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Copy pathNormalizingRandomAccess.java
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163 lines (134 loc) · 3.77 KB
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package data;
import net.imglib2.Localizable;
import net.imglib2.RandomAccess;
import net.imglib2.type.numeric.real.DoubleType;
public class NormalizingRandomAccess implements RandomAccess< DoubleType >
{
final protected DoubleType value = new DoubleType();
final RandomAccess< DoubleType > inputRandomAccess;
final RandomAccess< DoubleType > sumsPerLocationRandomAccess;
public NormalizingRandomAccess(
final RandomAccess< DoubleType > inputRandomAccess,
final RandomAccess< DoubleType > sumsPerLocationRandomAccess )
{
this.inputRandomAccess = inputRandomAccess;
this.sumsPerLocationRandomAccess = sumsPerLocationRandomAccess;
}
@Override
public DoubleType get()
{
// d_mn -> d_mn = log ( 10^5 * d_mn / sum_k(d_mk) + 1 )
//
// d_{mn} is an entry of the matrix, with {n} denoting the
// cell/location and {m} the gene.
//
// - cell means location, yes.
// - {k} is a dummy index, you just sum over it
//
// Basically you sum all raw UMIs/counts for a given cell/location,
// then you divide those counts by that number, multiply
// by 10*5 to get meaningful numbers, add 1 to escape infinities
// and take a logarithm of that.
final double d_mn = inputRandomAccess.get().get();
final double sum_k = sumsPerLocationRandomAccess.get().get();
if ( sum_k == 0 || d_mn == 0 )
value.set( 0 );
else
value.set( Math.log( 10000 * d_mn / sum_k + 1 ) );
return value;
}
@Override
public NormalizingRandomAccess copy() {
final NormalizingRandomAccess r = new NormalizingRandomAccess(inputRandomAccess.copy(), sumsPerLocationRandomAccess.copy());
r.setPosition(this);
return r;
}
@Override
public void fwd( final int d )
{
inputRandomAccess.fwd( d );
if ( d == 1 )
sumsPerLocationRandomAccess.fwd( 0 );
}
@Override
public void bck( final int d )
{
inputRandomAccess.bck( d );
if ( d == 1 )
sumsPerLocationRandomAccess.bck( 0 );
}
@Override
public void move( final int distance, final int d )
{
inputRandomAccess.move( distance, d );
if ( d == 1 )
sumsPerLocationRandomAccess.move( distance, 0 );
}
@Override
public void move( final long distance, final int d )
{
inputRandomAccess.move( distance, d );
if ( d == 1 )
sumsPerLocationRandomAccess.move( distance, 0 );
}
@Override
public void move( final Localizable localizable )
{
inputRandomAccess.move( localizable );
sumsPerLocationRandomAccess.move( localizable.getLongPosition( 1 ), 0 );
}
@Override
public void move( final int[] distance )
{
inputRandomAccess.move( distance );
sumsPerLocationRandomAccess.move( distance[ 1 ], 0 );
}
@Override
public void move( final long[] distance )
{
inputRandomAccess.move( distance );
sumsPerLocationRandomAccess.move( distance[ 1 ], 0 );
}
@Override
public void setPosition( final Localizable localizable )
{
inputRandomAccess.setPosition( localizable );
sumsPerLocationRandomAccess.setPosition( localizable.getLongPosition( 1 ), 0 );
}
@Override
public void setPosition( final int[] pos )
{
inputRandomAccess.setPosition( pos );
sumsPerLocationRandomAccess.setPosition( pos[ 1 ], 0 );
}
@Override
public void setPosition( final long[] pos )
{
inputRandomAccess.setPosition( pos );
sumsPerLocationRandomAccess.setPosition( pos[ 1 ], 0 );
}
@Override
public void setPosition( final int pos, final int d )
{
inputRandomAccess.setPosition( pos, d );
if ( d == 1 )
sumsPerLocationRandomAccess.setPosition( pos, 0 );
}
@Override
public void setPosition( final long pos, final int d )
{
inputRandomAccess.setPosition( pos, d );
if ( d == 1 )
sumsPerLocationRandomAccess.setPosition( pos, 0 );
}
@Override
public long getLongPosition( int d )
{
return inputRandomAccess.getLongPosition( d );
}
@Override
public int numDimensions()
{
return inputRandomAccess.numDimensions();
}
}