AllToAllRegistration.java

/*-
 * #%L
 * Fiji distribution of ImageJ for the life sciences.
 * %%
 * Copyright (C) 2007 - 2017 Fiji developers.
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as
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 * 
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 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
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 * You should have received a copy of the GNU General Public
 * License along with this program.  If not, see
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package spim.process.interestpointregistration.optimizationtypes;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;

import mpicbg.spim.data.sequence.TimePoint;
import mpicbg.spim.data.sequence.ViewId;
import spim.fiji.spimdata.SpimData2;
import spim.process.interestpointregistration.ChannelProcess;
import spim.process.interestpointregistration.MatchPointList;
import spim.process.interestpointregistration.PairwiseMatch;

public class AllToAllRegistration extends GlobalOptimizationType
{
	public AllToAllRegistration(
			final SpimData2 spimData,
			final List< ViewId > viewIdsToProcess,
			final List< ChannelProcess > channelsToProcess,
			final boolean considerTimePointsAsUnit )
	{ 
		super( spimData, viewIdsToProcess, channelsToProcess, considerTimePointsAsUnit );
	}

	@Override
	public List< GlobalOptimizationSubset > assembleAllViewPairs()
	{
		final HashMap< ViewId, MatchPointList > allPointLists = new HashMap< ViewId, MatchPointList >();
		
		// collect all point lists from all timepoints
		for ( final TimePoint timepoint : SpimData2.getAllTimePointsSorted( spimData, viewIdsToProcess ) )
		{
			final HashMap< ViewId, MatchPointList > pointLists = this.getInterestPoints( timepoint );
			
			allPointLists.putAll( pointLists );
		}
		
		// all viewids of all timepoints
		final ArrayList< ViewId > views = new ArrayList< ViewId >();
		views.addAll( allPointLists.keySet() );
		Collections.sort( views );

		// all pairs that need to be compared
		final ArrayList< PairwiseMatch > viewPairs = new ArrayList< PairwiseMatch >();		

		for ( int a = 0; a < views.size() - 1; ++a )
			for ( int b = a + 1; b < views.size(); ++b )
			{
				final ViewId viewIdA = views.get( a );
				final ViewId viewIdB = views.get( b );
				
				// only compare those to views if not both are fixed
				if ( !isFixedTile( viewIdA ) && !isFixedTile( viewIdB ) )
				{
					final MatchPointList listA = allPointLists.get( viewIdA );
					final MatchPointList listB = allPointLists.get( viewIdB );

					if ( !isValid( viewIdA, listA ) )
						continue;

					if ( !isValid( viewIdB, listB ) )
						continue;

					// in case we consider timepoints as units and the pair has the same timepoint, do not add;
					// i.e. add the pair always if the above statement is false
					if ( !( considerTimePointsAsUnit() && ( viewIdA.getTimePointId() == viewIdB.getTimePointId() ) ) )
						viewPairs.add( new PairwiseMatch( viewIdA, viewIdB, listA, listB ) );
				}
			}

		final ArrayList< GlobalOptimizationSubset > list = new ArrayList< GlobalOptimizationSubset >();
		list.add( new GlobalOptimizationSubset( viewPairs, "all-to-all matching over all timepoints" ) );
		
		return list;
	}
}