/*
* ------------------------------------------------------------------------
*
* Copyright (C) 2003 - 2016
* 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.
* ---------------------------------------------------------------------
*
* Created on Feb 28, 2016 by hornm
*/
package org.knime.knip.base.nodes.proc.binner;
import java.util.List;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.port.PortObjectSpec;
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.ValueToCellNodeModel;
import org.knime.knip.core.KNIPGateway;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.Cursor;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
/**
*
* @author <a href="mailto:horn_martin@gmx.de">Martin Horn</a>
*/
public class IntensityBinnerNodeModel<T1 extends RealType<T1>, T2 extends RealType<T2> & NativeType<T2>>
extends ValueToCellNodeModel<ImgPlusValue<T1>, ImgPlusCell<T2>> {
static final String KEY_BIN_SETTINGS = "bin_settings";
private IntensityBins m_bins = new IntensityBins(0);
private ImgPlusCellFactory m_imgCellFactory;
private T2 m_resType;
/**
* {@inheritDoc}
*/
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
//no settings models to be added since dialog components are not used to compose the dialog
}
/**
* {@inheritDoc}
*/
@Override
protected PortObjectSpec[] configure(final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
if (m_bins.getNumBins() == 0) {
throw new InvalidSettingsException("No pixel bins have been specified.");
} else {
return super.configure(inSpecs);
}
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
m_resType = m_bins.getPixelType();
}
/**
* {@inheritDoc}
*/
@Override
protected ImgPlusCell<T2> compute(final ImgPlusValue<T1> cellValue) throws Exception {
final ImgPlus<T1> fromCell = cellValue.getImgPlus();
final ImgPlus<T1> zeroMinFromCell = MinimaUtils.getZeroMinImgPlus(fromCell);
Img<T2> res = KNIPGateway.ops().create().img(zeroMinFromCell, m_resType);
Cursor<T2> resCur = res.cursor();
for (T1 type : zeroMinFromCell) {
resCur.fwd();
m_bins.covers(type, resCur.get());
}
return m_imgCellFactory
.createCell(MinimaUtils.getTranslatedImgPlus(fromCell, new ImgPlus<T2>(res, zeroMinFromCell)));
}
/**
* {@inheritDoc}
*/
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
super.loadValidatedSettingsFrom(settings);
m_bins = new IntensityBins(settings.getNodeSettings(KEY_BIN_SETTINGS));
}
/**
* {@inheritDoc}
*/
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
super.saveSettingsTo(settings);
m_bins.saveToSettings(settings.addNodeSettings(KEY_BIN_SETTINGS));
}
/**
* {@inheritDoc}
*/
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
super.validateSettings(settings);
new IntensityBins(settings.getNodeSettings(KEY_BIN_SETTINGS));
}
}