package data;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.RealInterval;

import net.imglib2.type.NativeType;

import net.imglib2.type.numeric.real.DoubleType;

/**

* An implementation of STData that uses ImgLib2 datastructures to hold the actual data

*

* @author spreibi

*

*/

public class STDataImgLib2 extends STDataAbstract

{

/**

* a 2d datastructure that holds all sequenced locations, size: [numLocations x numDimensions]

*/

private final RandomAccessibleInterval< DoubleType > locations;

/**

* a 2d datastructure that holds all expression values, size: [numGenes x numLocations]

*/

private final RandomAccessibleInterval< DoubleType > exprValues;

private final List< String > geneNames, barcodes;

private final HashMap< String, Integer > geneLookup;

private final Map<String, RandomAccessibleInterval<? extends NativeType< ? >>> annotations;

private final Map<String, RandomAccessibleInterval<? extends NativeType< ? >>> geneAnnotations;

private RealInterval realInterval;

public static class STDataImgLib2Factory

{

public RandomAccessibleInterval< DoubleType > locations, exprValues;

public List< String > geneNames, barcodes;

public HashMap< String, Integer > geneLookup;

}

public STDataImgLib2( final STDataImgLib2Factory factory )

{

this( factory.locations, factory.exprValues, factory.geneNames, factory.barcodes, factory.geneLookup );

}

public STDataImgLib2(

final RandomAccessibleInterval< DoubleType > locations,

final RandomAccessibleInterval< DoubleType > exprValues,

final List< String > geneNames,

final List< String > barcodes,

final HashMap< String, Integer > geneLookup )

{

super( (int)locations.dimension( 1 ), (int)locations.dimension( 0 ), (int)exprValues.dimension( 0 ) );

this.locations = locations;

this.exprValues = exprValues;

this.geneNames = geneNames;

this.barcodes = barcodes;

this.geneLookup = geneLookup;

this.annotations = new HashMap<>();

this.geneAnnotations = new HashMap<>();

this.realInterval = STDataUtils.computeRealInterval( this );

}

@Override

public Map<String, RandomAccessibleInterval<? extends NativeType< ? >>> getAnnotations()

{

return annotations;

}

@Override

public Map<String, RandomAccessibleInterval<? extends NativeType< ? >>> getGeneAnnotations()

{

return geneAnnotations;

}

@Override

protected RealInterval getLocationRealInterval()

{

return realInterval;

}

@Override

public void setLocations( final List< double[] > locations )

{

STDataText.setLocations( locations, this.locations );

this.realInterval = STDataUtils.computeRealInterval( this );

}

@Override

public int getIndexForGene( final String gene )

{

return geneLookup.get( gene );

}

@Override

public List< String > getGeneNames() { return geneNames; }

@Override

public List< String > getBarcodes() { return barcodes; }

@Override

public RandomAccessibleInterval< DoubleType > getAllExprValues()

{

return exprValues;

}

@Override

public RandomAccessibleInterval< DoubleType > getLocations()

{

return locations;

}

}