/**
* License: GPL
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License 2
* as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
import java.awt.Rectangle;
import ij.IJ;
import ij.ImagePlus;
import ij.Undo;
import ij.gui.GenericDialog;
import ij.gui.Roi;
import ij.plugin.PlugIn;
import ij.process.ByteProcessor;
import ij.process.ImageProcessor;
/**
* &lsquot;Contrast Limited Adaptive Histogram Equalization&rsquot; as
* described in
*
*
BibTeX:
*
* @article{zuiderveld94,
* author = {Zuiderveld, Karel},
* title = {Contrast limited adaptive histogram equalization},
* book = {Graphics gems IV},
* year = {1994},
* isbn = {0-12-336155-9},
* pages = {474--485},
* publisher = {Academic Press Professional, Inc.},
* address = {San Diego, CA, USA},
* }
*
*
* @author Stephan Saalfeld
* @version 0.1b
*/
public class CLAHE_ implements PlugIn
{
static private int blockRadius = 63;
static private int bins = 255;
static private float slope = 3;
final static boolean setup()
{
final GenericDialog gd = new GenericDialog( "CLAHE" );
gd.addNumericField( "blocksize : ", blockRadius * 2 + 1, 0 );
gd.addNumericField( "histogram bins : ", bins + 1, 0 );
gd.addNumericField( "maximum slope : ", slope, 2 );
gd.addHelp( "http://pacific.mpi-cbg.de/wiki/index.php/Enhance_Local_Contrast_(CLAHE)" );
gd.showDialog();
if ( gd.wasCanceled() ) return false;
blockRadius = ( ( int )gd.getNextNumber() - 1 ) / 2;
bins = ( int )gd.getNextNumber() - 1;
slope = ( float )gd.getNextNumber();
return true;
}
final public void run( final String arg )
{
final ImagePlus imp = IJ.getImage();
synchronized ( imp )
{
if ( !imp.isLocked() )
imp.lock();
else
{
IJ.error( "The image '" + imp.getTitle() + "' is in use currently.\nPlease wait until the process is done and try again." );
return;
}
}
if ( !setup() )
{
imp.unlock();
return;
}
Undo.setup( Undo.TRANSFORM, imp );
run( imp );
imp.unlock();
}
/**
* Process an {@link ImagePlus} with the static parameters. Create mask
* and bounding box from the {@link Roi} of that {@link ImagePlus}.
*
* @param imp
*/
final static public void run( final ImagePlus imp )
{
run( imp, blockRadius, bins, slope );
}
/**
* Process and {@link ImagePlus} with a given set of parameters. Create
* mask and bounding box from the {@link Roi} of that {@link ImagePlus}.
*
* @param imp
* @param blockRadius
* @param bins
* @param slope
*/
final static public void run(
final ImagePlus imp,
final int blockRadius,
final int bins,
final float slope )
{
final Roi roi = imp.getRoi();
if ( roi == null )
run( imp, blockRadius, bins, slope, null, null );
else
{
final Rectangle roiBox = roi.getBounds();
final ImageProcessor mask = roi.getMask();
if ( mask != null )
run( imp, blockRadius, bins, slope, roiBox, ( ByteProcessor )mask.convertToByte( false ) );
else
run( imp, blockRadius, bins, slope, roiBox, null );
}
}
/**
* Process and {@link ImagePlus} with a given set of parameters including
* the bounding box and mask.
*
* @param imp
* @param blockRadius
* @param bins
* @param slope
* @param roiBox can be null
* @param mask can be null
*/
final static public void run(
final ImagePlus imp,
final int blockRadius,
final int bins,
final float slope,
final java.awt.Rectangle roiBox,
final ByteProcessor mask )
{
/* initialize box if necessary */
final Rectangle box;
if ( roiBox == null )
{
if ( mask == null )
box = new Rectangle( 0, 0, imp.getWidth(), imp.getHeight() );
else
box = new Rectangle( 0, 0, Math.min( imp.getWidth(), mask.getWidth() ), Math.min( imp.getHeight(), mask.getHeight() ) );
}
else
box = roiBox;
/* make sure that the box is not larger than the mask */
if ( mask != null )
{
box.width = Math.min( mask.getWidth(), box.width );
box.height = Math.min( mask.getHeight(), box.height );
}
/* make sure that the box is not larger than the image */
box.width = Math.min( imp.getWidth() - box.x, box.width );
box.height = Math.min( imp.getHeight() - box.y, box.height );
final int boxXMax = box.x + box.width;
final int boxYMax = box.y + box.height;
/* convert 8bit processors with a LUT to RGB and create Undo-step */
final ImageProcessor ip;
if ( imp.getType() == ImagePlus.COLOR_256 )
{
ip = imp.getProcessor().convertToRGB();
imp.setProcessor( imp.getTitle(), ip );
}
else
ip = imp.getProcessor();
/* work on ByteProcessors that reflect the user defined intensity range */
final ByteProcessor src;
if ( imp.getType() == ImagePlus.GRAY8 )
src = ( ByteProcessor )ip.convertToByte( true ).duplicate();
else
src = ( ByteProcessor )ip.convertToByte( true );
final ByteProcessor dst = ( ByteProcessor )src.duplicate();
for ( int y = box.y; y < boxYMax; ++y )
{
final int yMin = Math.max( 0, y - blockRadius );
final int yMax = Math.min( imp.getHeight(), y + blockRadius + 1 );
final int h = yMax - yMin;
final int xMin0 = Math.max( 0, box.x - blockRadius );
final int xMax0 = Math.min( imp.getWidth() - 1, box.x + blockRadius );
/* initially fill histogram */
final int[] hist = new int[ bins + 1 ];
final int[] clippedHist = new int[ bins + 1 ];
for ( int yi = yMin; yi < yMax; ++yi )
for ( int xi = xMin0; xi < xMax0; ++xi )
++hist[ roundPositive( src.get( xi, yi ) / 255.0f * bins ) ];
for ( int x = box.x; x < boxXMax; ++x )
{
final int v = roundPositive( src.get( x, y ) / 255.0f * bins );
final int xMin = Math.max( 0, x - blockRadius );
final int xMax = x + blockRadius + 1;
final int w = Math.min( imp.getWidth(), xMax ) - xMin;
final int n = h * w;
final int limit;
if ( mask == null )
limit = ( int )( slope * n / bins + 0.5f );
else
limit = ( int )( ( 1 + mask.get( x - box.x, y - box.y ) / 255.0f * ( slope - 1 ) ) * n / bins + 0.5f );
/* remove left behind values from histogram */
if ( xMin > 0 )
{
final int xMin1 = xMin - 1;
for ( int yi = yMin; yi < yMax; ++yi )
--hist[ roundPositive( src.get( xMin1, yi ) / 255.0f * bins ) ];
}
/* add newly included values to histogram */
if ( xMax <= imp.getWidth() )
{
final int xMax1 = xMax - 1;
for ( int yi = yMin; yi < yMax; ++yi )
++hist[ roundPositive( src.get( xMax1, yi ) / 255.0f * bins ) ];
}
/* clip histogram and redistribute clipped entries */
System.arraycopy( hist, 0, clippedHist, 0, hist.length );
int clippedEntries = 0, clippedEntriesBefore;
do
{
clippedEntriesBefore = clippedEntries;
clippedEntries = 0;
for ( int i = 0; i <= bins; ++i )
{
final int d = clippedHist[ i ] - limit;
if ( d > 0 )
{
clippedEntries += d;
clippedHist[ i ] = limit;
}
}
final int d = clippedEntries / ( bins + 1 );
final int m = clippedEntries % ( bins + 1 );
for ( int i = 0; i <= bins; ++i)
clippedHist[ i ] += d;
if ( m != 0 )
{
final int s = bins / m;
for ( int i = 0; i <= bins; i += s )
++clippedHist[ i ];
}
}
while ( clippedEntries != clippedEntriesBefore );
/* build cdf of clipped histogram */
int hMin = bins;
for ( int i = 0; i < hMin; ++i )
if ( clippedHist[ i ] != 0 ) hMin = i;
int cdf = 0;
for ( int i = hMin; i <= v; ++i )
cdf += clippedHist[ i ];
int cdfMax = cdf;
for ( int i = v + 1; i <= bins; ++i )
cdfMax += clippedHist[ i ];
final int cdfMin = clippedHist[ hMin ];
dst.set( x, y, roundPositive( ( cdf - cdfMin ) / ( float )( cdfMax - cdfMin ) * 255.0f ) );
}
/* multiply the current row into ip */
final int t = y * imp.getWidth();
if ( imp.getType() == ImagePlus.GRAY8 )
{
for ( int x = box.x; x < boxXMax; ++x )
{
final int i = t + x;
ip.set( i, dst.get( i ) );
}
}
else if ( imp.getType() == ImagePlus.GRAY16 )
{
final int min = ( int )ip.getMin();
for ( int x = box.x; x < boxXMax; ++x )
{
final int i = t + x;
final int v = ip.get( i );
final float a = ( float )dst.get( i ) / src.get( i );
ip.set( i, Math.max( 0, Math.min( 65535, roundPositive( a * ( v - min ) + min ) ) ) );
}
}
else if ( imp.getType() == ImagePlus.GRAY32 )
{
final float min = ( float )ip.getMin();
for ( int x = box.x; x < boxXMax; ++x )
{
final int i = t + x;
final float v = ip.getf( i );
final float a = ( float )dst.get( i ) / src.get( i );
ip.setf( i, a * ( v - min ) + min );
}
}
else if ( imp.getType() == ImagePlus.COLOR_RGB )
{
for ( int x = box.x; x < boxXMax; ++x )
{
final int i = t + x;
final int argb = ip.get( i );
final float a = ( float )dst.get( i ) / src.get( i );
final int r = Math.max( 0, Math.min( 255, roundPositive( a * ( ( argb >> 16 ) & 0xff ) ) ) );
final int g = Math.max( 0, Math.min( 255, roundPositive( a * ( ( argb >> 8 ) & 0xff ) ) ) );
final int b = Math.max( 0, Math.min( 255, roundPositive( a * ( argb & 0xff ) ) ) );
ip.set( i, ( r << 16 ) | ( g << 8 ) | b );
}
}
imp.updateAndDraw();
}
}
final static private int roundPositive( float a )
{
return ( int )( a + 0.5f );
}
}