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Commit 9462689d authored by Stephan Saalfeld's avatar Stephan Saalfeld
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Merge remote-tracking branch 'origin/master' 

# Conflicts:
#	pom.xml
parents 4d5b5b96 b169d78d
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.travis.yml 0 → 100644
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language: java
jdk: oraclejdk8
branches:
only: master
install: true
script: ".travis/build.sh"
after_success: ".travis/notify.sh Travis-Success"
after_failure: ".travis/notify.sh Travis-Failure"
env:
global:
- secure: NqQnD838jkrZYdEdVBigS1nKaYDwf1u9mWidxenU+wE2/PLSYz8yO/mD9XTy1uaAji6yazNN/odQinIukcUr0rAGcFoxZg93GiXLGuLBosgUKx9OHm2IThOimhPoUjeoR2BcqA/EV7bordLTNHnM5ZCg4uQkasIIDZFZk7lPx9w=
- secure: JvJcNdcbec8ybGIXj7jGAzQiayeGPWxXzOKm7Ek7T0qg1O7aozqWl3qX+VcH5Q0wiLlhtJjshjhCn3FT0CW/ART3AyKt3rmYvujERYVapIFAfceI/4aHFuUfryOYlunHF58+STOKWrDAaotxk/yeILBB4kQMLSFgm2B3f/iAuUU=
.travis/build.sh 0 → 100755
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#!/bin/sh
dir="$(dirname "$0")"
if [ "$TRAVIS_SECURE_ENV_VARS" = true \
-a "$TRAVIS_PULL_REQUEST" = false \
-a "$TRAVIS_BRANCH" = master ]
then
mvn -Pdeploy-to-imagej deploy --settings "$dir/settings.xml"
else
mvn install
fi
.travis/notify.sh 0 → 100755
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#!/bin/sh
curl -fs "https://jenkins.imagej.net/job/$1/buildWithParameters?token=$TOKEN_NAME&repo=$TRAVIS_REPO_SLUG&commit=$TRAVIS_COMMIT&pr=$TRAVIS_PULL_REQUEST"
.travis/settings.xml 0 → 100644
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<settings>
<servers>
<server>
<id>imagej.releases</id>
<username>travis</username>
<password>${env.MAVEN_PASS}</password>
</server>
<server>
<id>imagej.snapshots</id>
<username>travis</username>
<password>${env.MAVEN_PASS}</password>
</server>
</servers>
</settings>
pom.xml
+ 75
− 47
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...@@ -3,32 +3,90 @@ ...@@ -3,32 +3,90 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<parent> <parent>
<groupId>sc.fiji</groupId> <groupId>org.scijava</groupId>
<artifactId>pom-bigdataviewer</artifactId> <artifactId>pom-scijava</artifactId>
<version>3.3.0-SNAPSHOT</version> <version>14.0.0</version>
<relativePath />
</parent> </parent>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-server</artifactId> <artifactId>bigdataviewer-server</artifactId>
<version>2.0.1-SNAPSHOT</version> <version>2.1.1-SNAPSHOT</version>
<name>BigDataServer</name> <name>BigDataServer</name>
<description>A web server for BigDataViewer datasets</description> <description>A web server for BigDataViewer datasets.</description>
<url>https://imagej.net/BigDataServer</url>
<inceptionYear>2014</inceptionYear>
<organization>
<name>BigDataViewer</name>
<url>https://imagej.net/BigDataViewer</url>
</organization>
<licenses>
<license>
<name>GNU General Public License v3+</name>
<url>https://www.gnu.org/licenses/gpl.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>tpietzsch</id>
<name>Tobias Pietzsch</name>
<url>http://imagej.net/User:Pietzsch</url>
<roles>
<role>founder</role>
<role>lead</role>
<role>developer</role>
<role>debugger</role>
<role>reviewer</role>
<role>support</role>
<role>maintainer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>HongKee Moon</name>
<url>http://imagej.net/User:Moon</url>
<properties><id>hkmoon</id></properties>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>ImageJ Forum</name>
<archive>http://forum.imagej.net/</archive>
</mailingList>
</mailingLists>
<scm>
<connection>scm:git:git://github.com/bigdataviewer/bigdataviewer-server</connection>
<developerConnection>scm:git:git@github.com:bigdataviewer/bigdataviewer-server</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/bigdataviewer/bigdataviewer-server</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/bigdataviewer/bigdataviewer-server/issues</url>
</issueManagement>
<ciManagement>
<system>Travis CI</system>
<url>https://travis-ci.org/bigdataviewer/bigdataviewer-server</url>
</ciManagement>
<properties> <properties>
<scijava.jvm.version>1.8</scijava.jvm.version> <package-name>bdv.server</package-name>
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>BigDataViewer developers.</license.copyrightOwners>
</properties> </properties>
<build> <repositories>
<plugins> <repository>
<plugin> <id>imagej.public</id>
<artifactId>maven-compiler-plugin</artifactId> <url>http://maven.imagej.net/content/groups/public</url>
<configuration> </repository>
<source>1.7</source> </repositories>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies> <dependencies>
<dependency> <dependency>
...@@ -50,34 +108,4 @@ ...@@ -50,34 +108,4 @@
<version>1.2</version> <version>1.2</version>
</dependency> </dependency>
</dependencies> </dependencies>
<developers>
<developer>
<id>tpietzsch</id>
<name>Tobias Pietzsch</name>
<email>pietzsch@mpi-cbg.de</email>
<url />
<organization>MPI-CBG</organization>
<organizationUrl>http://www.mpi-cbg.de/</organizationUrl>
<roles>
<role>architect</role>
<role>developer</role>
</roles>
<timezone>+1</timezone>
</developer>
</developers>
<repositories>
<repository>
<id>imagej.public</id>
<url>http://maven.imagej.net/content/groups/public</url>
</repository>
</repositories>
<scm>
<connection>scm:git:git://github.com/tpietzsch/spimviewer</connection>
<developerConnection>scm:git:git@github.com:tpietzsch/spimviewer</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/tpietzsch/spimviewer</url>
</scm>
</project> </project>
src/main/java/bdv/server/CellHandler.java
+ 13
− 11
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...@@ -14,10 +14,6 @@ import javax.imageio.ImageIO; ...@@ -14,10 +14,6 @@ import javax.imageio.ImageIO;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import mpicbg.spim.data.SpimDataException;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.realtransform.AffineTransform3D;
import org.eclipse.jetty.server.Request; import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.handler.ContextHandler; import org.eclipse.jetty.server.handler.ContextHandler;
import org.eclipse.jetty.util.log.Log; import org.eclipse.jetty.util.log.Log;
...@@ -27,11 +23,15 @@ import org.jdom2.input.SAXBuilder; ...@@ -27,11 +23,15 @@ import org.jdom2.input.SAXBuilder;
import org.jdom2.output.Format; import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter; import org.jdom2.output.XMLOutputter;
import com.google.gson.GsonBuilder;
import bdv.BigDataViewer; import bdv.BigDataViewer;
import bdv.img.cache.CacheHints; import bdv.cache.CacheHints;
import bdv.img.cache.LoadingStrategy; import bdv.cache.LoadingStrategy;
import bdv.img.cache.VolatileCell; import bdv.img.cache.VolatileCell;
import bdv.img.cache.VolatileGlobalCellCache; import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.cache.VolatileGlobalCellCache.Key;
import bdv.img.cache.VolatileGlobalCellCache.VolatileCellLoader;
import bdv.img.hdf5.Hdf5ImageLoader; import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.img.hdf5.Hdf5VolatileShortArrayLoader; import bdv.img.hdf5.Hdf5VolatileShortArrayLoader;
import bdv.img.remote.AffineTransform3DJsonSerializer; import bdv.img.remote.AffineTransform3DJsonSerializer;
...@@ -41,8 +41,9 @@ import bdv.spimdata.SequenceDescriptionMinimal; ...@@ -41,8 +41,9 @@ import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal; import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal; import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.ThumbnailGenerator; import bdv.util.ThumbnailGenerator;
import mpicbg.spim.data.SpimDataException;
import com.google.gson.GsonBuilder; import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.realtransform.AffineTransform3D;
public class CellHandler extends ContextHandler public class CellHandler extends ContextHandler
{ {
...@@ -97,7 +98,7 @@ public class CellHandler extends ContextHandler ...@@ -97,7 +98,7 @@ public class CellHandler extends ContextHandler
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription(); final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader(); final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
cache = imgLoader.getCache(); cache = imgLoader.getCacheControl();
loader = imgLoader.getShortArrayLoader(); loader = imgLoader.getShortArrayLoader();
cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false ); cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
...@@ -144,7 +145,8 @@ public class CellHandler extends ContextHandler ...@@ -144,7 +145,8 @@ public class CellHandler extends ContextHandler
final int timepoint = Integer.parseInt( parts[ 2 ] ); final int timepoint = Integer.parseInt( parts[ 2 ] );
final int setup = Integer.parseInt( parts[ 3 ] ); final int setup = Integer.parseInt( parts[ 3 ] );
final int level = Integer.parseInt( parts[ 4 ] ); final int level = Integer.parseInt( parts[ 4 ] );
VolatileCell< ? > cell = cache.getGlobalIfCached( timepoint, setup, level, index, cacheHints ); final Key key = new VolatileGlobalCellCache.Key( timepoint, setup, level, index );
VolatileCell< ? > cell = cache.getLoadingVolatileCache().getIfPresent( key, cacheHints );
if ( cell == null ) if ( cell == null )
{ {
final int[] cellDims = new int[] { final int[] cellDims = new int[] {
...@@ -155,7 +157,7 @@ public class CellHandler extends ContextHandler ...@@ -155,7 +157,7 @@ public class CellHandler extends ContextHandler
Long.parseLong( parts[ 8 ] ), Long.parseLong( parts[ 8 ] ),
Long.parseLong( parts[ 9 ] ), Long.parseLong( parts[ 9 ] ),
Long.parseLong( parts[ 10 ] ) }; Long.parseLong( parts[ 10 ] ) };
cell = cache.createGlobal( cellDims, cellMin, timepoint, setup, level, index, cacheHints, loader ); cell = cache.getLoadingVolatileCache().get( key, cacheHints, new VolatileCellLoader<>( loader, timepoint, setup, level, cellDims, cellMin ) );
} }
@SuppressWarnings( "unchecked" ) @SuppressWarnings( "unchecked" )
......
src/main/java/bdv/server/ManagerHandler.java
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...@@ -87,10 +87,6 @@ public class ManagerHandler extends ContextHandler ...@@ -87,10 +87,6 @@ public class ManagerHandler extends ContextHandler
final String ds = request.getParameter( "ds" ); final String ds = request.getParameter( "ds" );
undeploy( ds, baseRequest, response ); undeploy( ds, baseRequest, response );
} }
else
{
return;
}
} }
public String getByteSizeString( final long size ) public String getByteSizeString( final long size )
......
src/main/java/bdv/util/ThumbnailGenerator.java
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...@@ -7,16 +7,12 @@ import java.util.List; ...@@ -7,16 +7,12 @@ import java.util.List;
import javax.imageio.ImageIO; import javax.imageio.ImageIO;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.ui.PainterThread;
import net.imglib2.ui.RenderTarget;
import org.jdom2.Document; import org.jdom2.Document;
import org.jdom2.Element; import org.jdom2.Element;
import org.jdom2.input.SAXBuilder; import org.jdom2.input.SAXBuilder;
import bdv.BigDataViewer; import bdv.BigDataViewer;
import bdv.img.cache.Cache; import bdv.cache.CacheControl;
import bdv.spimdata.SpimDataMinimal; import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal; import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.tools.InitializeViewerState; import bdv.tools.InitializeViewerState;
...@@ -32,6 +28,9 @@ import bdv.viewer.state.SourceGroup; ...@@ -32,6 +28,9 @@ import bdv.viewer.state.SourceGroup;
import bdv.viewer.state.SourceState; import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState; import bdv.viewer.state.ViewerState;
import bdv.viewer.state.XmlIoViewerState; import bdv.viewer.state.XmlIoViewerState;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.ui.PainterThread;
import net.imglib2.ui.RenderTarget;
/** /**
* Created by moon on 2/5/15. * Created by moon on 2/5/15.
...@@ -94,7 +93,7 @@ public class ThumbnailGenerator ...@@ -94,7 +93,7 @@ public class ThumbnailGenerator
} }
} }
final ThumbnailTarget renderTarget = new ThumbnailTarget(); final ThumbnailTarget renderTarget = new ThumbnailTarget();
new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, AccumulateProjectorARGB.factory, new Cache.Dummy() ).paint( state ); new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, AccumulateProjectorARGB.factory, new CacheControl.Dummy() ).paint( state );
return renderTarget.bi; return renderTarget.bi;
} }
......
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