/*
* ------------------------------------------------------------------------
*
* 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.lab2table;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.knime.core.data.DataCell;
import org.knime.core.data.DataColumnProperties;
import org.knime.core.data.DataColumnSpec;
import org.knime.core.data.DataColumnSpecCreator;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.RowIterator;
import org.knime.core.data.def.DefaultRow;
import org.knime.core.data.def.IntervalCell;
import org.knime.core.data.def.StringCell;
import org.knime.core.data.renderer.DataValueRenderer;
import org.knime.core.node.BufferedDataContainer;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.knip.base.KNIPConstants;
import org.knime.knip.base.data.img.ImgPlusCell;
import org.knime.knip.base.data.img.ImgPlusCellFactory;
import org.knime.knip.base.data.labeling.LabelingCell;
import org.knime.knip.base.data.labeling.LabelingValue;
import org.knime.knip.base.node.NodeUtils;
import org.knime.knip.core.KNIPGateway;
import org.knime.knip.core.data.DefaultNamed;
import org.knime.knip.core.data.DefaultSourced;
import org.knime.knip.core.data.img.DefaultImageMetadata;
import org.knime.knip.core.data.img.DefaultImgMetadata;
import org.knime.knip.core.data.img.LabelingMetadata;
import net.imagej.ImgPlus;
import net.imagej.ImgPlusMetadata;
import net.imglib2.Cursor;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.ImgView;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.roi.IterableRegion;
import net.imglib2.roi.Regions;
import net.imglib2.roi.labeling.LabelRegion;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.logic.BoolType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.view.Views;
/**
* Labeling is converted into a KNIME table. For each possible label the region of interest is extracted and put into a
* {@link IntervalCell} together with a {@link BitType} {@link Img}
*
* @param <T>
* @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>
*/
@Deprecated
public class Lab2TableNodeModel<L extends Comparable<L>, II extends IntegerType<II>> extends NodeModel {
private static final NodeLogger LOGGER = NodeLogger.getLogger(Lab2TableNodeModel.class);
public static final String CFG_LABELING_COLUMN = "labeling_column";
private final SettingsModelString m_labColumn = new SettingsModelString(CFG_LABELING_COLUMN, "");
private DataTableSpec m_outSpec;
/**
* One input one output.
*/
public Lab2TableNodeModel() {
super(1, 1);
}
@Override
protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
getLabColIdx(inSpecs[0]);
// create outspec according to the selected features
final ArrayList<DataColumnSpec> specs = new ArrayList<DataColumnSpec>();
specs.add(new DataColumnSpecCreator("Bitmask", ImgPlusCell.TYPE).createSpec());
specs.add(new DataColumnSpecCreator("Label", StringCell.TYPE).createSpec());
final DataColumnSpecCreator colspecCreator = new DataColumnSpecCreator("Source Labeling", LabelingCell.TYPE);
colspecCreator.setProperties(new DataColumnProperties(Collections
.singletonMap(DataValueRenderer.PROPERTY_PREFERRED_RENDERER, "String")));
specs.add(colspecCreator.createSpec());
m_outSpec = new DataTableSpec(specs.toArray(new DataColumnSpec[specs.size()]));
return new DataTableSpec[]{m_outSpec};
}
/*
* Helper to create a binary mask from a region of interest.
*/
private Img<BitType> createBinaryMask(final IterableRegion<BoolType> ir) {
final Img<BitType> mask = new ArrayImgFactory<BitType>().create(ir, new BitType());
final RandomAccess<BitType> maskRA = mask.randomAccess();
final Cursor<Void> cur = ir.localizingCursor();
while (cur.hasNext()) {
cur.fwd();
for (int d = 0; d < cur.numDimensions(); d++) {
maskRA.setPosition(cur.getLongPosition(d) - ir.min(d), d);
}
maskRA.get().set(true);
}
return mask;
}
@Override
protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
throws Exception {
final BufferedDataContainer con = exec.createDataContainer(m_outSpec);
final RowIterator it = inData[0].iterator();
DataRow row;
final int count = inData[0].getRowCount();
int i = 0;
final int labColIdx = getLabColIdx(inData[0].getDataTableSpec());
final ImgPlusCellFactory imgCellFactory = new ImgPlusCellFactory(exec);
while (it.hasNext()) {
row = it.next();
if (row.getCell(labColIdx).isMissing()) {
setWarningMessage("Some missing cells have been ignored!");
LOGGER.warn("Missing cell was ignored at row " + row.getKey());
continue;
}
final LabelingValue<L> labVal = (LabelingValue<L>)row.getCell(labColIdx);
final RandomAccessibleInterval<LabelingType<L>> lab = labVal.getLabeling();
for (final LabelRegion<L> label : KNIPGateway.regions().regions(lab)) {
final IterableRegion<BoolType> ir = Regions.iterable(label);
final List<DataCell> cells = new ArrayList<DataCell>();
// segment image
final long[] min = new long[ir.numDimensions()];
for (int j = 0; j < min.length; j++) {
min[j] = ir.min(j);
}
final LabelingMetadata lmdata = labVal.getLabelingMetadata();
final ImgPlusMetadata mdata =
new DefaultImgMetadata(lmdata, new DefaultNamed(label.toString()), new DefaultSourced(
lmdata.getName()), new DefaultImageMetadata());
cells.add(imgCellFactory.createCell(new ImgPlus(
ImgView.wrap(Views.translate(createBinaryMask(ir), min), new ArrayImgFactory<BitType>()), mdata)));
// Segment label
cells.add(new StringCell(label.toString()));
// source labeling
cells.add(row.getCell(labColIdx));
con.addRowToTable(new DefaultRow(row.getKey() + KNIPConstants.IMGID_LABEL_DELIMITER + label.toString(),
cells));
}
exec.checkCanceled();
exec.setProgress((double)++i / count);
}
con.close();
return new BufferedDataTable[]{con.getTable()};
}
private int getLabColIdx(final DataTableSpec inSpec) throws InvalidSettingsException {
int idx = inSpec.findColumnIndex(m_labColumn.getStringValue());
if (idx == -1) {
idx = NodeUtils.autoOptionalColumnSelection(inSpec, m_labColumn, LabelingValue.class);
setWarningMessage("Auto-configure Labeling Column: " + m_labColumn.getStringValue());
}
if (idx == -1) {
throw new InvalidSettingsException("No labeling column found.");
}
return idx;
}
@Override
protected void loadInternals(final File nodeInternDir, final ExecutionMonitor exec) throws IOException,
CanceledExecutionException {
//
}
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
m_labColumn.loadSettingsFrom(settings);
}
@Override
protected void reset() {
//
}
@Override
protected void saveInternals(final File nodeInternDir, final ExecutionMonitor exec) throws IOException,
CanceledExecutionException {
//
}
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
m_labColumn.saveSettingsTo(settings);
}
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
m_labColumn.validateSettings(settings);
}
}