package data;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import imglib2.ExpValueRealIterable;

import net.imglib2.Cursor;

import net.imglib2.FinalRealInterval;

import net.imglib2.Interval;

import net.imglib2.IterableInterval;

import net.imglib2.IterableRealInterval;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.RealCursor;

import net.imglib2.RealLocalizable;

import net.imglib2.type.NativeType;

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

import net.imglib2.view.Views;

public class NormalizingSTData implements STData

{

final STData data;

final RandomAccessibleInterval< DoubleType > allExprValues;

/**

* Replaces the underlying data with a normalized version of it

*

* @param data - an STData instance

*/

public NormalizingSTData( final STData data )

{

this.data = data;

this.allExprValues = new NormalizingRandomAccessibleInterval( data.getAllExprValues() );

}

/*

* overwritten methods

*/

@Override

public RandomAccessibleInterval< DoubleType > getAllExprValues()

{

return allExprValues;

}

@Override

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

{

return data.getAnnotations();

}

@Override

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

{

return data.getGeneAnnotations();

}

@Override

public IterableRealInterval< DoubleType > getExprData( String geneName )

{

// TODO: use the entire values array so that the gene can be switched virtually

return new ExpValueRealIterable<>(

getLocations(),

getAllExprValues(),

data.getIndexForGene(geneName),

new FinalRealInterval(this));

}

@Override

public RandomAccessibleInterval< DoubleType > getExprValues( String geneName )

{

return Views.hyperSlice( getAllExprValues(), 0, data.getIndexForGene( geneName ) );

}

@Override

public RandomAccessibleInterval< DoubleType > getExprValues( long locationIndex )

{

return Views.hyperSlice( getAllExprValues(), 1, locationIndex );

}

@Override

public double[] getExpValuesCopy( final String geneName )

{

final IterableInterval< DoubleType > exprValues = Views.flatIterable( getExprValues( geneName ) );

final double[] exprValuesCopy = new double[ (int)exprValues.size() ];

final Cursor< DoubleType > cursor = exprValues.localizingCursor();

while ( cursor.hasNext() )

{

final DoubleType t = cursor.next();

exprValuesCopy[ cursor.getIntPosition( 0 ) ] = t.get();

}

return exprValuesCopy;

}

@Override

public void setExpValues( String geneName, double[] values )

{

throw new RuntimeException( "setting expression values not supported on virtual constructs." );

}

/*

* delegated methods

*/

@Override

public RealCursor< RealLocalizable > cursor()

{

return data.cursor();

}

@Override

public RealCursor< RealLocalizable > localizingCursor()

{

return data.localizingCursor();

}

@Override

public long size()

{

return data.size();

}

@Override

public RealLocalizable firstElement()

{

return data.firstElement();

}

@Override

public Object iterationOrder()

{

return data.iterationOrder();

}

@Override

public double realMin( int d )

{

return data.realMin( d );

}

@Override

public double realMax( int d )

{

return data.realMax( d );

}

@Override

public int numDimensions()

{

return data.numDimensions();

}

@Override

public Iterator< RealLocalizable > iterator()

{

return data.iterator();

}

@Override

public Interval getRenderInterval()

{

return data.getRenderInterval();

}

@Override

public Interval getRenderInterval( long border )

{

return data.getRenderInterval( border );

}

@Override

public Interval getRenderInterval( long[] border )

{

return data.getRenderInterval( border );

}

@Override

public long numLocations()

{

return data.numLocations();

}

@Override

public long numGenes()

{

return data.numGenes();

}

@Override

public List< String > getGeneNames()

{

return data.getGeneNames();

}

@Override

public List< String > getBarcodes()

{

return data.getBarcodes();

}

@Override

public RandomAccessibleInterval< DoubleType > getLocations()

{

return data.getLocations();

}

@Override

public List< double[] > getLocationsCopy()

{

return data.getLocationsCopy();

}

@Override

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

{

data.setLocations( locations );

}

@Override

public String toString()

{

return data.toString();

}

@Override

public int getIndexForGene( String geneName )

{

return data.getIndexForGene( geneName );

}

}