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fix ICP code
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@StephanPreibisch
StephanPreibisch committed Jun 26, 2024
1 parent 57cb9dd commit a5f5625
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Showing 2 changed files with 36 additions and 18 deletions.
1 change: 1 addition & 0 deletions src/main/java/net/preibisch/stitcher/plugin/Calculate_Pairwise_Shifts.java
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Original file line number Diff line number Diff line change
Expand Up @@ -419,6 +419,7 @@ public List< ViewId > getDefaultFixedViews()
ipMap,
brp.labelMap,
new GlobalOptimizationParameters(Double.MAX_VALUE, Double.MAX_VALUE, GlobalOptType.ONE_ROUND_SIMPLE, false ),
false, //matchacrosslabels
true ) )
continue;

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53 changes: 35 additions & 18 deletions src/main/java/net/preibisch/stitcher/process/ICPRefinement.java
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Original file line number Diff line number Diff line change
Expand Up @@ -426,13 +426,17 @@ public static void refine(
200,
IterativeClosestPointParameters.defaultMinNumPoints );

final Map< ViewId, String > labelMap = new HashMap<>();
final Map< ViewId, HashMap< String, Double > > labelMap = new HashMap<>();

for ( final ViewId viewId : params.viewIds )
labelMap.put( viewId, params.label );
{
final HashMap< String, Double > map = new HashMap<>();
map.put( params.label, 1.0 );
labelMap.put( viewId, map );
}

// load & transform all interest points
final Map< ViewId, List< InterestPoint > > interestpoints =
final Map< ViewId, HashMap< String, List< InterestPoint > > > interestpoints =
TransformationTools.getAllTransformedInterestPoints(
params.viewIds,
data.getViewRegistrations().getViewRegistrations(),
Expand Down Expand Up @@ -484,9 +488,9 @@ public static void refine(
HashMap< ViewId, mpicbg.models.Tile > models;

if ( Interest_Point_Registration.hasGroups( subsets ) )
models = groupedSubset( data, subset, interestpoints, labelMap, icpp, fixedViews, data.getSequenceDescription().getViewSetups(), data.getViewRegistrations().getViewRegistrations(), globalOptParameters, overlay );
models = groupedSubset( data, subset, interestpoints, labelMap, icpp, fixedViews, data.getSequenceDescription().getViewSetups(), data.getViewRegistrations().getViewRegistrations(), globalOptParameters, overlay, false );
else
models = pairSubset( data, subset, interestpoints, labelMap, icpp, fixedViews, data.getSequenceDescription().getViewSetups(), data.getViewRegistrations().getViewRegistrations(), globalOptParameters, overlay );
models = pairSubset( data, subset, interestpoints, labelMap, icpp, fixedViews, data.getSequenceDescription().getViewSetups(), data.getViewRegistrations().getViewRegistrations(), globalOptParameters, overlay, false );

if ( models == null )
continue;
Expand Down Expand Up @@ -515,14 +519,15 @@ public static void refine(
public static final HashMap< ViewId, mpicbg.models.Tile > pairSubset(
final SpimData2 spimData,
final Subset< ViewId > subset,
final Map< ViewId, List< InterestPoint > > interestpoints,
final Map< ViewId, String > labelMap,
final Map< ViewId, HashMap< String, List< InterestPoint > > > interestpoints,
final Map< ViewId, HashMap< String, Double > > labelMap,
final IterativeClosestPointParameters icpp,
final List< ViewId > fixedViews,
final Map< Integer, ? extends BasicViewSetup > viewSetups, // for two-round
final Map< ViewId, ViewRegistration > registrations, // for two-round
final GlobalOptimizationParameters globalOptParameters,
final DemoLinkOverlay overlay )
final DemoLinkOverlay overlay,
final boolean matchAcrossLabels )
{
final List< Pair< ViewId, ViewId > > pairs = subset.getPairs();

Expand All @@ -537,7 +542,7 @@ public static final HashMap< ViewId, mpicbg.models.Tile > pairSubset(

// compute all pairwise matchings
final List< Pair< Pair< ViewId, ViewId >, PairwiseResult< InterestPoint > > > resultsPairs =
MatcherPairwiseTools.computePairs( pairs, interestpoints, new IterativeClosestPointPairwise< InterestPoint >( icpp ) );
MatcherPairwiseTools.computePairs( pairs, interestpoints, new IterativeClosestPointPairwise< InterestPoint >( icpp ), matchAcrossLabels );

if ( overlay != null )
{
Expand All @@ -563,16 +568,26 @@ public static final HashMap< ViewId, mpicbg.models.Tile > pairSubset(
final ViewId vA = p.getA().getA();
final ViewId vB = p.getA().getB();

/*
final InterestPoints listA = spimData.getViewInterestPoints().getViewInterestPoints().get( vA ).getInterestPointList( labelMap.get( vA ) );
final InterestPoints listB = spimData.getViewInterestPoints().getViewInterestPoints().get( vB ).getInterestPointList( labelMap.get( vB ) );
MatcherPairwiseTools.addCorrespondences( p.getB().getInliers(), vA, vB, labelMap.get( vA ), labelMap.get( vB ), listA, listB );
*/

final String labelA = p.getB().getLabelA();
final String labelB = p.getB().getLabelB();

final InterestPoints listA = spimData.getViewInterestPoints().getViewInterestPoints().get( vA ).getInterestPointList( labelA );
final InterestPoints listB = spimData.getViewInterestPoints().getViewInterestPoints().get( vB ).getInterestPointList( labelB );

MatcherPairwiseTools.addCorrespondences( p.getB().getInliers(), vA, vB, labelA, labelB, listA, listB );

IOFunctions.println( p.getB().getFullDesc() );
}

// multiple solvers for ICP
final PointMatchCreator pmc = new InterestPointMatchCreator( resultsPairs );
final PointMatchCreator pmc = new InterestPointMatchCreator( resultsPairs, labelMap );
final HashMap< ViewId, mpicbg.models.Tile > models;

if ( globalOptParameters.method == GlobalOptType.ONE_ROUND_SIMPLE )
Expand Down Expand Up @@ -620,17 +635,18 @@ else if ( globalOptParameters.method == GlobalOptType.ONE_ROUND_ITERATIVE )
public static HashMap< ViewId, mpicbg.models.Tile > groupedSubset(
final SpimData2 spimData,
final Subset< ViewId > subset,
final Map< ViewId, List< InterestPoint > > interestpoints,
final Map< ViewId, String > labelMap,
final Map< ViewId, HashMap< String, List< InterestPoint > > > interestpoints,
final Map< ViewId, HashMap< String, Double > > labelMap,
final IterativeClosestPointParameters icpp,
final List< ViewId > fixedViews,
final Map< Integer, ? extends BasicViewSetup > viewSetups, // for two-round
final Map< ViewId, ViewRegistration > registrations, // for two-round
final GlobalOptimizationParameters globalOptParameters,
final DemoLinkOverlay overlay )
final DemoLinkOverlay overlay,
final boolean matchAcrossLabels )
{
final List< Pair< Group< ViewId >, Group< ViewId > > > groupedPairs = subset.getGroupedPairs();
final Map< Group< ViewId >, List< GroupedInterestPoint< ViewId > > > groupedInterestpoints = new HashMap<>();
final Map< Group< ViewId >, HashMap< String, List< GroupedInterestPoint< ViewId > > > > groupedInterestpoints = new HashMap<>();
final InterestPointGrouping< ViewId > ipGrouping = new InterestPointGroupingMinDistance<>( interestpoints );

if ( groupedPairs.size() <= 0 )
Expand Down Expand Up @@ -667,7 +683,7 @@ public static HashMap< ViewId, mpicbg.models.Tile > groupedSubset(
}

final List< Pair< Pair< Group< ViewId >, Group< ViewId > >, PairwiseResult< GroupedInterestPoint< ViewId > > > > resultsGroups =
MatcherPairwiseTools.computePairs( groupedPairs, groupedInterestpoints, new IterativeClosestPointPairwise< GroupedInterestPoint< ViewId > >( icpp ) );
MatcherPairwiseTools.computePairs( groupedPairs, groupedInterestpoints, new IterativeClosestPointPairwise< GroupedInterestPoint< ViewId > >( icpp ), false );

if ( overlay != null )
{
Expand All @@ -681,14 +697,15 @@ public static HashMap< ViewId, mpicbg.models.Tile > groupedSubset(
}

// clear correspondences and get a map linking ViewIds to the correspondence lists
final Map< ViewId, List< CorrespondingInterestPoints > > cMap = MatcherPairwiseTools.clearCorrespondences( subset.getViews(), spimData.getViewInterestPoints().getViewInterestPoints(), labelMap );
final Map< ViewId, HashMap< String, List< CorrespondingInterestPoints > > > cMap =
MatcherPairwiseTools.clearCorrespondences( subset.getViews(), spimData.getViewInterestPoints().getViewInterestPoints(), labelMap );

// add the corresponding detections and output result
final List< Pair< Pair< ViewId, ViewId >, PairwiseResult< GroupedInterestPoint< ViewId > > > > resultG =
MatcherPairwiseTools.addCorrespondencesFromGroups( resultsGroups, spimData.getViewInterestPoints().getViewInterestPoints(), labelMap, cMap );
MatcherPairwiseTools.addCorrespondencesFromGroups( resultsGroups, spimData.getViewInterestPoints().getViewInterestPoints(), cMap );

// run global optimization
final PointMatchCreator pmc = new InterestPointMatchCreator( resultG );
final PointMatchCreator pmc = new InterestPointMatchCreator( resultG, labelMap );

// multiple solvers for ICP
final HashMap< ViewId, mpicbg.models.Tile > models;
Expand Down

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