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add default implementations of boundingbox() and centerofmass() to Bl…
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…ockDataSolveParameters.java, assuming the alignment does not change
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@StephanPreibisch
StephanPreibisch committed Aug 27, 2023
1 parent 8e65023 commit 4711bca
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Showing 5 changed files with 68 additions and 36 deletions.
10 changes: 6 additions & 4 deletions render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/BlockData.java
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Expand Up @@ -100,10 +100,12 @@ public ArrayList< Function< Double, Double > > createWeightFunctions()
/**
* @return - the center of mass of all tiles that are part of this solve. If the coordinates are changed, the current ones should be used.
*/
public double[] centerOfMass()
{
return solveTypeParameters().centerOfMass( this );
}
public double[] centerOfMass() { return solveTypeParameters().centerOfMass( this ); }

/**
* @return - the bounding box of all tiles that are part of this solve. If the coordinates are changed, the current ones should be used.
*/
public Pair<double[],double[]> boundingBox( final BlockData<M, R, P, F> blockData ) { return solveTypeParameters().boundingBox( blockData ); }

public P solveTypeParameters() { return solveTypeParameters; }
public F blockFactory() { return blockFactory; }
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58 changes: 57 additions & 1 deletion ...va/org/janelia/render/client/newsolver/blocksolveparameters/BlockDataSolveParameters.java
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Expand Up @@ -2,9 +2,13 @@

import java.io.Serializable;

import org.janelia.alignment.spec.TileSpec;
import org.janelia.render.client.newsolver.BlockData;
import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
import org.janelia.render.client.newsolver.solvers.Worker;
import org.janelia.render.client.solver.SerializableValuePair;

import net.imglib2.util.Pair;

/**
*
Expand Down Expand Up @@ -44,10 +48,62 @@ public BlockDataSolveParameters(

public M blockSolveModel() { return blockSolveModel; }

/**
* @return - the bounding box of all tiles that are part of this solve. If the coordinates are changed, the current ones should be used.
*/
public <F extends BlockFactory<F>> Pair<double[],double[]> boundingBox( final BlockData<M, R, P, F> blockData )
{
double minX = Double.MAX_VALUE;
double maxX = -Double.MAX_VALUE;

double minY = Double.MAX_VALUE;
double maxY = -Double.MAX_VALUE;

double minZ = Double.MAX_VALUE;
double maxZ = -Double.MAX_VALUE;

for ( final TileSpec ts : blockData.rtsc().getTileSpecs() )
{
minX = Math.min( minX, ts.getMinX() );
minY = Math.min( minY, ts.getMinY() );
minZ = Math.min( minZ, ts.getZ() );

maxX = Math.max( maxX, ts.getMaxX() );
maxY = Math.max( maxY, ts.getMaxY() );
maxZ = Math.max( maxZ, ts.getZ() );
}

return new SerializableValuePair<>( new double[]{minX,minY,minZ}, new double[]{maxX,maxY,maxZ} );
}

/**
* @return - the center of mass of all tiles that are part of this solve. If the coordinates are changed, the current ones should be used.
*/
public abstract < F extends BlockFactory< F > > double[] centerOfMass( final BlockData<M, R, P, F > blockData );
public < F extends BlockFactory< F > > double[] centerOfMass( final BlockData< M, R, P, F > blockData )
{

final double[] c = new double[ 3 ];
int count = 0;

for ( final String tileId : blockData.idToNewModel().keySet() )
{
final TileSpec ts = blockData.rtsc().getTileSpec( tileId );

// the affine transform for the tile
final double[] tmp = ts.getWorldCoordinates( (ts.getWidth() - 1) /2.0, (ts.getHeight() - 1) /2.0 );

c[ 0 ] += tmp[ 0 ];
c[ 1 ] += tmp[ 1 ];
c[ 2 ] += ts.getZ();
++count;
}

c[ 0 ] /= (double)count;
c[ 1 ] /= (double)count;
c[ 2 ] /= (double)count;

return c;
}

public abstract < F extends BlockFactory< F > > Worker< M, R, P, F > createWorker(
final BlockData< M, R, P, F > blockData,
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3 changes: 3 additions & 0 deletions ...a/org/janelia/render/client/newsolver/blocksolveparameters/FIBSEMAlignmentParameters.java
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Expand Up @@ -151,6 +151,9 @@ public < F extends BlockFactory< F > > Worker< M, AffineModel2D, FIBSEMAlignment
@Override
public <F extends BlockFactory<F>> double[] centerOfMass( final BlockData<M, AffineModel2D, FIBSEMAlignmentParameters<M, S>, F> blockData)
{
if ( blockData.idToNewModel() == null || blockData.idToNewModel().size() == 0 )
return super.centerOfMass( blockData );

final HashMap<String, AffineModel2D> models = blockData.idToNewModel();

final double[] c = new double[ 3 ];
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28 changes: 0 additions & 28 deletions ...lia/render/client/newsolver/blocksolveparameters/FIBSEMIntensityCorrectionParameters.java
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Expand Up @@ -3,7 +3,6 @@
import java.io.IOException;
import java.util.ArrayList;

import org.janelia.alignment.spec.TileSpec;
import org.janelia.render.client.newsolver.BlockData;
import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
import org.janelia.render.client.newsolver.solvers.Worker;
Expand Down Expand Up @@ -68,31 +67,4 @@ public <F extends BlockFactory<F>> Worker<M, ArrayList<AffineModel1D>, FIBSEMInt
throw new RuntimeException(e);
}
}

@Override
public <F extends BlockFactory<F>> double[] centerOfMass( final BlockData<M, ArrayList<AffineModel1D>, FIBSEMIntensityCorrectionParameters<M>, F> blockData)
{

final double[] c = new double[ 3 ];
int count = 0;

for ( final String tileId : blockData.idToNewModel().keySet() )
{
final TileSpec ts = blockData.rtsc().getTileSpec( tileId );

// the affine transform for the tile
final double[] tmp = ts.getWorldCoordinates( (ts.getWidth() - 1) /2.0, (ts.getHeight() - 1) /2.0 );

c[ 0 ] += tmp[ 0 ];
c[ 1 ] += tmp[ 1 ];
c[ 2 ] += ts.getZ();
++count;
}

c[ 0 ] /= (double)count;
c[ 1 ] /= (double)count;
c[ 2 ] /= (double)count;

return c;
}
}
5 changes: 2 additions & 3 deletions .../main/java/org/janelia/render/client/newsolver/solvers/affine/AffineAlignBlockWorker.java
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Expand Up @@ -26,9 +26,8 @@
import org.janelia.render.client.newsolver.solvers.WorkerTools.LayerDetails;
import org.janelia.render.client.solver.ConstantAffineModel2D;
import org.janelia.render.client.solver.Graph;
import org.janelia.render.client.solver.SolveTools;
import org.janelia.render.client.solver.SerializableValuePair;
import org.janelia.render.client.solver.SolveItem;
import org.janelia.render.client.solver.SolveTools;
import org.janelia.render.client.solver.StabilizingAffineModel2D;
import org.janelia.render.client.solver.matchfilter.MatchFilter;
import org.janelia.render.client.solver.matchfilter.NoMatchFilter;
Expand Down Expand Up @@ -281,7 +280,7 @@ protected Tile<M> getOrBuildTile( final String id, final TileSpec tileSpec )
if (!inputSolveItem.idToTileMap().containsKey(id))
{
final Pair<Tile<M>, AffineModel2D> pair =
SolveTools.buildTileFromSpec( inputSolveItem.blockData().solveTypeParameters().blockSolveModel().copy(), SolveItem.samplesPerDimension, tileSpec );
SolveTools.buildTileFromSpec( inputSolveItem.blockData().solveTypeParameters().blockSolveModel().copy(), AffineBlockDataWrapper.samplesPerDimension, tileSpec );
tile = pair.getA();
inputSolveItem.idToTileMap().put(id, tile);
inputSolveItem.tileToIdMap().put(tile, id);
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