/*
* ------------------------------------------------------------------------
*
* 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.knimeimagebridge;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import javax.imageio.ImageIO;
import org.knime.core.data.DataCell;
import org.knime.core.data.DataType;
import org.knime.core.data.collection.CollectionCellFactory;
import org.knime.core.data.collection.ListCell;
import org.knime.core.data.image.png.PNGImageCell;
import org.knime.core.data.image.png.PNGImageContent;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.knip.base.data.img.ImgPlusValue;
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.nodesettings.SettingsModelDimSelection;
import org.knime.knip.core.awt.AWTImageTools;
import org.knime.knip.core.awt.Real2GreyColorRenderer;
import org.knime.knip.core.util.MinimaUtils;
import net.imagej.ImgPlus;
import net.imglib2.Interval;
import net.imglib2.ops.operation.interval.binary.IntervalsFromDimSelection;
import net.imglib2.type.numeric.RealType;
/**
* Converts ImgPlusValue<T> of any type to PNGImageCell
*
* @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 ImgPlusCellToPNGValueNodeFactory<T extends RealType<T>> extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private NodeLogger LOGGER = NodeLogger.getLogger(ImgPlusCellToPNGValueNodeFactory.class);
static SettingsModelDimSelection createXYDimSelectionModel() {
return new SettingsModelDimSelection("dimensions_plane_xy", "X", "Y");
}
static SettingsModelDimSelection createChannelDimSelectionModel() {
return new SettingsModelDimSelection("dimensions_plane_channel", "Channel");
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
private SettingsModelDimSelection m_channelSelection;
private SettingsModelDimSelection m_xySelection;
/**
* {@inheritDoc}
*/
@Override
public void addDialogComponents() {
addDialogComponent("Options", "XY Dimension Selection", new DialogComponentDimSelection(
m_xySelection = createXYDimSelectionModel(), "Dimensions Plane", 2, 2));
addDialogComponent("Options", "Channel Dimension Selection", new DialogComponentDimSelection(
m_channelSelection = createChannelDimSelectionModel(), "Dimensions Plane", 0, 1));
}
/**
* {@inheritDoc}
*/
@Override
public void saveAdditionalSettingsTo(final NodeSettingsWO settings) throws InvalidSettingsException {
super.saveAdditionalSettingsTo(settings);
if (m_channelSelection.getNumSelectedDimLabels() > 0) {
String channelLabel = m_channelSelection.getSelectedDimLabels().iterator().next();
for (String xyLabel : m_xySelection.getSelectedDimLabels()) {
if (xyLabel.equalsIgnoreCase(channelLabel)) {
throw new InvalidSettingsException("XY Dimensions must not contain the channel dimension!");
}
}
}
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_IPtoPNG";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, ListCell> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, ListCell>() {
SettingsModelDimSelection m_dimensionsSelectionXY = createXYDimSelectionModel();
SettingsModelDimSelection m_dimensionsSelectionChannel = createChannelDimSelectionModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_dimensionsSelectionXY);
settingsModels.add(m_dimensionsSelectionChannel);
}
/**
* {@inheritDoc}
*
* @throws IllegalArgumentException
*/
@Override
protected ListCell compute(final ImgPlusValue<T> cellValue) throws IOException {
// Order of dimensions always X Y C
final ImgPlus<T> imgPlus = MinimaUtils.getZeroMinImgPlus(cellValue.getImgPlus());
final List<DataCell> cells = new ArrayList<DataCell>(0);
final int[] channelDim =
m_dimensionsSelectionChannel.getSelectedDimIndices(imgPlus.numDimensions(), imgPlus);
final int[] planeDim = m_dimensionsSelectionXY.getSelectedDimIndices(imgPlus.numDimensions(), imgPlus);
if (planeDim.length != 2) {
LOGGER.warn("The two selected plane dimensions must be contained in the source image. Missing Cell returned.");
cells.add(DataType.getMissingCell());
return CollectionCellFactory.createListCell(cells);
}
// Properties of input are read in
final boolean channelSelected = channelDim.length == 1;
if (channelSelected) {
if ((imgPlus.dimension(channelDim[0]) != 2) && (imgPlus.dimension(channelDim[0]) != 3)) {
LOGGER.warn("Channel selected, but invalid amount of dimensions. Only dimensions of size two or three can be rendered as RGB images. Therefore a grey value image is rendered.");
}
}
// Combining the both dim selections
ArrayList<Integer> indicesAsList = new ArrayList<Integer>();
if (channelSelected) {
indicesAsList.add(channelDim[0]);
}
indicesAsList.add(planeDim[0]);
indicesAsList.add(planeDim[1]);
Collections.sort(indicesAsList);
int[] indices = new int[indicesAsList.size()];
for (int i = 0; i < indicesAsList.size(); i++) {
indices[i] = indicesAsList.get(i);
}
final Interval[] intervals = IntervalsFromDimSelection.compute(indices, imgPlus);
final long[] min = new long[imgPlus.numDimensions()];
for (final Interval interval : intervals) {
interval.min(min);
final Real2GreyColorRenderer<T> renderer = new Real2GreyColorRenderer<T>(
channelSelected ? channelDim[0] : -1, imgPlus.firstElement().getMinValue());
final ByteArrayOutputStream out = new ByteArrayOutputStream();
ImageIO.write(AWTImageTools
.makeBuffered(renderer.render(imgPlus, planeDim[0], planeDim[1], min).image()), "PNG", out);
cells.add(new PNGImageContent(out.toByteArray()).toImageCell());
}
return CollectionCellFactory.createListCell(cells);
}
@Override
protected DataType getOutDataCellListCellType() {
return DataType.getType(PNGImageCell.class);
}
};
}
}