/*
* ------------------------------------------------------------------------
*
* 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.Set;
import java.util.stream.Collectors;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTableSpec;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.defaultnodesettings.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.DialogComponentColumnNameSelection;
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.SettingsModelInteger;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.core.node.port.PortObject;
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.exceptions.KNIPRuntimeException;
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.awt.labelingcolortable.DefaultLabelingColorTable;
import org.knime.knip.core.data.img.DefaultLabelingMetadata;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.Cursor;
import net.imglib2.IterableInterval;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelingMapping;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.view.Views;
/**
* NodeFactory for the Lab2Table 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 ImgToLabelingNodeFactory<T extends IntegerType<T> & NativeType<T>, L>
extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private static SettingsModelInteger createBackgroundValueModel() {
return new SettingsModelInteger("background value", 0);
}
private static SettingsModelString createLabelingMapColModel() {
return new SettingsModelString("labeling_mapping", "");
}
private static SettingsModelBoolean createSetBackgroundModel() {
return new SettingsModelBoolean("has_background", true);
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
/**
* {@inheritDoc}
*/
@SuppressWarnings("unchecked")
@Override
public void addDialogComponents() {
final SettingsModelString labCol = createLabelingMapColModel();
addDialogComponent("Labeling Settings", "", new DialogComponentColumnNameSelection(labCol,
"Labels from ...", 0, false, true, LabelingValue.class));
final SettingsModelBoolean setBackground = createSetBackgroundModel();
final SettingsModelInteger backgroundValue = createBackgroundValueModel();
setBackground.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent arg0) {
backgroundValue.setEnabled(setBackground.getBooleanValue());
}
});
addDialogComponent("Options", "Background",
new DialogComponentBoolean(setBackground, "Use background value as background?"));
addDialogComponent("Options", "Background",
new DialogComponentNumber(backgroundValue, "Background value", 1));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_itl";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, LabelingCell<L>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, LabelingCell<L>>() {
private final NodeLogger LOGGER = NodeLogger.getLogger(this.getClass());
private final SettingsModelInteger m_background = createBackgroundValueModel();
private LabelingCellFactory m_labCellFactory;
private int m_labelingMappingColIdx = -1;
private LabelingMapping<L> m_currentLabelingMapping;
private final SettingsModelString m_labelingMappingColumn = createLabelingMapColModel();
private final SettingsModelBoolean m_setBackground = createSetBackgroundModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_labelingMappingColumn);
settingsModels.add(m_background);
settingsModels.add(m_setBackground);
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_labCellFactory = new LabelingCellFactory(exec);
}
/**
* {@inheritDoc}
*
* @throws IOException
*/
@Override
protected LabelingCell<L> compute(final ImgPlusValue<T> cellValue) throws IOException {
final ImgPlus<T> fromCell = cellValue.getImgPlus();
if (!(fromCell.firstElement() instanceof IntegerType)) {
throw new KNIPRuntimeException(
"Only Images of type IntegerType can be converted into a Labeling. Use the converter to convert your Image e.g. to ShortType, IntType, ByteType or BitType.");
}
final ImgPlus<T> zeroMinFromCell = MinimaUtils.getZeroMinImgPlus(fromCell);
ImgLabeling<L, ?> res;
T type = zeroMinFromCell.firstElement().createVariable();
int maxNumLabelSets = (int) (type.getMaxValue() - type.getMinValue());
if (!m_setBackground.getBooleanValue()) {
//if the background is not set to a certain value, we need to reserve an extra label for the additional background
maxNumLabelSets++;
}
if (m_currentLabelingMapping == null) {
final ImgLabeling<Integer, ?> tmp = KNIPGateway.ops().create()
.imgLabeling(zeroMinFromCell, null, fromCell.factory(), maxNumLabelSets);
final boolean setBGValue = m_setBackground.getBooleanValue();
final Cursor<T> cursor = zeroMinFromCell.cursor();
final Cursor<LabelingType<Integer>> labType = tmp.cursor();
while (cursor.hasNext()) {
int val = cursor.next().getInteger();
if (!setBGValue || val != m_background.getIntValue()) {
labType.next().add(val);
} else {
labType.fwd();
}
}
res = (ImgLabeling<L, ?>)tmp;
} else {
final ImgLabeling<String, ?> tmp = KNIPGateway.ops().create()
.imgLabeling(zeroMinFromCell, null, fromCell.factory(), maxNumLabelSets);
final boolean setBGValue = m_setBackground.getBooleanValue();
final Cursor<T> cursor = zeroMinFromCell.cursor();
final Cursor<LabelingType<String>> labType = tmp.cursor();
while (cursor.hasNext()) {
int index = cursor.next().getInteger();
if (setBGValue && index == m_background.getIntValue()) {
//do nothing
labType.fwd();
} else if (index >= 0 && index < m_currentLabelingMapping.numSets()) {
Set<String> labels = m_currentLabelingMapping.labelsAtIndex(index).stream()
.map(o -> o.toString()).collect(Collectors.toSet());
if (!setBGValue || index != m_background.getIntValue()) {
labType.next().addAll(labels);
} else {
labType.fwd();
}
} else {
//no labels found in the labeling mapping for the given index
//add the index (as string) as label
labType.next().add(String.valueOf(index));
}
}
res = (ImgLabeling<L, ?>)tmp;
}
return m_labCellFactory.createCell(MinimaUtils.getTranslatedLabeling(fromCell, res),
new DefaultLabelingMetadata(cellValue.getMetadata(),
cellValue.getMetadata(), cellValue.getMetadata(),
new DefaultLabelingColorTable()));
}
/**
* {@inheritDoc}
*/
@Override
protected void computeDataRow(final DataRow row) {
if (m_labelingMappingColIdx != -1) {
if (row.getCell(m_labelingMappingColIdx).isMissing()) {
LOGGER.warn("Labeling is missing. No labeling mapping can be used.");
m_currentLabelingMapping = null;
return;
}
IterableInterval<LabelingType<L>> labeling =
Views.iterable(((LabelingValue<L>)row.getCell(m_labelingMappingColIdx)).getLabeling());
if (!(labeling.firstElement().getMapping().getLabels().iterator().next() instanceof String)) {
LOGGER.warn("Labeling for the Labeling Mapping not compatible with String. Labeling Mapping ignored for row "
+ row.getKey());
m_currentLabelingMapping = null;
} else {
m_currentLabelingMapping = labeling.firstElement().getMapping();
}
} else {
m_currentLabelingMapping = null;
}
}
/**
* {@inheritDoc}
*/
@Override
protected PortObject[] execute(final PortObject[] inObjects, final ExecutionContext exec) throws Exception {
BufferedDataTable inTable = (BufferedDataTable)inObjects[0];
m_labelingMappingColIdx = getLabelingMappingColIdx(inTable.getDataTableSpec());
if (m_labelingMappingColIdx == -1) {
m_currentLabelingMapping = null;
}
return super.execute(inObjects, exec);
}
private int getLabelingMappingColIdx(final DataTableSpec inSpec) {
return inSpec.findColumnIndex(m_labelingMappingColumn.getStringValue());
}
};
}
}