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Set number of BDV render threads to number of IO threads
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@tischi
tischi committed Dec 16, 2023
1 parent 4fb63b7 commit a3c5cf0
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Showing 4 changed files with 34 additions and 34 deletions.
1 change: 0 additions & 1 deletion src/main/java/org/embl/mobie/MoBIE.java
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Expand Up @@ -265,7 +265,6 @@ private void openHCSDataset( double wellMargin, double siteMargin ) throws IOExc
{
initProject( "HCS" );
final Plate plate = new Plate( projectLocation );
IJ.log( "HCS Pattern: " + plate.getHcsPattern() );
new HCSDataAdder( plate, wellMargin, siteMargin ).addData( dataset );
initUIandShowView( dataset.views().keySet().iterator().next() );
}
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2 changes: 0 additions & 2 deletions src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java
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Expand Up @@ -49,9 +49,7 @@
import java.awt.*;

public class MobieBdvSupplier implements IBdvSupplier {

public final MobieSerializableBdvOptions sOptions;

public MobieBdvSupplier( MobieSerializableBdvOptions sOptions )
{
this.sOptions = sOptions;
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11 changes: 6 additions & 5 deletions src/main/java/org/embl/mobie/lib/bdv/MobieSerializableBdvOptions.java
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Expand Up @@ -31,6 +31,7 @@
import bdv.util.AxisOrder;
import bdv.util.BdvOptions;
import bdv.viewer.render.AccumulateProjectorFactory;
import org.embl.mobie.lib.ThreadHelper;
import org.embl.mobie.lib.bdv.blend.AccumulateAlphaBlendingProjectorARGBFactory;
import net.imglib2.type.numeric.ARGBType;

Expand Down Expand Up @@ -59,21 +60,21 @@ public class MobieSerializableBdvOptions {
public AccumulateProjectorFactory<ARGBType> accumulateProjectorFactory = new AccumulateAlphaBlendingProjectorARGBFactory();

public BdvOptions getBdvOptions() {
BdvOptions o =
BdvOptions bdvOptions =
BdvOptions.options()
.screenScales(this.screenScales)
.targetRenderNanos(this.targetRenderNanos)
.numRenderingThreads(this.numRenderingThreads)
.numRenderingThreads(ThreadHelper.getNumIoThreads())
.numSourceGroups(this.numSourceGroups)
.axisOrder(this.axisOrder)
.preferredSize(this.width, this.height)
.frameTitle(this.frameTitle);
if (this.accumulateProjectorFactory!=null) {
o = o.accumulateProjectorFactory(this.accumulateProjectorFactory);
bdvOptions = bdvOptions.accumulateProjectorFactory(this.accumulateProjectorFactory);
}
if (this.is2D) o = o.is2D();
if (this.is2D) bdvOptions = bdvOptions.is2D();

return o;
return bdvOptions;
}

}
54 changes: 28 additions & 26 deletions src/main/java/org/embl/mobie/lib/hcs/Plate.java
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Original file line number Diff line number Diff line change
Expand Up @@ -88,9 +88,10 @@ public Plate( String hcsDirectory ) throws IOException
// FIXME: fetch operetta paths from XML?!
// FIXME: fetch OME-Zarr paths entry point JSON?!

IJ.log( "Fetching paths..." );
IJ.log( "Looking for image files..." );
long start = System.currentTimeMillis();
List< String > imageSitePaths;
List< String > imagePaths;

if ( hcsDirectory.endsWith( ".zarr" ) )
{
hcsPattern = HCSPattern.OMEZarr;
Expand All @@ -105,9 +106,9 @@ public Plate( String hcsDirectory ) throws IOException
imageDataFormat = ImageDataFormat.OmeZarr;
}

imageSitePaths = OMEZarrHCSHelper.sitePathsFromMetadata( hcsDirectory );
imagePaths = OMEZarrHCSHelper.sitePathsFromMetadata( hcsDirectory );

final String firstImagePath = imageSitePaths.get( 0 );
final String firstImagePath = imagePaths.get( 0 );
AbstractSpimData< ? > spimData = DataStore.fetchSpimData( firstImagePath, imageDataFormat, ThreadHelper.sharedQueue );
List< ViewSetup > viewSetupsOrdered = ( List< ViewSetup > ) spimData.getSequenceDescription().getViewSetupsOrdered();
List< String > channels = viewSetupsOrdered.stream().map( vs -> vs.getChannel().getName() ).collect( Collectors.toList() );
Expand All @@ -118,19 +119,19 @@ public Plate( String hcsDirectory ) throws IOException
if( IOHelper.getType( hcsDirectory ).equals( IOHelper.ResourceType.S3 ) )
{
imageDataFormat = ImageDataFormat.BioFormatsS3;
imageSitePaths = S3Utils.getS3FilePaths( hcsDirectory );
imagePaths = S3Utils.getS3FilePaths( hcsDirectory );
ThreadHelper.setNumIoThreads( Math.max( 16, ThreadHelper.getNumIoThreads() ) );
}
else
{
imageDataFormat = ImageDataFormat.BioFormats;
imageSitePaths = Files.walk( Paths.get( hcsDirectory ), 3 )
imagePaths = Files.walk( Paths.get( hcsDirectory ), 3 )
.map( p -> p.toString() )
.collect( Collectors.toList() );
}

hcsPattern = determineHCSPattern( hcsDirectory, imageSitePaths );
imageSitePaths = imageSitePaths.stream()
hcsPattern = determineHCSPattern( hcsDirectory, imagePaths );
imagePaths = imagePaths.stream()
.filter( path -> hcsPattern.setMatcher( path ) ) // skip files like .DS_Store a.s.o.
.collect( Collectors.toList() );

Expand All @@ -140,26 +141,27 @@ public Plate( String hcsDirectory ) throws IOException
//final File xml = new File( hcsDirectory, "Index.idx.xml" );
final File xml = new File( hcsDirectory, "Index.xml" );
operettaMetadata = new OperettaMetadata( xml );
imageSitePaths = imageSitePaths.stream()
imagePaths = imagePaths.stream()
.filter( path -> operettaMetadata.contains( path ) ) // skip files like .DS_Store a.s.o.
.collect( Collectors.toList() );
}
}
IJ.log( "Done fetching " + imageSitePaths.size() + " paths in " + ( System.currentTimeMillis() - start ) + " ms." );
IJ.log( "Found " + imagePaths.size() + " image files in " + ( System.currentTimeMillis() - start ) + " ms." );
IJ.log( "HCS pattern: " + getHcsPattern() );

buildPlateMap( imageSitePaths );
buildPlateMap( imagePaths );
}

private void buildPlateMap( List< String > sitePaths )
private void buildPlateMap( List< String > imagePaths )
{
channelWellSites = new HashMap<>();
tPositions = new HashSet<>();

IJ.log("Parsing " + sitePaths.size() + " sites...");
IJ.log("Parsing metadata...");

for ( String sitePath : sitePaths )
for ( String imagePath : imagePaths )
{
hcsPattern.setMatcher( sitePath );
hcsPattern.setMatcher( imagePath );

// some formats contain multiple channels in one file
List< String > channelNames = hcsPattern.getChannels();
Expand All @@ -176,22 +178,22 @@ private void buildPlateMap( List< String > sitePaths )
channelWellSites.put( channel, new HashMap<>() );

// FIXME Replace with MoBIEHelper.getMetadataFromImageFile
IJ.log( "Fetching metadata for setup " + channelName + " from " + sitePath );
ImagePlus singleChannelImagePlus = operettaMetadata == null ? MoBIEHelper.openAsImagePlus( sitePath, channel.getChannelIndex(), imageDataFormat ) : null;
IJ.log( "Fetching metadata for setup " + channelName + " from " + imagePath );
ImagePlus singleChannelImagePlus = operettaMetadata == null ? MoBIEHelper.openAsImagePlus( imagePath, channel.getChannelIndex(), imageDataFormat ) : null;
if ( singleChannelImagePlus.getNSlices() > 1 )
is2d = false;

// set channel metadata
//
if ( operettaMetadata != null )
{
final String color = operettaMetadata.getColor( sitePath );
final String color = operettaMetadata.getColor( imagePath );
channel.setColor( color );

// TODO: There does not always seem to be enough metadata for the
// contrast limits, thus opening one image may be worth it
// then convert to image plus and run once auto contrast on it
final double[] contrastLimits = operettaMetadata.getContrastLimits( sitePath );
final double[] contrastLimits = operettaMetadata.getContrastLimits( imagePath );
channel.setContrastLimits( contrastLimits );
}
else // from image file
Expand All @@ -213,8 +215,8 @@ private void buildPlateMap( List< String > sitePaths )
{
if ( operettaMetadata != null )
{
voxelDimensions = operettaMetadata.getVoxelDimensions( sitePath );
siteDimensions = operettaMetadata.getSiteDimensions( sitePath );
voxelDimensions = operettaMetadata.getVoxelDimensions( imagePath );
siteDimensions = operettaMetadata.getSiteDimensions( imagePath );
}
else // from image file
{
Expand Down Expand Up @@ -256,14 +258,14 @@ private void buildPlateMap( List< String > sitePaths )
{
if ( imageDataFormat.equals( ImageDataFormat.SpimData ) )
{
final int imageIndex = operettaMetadata.getImageIndex( sitePath );
final int imageIndex = operettaMetadata.getImageIndex( imagePath );
final BasicViewSetup viewSetup = spimDataPlate.getSequenceDescription().getViewSetupsOrdered().get( imageIndex );
IJ.log( "" );
final Map< String, Entity > attributes = viewSetup.getAttributes();
IJ.log( "Image index:" + imageIndex );
IJ.log( "Series index: " + ( ( SeriesIndex ) attributes.get( "seriesindex" ) ).getId() );
IJ.log( "Setup name: " + viewSetup.getName() );
IJ.log( "File name: " + new File( sitePath ).getName() );
IJ.log( "File name: " + new File( imagePath ).getName() );
site = new Site( siteGroup, imageDataFormat, spimDataPlate, imageIndex );
}
else
Expand All @@ -282,14 +284,14 @@ private void buildPlateMap( List< String > sitePaths )

if ( hcsPattern.equals( hcsPattern.OMEZarr ) )
{
site.absolutePath = sitePath;
site.absolutePath = imagePath;
site.channelIndex = channel.getChannelIndex();
}
else
{
final String t = hcsPattern.getT();
final String z = hcsPattern.getZ();
site.addPath( t, z, sitePath );
site.addPath( t, z, imagePath );
tPositions.add( new TPosition( t ) );
}
}
Expand All @@ -298,8 +300,8 @@ private void buildPlateMap( List< String > sitePaths )
IJ.log( "Initialised HCS plate: " + getName() );
IJ.log( "Wells: " + wellsPerPlate );
IJ.log( "Sites per well: " + sitesPerWell );
IJ.log( "Sites: " + sitePaths.size() );
IJ.log( "Channels: " + channelWellSites.keySet().size() );
IJ.log( "Frames: " + tPositions.size() );
}

private ImagePlus openImagePlus( String path, int channelID )
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