/*
* ------------------------------------------------------------------------
*
* 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.DialogComponentStringSelection;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
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.TwoValuesToCellNodeDialog;
import org.knime.knip.base.node.TwoValuesToCellNodeFactory;
import org.knime.knip.base.node.TwoValuesToCellNodeModel;
import org.knime.knip.base.node.dialog.DialogComponentDimSelection;
import org.knime.knip.base.node.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.ops.operation.SubsetOperations;
import net.imglib2.ops.operation.UnaryOperation;
import net.imglib2.ops.operation.randomaccessibleinterval.unary.GrayscaleReconstructionByDilation;
import net.imglib2.ops.operation.randomaccessibleinterval.unary.GrayscaleReconstructionByErosion;
import net.imglib2.ops.types.ConnectedType;
import net.imglib2.type.numeric.RealType;
/**
* Grayscale Reconstruction NodeFactory
*
* @author <a href="mailto:dietzc85@googlemail.com">Christian Dietz</a>
* @author <a href="mailto:horn_martin@gmx.de">Martin Horn</a>
* @author muethingc, University of Konstanz
*
* @param <T>
*/
public final class GrayscaleReconstructionNodeFactory<T extends RealType<T>>
extends TwoValuesToCellNodeFactory<ImgPlusValue<T>, ImgPlusValue<T>> {
/**
* Operating type
*/
public enum OperationType {
/**
* dilate operator
*/
DILATE("By Dilation"), /**
* erode operator
*/
ERODE("By Erosion");
/**
* Names of operators
*/
public static final List<String> NAMES = new ArrayList<String>();
static {
for (final OperationType e : OperationType.values()) {
NAMES.add(e.toString());
}
}
/**
* @param name string representation of the {@link OperationType}
* @return return operator according to name
*/
public static OperationType value(final String name) {
return values()[NAMES.indexOf(name)];
}
private final String m_name;
private OperationType(final String name) {
m_name = name;
}
@Override
public String toString() {
return m_name;
}
}
private static SettingsModelString createConnectionTypeModel() {
return new SettingsModelString("connection_type", ConnectedType.FOUR_CONNECTED.toString());
}
private static SettingsModelDimSelection createDimSelectionModel() {
return new SettingsModelDimSelection("dim_selection", "X", "Y");
}
private static SettingsModelString createOperationTypeModel() {
return new SettingsModelString("operation_type", OperationType.DILATE.toString());
}
/**
* {@inheritDoc}
*/
@Override
protected TwoValuesToCellNodeDialog<ImgPlusValue<T>, ImgPlusValue<T>> createNodeDialog() {
return new TwoValuesToCellNodeDialog<ImgPlusValue<T>, ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
addDialogComponent("Options", "Dimension Selection", new DialogComponentDimSelection(
createDimSelectionModel(), "Dimension selection", 2, 5));
addDialogComponent("Options", "Grayscale Reconstruction Options", new DialogComponentStringSelection(
createConnectionTypeModel(), "Connection Type", ConnectedType.NAMES));
addDialogComponent("Options", "Grayscale Reconstruction Options", new DialogComponentStringSelection(
createOperationTypeModel(), "Operation Type", OperationType.NAMES));
}
@Override
protected String getFirstColumnSelectionLabel() {
return "Column of Image";
}
@Override
protected String getSecondColumnSelectionLabel() {
return "Column of Marker Image (BitType)";
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_gr";
}
};
}
@Override
public TwoValuesToCellNodeModel<ImgPlusValue<T>, ImgPlusValue<T>, ImgPlusCell<T>> createNodeModel() {
return new TwoValuesToCellNodeModel<ImgPlusValue<T>, ImgPlusValue<T>, ImgPlusCell<T>>() {
private final SettingsModelString m_connection = createConnectionTypeModel();
private final SettingsModelDimSelection m_dimSelection = createDimSelectionModel();
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelString m_operation = createOperationTypeModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_dimSelection);
settingsModels.add(m_connection);
settingsModels.add(m_operation);
}
@Override
protected ImgPlusCell<T> compute(final ImgPlusValue<T> cellValue1, final ImgPlusValue<T> cellValue2)
throws Exception {
final ImgPlus<T> fromCellA = cellValue1.getImgPlus();
final ImgPlus<T> mask = MinimaUtils.getZeroMinImgPlus(fromCellA);
final ImgPlus<T> fromCellB = cellValue2.getImgPlus();
final ImgPlus<T> marker = MinimaUtils.getZeroMinImgPlus(fromCellB);
if (!fromCellA.iterationOrder().equals(fromCellB.iterationOrder())) {
throw new KNIPException(
"Marker and mask don't have same iteration order. Reasons: Either min/max or dimensionality are not the same or the underlying data structures (e.g. ArrayImg vs CellImg) differ.");
}
if (mask.numDimensions() == 1) {
throw new KNIPException("One dimensional images are not supported by GrayScaleReconstruction");
}
final int[] selectedDimIndices = m_dimSelection.getSelectedDimIndices(mask);
int dim1 = 0;
for (int idx : selectedDimIndices) {
if (mask.dimension(idx) <= 1) {
dim1++;
}
}
if (selectedDimIndices.length - dim1 <= 1) {
throw new KNIPException(
"Image would be reduced to a one dimensional image, which can't be processed using the Grayscale Reconstruction. Please select different dimensions in the dimension selection.");
}
final ConnectedType type = ConnectedType.value(m_connection.getStringValue());
UnaryOperation<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>> op;
if (OperationType.value(m_operation.getStringValue()) == OperationType.DILATE) {
op = new GrayscaleReconstructionByDilation<T, T>(type);
} else {
op = new GrayscaleReconstructionByErosion<T, T>(type);
}
Img<T> out = marker.copy();
SubsetOperations.iterate(op, selectedDimIndices, mask, out, getExecutorService());
return m_imgCellFactory.createCell(new ImgPlus(out, cellValue1.getMetadata()));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}