/*
* ------------------------------------------------------------------------
*
* 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.proc.ucm;
import java.util.List;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.NodeModel;
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.data.img.ImgPlusCell;
import org.knime.knip.base.data.img.ImgPlusCellFactory;
import org.knime.knip.base.data.img.ImgPlusValue;
import org.knime.knip.base.data.labeling.LabelingValue;
import org.knime.knip.base.node.TwoValuesToCellNodeModel;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imagej.ops.MetadataUtil;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;
/**
* {@link NodeModel} for {@link UCMOp}
*
* @author <a href="mailto:dietzc85@googlemail.com">Christian Dietz</a>
* @author <a href="mailto:horn_martin@gmx.de">Martin Horn</a>
*
* @param <T>
* @param <L>
*/
public class UCMNodeModel<T extends RealType<T>, L extends Comparable<L>>
extends TwoValuesToCellNodeModel<LabelingValue<L>, ImgPlusValue<T>, ImgPlusCell<FloatType>> {
/**
* @return SettingsModel to store max number of faces
*/
static SettingsModelInteger createMaxFacesAmountModel() {
return new SettingsModelInteger("max_faces_num", 9999);
}
/**
* @return SettingsModel to store max face percent
*/
static SettingsModelDouble createMaxFacePercentModel() {
return new SettingsModelDouble("max_face_percent", 100);
}
/**
* @return SettingsModel to store min boundary weight model
*/
static SettingsModelInteger createMinBoundaryWeightModel() {
return new SettingsModelInteger("min_boundary_weight", 0);
}
/**
* @return SettingsModel to store boundary label
*/
static SettingsModelString createBoundaryLabelModel() {
return new SettingsModelString("boundary_label", "Boundary");
}
/**
* @return SettingsModel to store dimension selection
*/
static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("dim_selection", "X", "Y");
}
private SettingsModelInteger m_maxNumFaces = createMaxFacesAmountModel();
private SettingsModelDouble m_maxFacePercent = createMaxFacePercentModel();
private SettingsModelInteger m_minBoundaryWeight = createMinBoundaryWeightModel();
private SettingsModelString m_boundaryLabel = createBoundaryLabelModel();
private SettingsModelDimSelection m_dimSelection = createDimSelectionModel();
private ImgPlusCellFactory m_imgCellFactory;
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
@Override
protected ImgPlusCell<FloatType> compute(final LabelingValue<L> labelingValue, final ImgPlusValue<T> imgValue)
throws Exception {
// containers to work on
final RandomAccessibleInterval<LabelingType<L>> fromCellLabeling = labelingValue.getLabeling();
final RandomAccessibleInterval<LabelingType<L>> zeroMinFromCellLabeling =
MinimaUtils.getZeroMinLabeling(fromCellLabeling);
final ImgPlus<T> fromCellImg = imgValue.getImgPlus();
final ImgPlus<T> zeroMinFromCellImg = MinimaUtils.getZeroMinImgPlus(fromCellImg);
final Img<FloatType> result = new ArrayImgFactory<FloatType>().create(zeroMinFromCellImg, new FloatType());
// create new UCMOp with parameters
final UCMOp<L, T> ucmOp = new UCMOp<L, T>(m_maxNumFaces.getIntValue(), m_maxFacePercent.getDoubleValue(),
m_minBoundaryWeight.getIntValue(), m_boundaryLabel.getStringValue());
SubsetOperations.iterate(ucmOp, m_dimSelection.getSelectedDimIndices(zeroMinFromCellImg),
zeroMinFromCellLabeling, zeroMinFromCellImg, result, getExecutorService());
final ImgPlus<FloatType> res = new ImgPlus<>(result, imgValue.getMetadata());
MetadataUtil.copySource(imgValue.getMetadata(), res);
return m_imgCellFactory.createCell(MinimaUtils.getTranslatedImgPlus(fromCellImg, res));
}
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_maxNumFaces);
settingsModels.add(m_maxFacePercent);
settingsModels.add(m_minBoundaryWeight);
settingsModels.add(m_boundaryLabel);
settingsModels.add(m_dimSelection);
}
}