/*
* ------------------------------------------------------------------------
*
* 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.misc;
import java.util.Iterator;
import java.util.List;
import java.util.StringTokenizer;
import org.knime.core.data.DataCell;
import org.knime.core.data.DoubleValue;
import org.knime.core.data.collection.CollectionDataValue;
import org.knime.core.data.def.DoubleCell;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.defaultnodesettings.DialogComponentLabel;
import org.knime.core.node.defaultnodesettings.DialogComponentString;
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.exceptions.KNIPException;
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.core.types.NativeTypes;
import org.knime.knip.core.util.EnumUtils;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
import net.imagej.axis.AxisType;
import net.imglib2.Cursor;
import net.imglib2.img.Img;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
/**
* Converts a Collection of {@link DoubleCell}s to {@link Img}
*
* @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>
*/
public class DataRowToImgNodeFactory<T extends RealType<T> & NativeType<T>> extends
ValueToCellNodeFactory<CollectionDataValue> {
private static final SettingsModelString createDimenionsModel() {
return new SettingsModelString("dimensions", "100,100");
}
private static final SettingsModelString createDimensionLabelsModel() {
return new SettingsModelString("dimension_labels", "X,Y");
}
private static SettingsModelString createPixelTypeModel() {
return new SettingsModelString("pixel_type", NativeTypes.BYTETYPE.toString());
}
@Override
public ValueToCellNodeModel<CollectionDataValue, ImgPlusCell<T>> createNodeModel() {
return new ValueToCellNodeModel<CollectionDataValue, ImgPlusCell<T>>() {
private SettingsModelString m_smDims = createDimenionsModel();
private SettingsModelString m_smDimLabels = createDimensionLabelsModel();
private SettingsModelString m_smPixType = createPixelTypeModel();
private ImgPlusCellFactory m_cellFactory;
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_cellFactory = new ImgPlusCellFactory(exec);
}
@Override
protected ImgPlusCell<T> compute(final CollectionDataValue cellValue) throws Exception {
if (!cellValue.getElementType().isCompatible(DoubleValue.class)) {
throw new KNIPException(
"Collection of cells does not contain exclusively numbers! According row is skipped.");
}
//get dimensions and labels
long[] dims = parseDimensions(m_smDims.getStringValue());
String[] dimLabels = parseDimensionLabels(m_smDimLabels.getStringValue());
//if number of dimension are one less than the number of labels
//then determine the size of the last dimension
if (dims.length == dimLabels.length - 1) {
long[] tmpA = new long[dims.length + 1];
double tmp = 1;
for (int i = 0; i < dims.length; i++) {
tmp *= dims[i];
tmpA[i] = dims[i];
}
tmpA[tmpA.length - 1] = (long)Math.ceil(cellValue.size() / tmp);
dims = tmpA;
}
//pixel type
T type = (T)NativeTypes.valueOf(m_smPixType.getStringValue()).getTypeInstance();
//create image
Img<T> img = new ArrayImgFactory<T>().create(dims, type);
if (img.size() != cellValue.size()) {
//if the number pixels of the result image and the number of provided double values don't fit
getLogger().warn("The number of provided numbers (" + cellValue.size()
+ ") doesn't comply with the number of pixels of the result image ("
+ img.size() + ")");
setWarningMessage("The collection of values doesn't fit into the result image for some rows. See console log for details.");
}
//transfer data to the image
Cursor<T> cur = img.cursor();
Iterator<DataCell> it = cellValue.iterator();
while (cur.hasNext() && it.hasNext()) {
cur.fwd();
double val = ((DoubleValue)it.next()).getDoubleValue();
cur.get().setReal(val);
}
//set meta data
AxisType[] axes = new AxisType[dimLabels.length];
for (int i = 0; i < axes.length; i++) {
axes[i] = Axes.get(dimLabels[i]);
}
ImgPlus<T> imgPlus = new ImgPlus<T>(img, "", axes);
return m_cellFactory.createCell(imgPlus);
}
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_smDims);
settingsModels.add(m_smDimLabels);
settingsModels.add(m_smPixType);
}
};
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<CollectionDataValue> createNodeDialog() {
return new ValueToCellNodeDialog<CollectionDataValue>() {
private SettingsModelString m_smDims;
private SettingsModelString m_smDimLabels;
@Override
public void addDialogComponents() {
m_smDims = createDimenionsModel();
m_smDimLabels = createDimensionLabelsModel();
addDialogComponent("Options", "Image Dimensions", new DialogComponentString(m_smDims, "Dimensions"));
addDialogComponent("Options", "Image Dimensions", new DialogComponentString(m_smDimLabels,
"Dimension labels"));
addDialogComponent("Options", "Image Dimensions", new DialogComponentLabel(
"(Dimensions and labels are specified ','-separated)"));
addDialogComponent("Options", "Image Pixel Type", new DialogComponentStringSelection(
createPixelTypeModel(), "", EnumUtils.getStringListFromToString(NativeTypes.values())));
}
/**
* {@inheritDoc}
*/
@Override
public void saveAdditionalSettingsTo(final NodeSettingsWO settings) throws InvalidSettingsException {
super.saveAdditionalSettingsTo(settings);
//check configuration
long[] dims = parseDimensions(m_smDims.getStringValue());
String[] dimLabels = parseDimensionLabels(m_smDimLabels.getStringValue());
if (!(dims.length == dimLabels.length || dims.length == dimLabels.length - 1)) {
throw new InvalidSettingsException(
"Number of dimensions must be equal to the number of labels (or one less).");
}
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_drti";
}
};
}
private long[] parseDimensions(final String s) {
StringTokenizer st = new StringTokenizer(s, ",");
long[] dims = new long[st.countTokens()];
for (int i = 0; i < dims.length; i++) {
dims[i] = Long.parseLong(st.nextToken().trim());
}
return dims;
}
private String[] parseDimensionLabels(final String s) {
StringTokenizer st = new StringTokenizer(s, ",");
String[] dimLabels = new String[st.countTokens()];
for (int i = 0; i < dimLabels.length; i++) {
dimLabels[i] = st.nextToken().trim();
}
return dimLabels;
}
}