From d2eb1f856cf5dbaba27e22ba521cd5d22145bbf5 Mon Sep 17 00:00:00 2001 From: Stephan Saalfeld Date: Thu, 2 Oct 2014 14:37:42 -0400 Subject: [PATCH] auto-removed some training whitespaces --- .../src/main/java/mpicbg/trakem2/align/Align.java | 405 +++++++++++---------- 1 file changed, 203 insertions(+), 202 deletions(-) diff --git a/TrakEM2_/src/main/java/mpicbg/trakem2/align/Align.java b/TrakEM2_/src/main/java/mpicbg/trakem2/align/Align.java index 4e70820f..c25611fc 100644 --- a/TrakEM2_/src/main/java/mpicbg/trakem2/align/Align.java +++ b/TrakEM2_/src/main/java/mpicbg/trakem2/align/Align.java @@ -1,5 +1,5 @@ /** - * + * */ package mpicbg.trakem2.align; @@ -47,15 +47,15 @@ import mpicbg.trakem2.transform.TranslationModel2D; /** * A collection of methods regarding SIFT-based alignment - * + * * TODO Bring the methods and tasks into a class for each method and clean up this mess. - * + * * @author Stephan Saalfeld */ public class Align { static public class Param implements Serializable - { + { private static final long serialVersionUID = -6469820142091971052L; final public FloatArray2DSIFT.Param sift = new FloatArray2DSIFT.Param(); @@ -64,60 +64,61 @@ public class Align * Closest/next closest neighbour distance ratio */ public float rod = 0.92f; - + /** * Maximal allowed alignment error in px */ public float maxEpsilon = 100.0f; - + /** * Inlier/candidates ratio */ public float minInlierRatio = 0.2f; - + /** * Minimal absolute number of inliers */ public int minNumInliers = 7; - + /** * Implemeted transformation models for choice */ +// final static public String[] modelStrings = new String[]{ "Translation", "Rigid", "Similarity", "Affine", "Homography" }; final static public String[] modelStrings = new String[]{ "Translation", "Rigid", "Similarity", "Affine" }; public int expectedModelIndex = 1; public int desiredModelIndex = 1; public int regularizerModelIndex = 1; - + /** * Use a regularized model instead of a pure one. */ public boolean regularize = false; - + /** * Regularization weight. */ public double lambda = 0.1; - + public float correspondenceWeight = 1; - + /** * Ignore identity transform up to a given tolerance */ public boolean rejectIdentity = false; public float identityTolerance = 0.5f; - + public Param() { sift.maxOctaveSize = 600; sift.fdSize = 8; } - + public void addSIFTFields( final GenericDialog gd ) { - SIFT.addFields( gd, sift ); + SIFT.addFields( gd, sift ); gd.addNumericField( "closest/next_closest_ratio :", rod, 2 ); } - + public void addGeometricConsensusFilterFields( final GenericDialog gd ) { gd.addNumericField( "maximal_alignment_error :", maxEpsilon, 2, 6, "px" ); @@ -127,73 +128,73 @@ public class Align gd.addCheckbox( "ignore constant background", rejectIdentity ); gd.addNumericField( "tolerance :", identityTolerance, 2, 6, "px" ); } - + public void addAlignmentFields( final GenericDialog gd ) { gd.addChoice( "desired_transformation :", modelStrings, modelStrings[ desiredModelIndex ] ); gd.addNumericField( "correspondence weight :", correspondenceWeight, 2 ); gd.addCheckbox( "regularize", regularize ); } - + public void addRegularizationFields( final GenericDialog gd ) { gd.addChoice( "regularizer :", modelStrings, modelStrings[ regularizerModelIndex ] ); gd.addNumericField( "lambda :", lambda, 2 ); } - - + + public void addFields( final GenericDialog gd ) { addSIFTFields( gd ); - + gd.addMessage( "Geometric Consensus Filter:" ); - + addGeometricConsensusFilterFields( gd ); - + gd.addMessage( "Alignment:" ); - + addAlignmentFields( gd ); addRegularizationFields( gd ); } - + public boolean readSIFTFields( final GenericDialog gd ) { SIFT.readFields( gd, sift ); rod = ( float )gd.getNextNumber(); - + return !gd.invalidNumber(); } - + public boolean readGeometricConsensusFilterFields( final GenericDialog gd ) - { + { maxEpsilon = ( float )gd.getNextNumber(); minInlierRatio = ( float )gd.getNextNumber(); minNumInliers = ( int )gd.getNextNumber(); expectedModelIndex = gd.getNextChoiceIndex(); - + rejectIdentity = gd.getNextBoolean(); identityTolerance = ( float )gd.getNextNumber(); - + return !gd.invalidNumber(); } - + public boolean readAlignmentFields( final GenericDialog gd ) { desiredModelIndex = gd.getNextChoiceIndex(); correspondenceWeight = ( float )gd.getNextNumber(); regularize = gd.getNextBoolean(); - + return !gd.invalidNumber(); } - + public boolean readRegularizationFields( final GenericDialog gd ) { regularizerModelIndex = gd.getNextChoiceIndex(); lambda = gd.getNextNumber(); - + return !gd.invalidNumber(); } - + public boolean readFields( final GenericDialog gd ) { boolean b = readSIFTFields( gd ); @@ -202,7 +203,7 @@ public class Align b &= readRegularizationFields( gd ); return b; } - + final public boolean setup( final String title ) { /* SIFT */ @@ -212,9 +213,9 @@ public class Align { gdSIFT.showDialog(); if ( gdSIFT.wasCanceled() ) return false; - } + } while ( !readSIFTFields( gdSIFT ) ); - + /* Geometric consensus */ final GenericDialog gdGeometricConsensusFilter = new GenericDialog( title + ": Geometric Consensus Filter" ); addGeometricConsensusFilterFields( gdGeometricConsensusFilter ); @@ -222,9 +223,9 @@ public class Align { gdGeometricConsensusFilter.showDialog(); if ( gdGeometricConsensusFilter.wasCanceled() ) return false; - } + } while ( !readGeometricConsensusFilterFields( gdGeometricConsensusFilter ) ); - + /* Alignment */ final GenericDialog gdAlignment = new GenericDialog( title + ": Alignment parameters" ); addAlignmentFields( gdAlignment ); @@ -232,9 +233,9 @@ public class Align { gdAlignment.showDialog(); if ( gdAlignment.wasCanceled() ) return false; - } + } while ( !readAlignmentFields( gdAlignment ) ); - + /* Regularization */ if ( regularize ) { @@ -244,25 +245,25 @@ public class Align { gdRegularization.showDialog(); if ( gdRegularization.wasCanceled() ) return false; - } + } while ( !readRegularizationFields( gdRegularization ) ); } - + return true; } - + @Override public Param clone() { final Param p = new Param(); - + p.sift.initialSigma = this.sift.initialSigma; p.sift.steps = this.sift.steps; p.sift.minOctaveSize = this.sift.minOctaveSize; p.sift.maxOctaveSize = this.sift.maxOctaveSize; p.sift.fdSize = this.sift.fdSize; p.sift.fdBins = this.sift.fdBins; - + p.rod = rod; p.maxEpsilon = maxEpsilon; p.minInlierRatio = minInlierRatio; @@ -270,25 +271,25 @@ public class Align p.expectedModelIndex = expectedModelIndex; p.rejectIdentity = rejectIdentity; p.identityTolerance = identityTolerance; - + p.desiredModelIndex = desiredModelIndex; p.correspondenceWeight = correspondenceWeight; p.regularize = regularize; p.regularizerModelIndex = regularizerModelIndex; p.lambda = lambda; - + return p; } - + /** * Check if two parameter sets are equal. So far, this method ignores * the parameter {@link #desiredModelIndex} which defines the * transformation class to be used for {@link Tile} alignment. This * makes sense for the current use in {@link PointMatch} serialization * but might be misleading for other applications. - * + * * TODO Think about this. - * + * * @param p * @return */ @@ -306,9 +307,9 @@ public class Align // && ( desiredModelIndex == p.desiredModelIndex ); } } - + final static public Param param = new Param(); - + static public class ParamOptimize extends Param { private static final long serialVersionUID = 2173278806083343006L; @@ -317,83 +318,83 @@ public class Align * Maximal number of iteration allowed for the optimizer. */ public int maxIterations = 2000; - + /** * Maximal number of iterations allowed to not change the parameter to * be optimized. */ public int maxPlateauwidth = 200; - + /** * Filter outliers */ public boolean filterOutliers = false; public float meanFactor = 3.0f; - + @Override public void addAlignmentFields( final GenericDialog gd ) { super.addAlignmentFields( gd ); - + gd.addMessage( "Optimization:" ); - + gd.addNumericField( "maximal_iterations :", maxIterations, 0 ); gd.addNumericField( "maximal_plateauwidth :", maxPlateauwidth, 0 ); gd.addCheckbox( "filter outliers", filterOutliers ); gd.addNumericField( "mean_factor :", meanFactor, 2 ); } - + @Override public boolean readAlignmentFields( final GenericDialog gd ) { super.readAlignmentFields( gd ); - + maxIterations = ( int )gd.getNextNumber(); maxPlateauwidth = ( int )gd.getNextNumber(); filterOutliers = gd.getNextBoolean(); meanFactor = ( float )gd.getNextNumber(); - + return !gd.invalidNumber(); } - + @Override public void addFields( final GenericDialog gd ) { super.addFields( gd ); - + gd.addNumericField( "maximal_iterations :", maxIterations, 0 ); gd.addNumericField( "maximal_plateauwidth :", maxPlateauwidth, 0 ); gd.addCheckbox( "filter outliers", filterOutliers ); gd.addNumericField( "mean_factor :", meanFactor, 2 ); } - + @Override public boolean readFields( final GenericDialog gd ) { super.readFields( gd ); - + maxIterations = ( int )gd.getNextNumber(); maxPlateauwidth = ( int )gd.getNextNumber(); filterOutliers = gd.getNextBoolean(); meanFactor = ( float )gd.getNextNumber(); - + return !gd.invalidNumber(); } - - - + + + @Override final public ParamOptimize clone() { final ParamOptimize p = new ParamOptimize(); - + p.sift.initialSigma = this.sift.initialSigma; p.sift.steps = this.sift.steps; p.sift.minOctaveSize = this.sift.minOctaveSize; p.sift.maxOctaveSize = this.sift.maxOctaveSize; p.sift.fdSize = this.sift.fdSize; p.sift.fdBins = this.sift.fdBins; - + p.rod = rod; p.maxEpsilon = maxEpsilon; p.minInlierRatio = minInlierRatio; @@ -401,7 +402,7 @@ public class Align p.expectedModelIndex = expectedModelIndex; p.rejectIdentity = rejectIdentity; p.identityTolerance = identityTolerance; - + p.desiredModelIndex = desiredModelIndex; p.regularize = regularize; p.regularizerModelIndex = regularizerModelIndex; @@ -410,10 +411,10 @@ public class Align p.maxPlateauwidth = maxPlateauwidth; p.filterOutliers = filterOutliers; p.meanFactor = meanFactor; - + return p; } - + public boolean equals( final ParamOptimize p ) { return @@ -424,13 +425,13 @@ public class Align ( meanFactor == p.meanFactor ); } } - + final static public ParamOptimize paramOptimize = new ParamOptimize(); - + final static private class Features implements Serializable { private static final long serialVersionUID = 2689219384710526198L; - + FloatArray2DSIFT.Param p; ArrayList< Feature > features; Features( final FloatArray2DSIFT.Param p, final ArrayList< Feature > features ) @@ -439,11 +440,11 @@ public class Align this.features = features; } } - + final static private class PointMatches implements Serializable { private static final long serialVersionUID = -2564147268101223484L; - + Param p; ArrayList< PointMatch > pointMatches; PointMatches( final Param p, final ArrayList< PointMatch > pointMatches ) @@ -452,7 +453,7 @@ public class Align this.pointMatches = pointMatches; } } - + /** * Extracts {@link Feature SIFT-features} from a {@link List} of * {@link AbstractAffineTile2D Tiles} and saves them to disk. @@ -465,7 +466,7 @@ public class Align final protected AtomicInteger ai; final protected AtomicInteger ap; final protected int steps; - + public ExtractFeaturesThread( final Param p, final List< AbstractAffineTile2D< ? > > tiles, @@ -480,7 +481,7 @@ public class Align this.ap = ap; this.steps = steps; } - + @Override final public void run() { @@ -521,12 +522,12 @@ public class Align { Utils.log( features.size() + " features loaded for tile " + i + " \"" + tile.getPatch().getTitle() + "\"." ); } - IJ.showProgress( ap.getAndIncrement(), steps ); + IJ.showProgress( ap.getAndIncrement(), steps ); } } } - - + + final static protected class MatchFeaturesAndFindModelThread extends Thread { final protected Param p; @@ -536,7 +537,7 @@ public class Align final protected AtomicInteger ai; final protected AtomicInteger ap; final protected int steps; - + public MatchFeaturesAndFindModelThread( final Param p, final List< AbstractAffineTile2D< ? > > tiles, @@ -552,32 +553,32 @@ public class Align this.ap = ap; this.steps = steps; } - + @Override final public void run() { final List< PointMatch > candidates = new ArrayList< PointMatch >(); - + for ( int i = ai.getAndIncrement(); i < tilePairs.size() && !isInterrupted(); i = ai.getAndIncrement() ) { if (isInterrupted()) return; candidates.clear(); final AbstractAffineTile2D< ? >[] tilePair = tilePairs.get( i ); - + Collection< PointMatch > inliers = deserializePointMatches( p, tilePair[ 0 ], tilePair[ 1 ] ); - + if ( inliers == null ) { inliers = new ArrayList< PointMatch >(); - + final long s = System.currentTimeMillis(); - + FeatureTransform.matchFeatures( fetchFeatures( p, tilePair[ 0 ] ), fetchFeatures( p, tilePair[ 1 ] ), candidates, p.rod ); - + /* find the model */ final AbstractAffineModel2D< ? > model; switch ( p.expectedModelIndex ) @@ -597,7 +598,7 @@ public class Align default: return; } - + final boolean modelFound = findModel( model, candidates, @@ -607,25 +608,25 @@ public class Align p.minNumInliers, p.rejectIdentity, p.identityTolerance ); - + if ( modelFound ) Utils.log( "Model found for tiles \"" + tilePair[ 0 ].getPatch() + "\" and \"" + tilePair[ 1 ].getPatch() + "\":\n correspondences " + inliers.size() + " of " + candidates.size() + "\n average residual error " + model.getCost() + " px\n took " + ( System.currentTimeMillis() - s ) + " ms" ); else Utils.log( "No model found for tiles \"" + tilePair[ 0 ].getPatch() + "\" and \"" + tilePair[ 1 ].getPatch() + "\":\n correspondence candidates " + candidates.size() + "\n took " + ( System.currentTimeMillis() - s ) + " ms" ); - + if ( !serializePointMatches( p, tilePair[ 0 ], tilePair[ 1 ], inliers ) ) Utils.log( "Saving point matches failed for tiles \"" + tilePair[ 0 ].getPatch() + "\" and \"" + tilePair[ 1 ].getPatch() + "\"" ); - + } else Utils.log( "Point matches for tiles \"" + tilePair[ 0 ].getPatch().getTitle() + "\" and \"" + tilePair[ 1 ].getPatch().getTitle() + "\" fetched from disk cache" ); - + if ( inliers != null && inliers.size() > 0 ) { /* weight the inliers */ for ( final PointMatch pm : inliers ) pm.setWeights( new float[]{ p.correspondenceWeight } ); - + synchronized ( tilePair[ 0 ] ) { synchronized ( tilePair[ 1 ] ) { tilePair[ 0 ].connect( tilePair[ 1 ], inliers ); } @@ -633,13 +634,13 @@ public class Align } synchronized ( tilePair[ 1 ] ) { tilePair[ 1 ].clearVirtualMatches(); } } - + IJ.showProgress( ap.getAndIncrement(), steps ); } } } - - + + final static public boolean findModel( final Model< ? > model, final List< PointMatch > candidates, @@ -684,11 +685,11 @@ public class Align { modelFound = false; } - + return modelFound; } - - + + final static protected boolean serializeFeatures( final Param p, final AbstractAffineTile2D< ? > t, final Collection< Feature > f ) { final ArrayList< Feature > list = new ArrayList< Feature >(); @@ -727,8 +728,8 @@ public class Align } return null; } - - + + final static protected Collection< Feature > fetchFeatures( final Param p, final AbstractAffineTile2D< ? > t ) @@ -747,13 +748,13 @@ public class Align } return features; } - + /** * Save a {@link Collection} of {@link PointMatch PointMatches} two-sided. * Creates two serialization files which is desperately required to clean * up properly invalid serializations on change of a {@link Patch}. - * + * * @param p * @param t1 * @param t2 @@ -781,8 +782,8 @@ public class Align new PointMatches( p, tsil ), new StringBuilder( loader.getUNUIdFolder() ).append( "pointmatches.ser/" ).append( FSLoader.createIdPath( Long.toString( p2.getId() ) + "_" + Long.toString( p1.getId() ), "pointmatches", ".ser" ) ).toString() ); } - - + + final static protected Collection< PointMatch > deserializePointMatches( final Param p, final AbstractAffineTile2D< ? > t1, @@ -791,10 +792,10 @@ public class Align final Patch p1 = t1.getPatch(); final Patch p2 = t2.getPatch(); final Loader loader = p1.getProject().getLoader(); - + final Object ob = loader.deserialize( new StringBuilder( loader.getUNUIdFolder() ).append( "pointmatches.ser/" ) .append( FSLoader.createIdPath( Long.toString( p1.getId() ) + "_" + Long.toString( p2.getId() ), "pointmatches", ".ser" ) ).toString() ); - + if ( null != ob ) { try @@ -812,13 +813,13 @@ public class Align } return null; } - - + + /** * Fetch a {@link Collection} of corresponding * {@link Feature SIFT-features}. Both {@link Feature SIFT-features} and * {@linkplain PointMatch corresponding points} are cached to disk. - * + * * @param p * @param t1 * @param t2 @@ -842,7 +843,7 @@ public class Align { final List< PointMatch > candidates = new ArrayList< PointMatch >(); final List< PointMatch > inliers = new ArrayList< PointMatch >(); - + final long s = System.currentTimeMillis(); FeatureTransform.matchFeatures( fetchFeatures( p, t1 ), @@ -868,7 +869,7 @@ public class Align default: return null; } - + final boolean modelFound = findModel( model, candidates, @@ -878,23 +879,23 @@ public class Align p.minNumInliers, p.rejectIdentity, p.identityTolerance ); - + if ( modelFound ) Utils.log( "Model found for tiles \"" + t1.getPatch() + "\" and \"" + t2.getPatch() + "\":\n correspondences " + inliers.size() + " of " + candidates.size() + "\n average residual error " + model.getCost() + " px\n took " + ( System.currentTimeMillis() - s ) + " ms" ); else Utils.log( "No model found for tiles \"" + t1.getPatch() + "\" and \"" + t2.getPatch() + "\":\n correspondence candidates " + candidates.size() + "\n took " + ( System.currentTimeMillis() - s ) + " ms" ); - + if ( !serializePointMatches( p, t1, t2, pointMatches ) ) Utils.log( "Saving point matches failed for tile \"" + t1.getPatch() + "\" and tile \"" + t2.getPatch() + "\"" ); } return pointMatches; } - - + + /** * Align a set of {@link AbstractAffineTile2D tiles} using * the following procedure: - * + * *
    *
  1. Extract {@link Feature SIFT-features} from all * {@link AbstractAffineTile2D tiles}.
    2. @@ -903,13 +904,13 @@ public class Align * optionally inspect only those that are already overlapping. *
  2. Globally align the tile configuration.
    3. *
- * + * * Both * {@link SIFT#extractFeatures(ij.process.ImageProcessor, Collection) feature extraction} * and {@link FeatureTransform#matchFeatures(Collection, Collection, List, float) matching} * are executed in multiple {@link Thread Threads}, with the number of * {@link Thread Threads} being a parameter of the method. - * + * * @param p * @param tiles * @param fixedTiles @@ -932,11 +933,11 @@ public class Align optimizeTileConfiguration( p, tiles, fixedTiles ); } - + /** * Align a set of overlapping {@link AbstractAffineTile2D tiles} using * the following procedure: - * + * *
    *
  1. Extract {@link Feature SIFT-features} from all * {@link AbstractAffineTile2D tiles}.
    2. @@ -945,13 +946,13 @@ public class Align * tiles. *
  2. Globally align the tile configuration.
    3. *
- * + * * Both * {@link SIFT#extractFeatures(ij.process.ImageProcessor, Collection) feature extraction} * and {@link FeatureTransform#matchFeatures(Collection, Collection, List, float) matching} * are executed in multiple {@link Thread Threads}, with the number of * {@link Thread Threads} being a parameter of the method. - * + * * @param p * @param tiles * @param numThreads @@ -964,9 +965,9 @@ public class Align { alignTiles( p, tiles, fixedTiles, true, numThreads ); } - - - + + + /** * Align a set of {@link AbstractAffineTile2D tiles} that are * interconnected by {@link PointMatch point-correspondences}. @@ -980,7 +981,7 @@ public class Align for ( final AbstractAffineTile2D< ? > t : tiles ) if ( t.getConnectedTiles().size() > 0 ) tc.addTile( t ); - + // ArrayList< Set< Tile< ? > > > graphs = Tile.identifyConnectedGraphs( tiles ); // for ( Set< Tile< ? > > graph : graphs ) // { @@ -997,7 +998,7 @@ public class Align // } for ( final Tile< ? > t : fixedTiles ) tc.fixTile( t ); - + try { if ( p.filterOutliers ) @@ -1007,8 +1008,8 @@ public class Align } catch ( final Exception e ) { IJ.error( e.getMessage() + " " + e.getStackTrace() ); } } - - + + final static protected void pairwiseAlign( final AbstractAffineTile2D< ? > tile, final Set< AbstractAffineTile2D< ? > > visited ) @@ -1021,19 +1022,19 @@ public class Align // TODO Actually do it ... } } - - + + final static public void pairwiseAlignTileConfiguration( final List< AbstractAffineTile2D< ? > > tiles ) { // TODO Implement it } - - + + /** * Connect a {@link List} of {@link AbstractAffineTile2D Tiles} by * geometrically consistent {@link Feature SIFT-feature} correspondences. - * + * * @param p * @param tiles * @param numThreads @@ -1049,7 +1050,7 @@ public class Align final int steps = tiles.size() + tilePairs.size(); final List< ExtractFeaturesThread > extractFeaturesThreads = new ArrayList< ExtractFeaturesThread >(); final List< MatchFeaturesAndFindModelThread > matchFeaturesAndFindModelThreads = new ArrayList< MatchFeaturesAndFindModelThread >(); - + /** Extract and save Features */ for ( int i = 0; i < numThreads; ++i ) { @@ -1057,7 +1058,7 @@ public class Align extractFeaturesThreads.add( thread ); thread.start(); } - + try { for ( final ExtractFeaturesThread thread : extractFeaturesThreads ) @@ -1078,7 +1079,7 @@ public class Align IJ.showProgress( 1.0 ); return; } - + /** Establish correspondences */ ai.set( 0 ); for ( int i = 0; i < numThreads; ++i ) @@ -1107,14 +1108,14 @@ public class Align IJ.showProgress( 1.0 ); } } - - + + /** * If a Patch is locked or in fixedPatches, its corresponding Tile is added to fixedTiles. - * - * @param p + * + * @param p * @param patches - * @param fixedPatches + * @param fixedPatches * @param tiles will contain the generated * {@link AbstractAffineTile2D Tiles} * @param fixedTiles will contain the {@link AbstractAffineTile2D Tiles} @@ -1136,14 +1137,14 @@ public class Align /* can only be affine per convention */ final AbstractAffineModel2D< ? > m = ( AbstractAffineModel2D< ? > )Util.createModel( p.desiredModelIndex ); final AbstractAffineModel2D< ? > r = ( AbstractAffineModel2D< ? > )Util.createModel( p.regularizerModelIndex ); - + /* for type safety one would test both models as for the simple * case below but here I will go for the easy route and let * Java cast it to what is required and ignore the warning. */ @SuppressWarnings( { } ) final InterpolatedAffineModel2D< ?, ? > interpolatedModel = new InterpolatedAffineModel2D( m, r, ( float )p.lambda ); - + t = new GenericAffineTile2D( interpolatedModel, patch ); } else @@ -1171,11 +1172,11 @@ public class Align fixedTiles.add( t ); } } - - + + /** * Align a selection of {@link Patch patches} in a Layer. - * + * * @param layer */ final static public void alignSelectedPatches( final Selection selection, final int numThreads ) @@ -1183,11 +1184,11 @@ public class Align final List< Patch > patches = new ArrayList< Patch >(); for ( final Displayable d : selection.getSelected() ) if ( d instanceof Patch ) patches.add( ( Patch )d ); - + if ( patches.size() < 2 ) return; - + if ( !paramOptimize.setup( "Align selected patches" ) ) return; - + final List< AbstractAffineTile2D< ? > > tiles = new ArrayList< AbstractAffineTile2D< ? > >(); final List< AbstractAffineTile2D< ? > > fixedTiles = new ArrayList< AbstractAffineTile2D< ? > >(); final List< Patch > fixedPatches = new ArrayList< Patch >(); @@ -1195,23 +1196,23 @@ public class Align if ( active != null && active instanceof Patch ) fixedPatches.add( ( Patch )active ); tilesFromPatches( paramOptimize, patches, fixedPatches, tiles, fixedTiles ); - + alignTiles( paramOptimize, tiles, fixedTiles, numThreads ); - + for ( final AbstractAffineTile2D< ? > t : tiles ) t.getPatch().setAffineTransform( t.getModel().createAffine() ); } - - + + /** * Align all {@link Patch patches} in a Layer. - * + * * @param layer */ final static public void alignLayer( final Layer layer, final int numThreads ) { if ( !paramOptimize.setup( "Align patches in layer" ) ) return; - + final List< Displayable > displayables = layer.getDisplayables( Patch.class ); final List< Patch > patches = new ArrayList< Patch >(); for ( final Displayable d : displayables ) @@ -1219,16 +1220,16 @@ public class Align final List< AbstractAffineTile2D< ? > > tiles = new ArrayList< AbstractAffineTile2D< ? > >(); final List< AbstractAffineTile2D< ? > > fixedTiles = new ArrayList< AbstractAffineTile2D< ? > >(); tilesFromPatches( paramOptimize, patches, null, tiles, fixedTiles ); - + alignTiles( paramOptimize, tiles, fixedTiles, numThreads ); - + for ( final AbstractAffineTile2D< ? > t : tiles ) t.getPatch().setAffineTransform( t.getModel().createAffine() ); } /** * Align a range of layers by accumulating pairwise alignments of contiguous layers. - * + * * @param layers The range of layers to align pairwise. * @param numThreads The number of threads to use. */ @@ -1239,7 +1240,7 @@ public class Align /** * Align a range of layers by accumulating pairwise alignments of contiguous layers. - * + * * @param layers The range of layers to align pairwise. * @param numThreads The number of threads to use. * @param filter The {@link Filter} to decide which {@link Patch} instances to use in each {@param Layer}. Can be null. @@ -1247,60 +1248,60 @@ public class Align final static public void alignLayersLinearly( final List< Layer > layers, final int numThreads, final Filter filter ) { param.sift.maxOctaveSize = 1600; - + if ( !param.setup( "Align layers linearly" ) ) return; - + final Rectangle box = layers.get( 0 ).getParent().getMinimalBoundingBox( Patch.class ); final float scale = Math.min( 1.0f, Math.min( ( float )param.sift.maxOctaveSize / ( float )box.width, ( float )param.sift.maxOctaveSize / ( float )box.height ) ); final Param p = param.clone(); p.maxEpsilon *= scale; - + final FloatArray2DSIFT sift = new FloatArray2DSIFT( p.sift ); final SIFT ijSIFT = new SIFT( sift ); - + Rectangle box1 = null; Rectangle box2 = null; final Collection< Feature > features1 = new ArrayList< Feature >(); final Collection< Feature > features2 = new ArrayList< Feature >(); final List< PointMatch > candidates = new ArrayList< PointMatch >(); final List< PointMatch > inliers = new ArrayList< PointMatch >(); - + final AffineTransform a = new AffineTransform(); - + int i = 0; for ( final Layer l : layers ) { long s = System.currentTimeMillis(); - + features1.clear(); features1.addAll( features2 ); features2.clear(); - + final Rectangle box3 = l.getMinimalBoundingBox( Patch.class ); - + if ( box3 == null ) continue; - + box1 = box2; box2 = box3; - + final List patches = l.getAll(Patch.class); if (null != filter) { for (final Iterator it = patches.iterator(); it.hasNext(); ) { if (!filter.accept(it.next())) it.remove(); } } - + ijSIFT.extractFeatures( l.getProject().getLoader().getFlatImage( l, box2, scale, 0xffffffff, ImagePlus.GRAY8, Patch.class, patches, true ).getProcessor(), features2 ); Utils.log( features2.size() + " features extracted in layer \"" + l.getTitle() + "\" (took " + ( System.currentTimeMillis() - s ) + " ms)." ); - + if ( features1.size() > 0 ) { s = System.currentTimeMillis(); - + candidates.clear(); - + FeatureTransform.matchFeatures( features2, features1, @@ -1325,7 +1326,7 @@ public class Align default: return; } - + boolean modelFound; boolean again = false; try @@ -1360,7 +1361,7 @@ public class Align { modelFound = false; } - + if ( modelFound ) { Utils.log( "Model found for layer \"" + l.getTitle() + "\" and its predecessor:\n correspondences " + inliers.size() + " of " + candidates.size() + "\n average residual error " + ( model.getCost() / scale ) + " px\n took " + ( System.currentTimeMillis() - s ) + " ms" ); @@ -1370,7 +1371,7 @@ public class Align b.concatenate( model.createAffine() ); b.scale( scale, scale ); b.translate( -box2.x, -box2.y); - + a.concatenate( b ); l.apply( Displayable.class, a ); Display.repaint( l ); @@ -1384,9 +1385,9 @@ public class Align IJ.showProgress( ++i, layers.size() ); } } - + /** - * Temporary helper method that creates + * Temporary helper method that creates * @param matches * @param alpha * @return @@ -1410,13 +1411,13 @@ public class Align } mlst.setModel( c ); mlst.setMatches( matches ); - + return mlst; } - - + + /** - * Align two collections of tiles + * Align two collections of tiles * @param p * @param a * @param b @@ -1429,10 +1430,10 @@ public class Align pa.add( t.getPatch() ); for ( final AbstractAffineTile2D< ? > t : b ) pb.add( t.getPatch() ); - + final Layer la = pa.iterator().next().getLayer(); final Layer lb = pb.iterator().next().getLayer(); - + final Rectangle boxA = Displayable.getBoundingBox( pa, null ); final Rectangle boxB = Displayable.getBoundingBox( pb, null ); @@ -1445,28 +1446,28 @@ public class Align Math.min( ( float )p.sift.maxOctaveSize / ( float )boxB.width, ( float )p.sift.maxOctaveSize / ( float )boxB.height ) ) ); - + final Param pp = p.clone(); pp.maxEpsilon *= scale; - + final FloatArray2DSIFT sift = new FloatArray2DSIFT( pp.sift ); final SIFT ijSIFT = new SIFT( sift ); - + final Collection< Feature > featuresA = new ArrayList< Feature >(); final Collection< Feature > featuresB = new ArrayList< Feature >(); final List< PointMatch > candidates = new ArrayList< PointMatch >(); final List< PointMatch > inliers = new ArrayList< PointMatch >(); - + long s = System.currentTimeMillis(); ijSIFT.extractFeatures( la.getProject().getLoader().getFlatImage( la, boxA, scale, 0xffffffff, ImagePlus.GRAY8, null, pa, true, Color.GRAY ).getProcessor(), featuresA ); Utils.log( featuresA.size() + " features extracted in graph A in layer \"" + la.getTitle() + "\" (took " + ( System.currentTimeMillis() - s ) + " ms)." ); - + s = System.currentTimeMillis(); ijSIFT.extractFeatures( lb.getProject().getLoader().getFlatImage( lb, boxB, scale, 0xffffffff, ImagePlus.GRAY8, null, pb, true, Color.GRAY ).getProcessor(), featuresB ); Utils.log( featuresB.size() + " features extracted in graph B in layer \"" + lb.getTitle() + "\" (took " + ( System.currentTimeMillis() - s ) + " ms)." ); - + if ( featuresA.size() > 0 && featuresB.size() > 0 ) { s = System.currentTimeMillis(); @@ -1529,7 +1530,7 @@ public class Align { modelFound = false; } - + if ( modelFound ) { Utils.log( "Model found for graph A and B in layers \"" + la.getTitle() + "\" and \"" + lb.getTitle() + "\":\n correspondences " + inliers.size() + " of " + candidates.size() + "\n average residual error " + ( model.getCost() / scale ) + " px\n took " + ( System.currentTimeMillis() - s ) + " ms" ); @@ -1539,7 +1540,7 @@ public class Align at.concatenate( model.createAffine() ); at.scale( scale, scale ); at.translate( -boxB.x, -boxB.y); - + for ( final Patch t : pa ) t.preTransform( at, false ); Display.repaint( la ); -- 2.11.4.GIT