ), imgLoader );
@@ -64,7 +65,7 @@ public class SpimRegistrationSequence
return viewRegistrations;
}
- protected static ImgLoader createImageLoader( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )
+ protected static ImgLoader< UnsignedShortType > createImageLoader( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )
{
final int numTimepoints = conf.timepoints.length;
final int numSetups = setups.size();
diff --git a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
index 0b082b7cb11b493bb1a4e8c18819004164d2873b..74ed2c5a1fe81898bbdc56a028e8c5b7348390a6 100644
--- a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
@@ -35,12 +35,12 @@ import org.jdom2.Element;
* template to get the slice filenames.
*
* This {@link ImgLoader} is used for exporting spim sequences to hdf5. Only the
- * {@link #getUnsignedShortImage(View)} method is implemented because this is
+ * {@link #getImage(View)} method is implemented because this is
* the only method required for exporting to hdf5.
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
+public class FusionImageLoader< T extends RealType< T > > implements ImgLoader< UnsignedShortType >
{
private final String pattern;
@@ -96,13 +96,13 @@ public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
* not implemented.
*/
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
final int tp = view.getTimepoint();
final int c = view.getSetup().getChannel();
diff --git a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
index f36c01245fbed61828ffcbcac9a31c17321b02e7..9d639b7bc44bfa6898c3c1367669df45f18b1533 100644
--- a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
@@ -29,7 +29,7 @@ import spimopener.SPIMExperiment;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class HuiskenImageLoader implements ImgLoader
+public class HuiskenImageLoader implements ImgLoader< UnsignedShortType >
{
private File expFile;
@@ -82,7 +82,7 @@ public class HuiskenImageLoader implements ImgLoader
}
@Override
- public ImgPlus< UnsignedShortType > getUnsignedShortImage( final View view )
+ public ImgPlus< UnsignedShortType > getImage( final View view )
{
ensureExpIsOpen();
@@ -106,7 +106,7 @@ public class HuiskenImageLoader implements ImgLoader
}
@Override
- public ImgPlus< FloatType > getImage( final View view )
+ public ImgPlus< FloatType > getFloatImage( final View view )
{
ensureExpIsOpen();
diff --git a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
index 5a11007e688410d7cb5ba0df00d77e64ce960f70..17081799f0b160b69fe0bc70e9bfa8a6087b50c9 100644
--- a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
@@ -22,12 +22,12 @@ import org.jdom2.Element;
/**
* This {@link ImgLoader} implementation returns a wrapped, converted
* {@link ImagePlus}. It is used for exporting {@link ImagePlus} to hdf5. Only
- * the {@link #getUnsignedShortImage(View)} method is implemented because this
+ * the {@link #getImage(View)} method is implemented because this
* is the only method required for exporting to hdf5.
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class ImagePlusImgLoader< T extends RealType< T > > implements ImgLoader
+public class ImagePlusImgLoader< T extends RealType< T > > implements ImgLoader< UnsignedShortType >
{
public static enum MinMaxOption
{
@@ -141,13 +141,13 @@ public class ImagePlusImgLoader< T extends RealType< T > > implements ImgLoader
* not implemented.
*/
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
RandomAccessibleInterval< T > img = wrappedImp;
if ( isMultiFrame )
diff --git a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
index f58e23e9996e8b0191cc7a93c9aa88a3d6129510..a3ac85e8610ee7169af4ae2bac3a09c87837971b 100644
--- a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
@@ -26,12 +26,12 @@ import org.jdom2.Element;
* <code>view.getSetupIndex() + numViewSetups * view.getTimepointIndex()</code>.
*
* This {@link ImgLoader} is used for exporting spim sequences to hdf5. Only the
- * {@link #getUnsignedShortImage(View)} method is implemented because this is
+ * {@link #getImage(View)} method is implemented because this is
* the only method required for exporting to hdf5.
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class StackImageLoader implements ImgLoader
+public class StackImageLoader implements ImgLoader< UnsignedShortType >
{
private final ImgOpener opener;
@@ -77,13 +77,13 @@ public class StackImageLoader implements ImgLoader
* not implemented.
*/
@Override
- public ImgPlus< FloatType > getImage( final View view )
+ public ImgPlus< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@Override
- public ImgPlus< UnsignedShortType > getUnsignedShortImage( final View view )
+ public ImgPlus< UnsignedShortType > getImage( final View view )
{
final int setup = view.getSetupIndex();
final int timepoint = view.getTimepointIndex();
diff --git a/src/main/java/bdv/ij/export/tiles/TileImgLoader.java b/src/main/java/bdv/ij/export/tiles/TileImgLoader.java
index 4a2bc22d4ec2ee169498706bad90cdf9ece3385c..d396c6b792100a7231dee25c61a81a869bb5816e 100644
--- a/src/main/java/bdv/ij/export/tiles/TileImgLoader.java
+++ b/src/main/java/bdv/ij/export/tiles/TileImgLoader.java
@@ -32,7 +32,7 @@ import org.jdom2.input.SAXBuilder;
import bdv.ij.export.tiles.CellVoyagerDataExporter.ChannelInfo;
-public class TileImgLoader implements ImgLoader
+public class TileImgLoader implements ImgLoader< UnsignedShortType >
{
private static final Namespace NAMESPACE = Namespace.getNamespace( "bts", "http://www.yokogawa.co.jp/BTS/BTSSchema/1.0" );
@@ -70,7 +70,7 @@ public class TileImgLoader implements ImgLoader
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
final int setupIndex = view.getSetupIndex();
@@ -187,7 +187,7 @@ public class TileImgLoader implements ImgLoader
}
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
diff --git a/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java b/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
index b12784f766eefe0f594593d1e3da311d58937a6c..dfbdca615817f853968fdd6655660a8e2d2795ea 100644
--- a/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
+++ b/src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
@@ -22,7 +22,7 @@ import bdv.img.cache.VolatileGlobalCellCache.LoadingStrategy;
import bdv.img.cache.VolatileImgCells;
import bdv.img.cache.VolatileImgCells.CellCache;
-public class CatmaidImageLoader implements ViewerImgLoader
+public class CatmaidImageLoader implements ViewerImgLoader< UnsignedShortType, VolatileUnsignedShortType >
{
private long width;
@@ -103,19 +103,19 @@ public class CatmaidImageLoader implements ViewerImgLoader
}
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
- return getUnsignedShortImage( view, 0 );
+ return getImage( view, 0 );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view, final int level )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view, final int level )
{
final CellImg< UnsignedShortType, VolatileShortArray, VolatileCell< VolatileShortArray > > img = prepareCachedImage( view, level, LoadingStrategy.BLOCKING );
final UnsignedShortType linkedType = new UnsignedShortType( img );
@@ -124,7 +124,7 @@ public class CatmaidImageLoader implements ViewerImgLoader
}
@Override
- public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileUnsignedShortImage( final View view, final int level )
+ public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileImage( final View view, final int level )
{
final CellImg< VolatileUnsignedShortType, VolatileShortArray, VolatileCell< VolatileShortArray > > img = prepareCachedImage( view, level, LoadingStrategy.VOLATILE );
final VolatileUnsignedShortType linkedType = new VolatileUnsignedShortType( img );
@@ -164,4 +164,21 @@ public class CatmaidImageLoader implements ViewerImgLoader
{
return cache;
}
+
+ private final UnsignedShortType type = new UnsignedShortType();
+
+ private final VolatileUnsignedShortType volatileType = new VolatileUnsignedShortType();
+
+ @Override
+ public UnsignedShortType getImageType()
+ {
+ return type;
+ }
+
+ @Override
+ public VolatileUnsignedShortType getVolatileImageType()
+ {
+ return volatileType;
+ }
+
}
diff --git a/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java b/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
index 3ee33b856543e535307dc22a6818b63b04e60769..1b6e87a1390a00635aa649d27631159ff55547d2 100644
--- a/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
+++ b/src/main/java/bdv/img/hdf5/Hdf5ImageLoader.java
@@ -34,7 +34,7 @@ import ch.systemsx.cisd.hdf5.HDF5DataSetInformation;
import ch.systemsx.cisd.hdf5.HDF5Factory;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
-public class Hdf5ImageLoader implements ViewerImgLoader
+public class Hdf5ImageLoader implements ViewerImgLoader< UnsignedShortType, VolatileUnsignedShortType >
{
protected File hdf5File;
@@ -222,19 +222,19 @@ public class Hdf5ImageLoader implements ViewerImgLoader
}
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "currently not used" );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
- return getUnsignedShortImage( view, 0 );
+ return getImage( view, 0 );
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view, final int level )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view, final int level )
{
if ( ! existsImageData( view, level ) )
{
@@ -248,7 +248,7 @@ public class Hdf5ImageLoader implements ViewerImgLoader
}
@Override
- public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileUnsignedShortImage( final View view, final int level )
+ public RandomAccessibleInterval< VolatileUnsignedShortType > getVolatileImage( final View view, final int level )
{
if ( ! existsImageData( view, level ) )
{
@@ -392,4 +392,20 @@ public class Hdf5ImageLoader implements ViewerImgLoader
}
}
}
+
+ private final UnsignedShortType type = new UnsignedShortType();
+
+ private final VolatileUnsignedShortType volatileType = new VolatileUnsignedShortType();
+
+ @Override
+ public UnsignedShortType getImageType()
+ {
+ return type;
+ }
+
+ @Override
+ public VolatileUnsignedShortType getVolatileImageType()
+ {
+ return volatileType;
+ }
}
diff --git a/src/main/java/bdv/tools/InitializeViewerState.java b/src/main/java/bdv/tools/InitializeViewerState.java
index f9d34ea8525b624585e34d375b136153c6e30449..7e671062000a9c1a748de1c48fe0f16faf0592ba 100644
--- a/src/main/java/bdv/tools/InitializeViewerState.java
+++ b/src/main/java/bdv/tools/InitializeViewerState.java
@@ -131,7 +131,10 @@ public class InitializeViewerState
{
final ViewerState state = viewer.getState();
final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource();
- final RandomAccessibleInterval< UnsignedShortType > img = ( RandomAccessibleInterval ) source.getSource( state.getCurrentTimepoint(), source.getNumMipmapLevels() - 1 );
+ if ( ! UnsignedShortType.class.isInstance( source.getType() ) )
+ return;
+ @SuppressWarnings( "unchecked" )
+ final RandomAccessibleInterval< UnsignedShortType > img = ( RandomAccessibleInterval< UnsignedShortType > ) source.getSource( state.getCurrentTimepoint(), source.getNumMipmapLevels() - 1 );
final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
final int numBins = 6535;
diff --git a/src/main/java/bdv/tools/crop/CropDialog.java b/src/main/java/bdv/tools/crop/CropDialog.java
index 7b23df7939715fcba68b9d384743e740df920274..4d59e4e357815d793578a2e68059aded022a089d 100644
--- a/src/main/java/bdv/tools/crop/CropDialog.java
+++ b/src/main/java/bdv/tools/crop/CropDialog.java
@@ -29,13 +29,6 @@ import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.filechooser.FileFilter;
-import bdv.export.WriteSequenceToHdf5;
-import bdv.export.WriteSequenceToXml;
-import bdv.img.hdf5.Hdf5ImageLoader;
-import bdv.img.hdf5.Util;
-import bdv.viewer.Source;
-import bdv.viewer.ViewerPanel;
-import bdv.viewer.state.SourceState;
import mpicbg.spim.data.SequenceDescription;
import mpicbg.spim.data.View;
import mpicbg.spim.data.ViewRegistration;
@@ -45,6 +38,13 @@ import net.imglib2.RealInterval;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.util.Intervals;
+import bdv.export.WriteSequenceToHdf5;
+import bdv.export.WriteSequenceToXml;
+import bdv.img.hdf5.Hdf5ImageLoader;
+import bdv.img.hdf5.Util;
+import bdv.viewer.Source;
+import bdv.viewer.ViewerPanel;
+import bdv.viewer.state.SourceState;
public class CropDialog extends JDialog
{
@@ -250,6 +250,7 @@ public class CropDialog extends JDialog
* @param hdf5File
* @param xmlFile
*/
+ @SuppressWarnings( "unchecked" )
public void cropGlobal( final int minTimepointIndex, final int maxTimepointIndex, final File hdf5File, final File xmlFile ) throws IOException
{
final AffineTransform3D globalToCropTransform = new AffineTransform3D();
@@ -265,7 +266,7 @@ public class CropDialog extends JDialog
final RealInterval cropInterval = Intervals.createMinSizeReal( x, y, z, w, h, d );
final ArrayList< Source< UnsignedShortType > > sources = new ArrayList< Source< UnsignedShortType > >();
for( final SourceState< ? > s : viewer.getState().getSources() )
- sources.add( ( Source ) s.getSpimSource() );
+ sources.add( ( Source< UnsignedShortType > ) s.getSpimSource() );
final ArrayList< Integer > timepoints = new ArrayList< Integer >();
final ArrayList< Integer > cropperTimepointMap = new ArrayList< Integer >();
for ( int tp = minTimepointIndex; tp <= maxTimepointIndex; ++tp )
diff --git a/src/main/java/bdv/tools/crop/CropImgLoader.java b/src/main/java/bdv/tools/crop/CropImgLoader.java
index 5fe19b5a7099c5a7310e9f60da76d76cdb188469..f05b216396d5db3b637da12378b63a3159982f74 100644
--- a/src/main/java/bdv/tools/crop/CropImgLoader.java
+++ b/src/main/java/bdv/tools/crop/CropImgLoader.java
@@ -33,7 +33,7 @@ import bdv.viewer.Source;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class CropImgLoader implements ImgLoader
+public class CropImgLoader implements ImgLoader< UnsignedShortType >
{
private final ArrayList< Source< UnsignedShortType > > sources;
@@ -73,7 +73,7 @@ public class CropImgLoader implements ImgLoader
* not implemented.
*/
@Override
- public RandomAccessibleInterval< FloatType > getImage( final View view )
+ public RandomAccessibleInterval< FloatType > getFloatImage( final View view )
{
throw new UnsupportedOperationException( "not implemented" );
}
@@ -86,7 +86,7 @@ public class CropImgLoader implements ImgLoader
}
@Override
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( final View view )
+ public RandomAccessibleInterval< UnsignedShortType > getImage( final View view )
{
final Pair< RandomAccessibleInterval< UnsignedShortType >, AffineTransform3D > pair = cropView( view );
return pair.getA();
diff --git a/src/main/java/mpicbg/spim/data/ImgLoader.java b/src/main/java/mpicbg/spim/data/ImgLoader.java
index 306ecb4e028450644ff112274722a33aeecee690..1b65ef397b980dbd2ce488b7b25524984b3c2190 100644
--- a/src/main/java/mpicbg/spim/data/ImgLoader.java
+++ b/src/main/java/mpicbg/spim/data/ImgLoader.java
@@ -8,7 +8,7 @@ import net.imglib2.type.numeric.real.FloatType;
import org.jdom2.Element;
-public interface ImgLoader
+public interface ImgLoader< T >
{
/**
* initialize the loader from a "ImageLoader" DOM element.
@@ -27,7 +27,7 @@ public interface ImgLoader
* timepoint and setup for which to retrieve the image.
* @return {@link FloatType} image normalized to range [0,1]
*/
- public RandomAccessibleInterval< FloatType > getImage( View view );
+ public RandomAccessibleInterval< FloatType > getFloatImage( View view );
/**
* Get {@link UnsignedShortType} un-normalized image.
@@ -36,5 +36,5 @@ public interface ImgLoader
* timepoint and setup for which to retrieve the image.
* @return {@link UnsignedShortType} image.
*/
- public RandomAccessibleInterval< UnsignedShortType > getUnsignedShortImage( View view );
+ public RandomAccessibleInterval< T > getImage( View view );
}
diff --git a/src/main/java/mpicbg/spim/data/SequenceDescription.java b/src/main/java/mpicbg/spim/data/SequenceDescription.java
index efea09fb8259dcae3f4c0545d9dc66902c3451a4..abc3f6c177357853da2e2b4b1a8f13dcad4aaf82 100644
--- a/src/main/java/mpicbg/spim/data/SequenceDescription.java
+++ b/src/main/java/mpicbg/spim/data/SequenceDescription.java
@@ -39,10 +39,10 @@ public class SequenceDescription
/**
* load images for every view. might be null.
*/
- public final ImgLoader imgLoader;
+ public final ImgLoader< ? > imgLoader;
// TODO: make protected and use getter
- public SequenceDescription( final List< ? extends ViewSetup > setups, final List< Integer > timepoints, final File basePath, final ImgLoader imgLoader )
+ public SequenceDescription( final List< ? extends ViewSetup > setups, final List< Integer > timepoints, final File basePath, final ImgLoader< ? > imgLoader )
{
this.timepoints = new ArrayList< Integer >( timepoints );
this.setups = new ArrayList< ViewSetup >( setups );
@@ -111,13 +111,13 @@ public class SequenceDescription
return basePath;
}
- protected static ImgLoader createImgLoaderFromXml( final Element sequenceDescription, final File basePath ) throws InstantiationException, IllegalAccessException, ClassNotFoundException
+ protected static ImgLoader< ? > createImgLoaderFromXml( final Element sequenceDescription, final File basePath ) throws InstantiationException, IllegalAccessException, ClassNotFoundException
{
final Element elem = sequenceDescription.getChild( "ImageLoader" );
String classn = elem.getAttributeValue( "class" );
if ( classn.equals( "viewer.hdf5.Hdf5ImageLoader" ) )
classn = "bdv.img.hdf5.Hdf5ImageLoader";
- final ImgLoader imgLoader = ( ImgLoader ) Class.forName( classn ).newInstance();
+ final ImgLoader< ? > imgLoader = ( ImgLoader< ? > ) Class.forName( classn ).newInstance();
imgLoader.init( elem, basePath );
return imgLoader;
}