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put minZ,maxZ,sectionIdToZMap into BlockData
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@StephanPreibisch
StephanPreibisch committed Aug 10, 2023
1 parent 4b75491 commit 1324ca1
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Showing 3 changed files with 85 additions and 88 deletions.
68 changes: 67 additions & 1 deletion render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/BlockData.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.janelia.render.client.newsolver;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
Expand All @@ -14,6 +15,8 @@
import org.janelia.render.client.newsolver.solvers.Worker;

import mpicbg.models.CoordinateTransform;
import net.imglib2.util.Pair;
import net.imglib2.util.ValuePair;

/**
* Should contain only geometric data, nothing specific to the type of solve
Expand Down Expand Up @@ -47,6 +50,12 @@ public class BlockData< M extends CoordinateTransform, P extends BlockDataSolveP
// contains the model as determined by the local solve
final private HashMap<String, M> idToNewModel = new HashMap<>();

// what z-range this block covers
final protected int minZ, maxZ;

// all z-layers as String map to List that only contains the z-layer as double
final protected Map<String, ArrayList<Double>> sectionIdToZMap;

public BlockData(
final F blockFactory, // knows how it was created for assembly later?
final P solveTypeParameters,
Expand All @@ -61,8 +70,18 @@ public BlockData(
this.allTileIds = new HashSet<>( allTileIds );
this.idToTileSpec = idToTileSpec;
this.weightF = weightF;

this.sectionIdToZMap = new HashMap<>();
final Pair<Integer, Integer> minmax = fetchRenderDetails( idToTileSpec().values(), sectionIdToZMap );

this.minZ = minmax.getA();
this.maxZ = minmax.getB();
}

public int minZ() { return minZ; }
public int maxZ() { return maxZ; }
public Map<String, ArrayList<Double>> sectionIdToZMap() { return sectionIdToZMap; }

public int getId() { return id; }
public double getWeight( final double location, final int dim ) { return weightF.get( dim ).apply( location ); }

Expand All @@ -80,5 +99,52 @@ public Worker< M, P, F > createWorker()
// should maybe ask the solveTypeParamters to create the object I think
return null;
}


/**
* Fetches basic data for all TileSpecs
*
* @param allTileSpecs - all TileSpec objects that are part of this solve
* @param sectionIdToZMap - will be filled
* @return a Pair< minZ, maxZ >
*/
public static Pair< Integer, Integer > fetchRenderDetails(
final Collection< TileSpec > allTileSpecs,
final Map<String, ArrayList<Double>> sectionIdToZMap )
{
int minZ = Integer.MAX_VALUE;
int maxZ = Integer.MIN_VALUE;

for ( final TileSpec t : allTileSpecs) //blockData.idToTileSpec().values() )
{
if ( sectionIdToZMap.containsKey( t.getSectionId() ))
{
final ArrayList<Double> z = sectionIdToZMap.get( t.getSectionId() );

if ( !z.contains( t.getZ() ) )
z.add( t.getZ() );
}
else
{
final ArrayList<Double> z = new ArrayList<>();
z.add( t.getZ() );
sectionIdToZMap.put( t.getSectionId(), z );
}

final int z = (int)Math.round( t.getZ() );
minZ = Math.min( z, minZ );
maxZ = Math.max( z, maxZ );
}

return new ValuePair<>( minZ, maxZ );

//final private HashSet<String> allTileIds;
//final private Map<String, MinimalTileSpec> idToTileSpec;

// tileId > String (this is the pId, qId)
// sectionId > String (this is the pGroupId, qGroupId)

//TileSpec ts = blockData.idToTileSpec().values().iterator().next();
//String sectionId = ts.getLayout().getSectionId(); //

}
}
63 changes: 0 additions & 63 deletions render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/solvers/Worker.java
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Original file line number Diff line number Diff line change
@@ -1,23 +1,16 @@
package org.janelia.render.client.newsolver.solvers;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutionException;

import org.janelia.alignment.spec.TileSpec;
import org.janelia.render.client.RenderDataClient;
import org.janelia.render.client.newsolver.BlockData;
import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
import org.janelia.render.client.newsolver.blocksolveparameters.BlockDataSolveParameters;

import mpicbg.models.CoordinateTransform;
import mpicbg.models.NoninvertibleModelException;
import net.imglib2.util.Pair;
import net.imglib2.util.ValuePair;

public abstract class Worker < M extends CoordinateTransform, P extends BlockDataSolveParameters< M, P >, F extends BlockFactory< F > >
{
Expand All @@ -28,12 +21,6 @@ public abstract class Worker < M extends CoordinateTransform, P extends BlockDat
final protected RenderDataClient renderDataClient;
final protected String renderStack;

// what z-range this block covers
final protected int minZ, maxZ;

// all z-layers as String map to List that only contains the z-layer as double
final protected Map<String, ArrayList<Double>> sectionIdToZMap;

final protected int numThreads;

public Worker(
Expand All @@ -49,19 +36,10 @@ public Worker(
blockData.solveTypeParameters().owner(),
blockData.solveTypeParameters().project() );
this.renderStack = blockData.solveTypeParameters().stack();
this.sectionIdToZMap = new HashMap<>();

final Pair<Integer, Integer> minmax = fetchRenderDetails( blockData.idToTileSpec().values(), sectionIdToZMap );

this.minZ = minmax.getA();
this.maxZ = minmax.getB();

this.numThreads = numThreads;
}

public int minZ() { return minZ; }
public int maxZ() { return maxZ; }

/**
* runs the Worker
*/
Expand All @@ -71,45 +49,4 @@ public Worker(
* @return - the result(s) of the solve, multiple ones if they were not connected
*/
public abstract List< BlockData< M, P, F > > getBlockDataList();

public static Pair< Integer, Integer > fetchRenderDetails(
final Collection< TileSpec > allTileSpecs,
final Map<String, ArrayList<Double>> sectionIdToZMap )
{
int minZ = Integer.MAX_VALUE;
int maxZ = Integer.MIN_VALUE;

for ( final TileSpec t : allTileSpecs) //blockData.idToTileSpec().values() )
{
if ( sectionIdToZMap.containsKey( t.getSectionId() ))
{
final ArrayList<Double> z = sectionIdToZMap.get( t.getSectionId() );

if ( !z.contains( t.getZ() ) )
z.add( t.getZ() );
}
else
{
final ArrayList<Double> z = new ArrayList<>();
z.add( t.getZ() );
sectionIdToZMap.put( t.getSectionId(), z );
}

final int z = (int)Math.round( t.getZ() );
minZ = Math.min( z, minZ );
maxZ = Math.max( z, maxZ );
}

return new ValuePair<>( minZ, maxZ );

//final private HashSet<String> allTileIds;
//final private Map<String, MinimalTileSpec> idToTileSpec;

// tileId > String (this is the pId, qId)
// sectionId > String (this is the pGroupId, qGroupId)

//TileSpec ts = blockData.idToTileSpec().values().iterator().next();
//String sectionId = ts.getLayout().getSectionId(); //

}
}
42 changes: 18 additions & 24 deletions .../main/java/org/janelia/render/client/newsolver/solvers/affine/AffineAlignBlockWorker.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -140,25 +140,17 @@ public List< BlockData< M, FIBSEMAlignmentParameters< M, S >, F > > getBlockData
@Override
public void run() throws IOException, ExecutionException, InterruptedException, NoninvertibleModelException
{
this.canvasMatches = assembleMatchData(
inputSolveItem, sectionIdToZMap, matchFilter, minZ, maxZ, matchDataClient, renderDataClient, renderStack,
pairs, zToPairs, blockData.solveTypeParameters().maxZRangeMatches() );
this.canvasMatches = assembleMatchData( inputSolveItem, matchFilter, matchDataClient, renderDataClient, renderStack, pairs, zToPairs );

// minStitchingInliersSupplier:
// how many stitching inliers are needed to stitch first
// reason: if tiles are rarely connected and it is stitched first, a useful
// common alignment model after stitching cannot be found
stitchSectionsAndCreateGroupedTiles(
inputSolveItem, pairs, zToPairs,
blockData.solveTypeParameters().maxPlateauWidthStitching(),
blockData.solveTypeParameters().maxAllowedErrorStitching(),
blockData.solveTypeParameters().maxIterationsStitching(),
blockData.solveTypeParameters().minStitchingInliersSupplier(),
stitchFirst, numThreads );
stitchSectionsAndCreateGroupedTiles( inputSolveItem, pairs, zToPairs, stitchFirst, numThreads );

connectGroupedTiles( pairs, inputSolveItem );

this.solveItems = splitSolveItem( inputSolveItem, startId, minZ, maxZ );
this.solveItems = splitSolveItem( inputSolveItem, startId );

for ( final AffineBlockDataWrapper< M, S, F > solveItem : solveItems )
{
Expand Down Expand Up @@ -187,23 +179,24 @@ public void run() throws IOException, ExecutionException, InterruptedException,

protected ArrayList< CanvasMatches > assembleMatchData(
final AffineBlockDataWrapper< M, S, F > inputSolveItem,
final Map<String, ArrayList<Double>> sectionIdToZMap,
final MatchFilter matchFilter,
final int minZ,
final int maxZ,
final RenderDataClient matchDataClient,
final RenderDataClient renderDataClient,
final String renderStack,
final ArrayList< Pair< Pair< Tile< ? >, Tile< ? > >, List< PointMatch > > > pairs,
final HashMap< Integer, List< Integer > > zToPairs,
final double maxZRangeMatches ) throws IOException
final HashMap< Integer, List< Integer > > zToPairs ) throws IOException
{
final Map<String, ArrayList<Double>> sectionIdToZMap = inputSolveItem.blockData().sectionIdToZMap();
final int minZ = inputSolveItem.blockData().minZ();
final int maxZ = inputSolveItem.blockData().maxZ();
final int maxZRangeMatches = inputSolveItem.blockData().solveTypeParameters().maxZRangeMatches();

final ArrayList< CanvasMatches > canvasMatches = new ArrayList<>();
final Map<Double, ResolvedTileSpecCollection> zToTileSpecsMap = new HashMap<>();

LOG.info( "block " + inputSolveItem.blockData().getId() + ": Loading transforms and matches for " + inputSolveItem.blockData().allTileIds().size() + "tiles, from " + this.minZ + " to layer " + this.maxZ );
LOG.info( "block " + inputSolveItem.blockData().getId() + ": Loading transforms and matches for " + inputSolveItem.blockData().allTileIds().size() + "tiles, from " + minZ + " to layer " + maxZ );

if ( !Double.isNaN( maxZRangeMatches ) )
if ( maxZRangeMatches >= 0 )
LOG.info( "block " + inputSolveItem.blockData().getId() + ": WARNING! max z range for matching is " + maxZRangeMatches );

// Note: this is not sorted anymore
Expand Down Expand Up @@ -247,7 +240,7 @@ protected ArrayList< CanvasMatches > assembleMatchData(
}

// max range
if ( !Double.isNaN( maxZRangeMatches ) && Math.abs( pTileSpec.getZ() - qTileSpec.getZ() ) > maxZRangeMatches )
if ( maxZRangeMatches >= 0 && Math.abs( pTileSpec.getZ() - qTileSpec.getZ() ) > maxZRangeMatches )
continue;

final Tile<M> p = getOrBuildTile(pId, pTileSpec);
Expand Down Expand Up @@ -600,13 +593,14 @@ protected void stitchSectionsAndCreateGroupedTiles(
final AffineBlockDataWrapper< M, S, F > solveItem,
final ArrayList< Pair< Pair< Tile< ? >, Tile< ? > >, List< PointMatch > > > pairs,
final HashMap< Integer, List< Integer > > zToPairs,
final int maxPlateauWidthStitching,
final double maxAllowedErrorStitching,
final int maxIterationsStitching,
final Function< Integer, Integer > minStitchingInliersSupplier,
final boolean stitchFirst,
final int numThreads )
{
final int maxPlateauWidthStitching = solveItem.blockData().solveTypeParameters().maxPlateauWidthStitching();
final double maxAllowedErrorStitching = solveItem.blockData().solveTypeParameters().maxAllowedErrorStitching();
final int maxIterationsStitching = solveItem.blockData().solveTypeParameters().maxIterationsStitching();
final Function< Integer, Integer > minStitchingInliersSupplier = solveItem.blockData().solveTypeParameters().minStitchingInliersSupplier();

//final S model = solveItem.stitchingSolveModelInstance();

// combine tiles per layer that are be stitched first, but iterate over all z's
Expand Down Expand Up @@ -815,7 +809,7 @@ protected void stitchSectionsAndCreateGroupedTiles(
}
}

protected List< AffineBlockDataWrapper< M, S, F > > splitSolveItem( final AffineBlockDataWrapper< M, S, F > inputSolveItem, final int startId, final int minZ, final int maxZ )
protected List< AffineBlockDataWrapper< M, S, F > > splitSolveItem( final AffineBlockDataWrapper< M, S, F > inputSolveItem, final int startId )
{
// assigning new id's to the solve items (they collide for now with other workers, fix upon merging)
int id = startId + 1;
Expand Down

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