/*
* ------------------------------------------------------------------------
*
* University of Konstanz, Germany and
* KNIME GmbH, Konstanz, Germany
* Website: http://www.knime.org; Email: contact@knime.org
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License, Version 3, as
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* along with this program; if not, see <http://www.gnu.org/licenses>.
*
* Additional permission under GNU GPL version 3 section 7:
*
* KNIME interoperates with ECLIPSE solely via ECLIPSE's plug-in APIs.
* Hence, KNIME and ECLIPSE are both independent programs and are not
* derived from each other. Should, however, the interpretation of the
* GNU GPL Version 3 ("License") under any applicable laws result in
* KNIME and ECLIPSE being a combined program, KNIME GMBH herewith grants
* you the additional permission to use and propagate KNIME together with
* ECLIPSE with only the license terms in place for ECLIPSE applying to
* ECLIPSE and the GNU GPL Version 3 applying for KNIME, provided the
* license terms of ECLIPSE themselves allow for the respective use and
* propagation of ECLIPSE together with KNIME.
*
* Additional permission relating to nodes for KNIME that extend the Node
* Extension (and in particular that are based on subclasses of NodeModel,
* NodeDialog, and NodeView) and that only interoperate with KNIME through
* standard APIs ("Nodes"):
* Nodes are deemed to be separate and independent programs and to not be
* covered works. Notwithstanding anything to the contrary in the
* License, the License does not apply to Nodes, you are not required to
* license Nodes under the License, and you are granted a license to
* prepare and propagate Nodes, in each case even if such Nodes are
* propagated with or for interoperation with KNIME. The owner of a Node
* may freely choose the license terms applicable to such Node, including
* when such Node is propagated with or for interoperation with KNIME.
---------------------------------------------------------------------
*
*/
package org.knime.knip.features.sets;
import net.imagej.ops.Contingent;
import net.imagej.ops.features.haralick.HaralickFeature;
import net.imglib2.IterableInterval;
import net.imglib2.type.numeric.RealType;
import org.scijava.ItemIO;
import org.scijava.plugin.Attr;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
/**
* {@link FeatureSet} for {@link HaralickFeature}s
*
* @author Christian Dietz, University of Konstanz
* @param <T>
* @param <O>
*/
@Plugin(type = FeatureSet.class, label = "Haralick 2D Features", description = "<h1> Haralick 2D Feature Set</h1> <h2>Description</h2> The basis for these features is the gray-level co-occurrence matrix. This matrix is square with dimension Ng, where Ng is the number of gray levels in the image. Element [i,j] of the matrix is generated by counting the number of times a pixel with value i is adjacent to a pixel with value j and then dividing the entire matrix by the total number of such comparisons made. Each entry is therefore considered to be the probability that a pixel with value i will be found adjacent to a pixel of value j. For more information see <a href=\"http://murphylab.web.cmu.edu/publications/boland/boland_node26.html\">Haralick Features</a><h2>Parameters</h2> <ul><li><strong>Num. Grey Levels:</strong> The number of grey values determines the size of the co-occurence matrix on which the Haralick features are calculated.</li><li><strong>Distance:</strong> The maximum distance between pairs of pixels which will be added to the co-occurence matrix.</li><li><strong>Orientation:</strong> Orientation of the pairs of pixels which will be added to the co-occurence matrix.</li></ul>")
public class Haralick2DFeatureSet<T extends RealType<T>, O extends RealType<O>>
extends AbstractOpRefFeatureSet<IterableInterval<T>, O> implements Contingent {
private static final String PKG = "net.imagej.ops.Ops$Haralick$";
@Parameter(type = ItemIO.INPUT, label = "Number Grey Levels", description = "The number of grey values determines the size of the co-occurence matrix on which the Haralick features are calculated.", min = "1", max = "2147483647", stepSize = "1")
private int numGreyLevels = 32;
@Parameter(type = ItemIO.INPUT, label = "Distance", description = "The maximum distance between pairs of pixels which will be added to the co-occurence matrix.", min = "1", max = "2147483647", stepSize = "1")
private int distance = 1;
@Parameter(type = ItemIO.INPUT, label = "Orientation", description = "Orientation of the pairs of pixels which will be added to the co-occurence matrix", choices = {
"DIAGONAL 2D", "ANTIDIAGONAL 2D", "HORIZONTAL 2D", "VERTICAL 2D" })
private String orientation = "HORIZONTAL";
@Parameter(required = false, label = "ASM", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "ASM") })
private boolean isASMActive = true;
@Parameter(required = false, label = "Cluster Promenence", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "ClusterPromenence") })
private boolean isClusterPromenenceActive = true;
@Parameter(required = false, label = "Cluster Shade", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "ClusterShade") })
private boolean isClusterShadeActive = true;
@Parameter(required = false, label = "Contrast", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "Contrast") })
private boolean isContrastActive = true;
@Parameter(required = false, label = "Correlation", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "Correlation") })
private boolean isCorrelationActive = true;
@Parameter(required = false, label = "Difference Entropy", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "DifferenceEntropy") })
private boolean isDifferenceEntropyActive = true;
@Parameter(required = false, label = "Difference Variance", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "DifferenceVariance") })
private boolean isDifferenceVarianceActive = true;
@Parameter(required = false, label = "Entropy", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "Entropy") })
private boolean isEntropyActive = true;
@Parameter(required = false, label = "ICM1", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "ICM1") })
private boolean isICM1Active = true;
@Parameter(required = false, label = "ICM2", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "ICM2") })
private boolean isICM2Active = true;
@Parameter(required = false, label = "IFDM", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "IFDM") })
private boolean isIFDMActive = true;
@Parameter(required = false, label = "Max Probability", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "MaxProbability") })
private boolean isMaxProbabilityActive = true;
@Parameter(required = false, label = "Sum Average", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "SumAverage") })
private boolean isSumAverageActive = true;
@Parameter(required = false, label = "Sum Entropy", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "SumEntropy") })
private boolean isSumEntropyActive = true;
@Parameter(required = false, label = "Sum Variance", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "SumVariance") })
private boolean isSumVarianceActive = true;
@Parameter(required = false, label = "Texture Homogenity", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "TextureHomogeneity") })
private boolean isTextureHomogeneityActive = true;
@Parameter(required = false, label = "Variance", attrs = { @Attr(name = ATTR_FEATURE),
@Attr(name = ATTR_PARAMS, value = "numGreyLevels,distance,orientation"),
@Attr(name = ATTR_TYPE, value = PKG + "Variance") })
private boolean isVarianceActive = true;
@Override
public boolean conforms() {
return in().numDimensions() == 2;
}
@Override
public boolean isCompatible(final Class<?> object, final Class<?> type) {
return IterableInterval.class.isAssignableFrom(object) && RealType.class.isAssignableFrom(type);
}
}