/*
* ------------------------------------------------------------------------
*
* 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.ArrayList;
import java.util.List;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.defaultnodesettings.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
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.KNIPException;
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.DialogComponentSubsetSelection;
import org.knime.knip.base.node.dialog.DialogComponentSubsetSelection2;
import org.knime.knip.base.node.nodesettings.SettingsModelSubsetSelection2;
import org.knime.knip.core.data.DefaultNamed;
import org.knime.knip.core.data.DefaultSourced;
import org.knime.knip.core.data.img.DefaultLabelingMetadata;
import net.imagej.axis.CalibratedAxis;
import net.imagej.space.DefaultCalibratedSpace;
import net.imglib2.Interval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.ops.operation.Operations;
import net.imglib2.ops.operation.labeling.unary.MergeLabelings;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelingType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.util.Intervals;
import net.imglib2.util.Util;
import net.imglib2.view.Views;
/**
* Factory class to produce the Histogram Operations Node. Uses {@link DialogComponentSubsetSelection2} instead of
* {@link DialogComponentSubsetSelection};
*
* @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>
*/
public class LabelingOrthoCropperNodeFactory2<L extends Comparable<L>>
extends ValueToCellNodeFactory<LabelingValue<L>> {
private static SettingsModelBoolean createAdjustDimModel() {
return new SettingsModelBoolean("cfg_adjust_dimensionality", false);
}
private static SettingsModelSubsetSelection2 createSubsetSelectionModel() {
return new SettingsModelSubsetSelection2("subset_selection");
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<LabelingValue<L>> createNodeDialog() {
return new ValueToCellNodeDialog<LabelingValue<L>>() {
@Override
public void addDialogComponents() {
addDialogComponent("Options", "Subset Selection",
new DialogComponentSubsetSelection2(createSubsetSelectionModel(), true, true));
addDialogComponent("Options", "Options",
new DialogComponentBoolean(createAdjustDimModel(), "Adjust Dimensionality?"));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_cropped";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<LabelingValue<L>, LabelingCell<L>> createNodeModel() {
return new ValueToCellNodeModel<LabelingValue<L>, LabelingCell<L>>() {
private LabelingCellFactory m_labCellFactory;
private final SettingsModelBoolean m_smAdjustDimensionality = createAdjustDimModel();
private final SettingsModelSubsetSelection2 m_subsetSel = createSubsetSelectionModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_subsetSel);
settingsModels.add(m_smAdjustDimensionality);
}
@Override
protected LabelingCell<L> compute(final LabelingValue<L> cellValue) throws Exception {
RandomAccessibleInterval<LabelingType<L>> res;
if (m_subsetSel.isCompletelySelected()) {
return m_labCellFactory.createCell(cellValue.getLabeling(), cellValue.getLabelingMetadata());
} else {
final RandomAccessibleInterval<LabelingType<L>> lab = cellValue.getLabeling();
final long[] dimensions = new long[lab.numDimensions()];
lab.dimensions(dimensions);
final Interval[] intervals =
m_subsetSel.createSelectedIntervals(Intervals.minAsLongArray(lab), dimensions,
cellValue.getLabelingMetadata());
@SuppressWarnings("unchecked")
final RandomAccessibleInterval<LabelingType<L>>[] subLab =
new RandomAccessibleInterval[intervals.length];
for (int i = 0; i < subLab.length; i++) {
subLab[i] = Views.offsetInterval(lab, intervals[i]);
}
// TODO: Assumption here is that
// Labeling =
// ImgLabeling
@SuppressWarnings("unchecked")
final MergeLabelings<L> mergeOp = new MergeLabelings<L>(
Util.getTypeFromInterval(((ImgLabeling<L, ? extends IntegerType<?>>)lab).getIndexImg()),
m_smAdjustDimensionality.getBooleanValue());
long totalSize = 0;
for (int i = 0; i < subLab.length; i++) {
totalSize += Views.iterable(subLab[i]).size();
}
if (subLab.length == totalSize) {
throw new KNIPException(
"There is no dimension left to create a new image in Labeling Cropper!");
}
res = Operations.compute(mergeOp, subLab);
final List<CalibratedAxis> validAxes = new ArrayList<CalibratedAxis>();
for (int d = 0; d < lab.numDimensions(); d++) {
if (!mergeOp.getInvalidDims().contains(d)) {
validAxes.add(cellValue.getLabelingMetadata().axis(d).copy());
}
}
return m_labCellFactory.createCell(res, new DefaultLabelingMetadata(
new DefaultCalibratedSpace(validAxes.toArray(new CalibratedAxis[validAxes.size()])),
new DefaultNamed(cellValue.getLabelingMetadata().getName()),
new DefaultSourced(cellValue.getLabelingMetadata().getSource()),
cellValue.getLabelingMetadata().getLabelingColorTable()));
}
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_labCellFactory = new LabelingCellFactory(exec);
}
};
}
}