/*
* ------------------------------------------------------------------------
*
* 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.io.IOException;
import java.util.List;
import java.util.concurrent.ExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.defaultnodesettings.DialogComponentNumber;
import org.knime.core.node.defaultnodesettings.DialogComponentStringSelection;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelInteger;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
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.node.ValueToCellNodeDialog;
import org.knime.knip.base.node.ValueToCellNodeFactory;
import org.knime.knip.base.node.ValueToCellNodeModel;
import org.knime.knip.base.node.dialog.DialogComponentDimSelection;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.KNIPGateway;
import org.knime.knip.core.awt.labelingcolortable.DefaultLabelingColorTable;
import org.knime.knip.core.data.img.DefaultLabelingMetadata;
import org.knime.knip.core.types.ImgFactoryTypes;
import org.knime.knip.core.util.EnumUtils;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.ops.operation.randomaccessibleinterval.unary.regiongrowing.AbstractRegionGrowing;
import net.imglib2.ops.operation.randomaccessibleinterval.unary.regiongrowing.CCA;
import net.imglib2.ops.types.ConnectedType;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.IntType;
/**
* Factory class to produce a Connected Component Analysis Node.
*
* @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 ConnectedCompAnalysisNodeFactory<T extends RealType<T> & Comparable<T> & NativeType<T>>
extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private static NodeLogger LOGGER = NodeLogger.getLogger(ConnectedCompAnalysisNodeFactory.class);
private static SettingsModelInteger createBackgroundModel() {
return new SettingsModelInteger("background", 0);
}
private static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("dimensions", "X", "Y");
}
private static SettingsModelString createFactoryModel() {
return new SettingsModelString("factoryselection", ImgFactoryTypes.SOURCE_FACTORY.toString());
}
private static SettingsModelString createTypeModel() {
return new SettingsModelString("connection_type", ConnectedType.values()[0].toString());
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
addDialogComponent("Settings", "Factory Selection",
new DialogComponentStringSelection(createFactoryModel(), "Factory Type",
EnumUtils.getStringListFromName(ImgFactoryTypes.values())));
addDialogComponent("Options", "Settings", new DialogComponentStringSelection(createTypeModel(),
"Connection Type", EnumUtils.getStringListFromName(ConnectedType.values())));
addDialogComponent("Options", "Settings",
new DialogComponentNumber(createBackgroundModel(), "Background", 1));
addDialogComponent("Options", "Dimensions",
new DialogComponentDimSelection(createDimSelectionModel(), "Dimensions", 0, 5));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_cca";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, LabelingCell<Integer>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, LabelingCell<Integer>>() {
private final SettingsModelInteger m_background = createBackgroundModel();
private final SettingsModelDimSelection m_dimSelection = createDimSelectionModel();
private final SettingsModelString m_factory = createFactoryModel();
private LabelingCellFactory m_labCellFactory;
private final SettingsModelString m_type = createTypeModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_factory);
settingsModels.add(m_background);
settingsModels.add(m_dimSelection);
settingsModels.add(m_type);
}
/**
* {@inheritDoc}
*/
@SuppressWarnings({"unchecked"})
@Override
protected LabelingCell<Integer> compute(final ImgPlusValue<T> cellValue) throws IOException {
final ImgPlus<T> fromCell = cellValue.getImgPlus();
final ImgPlus<T> zeroMinFromCell = MinimaUtils.getZeroMinImgPlus(fromCell);
final T background = zeroMinFromCell.firstElement().createVariable();
background.setReal(m_background.getIntValue());
if (((int)background.getRealDouble()) != m_background.getIntValue()) {
background.setReal(Math.min(background.getMaxValue(),
Math.max(background.getMinValue(), m_background.getIntValue())));
setWarningMessage("Background value has been adopted to the range of the input image (e.g. "
+ m_background.getIntValue() + "->" + background.getRealDouble() + ")");
}
long[][] structuringElement;
if (m_type.getStringValue().equals(ConnectedType.EIGHT_CONNECTED.name())) {
structuringElement = AbstractRegionGrowing
.get8ConStructuringElement(m_dimSelection.getSelectedDimIndices(zeroMinFromCell).length);
} else {
structuringElement = AbstractRegionGrowing
.get4ConStructuringElement(m_dimSelection.getSelectedDimIndices(zeroMinFromCell).length);
}
final CCA<T> cca = new CCA<T>(structuringElement, background);
final RandomAccessibleInterval<LabelingType<Integer>> lab = new ImgLabeling<Integer, IntType>(
KNIPGateway.ops().create().img(zeroMinFromCell.getImg(), new IntType(), ImgFactoryTypes
.getImgFactory(m_factory.getStringValue(), zeroMinFromCell.getImg())));
try {
SubsetOperations.iterate(cca, m_dimSelection.getSelectedDimIndices(zeroMinFromCell),
zeroMinFromCell.getImg(), lab, getExecutorService());
} catch (InterruptedException e) {
LOGGER.warn("Thread execution interrupted", e);
} catch (ExecutionException e) {
LOGGER.warn("Couldn't retrieve results because thread execution was interrupted/aborted", e);
}
return m_labCellFactory.createCell(MinimaUtils.getTranslatedLabeling(fromCell, lab),
new DefaultLabelingMetadata(zeroMinFromCell, zeroMinFromCell,
zeroMinFromCell, new DefaultLabelingColorTable()));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_labCellFactory = new LabelingCellFactory(exec);
}
};
}
}