package data;

import java.util.ArrayList;

import java.util.Collections;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.stream.Collectors;

import net.imglib2.RandomAccess;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.img.Img;

import net.imglib2.img.array.ArrayImgs;

import net.imglib2.img.cell.CellImgFactory;

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

import net.imglib2.util.Pair;

/**

* A text-input based implementation that can be used to convert to e.g. N5.

* <p>

* Computes the ImgLib2 datastructures on demand from a list of locations and a HashMap of geneName to expression values

*

*

* @author spreibi

*

*/

public class STDataText extends STDataImgLib2

{

public STDataText( final List< Pair< double[], String > > locations, final HashMap< String, double[] > exprValues )

{

super( create( locations, exprValues ) );

}

protected static STDataImgLib2Factory create( final List< Pair< double[], String > > locations, final HashMap< String, double[] > exprValues )

{

final STDataImgLib2Factory factory = new STDataImgLib2Factory();

factory.geneNames = new ArrayList<>( exprValues.keySet() );

Collections.sort( factory.geneNames );

factory.geneLookup = new HashMap<>();

for ( int i = 0; i < factory.geneNames.size(); ++i )

factory.geneLookup.put( factory.geneNames.get( i ), i );

factory.barcodes = locations.stream().map(Pair::getB).collect( Collectors.toList() );

factory.locations = locationsToImgLib2( locations );

factory.exprValues = exprValuesToImgLib2( factory.geneNames, exprValues );

return factory;

}

/**

* @param locations - the list of sequenced locations

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

*/

public static Img< DoubleType > locationsToImgLib2( final List< Pair< double[], String > > locations )

{

final int n = locations.get( 0 ).getA().length;

final int numLocations = locations.size();

final Img< DoubleType > img = ArrayImgs.doubles(numLocations, n);

setLocations( locations.stream().map(Pair::getA).collect( Collectors.toList() ), img );

return img;

}

public static void setLocations( final List< double[] > locations, final RandomAccessibleInterval< DoubleType > img )

{

final int numLocations = (int)img.dimension( 0 );

final int n = (int)img.dimension( 1 );

// TODO: use cursor

final RandomAccess< DoubleType > ra = img.randomAccess();

for ( int i = 0; i < numLocations; ++i )

{

ra.setPosition( i, 0 );

ra.setPosition( 0, 1 );

final double[] coord = locations.get( i );

for ( int d = 0; d < n; ++d )

{

ra.get().set( coord[ d ] );

if ( d != n - 1 )

ra.fwd( 1 );

}

}

}

/**

* @param geneList - the order of the genes defines the order in the imglib2 img

* @param exprValues - a map that links geneNames to their values

*

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

*/

public static Img< DoubleType > exprValuesToImgLib2( final List< String > geneList, final Map< String, double[] > exprValues )

{

final long numGenes = geneList.size();

final long numLocations = exprValues.values().iterator().next().length;

final Img< DoubleType > img = new CellImgFactory<>( new DoubleType(), 128 ).create(numGenes, numLocations);

// TODO: use cursor

final RandomAccess< DoubleType > ra = img.randomAccess();

for ( int i = 0; i < numGenes; ++i )

{

ra.setPosition( i, 0 );

ra.setPosition( 0, 1 );

final double[] values = exprValues.get( geneList.get( i ) );

for ( int j = 0; j < numLocations; ++j )

{

ra.get().set( values[ j ] );

if ( j != numLocations - 1 )

ra.fwd( 1 );

}

}

return img;

}

}