/*
* ------------------------------------------------------------------------
*
* 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.proc;
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.DialogComponentNumber;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModelDouble;
import org.knime.knip.base.data.img.ImgPlusCell;
import org.knime.knip.base.data.img.ImgPlusCellFactory;
import org.knime.knip.base.data.img.ImgPlusValue;
import org.knime.knip.base.node.ValueToCellNodeDialog;
import org.knime.knip.base.node.ValueToCellNodeFactory;
import org.knime.knip.base.node.ValueToCellNodeModel;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccess;
import net.imglib2.algorithm.math.PickImagePeaks;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
/**
* TODO: Add Dimension Selection?
*
* @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 ImgPeaksNodeFactory<T extends RealType<T>> extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private SettingsModelBoolean createDoSuppressionModel() {
return new SettingsModelBoolean("do_suppresion", false);
}
private SettingsModelDouble createSuppressionModel() {
return new SettingsModelDouble("suppression", 0);
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
addDialogComponent(new DialogComponentBoolean(createDoSuppressionModel(), "Do suppression?"));
addDialogComponent(new DialogComponentNumber(createSuppressionModel(),
"Peak suppression region radius", .1));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_peaks";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<BitType>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<BitType>>() {
private final SettingsModelBoolean m_doSuppression = createDoSuppressionModel();
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelDouble m_suppression = createSuppressionModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_suppression);
settingsModels.add(m_doSuppression);
}
@Override
protected ImgPlusCell<BitType> compute(final ImgPlusValue<T> cellValue) throws Exception {
final ImgPlus<T> imgPlus = cellValue.getImgPlus();
final PickImagePeaks<T> peakPicker = new PickImagePeaks<T>(imgPlus);
peakPicker.process();
final Img<BitType> res = peakPicker.getResult();
if (m_doSuppression.getBooleanValue()) {
peakPicker.setSuppression(m_suppression.getDoubleValue());
final ArrayList<long[]> peaks = peakPicker.getPeakList();
for (final BitType t : res) {
t.set(false);
}
final RandomAccess<BitType> access = res.randomAccess();
for (final long[] l : peaks) {
access.setPosition(l);
access.get().set(true);
}
}
return m_imgCellFactory.createCell(new ImgPlus<>(res, imgPlus));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}