/*
* ------------------------------------------------------------------------
*
* 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.node;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeModel;
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.exceptions.KNIPException;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.ops.operation.UnaryOutputOperation;
import net.imglib2.type.numeric.RealType;
/**
* {@link NodeModel} to map from one {@link ImgPlus} to another {@link ImgPlus} rowwise
*
* @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 <T> type of the incoming {@link ImgPlus}
* @param <V> type of the outgoing {@link ImgPlus}
*/
public abstract class ImgPlusToImgPlusNodeModel<T extends RealType<T>, V extends RealType<V>>
extends ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<V>> {
/**
* Global KNIME Logger
*/
protected final static NodeLogger LOGGER = NodeLogger.getLogger(ImgPlusToImgPlusNodeModel.class);
/**
* Create the {@link SettingsModelDimSelection}
*
* @param axes default axes
* @return the {@link SettingsModelDimSelection}
*/
protected static SettingsModelDimSelection createDimSelectionModel(final String... axes) {
return new SettingsModelDimSelection("dim_selection", axes);
}
/**
* {@link SettingsModelDimSelection} to store dimension selection
*/
protected SettingsModelDimSelection m_dimSelection;
/**
* {@link ImgPlusCellFactory} used to create {@link ImgPlusCell}
*/
protected ImgPlusCellFactory m_imgCellFactory;
/**
* if true, parallelization is active
*/
private boolean m_active = true;
/**
* Constructor
*
* @param isEnabled
* @param axes
*/
protected ImgPlusToImgPlusNodeModel(final boolean isEnabled, final String... axes) {
m_dimSelection = createDimSelectionModel(axes);
m_dimSelection.setEnabled(isEnabled);
}
/**
* Constructor
*
* @param axes default axes
*/
protected ImgPlusToImgPlusNodeModel(final String... axes) {
this(true, axes);
}
/**
* Will be removed in KNIP 2.0.0
*
* @param model
*/
@Deprecated
protected ImgPlusToImgPlusNodeModel(final SettingsModelDimSelection model) {
this(model, true);
}
/**
* Will be removed in KNIP 2.0.0
*
* @param model
* @param isEnabled
*/
@Deprecated
protected ImgPlusToImgPlusNodeModel(final SettingsModelDimSelection model, final boolean isEnabled) {
m_dimSelection = model;
m_dimSelection.setEnabled(isEnabled);
}
@Override
protected void collectSettingsModels() {
super.collectSettingsModels();
m_settingsModels.add(m_dimSelection);
}
@Override
protected ImgPlusCell<V> compute(final ImgPlusValue<T> cellValue) throws Exception {
if (!m_dimSelection.isContainedIn(cellValue.getMetadata())) {
LOGGER.warn("image " + cellValue.getMetadata().getName() + " does not provide all selected dimensions.");
}
if (m_dimSelection.getNumSelectedDimLabels(cellValue.getMetadata()) < getMinDimensions()) {
throw new KNIPException("not enough selected dimensions provided by image.");
}
final ImgPlus<T> imgPlus = MinimaUtils.getZeroMinImgPlus(cellValue.getImgPlus());
final UnaryOutputOperation<ImgPlus<T>, ImgPlus<V>> op = op(imgPlus);
final int[] selection = m_dimSelection.getSelectedDimIndices(cellValue.getMetadata());
final long[] inMin = new long[imgPlus.numDimensions()];
cellValue.getImgPlus().min(inMin);
final ImgPlus<V> out = op.bufferFactory().instantiate(imgPlus);
return m_imgCellFactory.createCell(MinimaUtils.getTranslatedImgPlus(cellValue.getImgPlus(), SubsetOperations
.iterate(op, selection, imgPlus, out, m_active ? getExecutorService() : null)));
}
/**
* Create {@link UnaryOutputOperation} to map from one {@link ImgPlus} to another {@link ImgPlus}.
*
* @param imgPlus The incoming {@link ImgPlus}
* @return {@link UnaryOutputOperation} which will be used to map from {@link ImgPlus} to another {@link ImgPlus}
*/
protected abstract UnaryOutputOperation<ImgPlus<T>, ImgPlus<V>> op(ImgPlus<T> imgPlus);
/**
* Enable/Disable plane-wise or rather hypercube-wise parallelization. NB: Disable parallelization, if the
* {@link UnaryOutputOperation} provided by the implementation is able to parallelize
*
* @param active
*/
protected void enableParallelization(final boolean active) {
this.m_active = active;
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
/**
* @return number of dimensions which an {@link ImgPlus} must provide to run this node
*/
protected abstract int getMinDimensions();
}