/*
* ------------------------------------------------------------------------
*
* 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.features.providers;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.knime.core.data.DataCell;
import org.knime.core.data.DataColumnSpec;
import org.knime.core.data.DataColumnSpecCreator;
import org.knime.core.data.DataType;
import org.knime.core.data.def.DoubleCell;
import org.knime.core.data.def.IntCell;
import org.knime.core.node.defaultnodesettings.DialogComponent;
import org.knime.core.node.defaultnodesettings.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.DialogComponentNumberEdit;
import org.knime.core.node.defaultnodesettings.DialogComponentString;
import org.knime.core.node.defaultnodesettings.DialogComponentStringListSelection;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModelIntegerBounded;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.core.node.defaultnodesettings.SettingsModelStringArray;
import org.knime.knip.core.features.FeatureFactory;
import org.knime.knip.core.features.seg.FirstOrderMomentsFeatureSet;
import net.imagej.space.CalibratedSpace;
import net.imglib2.Cursor;
import net.imglib2.IterableInterval;
import net.imglib2.type.numeric.RealType;
import net.imglib2.util.ValuePair;
/**
* TODO Auto-generated
*
* @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 FirstOrderMomentsFeatureSetProvider<T extends RealType<T>>
implements FeatureSetProvider<ValuePair<IterableInterval<T>, CalibratedSpace>> {
private SettingsModelBoolean m_appendHistogram;
private FeatureFactory m_featFac;
private FirstOrderMomentsFeatureSet<T> m_featSet;
private SettingsModelStringArray m_fosFeat;
private SettingsModelIntegerBounded m_histogramBins;
private SettingsModelString m_percentiles;
private final ArrayList<Double> m_percentileValues = new ArrayList<Double>();
/**
* {@inheritDoc}
*/
@Override
public void calcAndAddFeatures(final ValuePair<IterableInterval<T>, CalibratedSpace> roi,
final List<DataCell> cells) {
m_featFac.updateFeatureTarget(roi.a);
m_featFac.updateFeatureTarget(roi.b);
// Features
for (int featID = 0; featID < m_featFac.getNumFeatures(); featID++) {
final double val = m_featFac.getFeatureValue(featID);
if (Double.isNaN(val)) {
cells.add(DataType.getMissingCell());
} else {
cells.add(new DoubleCell(val));
}
}
if (m_appendHistogram.getBooleanValue()) {
final Cursor<T> c = roi.a.cursor();
final double min = c.get().createVariable().getMinValue();
final double max = c.get().createVariable().getMaxValue();
final int[] hist = new int[m_histogramBins.getIntValue()];
final double scale = (hist.length - 1) / (max - min);
while (c.hasNext()) {
c.fwd();
hist[(int)((c.get().getRealDouble() - min) * scale)]++;
}
for (int j = 0; j < m_histogramBins.getIntValue(); j++) {
cells.add(new IntCell(hist[j]));
}
}
for (int i = 0; i < m_percentileValues.size(); i++) {
cells.add(new DoubleCell(m_featSet.getPercentile(roi.a, m_percentileValues.get(i))));
}
}
private SettingsModelBoolean createAppendHistModel() {
return new SettingsModelBoolean("append_histogram", false);
}
private SettingsModelStringArray createFosFeatModel() {
return new SettingsModelStringArray("fos_feature_selection", FirstOrderMomentsFeatureSet.FEATURES);
}
private SettingsModelIntegerBounded createHistBinsModel() {
return new SettingsModelIntegerBounded("histogram_bins", 64, 1, Integer.MAX_VALUE);
}
private SettingsModelString createPercentilesModel() {
return new SettingsModelString("percentiles", "");
}
@Override
public String getFeatureSetName() {
return "First order statistics";
}
@Override
public String getFeatureSetId() {
return "First order statistics";
}
/**
* {@inheritDoc}
*/
@Override
public void initAndAddColumnSpecs(final List<DataColumnSpec> specs) {
m_featSet = new FirstOrderMomentsFeatureSet<T>();
m_featFac = new FeatureFactory(false, m_featSet);
// select the appropriate features
final String[] selectedFeatures = m_fosFeat.getStringArrayValue();
final String[] allFeat = FirstOrderMomentsFeatureSet.FEATURES;
final BitSet selection = new BitSet(allFeat.length);
int j = 0;
for (int i = 0; i < allFeat.length; i++) {
if ((j < selectedFeatures.length) && selectedFeatures[j].equals(allFeat[i])) {
selection.set(i);
j++;
}
}
m_featFac.initFeatureFactory(selection);
// create outspec according to the selected features
final String[] featNames = m_featFac.getFeatureNames();
for (int i = 0; i < featNames.length; i++) {
specs.add(new DataColumnSpecCreator(featNames[i], DoubleCell.TYPE).createSpec());
}
if (m_appendHistogram.getBooleanValue()) {
for (int i = 0; i < m_histogramBins.getIntValue(); i++) {
specs.add(new DataColumnSpecCreator("h_" + i, IntCell.TYPE).createSpec());
}
}
final String[] percentiles = m_percentiles.getStringValue().split(",");
m_percentileValues.clear();
for (int i = 0; i < percentiles.length; i++) {
if (percentiles[i].trim().length() == 0) {
continue;
}
try {
final double p = Double.parseDouble(percentiles[i]);
m_percentileValues.add(p);
specs.add(new DataColumnSpecCreator(percentiles[i] + "th Percentile_", DoubleCell.TYPE).createSpec());
} catch (final NumberFormatException e) {
throw new NumberFormatException("Wrong format of the percentile specification!");
}
}
}
@Override
public void initAndAddDialogComponents(final List<DialogComponent> dialogComponents) {
final SettingsModelBoolean appendHistogram = createAppendHistModel();
final SettingsModelIntegerBounded numBins = createHistBinsModel();
numBins.setEnabled(false);
appendHistogram.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent e) {
numBins.setEnabled(appendHistogram.getBooleanValue());
}
});
// necessary to avoid the enabling of this component from outside
numBins.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent e) {
numBins.setEnabled(appendHistogram.getBooleanValue());
}
});
dialogComponents.add(new DialogComponentStringListSelection(createFosFeatModel(), "Features",
Arrays.asList(FirstOrderMomentsFeatureSet.FEATURES), false, 5));
dialogComponents.add(new DialogComponentBoolean(appendHistogram, "Append Histogram"));
dialogComponents.add(new DialogComponentNumberEdit(numBins, "Histogram bins"));
dialogComponents.add(new DialogComponentString(createPercentilesModel(),
"The pth percentile (comma-separated list of p's)"));
}
@Override
public void initAndAddSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_appendHistogram = createAppendHistModel());
settingsModels.add(m_fosFeat = createFosFeatModel());
settingsModels.add(m_histogramBins = createHistBinsModel());
settingsModels.add(m_percentiles = createPercentilesModel());
}
/**
* {@inheritDoc}
*/
@Override
public void cleanUp() {
if (m_featFac != null) {
m_featFac.cleanUp();
}
}
}