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implemented a per-overlapping-interval maxspot limit
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@StephanPreibisch
StephanPreibisch committed Jul 14, 2024
1 parent 797989f commit 21327cb
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Showing 2 changed files with 133 additions and 11 deletions.
130 changes: 120 additions & 10 deletions src/main/java/net/preibisch/bigstitcher/spark/SparkInterestPointDetection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,9 @@ public enum Localization { NONE, QUADRATIC };
@Option(names = {"--maxSpots" }, description = "limit the number of spots per view (choose the brightest ones), e.g. --maxSpots 10000 (default: NO LIMIT)")
protected int maxSpots = -1;

@Option(names = { "--maxSpotsPerOverlap" }, description = "apply the maximum number of spots individually to every overlapping area, needs --overlappingOnly & --maxSpots to be set to work (default: false)")
protected boolean maxSpotsPerOverlap = false;

@Option(names = "--blockSize", description = "blockSize for running the interest point detection - at the scale of detection (default: 512,512,128)")
protected String blockSizeString = "512,512,128";

Expand All @@ -160,6 +163,12 @@ public enum Localization { NONE, QUADRATIC };
@Override
public Void call() throws Exception
{
if ( maxSpotsPerOverlap && ( !overlappingOnly || maxSpots <= 0 ) )
{
System.out.println( "--maxSpotsPerOverlap only works when --overlappingOnly AND --maxSpots is set.");
System.exit( 0 );
}

final SpimData2 dataGlobal = this.loadSpimData2();

if ( dataGlobal == null )
Expand All @@ -186,6 +195,7 @@ public Void call() throws Exception
final double combineDistance = SparkInterestPointDetection.combineDistance;
final Localization localization = this.localization;
final int maxSpots = this.maxSpots;
final boolean maxSpotsPerOverlap = this.maxSpotsPerOverlap;
final boolean prefetch = this.prefetch;
final boolean storeIntensities = this.storeIntensities;
final Integer medianFilter = this.medianFilter;
Expand All @@ -201,7 +211,10 @@ public Void call() throws Exception
System.out.println( "downsampleZ: " + downsampleZ );
System.out.println( "overlappingOnly: " + onlyOverlappingRegions );
System.out.println( "prefetching: " + prefetch );
if ( maxSpots > 0 ) System.out.println( "maxSpots: " + maxSpots );
if ( maxSpots > 0 ) {
System.out.println( "maxSpots: " + maxSpots );
System.out.println( "maxSpotsPerOverlap: " + maxSpotsPerOverlap );
}
System.out.println( "blockSize: " + Util.printCoordinates( blockSize ) );
System.out.println( "medianFilter: " + medianFilter );
System.out.println( "storeIntensities: " + storeIntensities );
Expand All @@ -211,6 +224,8 @@ public Void call() throws Exception
//
final ArrayList< Pair< ViewId, Interval > > toProcess = new ArrayList<>();

long maxIntervalSize = 0;

for ( final ViewId viewId : viewIdsGlobal )
{
final ViewDescription vd = dataGlobal.getSequenceDescription().getViewDescription( viewId );
Expand Down Expand Up @@ -263,8 +278,12 @@ public Void call() throws Exception
final Interval intersectionBoxes = Intervals.intersect( boundingBox, boundingBoxOther );
final Interval intersection = Intervals.intersect( input.getA(), intersectionBoxes ); // make sure it fits (e.g. rounding errors)

System.out.println( "intersectionBoxes=" + Util.printInterval( intersectionBoxes ) );
System.out.println( "intersection=" + Util.printInterval( intersection ) );
final long size = ViewUtil.size( intersection );

//System.out.println( "intersectionBoxes=" + Util.printInterval( intersectionBoxes ) );
System.out.println( "intersection=" + Util.printInterval( intersection ) + ", size (#px)=" + size );

maxIntervalSize = Math.max( maxIntervalSize, size );

allIntervals.add( intersection );
}
Expand All @@ -281,7 +300,7 @@ public Void call() throws Exception
}

//
// turn all areas into grids and serializable objects
// turn all areas into grids and serializable objects (ViewId, intervalOffset, gridEntry)
//
final ArrayList< Tuple3<int[], long[], long[][] > > sparkProcess = new ArrayList<>();

Expand Down Expand Up @@ -501,12 +520,10 @@ public Void call() throws Exception

System.out.println( "Computed all interest points, statistics:" );

final HashMap< ViewId, List< InterestPoint > > interestPoints = new HashMap<>();
final HashMap< ViewId, List< Double > > intensitiesIPs = new HashMap<>();

// assemble all interest point intervals per ViewId
final HashMap< ViewId, List< List< InterestPoint > > > interestPointsPerViewId = new HashMap<>();
final HashMap< ViewId, List< List< Double > > > intensitiesPerViewId = new HashMap<>();
final HashMap< ViewId, List< Interval > > intervalsPerViewId = new HashMap<>();

for ( final Tuple4<int[], long[][], double[][], double[]> tuple : results )
{
Expand All @@ -518,6 +535,9 @@ public Void call() throws Exception
interestPointsPerViewId.putIfAbsent(viewId, new ArrayList<>() );
interestPointsPerViewId.get( viewId ).add( Spark.deserializeInterestPoints(points) );

intervalsPerViewId.putIfAbsent(viewId, new ArrayList<>() );
intervalsPerViewId.get( viewId ).add( Spark.deserializeInterval( tuple._2() ) );

if ( storeIntensities || maxSpots > 0 )
{
intensitiesPerViewId.putIfAbsent(viewId, new ArrayList<>() );
Expand All @@ -526,10 +546,74 @@ public Void call() throws Exception
}
}

// now combine all jobs and fix potential overlap (overlappingOnly)
// assemble all ViewIds
final ArrayList< ViewId > viewIds = new ArrayList<>( interestPointsPerViewId.keySet() );
Collections.sort( viewIds );

// we need to filter per overlap before combining
if ( maxSpotsPerOverlap && maxSpots > 0 )
{
for ( final ViewId viewId : viewIds )
{
final List< List< InterestPoint > > ipsList = interestPointsPerViewId.get( viewId );
final List< List< Double > > intensitiesList = intensitiesPerViewId.get( viewId );
final List< Interval > intervalsList = intervalsPerViewId.get( viewId ); // note: in downsampled coordinates(!)

// find all intervals of this view, then assign points to it
final List< Tuple3< Interval, List< InterestPoint >, List< Double > > > intervalData = new ArrayList<>();

// for each toProcess block do
for ( final Pair< ViewId, Interval > p : toProcess )
{
if ( p.getA().equals( viewId ) )
{
final Interval toProcessInterval = p.getB();

final List< InterestPoint > ipsBlock = new ArrayList<>();
final List< Double > intensitiesBlock = new ArrayList<>();

// figure out which computed blockIntervals fall into this toProcessInterval
for ( int l = 0; l < ipsList.size(); ++l )
{
final Interval blockInterval = intervalsList.get( l );

if ( Intervals.contains( toProcessInterval, blockInterval ) )
{
ipsBlock.addAll( ipsList.get( l ) );
intensitiesBlock.addAll( intensitiesList.get( l ) );
}
}

intervalData.add( new Tuple3<>( toProcessInterval, ipsBlock, intensitiesBlock ) );
}
}

// to later put back into interestPointsPerViewId and intensitiesPerViewId
interestPointsPerViewId.get( viewId ).clear();
intensitiesPerViewId.get( viewId ).clear();

// now filter each interval of each view
for ( final Tuple3< Interval, List< InterestPoint >, List< Double > > tuple : intervalData )
{
final int myMaxSpots = (int)Math.round( maxSpots * ( (double)ViewUtil.size( tuple._1() ) /(double)maxIntervalSize ) );

if ( myMaxSpots > 0 && myMaxSpots < tuple._2().size() )
{
final int oldSize = tuple._2().size();
filterPoints( tuple._2(), tuple._3(), myMaxSpots );
System.out.println( "Filtered interval " + Util.printInterval( tuple._1() ) + " (" + Group.pvid( viewId ) + "): " + oldSize + " >>> " + tuple._2().size() );
}

interestPointsPerViewId.get( viewId ).add( tuple._2() );
intensitiesPerViewId.get( viewId ).add( tuple._3() );
}
}
}

// now combine all jobs and fix potential overlap (overlappingOnly)
final HashMap< ViewId, List< InterestPoint > > interestPoints = new HashMap<>();
final HashMap< ViewId, List< Double > > intensitiesIPs = new HashMap<>();

for ( final ViewId viewId : viewIds )
{
final ArrayList< InterestPoint > myIps = new ArrayList<>();
Expand Down Expand Up @@ -592,8 +676,10 @@ public Void call() throws Exception

System.out.println( Group.pvid( viewId ) + ": " + myIpsNewId.size() );

if ( maxSpots > 0 && maxSpots < myIpsNewId.size() )
if ( !maxSpotsPerOverlap && maxSpots > 0 && maxSpots < myIpsNewId.size() )
{
filterPoints( myIpsNewId, myIntensities, maxSpots );
/*
// filter for the brightnest N spots
final ArrayList< Pair< Double, InterestPoint > > combinedList = new ArrayList<>();
Expand All @@ -611,7 +697,7 @@ public Void call() throws Exception
myIntensities.add( combinedList.get( i ).getA() );
myIpsNewId.add( new InterestPoint( i, combinedList.get( i ).getB().getL() ) ); // new id's again ...
}

*/
System.out.println( Group.pvid( viewId ) + " (after applying maxSpots): " + myIpsNewId.size() );
}

Expand Down Expand Up @@ -703,6 +789,30 @@ public Void call() throws Exception
return null;
}

public static void filterPoints(
final List< InterestPoint > myIps,
final List< Double > myIntensities,
final int maxSpots )
{
// filter for the brightnest N spots
final ArrayList< Pair< Double, InterestPoint > > combinedList = new ArrayList<>();

for ( int i = 0; i < myIps.size(); ++i )
combinedList.add( new ValuePair<Double, InterestPoint>(myIntensities.get( i ), myIps.get( i )));

// sort from large to small
Collections.sort(combinedList, (a,b) -> b.getA().compareTo( a.getA() ) );

myIps.clear();
myIntensities.clear();

for ( int i = 0; i < maxSpots; ++i )
{
myIntensities.add( combinedList.get( i ).getA() );
myIps.add( new InterestPoint( i, combinedList.get( i ).getB().getL() ) ); // new id's again ...
}
}

// TODO: this has been pushed up to the multiview-reconstruction code, use new version
public static Pair<RandomAccessibleInterval, AffineTransform3D> openAndDownsample(
final BasicImgLoader imgLoader,
Expand Down
14 changes: 13 additions & 1 deletion src/main/java/net/preibisch/bigstitcher/spark/util/ViewUtil.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,11 @@
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.Callable;

import mpicbg.spim.data.SpimData;
import mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.registration.ViewRegistration;
import mpicbg.spim.data.registration.ViewRegistrations;
import mpicbg.spim.data.sequence.ImgLoader;
import mpicbg.spim.data.sequence.SetupImgLoader;
import mpicbg.spim.data.sequence.ViewId;
Expand All @@ -53,6 +53,18 @@

public class ViewUtil
{
public static long size( final Interval interval )
{
if ( interval == null || interval.numDimensions() == 0 )
return 0;

long size = interval.dimension( 0 );

for ( int d = 1; d < interval.numDimensions(); ++d )
size *= interval.dimension( d );

return size;
}

public static boolean overlaps( final Interval interval1, final Interval interval2 )
{
Expand Down

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