/*
* ------------------------------------------------------------------------
*
* 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 org.knime.core.node.ExecutionContext;
import org.knime.core.node.NodeFactory;
import org.knime.core.node.defaultnodesettings.DialogComponentStringSelection;
import org.knime.core.node.defaultnodesettings.SettingsModel;
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.labeling.LabelingValue;
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.core.KNIPGateway;
import org.knime.knip.core.types.NativeTypes;
import org.knime.knip.core.util.EnumUtils;
import net.imagej.ImgPlus;
import net.imglib2.Cursor;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.exception.IncompatibleTypeException;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
/**
* {@link NodeFactory} to convert {@link ImgLabeling} to an {@link ImgPlus} of arbitrary {@link RealType}
*
* @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>
*
* @param <L>
* @param <V>
*/
public class LabelingToImgNodeFactory<L extends Comparable<L>, V extends IntegerType<V> & NativeType<V>>
extends ValueToCellNodeFactory<LabelingValue<L>> {
private static SettingsModelString createOutputImgModel() {
return new SettingsModelString("output", NativeTypes.BITTYPE.toString());
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<LabelingValue<L>> createNodeDialog() {
return new ValueToCellNodeDialog<LabelingValue<L>>() {
/**
* {@inheritDoc}
*/
@SuppressWarnings("deprecation")
@Override
public void addDialogComponents() {
addDialogComponent("Options", "", new DialogComponentStringSelection(createOutputImgModel(),
"Img Output Type Selection", EnumUtils.getStringListFromName(NativeTypes.values())));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_lti";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<LabelingValue<L>, ImgPlusCell<V>> createNodeModel() {
return new ValueToCellNodeModel<LabelingValue<L>, ImgPlusCell<V>>() {
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelString m_outputImg = createOutputImgModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_outputImg);
}
/**
* {@inheritDoc}
*
* @throws IncompatibleTypeException
*/
@SuppressWarnings({"rawtypes", "unchecked"})
@Override
protected ImgPlusCell<V> compute(final LabelingValue<L> cellValue)
throws IncompatibleTypeException, IOException {
final RandomAccessibleInterval<LabelingType<L>> lab = cellValue.getLabeling();
final RealType outType =
(RealType)NativeTypes.getTypeInstance(NativeTypes.valueOf(m_outputImg.getStringValue()));
final ImgPlus<RealType> out = new ImgPlus(KNIPGateway.ops().create().img(lab, (NativeType)outType));
final Cursor<LabelingType<L>> inC = Views.iterable(lab).cursor();
final Cursor<RealType> outC = out.cursor();
double outMax = outType.getMaxValue();
while (outC.hasNext()) {
int val = inC.next().getIndex().getInteger();
if (val > outMax) {
outC.next().setReal(outMax);
} else {
outC.next().setReal(val);
}
}
for (int a = 0; a < cellValue.getDimensions().length; a++) {
out.setAxis(cellValue.getLabelingMetadata().axis(a).copy(), a);
}
out.setSource(cellValue.getLabelingMetadata().getSource());
out.setName(cellValue.getLabelingMetadata().getName());
ImgPlusCell cell = m_imgCellFactory.createCell(out);
return cell;
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}