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Generic N5ImageLoader #84

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Generic N5ImageLoader #84

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2cdd234
Make N5ImageLoader accept N5Reader in constructor
tischi Feb 6, 2020
0e5e006
Handle IOException in XmlIoN5ImageLoader
tischi Feb 6, 2020
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16 changes: 10 additions & 6 deletions src/main/java/bdv/img/n5/N5ImageLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@

public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
{
private final File n5File;
private final N5Reader n5;

// TODO: it would be good if this would not be needed
// find available setups from the n5
Expand All @@ -113,9 +113,9 @@ public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
*/
private final Map< Integer, SetupImgLoader > setupImgLoaders = new HashMap<>();

public N5ImageLoader( final File n5File, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
public N5ImageLoader( final N5Reader n5, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
this.n5File = n5File;
this.n5 = n5;
this.seq = sequenceDescription;
}

Expand All @@ -124,10 +124,16 @@ public File getN5File()
return n5File;
}

public void setN5File( File n5File )
{
this.n5File = n5File;
}

private File n5File;
private volatile boolean isOpen = false;
private FetcherThreads fetchers;
private VolatileGlobalCellCache cache;
private N5Reader n5;


private void open()
{
Expand All @@ -140,8 +146,6 @@ private void open()

try
{
this.n5 = new N5FSReader( n5File.getAbsolutePath() );

int maxNumLevels = 0;
final List< ? extends BasicViewSetup > setups = seq.getViewSetupsOrdered();
for ( final BasicViewSetup setup : setups )
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18 changes: 16 additions & 2 deletions src/main/java/bdv/img/n5/XmlIoN5ImageLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,13 @@
package bdv.img.n5;

import java.io.File;
import java.io.IOException;

import mpicbg.spim.data.XmlHelpers;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.ImgLoaderIo;
import mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.jdom2.Element;

import static mpicbg.spim.data.XmlHelpers.loadPath;
Expand All @@ -56,7 +59,18 @@ public Element toXml( final N5ImageLoader imgLoader, final File basePath )
public N5ImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
// final String version = elem.getAttributeValue( "version" );
final File path = loadPath( elem, "n5", basePath );
return new N5ImageLoader( path, sequenceDescription );

try
{
final File path = loadPath( elem, "n5", basePath );
final N5FSReader n5FSReader = new N5FSReader( path.getAbsolutePath() );
final N5ImageLoader n5ImageLoader = new N5ImageLoader( n5FSReader, sequenceDescription );
n5ImageLoader.setN5File( path );
return n5ImageLoader;
}
catch ( IOException e )
{
throw new RuntimeException( e );
}
}
}