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A multidimensional, type-agnostic image processing library.
/*
* #%L
* ImgLib2: a general-purpose, multidimensional image processing library.
* %%
* Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
* John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
* Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
* Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
* Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
* Jean-Yves Tinevez and Michael Zinsmaier.
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package net.imglib2.display.projector.specialized;
import net.imglib2.display.projector.AbstractProjector2D;
import net.imglib2.display.screenimage.awt.UnsignedByteAWTScreenImage;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.basictypeaccess.array.ShortArray;
import net.imglib2.img.planar.PlanarImg;
import net.imglib2.type.numeric.integer.GenericShortType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.util.IntervalIndexer;
/**
* Fast implementation of a {@link AbstractProjector2D} that selects a 2D data
* plain from an ShortType PlanarImg. The map method implements a normalization
* function. The resulting image is a ShortType ArrayImg. *
*
* @author Michael Zinsmaier
* @author Martin Horn
* @author Christian Dietz
*
* @param
*/
public class PlanarImgXYShortProjector< A extends GenericShortType< A >> extends AbstractProjector2D
{
private final PlanarImg< A, ShortArray > source;
private final short[] targetArray;
private final double min;
private final double normalizationFactor;
private final boolean isSigned;
private final long[] dims;
/**
* Normalizes a PlanarImg and writes the result into target. This can be
* used in conjunction with {@link UnsignedByteAWTScreenImage} for direct
* displaying. The normalization is based on a normalization factor and a
* minimum value with the following dependency:
*
* normalizationFactor = (typeMax - typeMin) / (newMax - newMin)
* min = newMin
*
* A value is normalized by: normalizedValue = (value - min) *
* normalizationFactor.
* Additionally the result gets clamped to the type range of target (that
* allows playing with saturation...).
*
* @param source
* Signed/Unsigned input data
* @param target
* Unsigned output
* @param normalizationFactor
* @param min
*/
public PlanarImgXYShortProjector( final PlanarImg< A, ShortArray > source, final ArrayImg< UnsignedShortType, ShortArray > target, final double normalizationFactor, final double min )
{
super( source.numDimensions() );
this.isSigned = source.firstElement().getMinValue() < 0;
this.targetArray = target.update( null ).getCurrentStorageArray();
this.normalizationFactor = normalizationFactor;
this.min = min;
this.dims = new long[ n ];
source.dimensions( dims );
this.source = source;
}
@Override
public void map()
{
// more detailed documentation of the binary arithmetic can be found in
// ArrayImgXYByteProjector
double minCopy = min;
final int offset = 0;
// positioning for every call to map because the plane index is
// position dependent
int planeIndex;
if ( position.length > 2 )
{
final long[] tmpPos = new long[ position.length - 2 ];
final long[] tmpDim = new long[ position.length - 2 ];
for ( int i = 0; i < tmpDim.length; i++ )
{
tmpPos[ i ] = position[ i + 2 ];
tmpDim[ i ] = source.dimension( i + 2 );
}
planeIndex = ( int ) IntervalIndexer.positionToIndex( tmpPos, tmpDim );
}
else
{
planeIndex = 0;
}
final short[] sourceArray = source.update( new PlanarImgContainerSamplerImpl( planeIndex ) ).getCurrentStorageArray();
// copy the selected part of the source array (e.g. a xy plane at time t
// in a video) into the target array.
System.arraycopy( sourceArray, offset, targetArray, 0, targetArray.length );
if ( isSigned )
{
for ( int i = 0; i < targetArray.length; i++ )
{
// Short.MIN => 0 && Short.MAX => 65535 (2^16 - 1) => unsigned
// short
targetArray[ i ] = ( short ) ( targetArray[ i ] - 0x8000 );
}
// old => unsigned short minimum
minCopy += 0x8000;
}
if ( normalizationFactor != 1 )
{
for ( int i = 0; i < targetArray.length; i++ )
{
// normalizedValue = (oldValue - min) * normalizationFactor
// clamped to 0 .. 65535
targetArray[ i ] = ( short ) Math.min( 65535, Math.max( 0, ( Math.round( ( ( targetArray[ i ] & 0xFFFF ) - minCopy ) * normalizationFactor ) ) ) );
}
}
}
}