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ImageStatistics.java
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ImageStatistics.java
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/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 2017 Fiji developers.
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* 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, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
/*
* Copyright (c) 2009--2010, Stephan Preibisch & Stephan Saalfeld
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer. 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. Neither the name of the Fiji project nor
* the names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* 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 HOLDER 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.
*/
package net.imglib2.algorithm.math;
import net.imglib2.Cursor;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.TwinCursor;
import net.imglib2.type.Type;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.util.RealSum;
import net.imglib2.view.Views;
/**
* This class contains some basic image statistics
* calculations.
*
* @author Dan White
* @author Tom Kazimiers
*/
public class ImageStatistics {
/**
* Calculates the number of pixels in the image.
*
* @param img The image to calculate the mean of
* @return The mean of the image passed
*/
final public static <T extends RealType<T>> long getNumPixels(
final RandomAccessibleInterval<T> img )
{
long numPixels = 1;
for (int d=0; d<img.numDimensions(); ++d)
numPixels = numPixels * img.dimension(d);
return numPixels;
}
/**
* Calculates the mean of an image with respect to a mask.
*
* @param img The image to calculate the mean of
* @param mask The mask to respect
* @return The mean of the image passed
*/
final public static <T extends RealType<T>> double getImageMean(
final RandomAccessibleInterval<T> img,
final RandomAccessibleInterval<BitType> mask )
{
final RealSum sum = new RealSum();
long numPixels = 0;
// create cursor to walk an image with respect to a mask
final TwinCursor<T> cursor = new TwinCursor<T>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).localizingCursor());
while (cursor.hasNext()) {
sum.add(cursor.getFirst().getRealDouble());
++numPixels;
}
return sum.getSum() / numPixels;
}
/**
* Calculates the mean of an image.
*
* @param img The image to calculate the mean of
* @return The mean of the image passed
*/
final public static <T extends RealType<T>> double getImageMean(
final RandomAccessibleInterval<T> img )
{
// Count all values using the RealSum class.
// It prevents numerical instabilities when adding up millions of pixels
RealSum realSum = new RealSum();
long count = 0;
for ( final T type : Views.iterable(img) )
{
realSum.add( type.getRealDouble() );
++count;
}
return realSum.getSum() / count;
}
/**
* Calculates the integral of the pixel values of an image.
*
* @param img The image to calculate the integral of
* @return The pixel values integral of the image passed
*/
final public static <T extends RealType<T>> double getImageIntegral(
final RandomAccessibleInterval<T> img )
{
final RealSum sum = new RealSum();
for ( final T type : Views.iterable(img) )
sum.add( type.getRealDouble() );
return sum.getSum();
}
/**
* Calculates the integral of the pixel values of an image.
*
* @param img The image to calculate the integral of
* @return The pixel values integral of the image passed
*/
final public static <T extends RealType<T>> double getImageIntegral(
final RandomAccessibleInterval<T> img,
final RandomAccessibleInterval<BitType> mask )
{
final RealSum sum = new RealSum();
// create cursor to walk an image with respect to a mask
final TwinCursor<T> cursor = new TwinCursor<T>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).cursor());
while (cursor.hasNext())
sum.add( cursor.getFirst().getRealDouble() );
return sum.getSum();
}
/**
* Calculates the min of an image.
*
* @param img The image to calculate the min of
* @return The min of the image passed
*/
final public static <T extends Type<T> & Comparable<T>> T getImageMin(
final RandomAccessibleInterval<T> img )
{
final Cursor<T> cursor = Views.iterable(img).cursor();
cursor.fwd();
// copy first element as current maximum
final T min = cursor.get().copy();
while ( cursor.hasNext() )
{
cursor.fwd();
final T currValue = cursor.get();
if ( currValue.compareTo( min ) < 0 )
min.set( currValue );
}
return min;
}
/**
* Calculates the min of an image with respect to a mask.
*
* @param img The image to calculate the min of
* @param mask The mask to respect
* @return The min of the image passed
*/
final public static <T extends Type<T> & Comparable<T>> T getImageMin(
final RandomAccessibleInterval<T> img,
final RandomAccessibleInterval<BitType> mask )
{
// create cursor to walk an image with respect to a mask
final TwinCursor<T> cursor = new TwinCursor<T>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).localizingCursor());
// forward one step to get the first value
cursor.fwd();
// copy first element as current minimum
final T min = cursor.getFirst().copy();
while ( cursor.hasNext() ) {
cursor.fwd();
final T currValue = cursor.getFirst();
if ( currValue.compareTo( min ) < 0 )
min.set( currValue );
}
return min;
}
/**
* Calculates the max of an image.
*
* @param img The image to calculate the max of
* @return The max of the image passed
*/
final public static <T extends Type<T> & Comparable<T>> T getImageMax(
final RandomAccessibleInterval<T> img ) {
final Cursor<T> cursor = Views.iterable(img).localizingCursor();
cursor.fwd();
// copy first element as current maximum
final T max = cursor.get().copy();
while ( cursor.hasNext() )
{
cursor.fwd();
final T currValue = cursor.get();
if ( currValue.compareTo( max ) > 0 )
max.set( currValue );
}
return max;
}
/**
* Calculates the max of an image with respect to a mask.
*
* @param img The image to calculate the min of
* @param mask The mask to respect
* @return The min of the image passed
*/
final public static <T extends Type<T> & Comparable<T>> T getImageMax(
final RandomAccessibleInterval<T> img,
final RandomAccessibleInterval<BitType> mask )
{
// create cursor to walk an image with respect to a mask
final TwinCursor<T> cursor = new TwinCursor<T>(
img.randomAccess(),
img.randomAccess(),
Views.iterable(mask).localizingCursor());
// forward one step to get the first value
cursor.fwd();
final T max = cursor.getFirst().copy();
while ( cursor.hasNext() ) {
cursor.fwd();
final T currValue = cursor.getFirst();
if ( currValue.compareTo( max ) > 0 )
max.set( currValue );
}
return max;
}
}

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