/*
* ------------------------------------------------------------------------
*
* 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;
import java.util.List;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.defaultnodesettings.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.DialogComponentNumber;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModelDouble;
import org.knime.knip.base.data.img.ImgPlusValue;
import org.knime.knip.base.data.labeling.LabelingCell;
import org.knime.knip.base.data.labeling.LabelingCellFactory;
import org.knime.knip.base.data.labeling.LabelingValue;
import org.knime.knip.base.node.TwoValuesToCellNodeDialog;
import org.knime.knip.base.node.TwoValuesToCellNodeFactory;
import org.knime.knip.base.node.TwoValuesToCellNodeModel;
import org.knime.knip.base.node.dialog.DialogComponentDimSelection;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.data.img.DefaultLabelingMetadata;
import org.knime.knip.core.ops.labeling.WatershedWithSheds;
import org.knime.knip.core.ops.labeling.WatershedWithThreshold;
import org.knime.knip.core.util.MinimaUtils;
import org.knime.knip.core.util.MiscViews;
import org.knime.knip.core.util.NeighborhoodUtils;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.ops.operation.BinaryOperation;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.ops.operation.randomaccessibleinterval.unary.regiongrowing.AbstractRegionGrowing;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.IntType;
/**
*
* @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>
*/
public class WatershedNodeFactory<T extends RealType<T>, L>
extends TwoValuesToCellNodeFactory<ImgPlusValue<T>, LabelingValue<L>> {
private final class WatershedOperationWrapper1 implements
BinaryOperation<Img<T>, RandomAccessibleInterval<LabelingType<L>>, RandomAccessibleInterval<LabelingType<L>>> {
private final WatershedWithThreshold<T, L> m_ws;
public WatershedOperationWrapper1(final WatershedWithThreshold<T, L> ws) {
m_ws = ws;
}
/**
* {@inheritDoc}
*/
@Override
public RandomAccessibleInterval<LabelingType<L>>
compute(final Img<T> inputA, final RandomAccessibleInterval<LabelingType<L>> inputB,
final RandomAccessibleInterval<LabelingType<L>> output) {
m_ws.setSeeds(inputB);
m_ws.setOutputLabeling(output);
m_ws.setIntensityImage(inputA);
m_ws.setStructuringElement(AbstractRegionGrowing.get4ConStructuringElement(inputA.numDimensions()));
// ws.setStructuringElement(AllConnectedComponents.getStructuringElement(lab
// .numDimensions()));
if (!m_ws.checkInput()) {
throw new IllegalArgumentException(m_ws.getErrorMessage());
}
m_ws.process();
return m_ws.getResult();
}
/**
* {@inheritDoc}
*/
@Override
public BinaryOperation<Img<T>, RandomAccessibleInterval<LabelingType<L>>, RandomAccessibleInterval<LabelingType<L>>>
copy() {
return new WatershedOperationWrapper1(m_ws);
}
}
private static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("dimension_selection", "X", "Y");
}
private static SettingsModelDouble createThresholdValueModel() {
return new SettingsModelDouble("threshold_value", 0);
}
private static SettingsModelBoolean createUseThresholdModel() {
return new SettingsModelBoolean("use_threshold", false);
}
private static SettingsModelBoolean createVirtualExtendModel() {
return new SettingsModelBoolean("virtual_extend", true);
}
private static SettingsModelBoolean createWithWatershedsModel() {
return new SettingsModelBoolean("with_watersheds", false);
}
/**
* {@inheritDoc}
*/
@SuppressWarnings("deprecation")
@Override
protected TwoValuesToCellNodeDialog<ImgPlusValue<T>, LabelingValue<L>> createNodeDialog() {
return new TwoValuesToCellNodeDialog<ImgPlusValue<T>, LabelingValue<L>>() {
@Override
public void addDialogComponents() {
final SettingsModelBoolean withWatersheds = createWithWatershedsModel();
addDialogComponent("Options", "", new DialogComponentBoolean(withWatersheds, "With Watersheds"));
final SettingsModelBoolean useThreshold = createUseThresholdModel();
addDialogComponent("Options", "", new DialogComponentBoolean(useThreshold, "Use Threshold"));
final SettingsModelDouble thresholdValue = createThresholdValueModel();
addDialogComponent("Options", "", new DialogComponentNumber(thresholdValue, "Threshold Value", 1));
useThreshold.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent arg0) {
thresholdValue.setEnabled(useThreshold.getBooleanValue());
}
});
withWatersheds.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent e) {
useThreshold.setEnabled(!withWatersheds.getBooleanValue());
thresholdValue.setEnabled(!withWatersheds.getBooleanValue());
}
});
addDialogComponent("Options", "",
new DialogComponentBoolean(createVirtualExtendModel(), "Virtually extend labeling"));
addDialogComponent("Options", "",
new DialogComponentDimSelection(createDimSelectionModel(), "Dimension selection"));
}
@Override
protected String getFirstColumnSelectionLabel() {
return "Column of Image";
}
@Override
protected String getSecondColumnSelectionLabel() {
return "Column of Labeling with Seeds";
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_sw";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public TwoValuesToCellNodeModel<ImgPlusValue<T>, LabelingValue<L>, LabelingCell<?>> createNodeModel() {
return new TwoValuesToCellNodeModel<ImgPlusValue<T>, LabelingValue<L>, LabelingCell<?>>() {
private final SettingsModelDimSelection m_dimSelection = createDimSelectionModel();
private LabelingCellFactory m_labCellFactory;
private final SettingsModelDouble m_thresholdValue = createThresholdValueModel();
private final SettingsModelBoolean m_useThreshold = createUseThresholdModel();
private final SettingsModelBoolean m_virtualExtend = createVirtualExtendModel();
private final SettingsModelBoolean m_withWatersheds = createWithWatershedsModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
m_thresholdValue.setEnabled(false);
settingsModels.add(m_useThreshold);
settingsModels.add(m_thresholdValue);
settingsModels.add(m_virtualExtend);
settingsModels.add(m_dimSelection);
settingsModels.add(m_withWatersheds);
}
@Override
protected LabelingCell<?> compute(final ImgPlusValue<T> imgValue, final LabelingValue<L> labelingValue)
throws Exception {
final RandomAccessibleInterval<LabelingType<L>> fromCellLabeling = labelingValue.getLabeling();
RandomAccessibleInterval<LabelingType<L>> zeroMinFromCellLabeling =
MinimaUtils.getZeroMinLabeling(fromCellLabeling);
final ImgPlus<T> fromCellImg = imgValue.getImgPlus();
final ImgPlus<T> zeroMinFromCellImg = MinimaUtils.getZeroMinImgPlus(fromCellImg);
final ImgLabeling<?, ?> out;
if (m_virtualExtend.getBooleanValue()) {
zeroMinFromCellLabeling = MiscViews
.synchronizeDimensionality(zeroMinFromCellLabeling, labelingValue.getLabelingMetadata(),
zeroMinFromCellImg, imgValue.getMetadata());
} else if (zeroMinFromCellLabeling.numDimensions() != zeroMinFromCellImg.numDimensions()) {
throw new IllegalArgumentException("The dimensionality of the seed labeling ("
+ zeroMinFromCellLabeling.numDimensions() + ") does not match that of the intensity image ("
+ zeroMinFromCellImg.numDimensions() + ")");
}
if (m_withWatersheds.getBooleanValue()) {
WatershedWithSheds<T, L> ws = new WatershedWithSheds<T, L>(
NeighborhoodUtils.get4ConStructuringElement(zeroMinFromCellImg.numDimensions()));
ImgLabeling<String, IntType> tmp = new ImgLabeling<String, IntType>(
new ArrayImgFactory<IntType>().create(zeroMinFromCellImg, new IntType()));
SubsetOperations.iterate(ws, m_dimSelection.getSelectedDimIndices(imgValue.getMetadata()),
zeroMinFromCellImg, zeroMinFromCellLabeling, tmp);
out = tmp;
} else {
final WatershedWithThreshold<T, L> ws = new WatershedWithThreshold<T, L>();
ImgLabeling<L, ?> tmp = new ImgLabeling<L, IntType>(
new ArrayImgFactory<IntType>().create(zeroMinFromCellImg, new IntType()));
if (m_useThreshold.getBooleanValue()) {
ws.setThreshold(m_thresholdValue.getDoubleValue());
}
final BinaryOperation<Img<T>, RandomAccessibleInterval<LabelingType<L>>, RandomAccessibleInterval<LabelingType<L>>> operation =
new WatershedOperationWrapper1(ws);
SubsetOperations.iterate(operation, m_dimSelection.getSelectedDimIndices(imgValue.getMetadata()),
zeroMinFromCellImg, zeroMinFromCellLabeling, tmp);
out = tmp;
}
return m_labCellFactory
.createCell(MinimaUtils.getTranslatedLabeling(fromCellLabeling, out),
new DefaultLabelingMetadata(imgValue.getMetadata(), imgValue.getMetadata(),
imgValue.getMetadata(),
labelingValue.getLabelingMetadata().getLabelingColorTable()));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_labCellFactory = new LabelingCellFactory(exec);
}
};
}
}