/*
* ------------------------------------------------------------------------
*
* 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.Arrays;
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.DataType;
import org.knime.core.data.DataValue;
import org.knime.core.data.collection.CollectionCellFactory;
import org.knime.core.data.collection.ListCell;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.defaultnodesettings.DialogComponentNumber;
import org.knime.core.node.defaultnodesettings.DialogComponentStringListSelection;
import org.knime.core.node.defaultnodesettings.SettingsModelDouble;
import org.knime.core.node.defaultnodesettings.SettingsModelStringArray;
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.exceptions.KNIPRuntimeException;
import org.knime.knip.base.node.ValueToCellNodeDialog;
import org.knime.knip.base.node.ValueToCellNodeFactory;
import org.knime.knip.base.node.ValueToCellNodeModel;
import org.knime.knip.base.node.dialog.DialogComponentDimSelection;
import org.knime.knip.base.node.dialog.Descriptions;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.KNIPGateway;
import org.knime.knip.core.algorithm.types.ThresholdingType;
import org.knime.knip.core.ops.interval.AutoThreshold;
import org.knime.knip.core.util.EnumUtils;
import org.knime.node.v210.KnimeNodeDocument.KnimeNode;
import net.imagej.ImgPlus;
import net.imglib2.ops.img.UnaryRelationAssigment;
import net.imglib2.ops.operation.ImgOperations;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.ops.operation.UnaryOutputOperation;
import net.imglib2.ops.relation.real.unary.RealGreaterThanConstant;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
/**
* Deprecated. Use ROI based ThresholderNodeFactory3 (ImgThresholder)
*
* @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>
*/
@SuppressWarnings("rawtypes")
@Deprecated
public class ThresholderNodeFactory2<T extends RealType<T>> extends ValueToCellNodeFactory {
private static final NodeLogger LOGGER = NodeLogger.getLogger(ThresholderNodeFactory2.class);
private static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("thresholder_dimselection", "X", "Y");
}
private static SettingsModelDouble createManualThresholdModel() {
return new SettingsModelDouble("manual_threshold", 0);
}
private static SettingsModelStringArray createThresholderSelectionModel() {
return new SettingsModelStringArray("thresholder", new String[]{ThresholdingType.MANUAL.name()});
}
/**
* {@inheritDoc}
*/
@Override
protected void addNodeDescriptionContent(final KnimeNode node) {
Descriptions
.createNodeDescriptionDimSelection(node.getFullDescription().getTabList().get(0).addNewOption());
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
final SettingsModelDouble settModManual = createManualThresholdModel();
addDialogComponent("Options", "Manual Threshold",
new DialogComponentNumber(settModManual, "Threshold Value", .01));
final SettingsModelStringArray method = createThresholderSelectionModel();
addDialogComponent("Options", "Thresholding Method", new DialogComponentStringListSelection(method,
"Method", EnumUtils.getStringListFromName(ThresholdingType.values())));
addDialogComponent("Options", "Dimension Selection",
new DialogComponentDimSelection(createDimSelectionModel(), "", 2, 5));
method.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent arg0) {
final String[] selectedMethods = method.getStringArrayValue();
for (final String s : selectedMethods) {
if (ThresholdingType.valueOf(s) == ThresholdingType.MANUAL) {
settModManual.setEnabled(true);
return;
}
}
settModManual.setEnabled(false);
}
});
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_thresholded";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel createNodeModel() {
return new ValueToCellNodeModel() {
/*
* The dimension selection
*/
private final SettingsModelDimSelection m_dimSelection = createDimSelectionModel();
/*
* ImgPlusCellFactory
*/
private ImgPlusCellFactory m_imgCellFactory;
/*
* The value of the manual threshold
*/
private final SettingsModelDouble m_manualThreshold = createManualThresholdModel();
/*
* The selected thresholder
*/
private final SettingsModelStringArray m_thresholderSettings = createThresholderSelectionModel();
/**
* {@inheritDoc}
*/
@SuppressWarnings("unchecked")
@Override
protected void addSettingsModels(final List settingsModels) {
m_manualThreshold.setEnabled(true);
settingsModels.add(m_dimSelection);
settingsModels.add(m_manualThreshold);
settingsModels.add(m_thresholderSettings);
}
@Override
protected DataCell compute(final DataValue cellValue) throws Exception {
@SuppressWarnings("unchecked")
final ImgPlusValue<T> imgPlusValue = (ImgPlusValue<T>)cellValue;
final ImgPlus<T> imgPlus = imgPlusValue.getImgPlus();
if (imgPlus.firstElement() instanceof BitType) {
LOGGER.warn("Threshold of BitType image cannot be calculated. Image is returned as is.");
return m_imgCellFactory.createCell(imgPlus);
}
final String[] methods = m_thresholderSettings.getStringArrayValue();
final ThresholdingType[] thresholders = new ThresholdingType[methods.length];
for (int i = 0; i < thresholders.length; i++) {
thresholders[i] = Enum.valueOf(ThresholdingType.class, methods[i]);
}
final ImgPlusCell[] resCells = new ImgPlusCell[thresholders.length];
for (int i = 0; i < resCells.length; i++) {
final ImgPlus<BitType> res =
new ImgPlus<BitType>(KNIPGateway.ops().create().img(imgPlus, new BitType()), imgPlus);
res.setName(res.getName());
if (thresholders[i] == ThresholdingType.MANUAL) {
final T type = imgPlus.firstElement().createVariable();
type.setReal(m_manualThreshold.getDoubleValue());
new UnaryRelationAssigment<T>(new RealGreaterThanConstant<T>(type)).compute(imgPlus, res);
resCells[i] = m_imgCellFactory.createCell(res);
} else if (thresholders[i] == ThresholdingType.INTERMODES
|| thresholders[i] == ThresholdingType.MINIMUM
|| thresholders[i] == ThresholdingType.ISODATA) {
LOGGER.warn("MINIMUM, INTERMODES and ISODATA are currently not supported because their implementation can result in incorrect results. A missing cell has been created.");
return m_imgCellFactory.createCell(imgPlus);
} else {
UnaryOutputOperation<ImgPlus<T>, ImgPlus<BitType>> op =
ImgOperations.wrapII(new AutoThreshold<T>(thresholders[i]), new BitType());
try {
SubsetOperations.iterate(op, m_dimSelection.getSelectedDimIndices(imgPlus), imgPlus, res,
getExecutorService());
} catch (Exception e) {
throw new KNIPRuntimeException(e.getMessage(), e);
}
resCells[i] = m_imgCellFactory.createCell(res);
}
}
if (resCells.length == 1) {
return resCells[0];
} else {
return CollectionCellFactory.createListCell(Arrays.asList(resCells));
}
}
/**
* {@inheritDoc}
*/
@SuppressWarnings("unchecked")
@Override
protected PortObjectSpec[] configure(final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
m_inValueClass = ImgPlusValue.class;
if (m_thresholderSettings.getStringArrayValue().length == 1) {
m_outCellClass = ImgPlusCell.class;
} else {
m_outCellClass = ListCell.class;
}
return super.configure(inSpecs);
}
/**
* {@inheritDoc}
*/
@Override
protected DataType getOutDataCellListCellType() {
if (m_thresholderSettings.getStringArrayValue().length == 1) {
return null;
} else {
return ImgPlusCell.TYPE;
}
}
/**
* {@inheritDoc}
*/
@Override
protected void getTypeArgumentClasses() {
// do nothing here
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}