/*
* ------------------------------------------------------------------------
*
* 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.spotdetection;
import java.util.List;
import net.imagej.ImgPlus;
import net.imglib2.ops.operation.Operations;
import net.imglib2.ops.operation.UnaryOutputOperation;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.knip.base.node.ImgPlusToImgPlusNodeModel;
import org.knime.knip.core.util.ImgPlusFactory;
/*
* Implementation status:
* Currently using B3SplineUDWT and WaveletConfigException from ICY both could be replaced by the imglib implementation
* but the array specific code runs faster than standard convolution. *
*/
/**
* Implementation of Extraction of spots in biological images using multiscale products (Pattern Recognition 35)<br>
* Jean-Christophe Olivo-Marin<br>
* <br>
* Allows the detection of bright spots over dark background using a multiscale wavelet partition of the image.
*
*
* @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>
*/
public class WaveletSpotDetectionNodeModel<T extends RealType<T>> extends ImgPlusToImgPlusNodeModel<T, BitType> {
private static final String MAD = "mad";
/* noise estimation statistics */
private static final String MEAN_MAD = "mean mad";
static SettingsModelString createAvgNodeModel() {
return new SettingsModelString("avgMethod", MEAN_MAD);
}
/**
* @return {@link SettingsModelDoubleArray} for a {@link DialogComponentScaleConfig} with three wavelet levels and
* enabled levels two and three.
*/
static SettingsModelDoubleArray createScaleModel() {
// TODO find good starting values (are these already good)
final double[] values =
DialogComponentScaleConfig.createModelArray(new boolean[]{false, true, true}, new double[]{1.0, 1.0,
1.0});
return new SettingsModelDoubleArray("scaleConfig", values);
}
static String[] getAvgOptions() {
return new String[]{MEAN_MAD, MAD};
}
private final SettingsModelString m_avgModel = createAvgNodeModel();
private final SettingsModelDoubleArray m_scaleModel = createScaleModel();
@SuppressWarnings("javadoc")
public WaveletSpotDetectionNodeModel(final String... axes) {
super(axes);
}
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_avgModel);
settingsModels.add(m_scaleModel);
}
@Override
protected UnaryOutputOperation<ImgPlus<T>, ImgPlus<BitType>> op(final ImgPlus<T> imgPlus) {
boolean useMeanMAD = true;
if (m_avgModel.getStringValue().equals(MAD)) {
useMeanMAD = false;
}
final boolean[] enabled = DialogComponentScaleConfig.getEnabledState(m_scaleModel);
final double[] factor = DialogComponentScaleConfig.getThresholdValues(m_scaleModel);
return Operations.wrap(new WaveletSpotDetection<T>(enabled, factor, useMeanMAD),
new ImgPlusFactory<T, BitType>(new BitType()));
}
/**
* {@inheritDoc}
*/
@Override
protected int getMinDimensions() {
return 2;
}
}