/*
* ------------------------------------------------------------------------
*
* Copyright (C) 2003 - 2013
* 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
* 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, 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.base.nodes.seg.local;
import java.util.Iterator;
import java.util.List;
import net.imagej.ImgPlus;
import net.imglib2.ops.operation.BinaryOperation;
import net.imglib2.ops.operation.Operations;
import net.imglib2.ops.operation.UnaryOutputOperation;
import net.imglib2.ops.operation.iterable.binary.localthresholder.Bernsen;
import net.imglib2.ops.operation.iterable.binary.localthresholder.MeanLocalThreshold;
import net.imglib2.ops.operation.iterable.binary.localthresholder.MedianLocalThreshold;
import net.imglib2.ops.operation.iterable.binary.localthresholder.MidGrey;
import net.imglib2.ops.operation.iterable.binary.localthresholder.Niblack;
import net.imglib2.ops.operation.iterable.binary.localthresholder.Sauvola;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelDouble;
import org.knime.core.node.defaultnodesettings.SettingsModelInteger;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.knip.base.node.ImgPlusToImgPlusNodeModel;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.ops.iterable.SlidingShapeOpBinaryInside;
import org.knime.knip.core.types.NeighborhoodType;
import org.knime.knip.core.types.OutOfBoundsStrategyEnum;
import org.knime.knip.core.types.OutOfBoundsStrategyFactory;
import org.knime.knip.core.util.ImgPlusFactory;
/**
*
* @author friedrichm, University of Konstanz
*
* @param <T> the pixel type of the input and output image
*/
// TODO Remove with 2.0
/**
* TODO Auto-generated
*
* @author <a href="mailto:dietzc85@googlemail.com">Christian Dietz</a>
* @author <a href="mailto:horn_martin@gmx.de">Martin Horn</a>
* @author <a href="mailto:michael.zinsmaier@googlemail.com">Michael Zinsmaier</a>
*/
@Deprecated
public class LocalThresholderNodeModel<T extends RealType<T>> extends ImgPlusToImgPlusNodeModel<T, BitType> {
protected static SettingsModelDouble createCModel() {
return new SettingsModelDouble("c", 0.0);
}
protected static SettingsModelDouble createContrastThreshold() {
return new SettingsModelDouble("contrastThreshold", 0.0);
}
protected static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("dimselection", "X", "Y");
}
protected static SettingsModelDouble createKModel() {
return new SettingsModelDouble("k", 0.5);
}
protected static SettingsModelString createNeighborhoodTypeNodeModel() {
return new SettingsModelString("neighborhood_type", NeighborhoodType.RECTANGULAR.toString());
}
protected static SettingsModelString createOutOfBoundsModel() {
return new SettingsModelString("outofboundsstrategy", OutOfBoundsStrategyEnum.BORDER.toString());
}
protected static SettingsModelDouble createRModel() {
return new SettingsModelDouble("r", 128.0);
}
protected static SettingsModelString createThresholderModel() {
return new SettingsModelString("thresholder", "");
}
protected static SettingsModelInteger createWindowSize() {
return new SettingsModelInteger("windowsize", 15);
}
private final SettingsModelDouble m_c = createCModel();
private final SettingsModelDouble m_contrastThreshold = createContrastThreshold();
private final SettingsModelDouble m_k = createKModel();
private final SettingsModelString m_neighborhoodType = createNeighborhoodTypeNodeModel();
private final SettingsModelString m_outOfBoundsStrategy = createOutOfBoundsModel();
private final SettingsModelDouble m_r = createRModel();
private final SettingsModelInteger m_span = createWindowSize();
private final SettingsModelString m_thresholder = createThresholderModel();
public LocalThresholderNodeModel() {
super(createDimSelectionModel());
}
/**
* {@inheritDoc}
*/
@Override
public void addSettingsModels(final List<SettingsModel> settingsModels) {
m_k.setEnabled(false);
m_c.setEnabled(false);
m_r.setEnabled(false);
settingsModels.add(m_thresholder);
settingsModels.add(m_outOfBoundsStrategy);
settingsModels.add(m_k);
settingsModels.add(m_c);
settingsModels.add(m_r);
settingsModels.add(m_span);
settingsModels.add(m_contrastThreshold);
settingsModels.add(m_neighborhoodType);
}
@Override
protected UnaryOutputOperation<ImgPlus<T>, ImgPlus<BitType>> op(final ImgPlus<T> imgPlus) {
final LocalThresholdingMethodsEnum method =
Enum.valueOf(LocalThresholdingMethodsEnum.class, m_thresholder.getStringValue());
final T inputValue = imgPlus.firstElement().createVariable();
BinaryOperation<Iterator<T>, T, BitType> thresholder = null;
// TODO: incoperate integral img calculation
switch (method) {
case BERNSEN:
// TODO integral img?
thresholder = new Bernsen<T>(m_contrastThreshold.getDoubleValue(), inputValue.getMaxValue());
break;
case MEAN:
// TODO use integral img wrapper?!
thresholder = new MeanLocalThreshold<T>(m_c.getDoubleValue());
break;
case MEDIAN:
thresholder = new MedianLocalThreshold<T>(m_c.getDoubleValue());
break;
case MIDGREY:
thresholder = new MidGrey<T, Iterator<T>>(m_c.getDoubleValue());
break;
case NIBLACK:
thresholder = new Niblack<T>(m_k.getDoubleValue(), m_c.getDoubleValue());
break;
case SAUVOLA:
thresholder = new Sauvola<T>(m_k.getDoubleValue(), m_r.getDoubleValue());
break;
default:
throw new RuntimeException(new IllegalArgumentException("Unknown thresholding type"));
}
return Operations.wrap(new SlidingShapeOpBinaryInside<T, BitType, ImgPlus<T>, ImgPlus<BitType>>(
NeighborhoodType.getNeighborhood(NeighborhoodType.valueOf(m_neighborhoodType
.getStringValue()), m_span.getIntValue()), thresholder,
OutOfBoundsStrategyFactory.<T, ImgPlus<T>> getStrategy(m_outOfBoundsStrategy
.getStringValue(), imgPlus.firstElement())), ImgPlusFactory
.<T, BitType> get(new BitType()));
}
/**
* {@inheritDoc}
*/
@Override
protected int getMinDimensions() {
return 1;
}
}