diff --git a/pom.xml b/pom.xml
index d38731343481f87eb6e83be72f910cf5e922a6d1..7db091a427c7d890a5b82c732ef49246627225cd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -2,6 +2,10 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
+ <properties>
+ <enforcer.skip>true</enforcer.skip>
+ </properties>
+
<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-bigdataviewer</artifactId>
diff --git a/src/main/java/bdv/BigDataViewer.java b/src/main/java/bdv/BigDataViewer.java
index 94100142476245e986df5f2b00ab296d1851e0b4..2ca421072b6247f19ed468cfc99256a2ee3d5ce6 100644
--- a/src/main/java/bdv/BigDataViewer.java
+++ b/src/main/java/bdv/BigDataViewer.java
@@ -7,13 +7,13 @@
* %%
* 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
@@ -690,7 +690,8 @@ public class BigDataViewer
// final String fn = "/Users/Pietzsch/Desktop/bdv example/drosophila 2.xml";
// final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml";
// final String fn = "/Users/Pietzsch/Desktop/data/catmaid.xml";
- final String fn = "src/main/resources/openconnectome-bock11-neariso.xml";
+// final String fn2 = "src/main/resources/openconnectome-bock11-neariso.xml";
+ final String fn1 = "/nrs/saalfeld/tomoko/24gb_n_10_l_9_tfac_m5_xlfac_0_ylfac_0_xfac_2_yfac_5_deg_2.xml";
// final String fn = "/home/saalfeld/catmaid.xml";
// final String fn = "/home/saalfeld/catmaid-fafb00-v9.xml";
// final String fn = "/home/saalfeld/catmaid-fafb00-sample_A_cutout_3k.xml";
@@ -712,7 +713,10 @@ public class BigDataViewer
{
System.setProperty( "apple.laf.useScreenMenuBar", "true" );
- final BigDataViewer bdv = open( fn, new File( fn ).getName(), new ProgressWriterConsole(), ViewerOptions.options() );
+ final BigDataViewer bdv1 = open( fn1, new File( fn1 ).getName(), new ProgressWriterConsole(), ViewerOptions.options() );
+// final BigDataViewer bdv2 = open( fn2, new File( fn2 ).getName(), new ProgressWriterConsole(), ViewerOptions.options() );
+
+ bdv1.getViewerFrame().setSize( 1248, 656 );
// DumpInputConfig.writeToYaml( System.getProperty( "user.home" ) + "/.bdv/bdvkeyconfig.yaml", bdv.getViewerFrame() );
}
diff --git a/src/main/java/bdv/img/openconnectome/OpenConnectomeImageLoader.java b/src/main/java/bdv/img/openconnectome/OpenConnectomeImageLoader.java
index 263c83fcccced7347a83aded2e58275d1355813b..3195e850d1a222b653300035d08a8db090be6050 100644
--- a/src/main/java/bdv/img/openconnectome/OpenConnectomeImageLoader.java
+++ b/src/main/java/bdv/img/openconnectome/OpenConnectomeImageLoader.java
@@ -7,13 +7,13 @@
* %%
* 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
@@ -244,7 +244,12 @@ public class OpenConnectomeImageLoader extends AbstractViewerSetupImgLoader< Uns
* Create a {@link VolatileCachedCellImg} backed by the cache. The type
* should be either {@link ARGBType} and {@link VolatileARGBType}.
*/
- protected < T extends NativeType< T > > VolatileCachedCellImg< T, VolatileByteArray > prepareCachedImage( final int timepointId, final int setupId, final int level, final LoadingStrategy loadingStrategy, final T type )
+ protected < T extends NativeType< T > > VolatileCachedCellImg< T, VolatileByteArray > prepareCachedImage(
+ final int timepointId,
+ final int setupId,
+ final int level,
+ final LoadingStrategy loadingStrategy,
+ final T type )
{
final long[] dimensions = imageDimensions[ level ];
final int[] cellDimensions = blockDimensions[ level ];
diff --git a/src/main/java/bdv/spimdata/tools/MergeExample.java b/src/main/java/bdv/spimdata/tools/MergeExample.java
index b31019a37471d7bbc7870e0104482fba1e33805d..9091b15bf19f7bebabbc5a60ec7cf70f1aeccebb 100644
--- a/src/main/java/bdv/spimdata/tools/MergeExample.java
+++ b/src/main/java/bdv/spimdata/tools/MergeExample.java
@@ -7,13 +7,13 @@
* %%
* 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
@@ -31,6 +31,7 @@ package bdv.spimdata.tools;
import java.io.File;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -38,10 +39,6 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import mpicbg.spim.data.SpimDataException;
-import mpicbg.spim.data.registration.ViewRegistration;
-import mpicbg.spim.data.registration.ViewRegistrations;
-import mpicbg.spim.data.registration.ViewTransform;
import bdv.export.ExportMipmapInfo;
import bdv.export.WriteSequenceToHdf5;
import bdv.img.hdf5.Hdf5ImageLoader;
@@ -49,6 +46,12 @@ import bdv.img.hdf5.Partition;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.data.registration.ViewRegistration;
+import mpicbg.spim.data.registration.ViewRegistrations;
+import mpicbg.spim.data.registration.ViewTransform;
+import mpicbg.spim.data.registration.ViewTransformAffine;
+import net.imglib2.realtransform.AffineTransform3D;
/**
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
@@ -136,4 +139,22 @@ public class MergeExample
WriteSequenceToHdf5.writeHdf5PartitionLinkFile( seq, newMipmapInfos );
io.save( spimData, xmlFilename );
}
+
+ public static void main( final String... args ) throws SpimDataException
+ {
+ final AffineTransform3D t1 = new AffineTransform3D();
+ final AffineTransform3D t2 = new AffineTransform3D();
+ t2.set( 70, 0, 3 );
+
+ mergeHdf5Views(
+ Arrays.asList( new String[]{
+ "/groups/saalfeld/home/saalfelds/tmp/dagmar/bdv-26.xml",
+ "/groups/saalfeld/home/saalfelds/tmp/dagmar/bdv-27.xml"
+ } ),
+ Arrays.asList( new ViewTransformAffine[]{
+ new ViewTransformAffine( "t1", t1 ),
+ new ViewTransformAffine( "t2", t2 )
+ } ),
+ "/groups/saalfeld/home/saalfelds/tmp/dagmar/bdv-26-27.xml" );
+ }
}
diff --git a/src/main/java/bdv/viewer/render/AccumulateProjectorARGB.java b/src/main/java/bdv/viewer/render/AccumulateProjectorARGB.java
index 5d35601449d80528134e75ea35fb89ab74598078..fcc4cb79928e25af526f82d8fcdf527c9f8edf06 100644
--- a/src/main/java/bdv/viewer/render/AccumulateProjectorARGB.java
+++ b/src/main/java/bdv/viewer/render/AccumulateProjectorARGB.java
@@ -7,13 +7,13 @@
* %%
* 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
@@ -32,11 +32,11 @@ package bdv.viewer.render;
import java.util.ArrayList;
import java.util.concurrent.ExecutorService;
+import bdv.viewer.Source;
import net.imglib2.Cursor;
import net.imglib2.RandomAccessible;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.numeric.ARGBType;
-import bdv.viewer.Source;
public class AccumulateProjectorARGB extends AccumulateProjector< ARGBType, ARGBType >
{
@@ -68,7 +68,7 @@ public class AccumulateProjectorARGB extends AccumulateProjector< ARGBType, ARGB
@Override
protected void accumulate( final Cursor< ARGBType >[] accesses, final ARGBType target )
{
- int aSum = 0, rSum = 0, gSum = 0, bSum = 0;
+ int aSum = 0, rSum = 255, gSum = 255, bSum = 255;
for ( final Cursor< ARGBType > access : accesses )
{
final int value = access.get().get();
@@ -76,19 +76,36 @@ public class AccumulateProjectorARGB extends AccumulateProjector< ARGBType, ARGB
final int r = ARGBType.red( value );
final int g = ARGBType.green( value );
final int b = ARGBType.blue( value );
- aSum += a;
- rSum += r;
- gSum += g;
- bSum += b;
+// aSum += a;
+// rSum += r;
+// gSum += g;
+// bSum += b;
+ if (!(r == 0 && g == 0 && b == 0))
+ {
+ aSum = Math.max( aSum, a );
+ rSum = Math.min( rSum, r );
+ gSum = Math.min( gSum, g );
+ bSum = Math.min( bSum, b );
+ }
}
- if ( aSum > 255 )
+ if ( aSum == 0 )
+ {
aSum = 255;
- if ( rSum > 255 )
- rSum = 255;
- if ( gSum > 255 )
- gSum = 255;
- if ( bSum > 255 )
- bSum = 255;
+ rSum = 0;
+ gSum = 0;
+ bSum = 0;
+ }
+ else
+ {
+ if ( aSum > 255 )
+ aSum = 255;
+ if ( rSum > 255 )
+ rSum = 255;
+ if ( gSum > 255 )
+ gSum = 255;
+ if ( bSum > 255 )
+ bSum = 255;
+ }
target.set( ARGBType.rgba( rSum, gSum, bSum, aSum ) );
}
}