/*
* ------------------------------------------------------------------------
*
* 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.io.IOException;
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.node.ValueToCellNodeDialog;
import org.knime.knip.base.node.ValueToCellNodeFactory;
import org.knime.knip.base.node.ValueToCellNodeModel;
import org.knime.knip.core.types.ImgFactoryTypes;
import org.knime.knip.core.types.NativeTypes;
import org.knime.knip.core.util.EnumUtils;
import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.converter.read.ConvertedRandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.ImgView;
import net.imglib2.ops.operation.Operations;
import net.imglib2.ops.operation.img.unary.ImgConvert.ImgConversionTypes;
import net.imglib2.ops.operation.iterableinterval.unary.MinMax;
import net.imglib2.ops.operation.real.unary.Convert;
import net.imglib2.ops.operation.real.unary.Convert.TypeConversionTypes;
import net.imglib2.ops.operation.real.unary.Normalize;
import net.imglib2.type.NativeType;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.type.numeric.integer.ShortType;
import net.imglib2.type.numeric.integer.Unsigned12BitType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.ValuePair;
import net.imglib2.view.Views;
/**
* Factory class to produce the Histogram Operations Node.
*
* @param <T>
*
* @author <a href="mailto:dietzc85@googlemail.com">Christian Dietz</a>
* @author <a href="mailto:horn_martin@gmx.de">Martin Horn</a>
*/
public class ConvertImgNodeFactory<T extends RealType<T> & NativeType<T>>
extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private static SettingsModelString createConversionTypeModel() {
return new SettingsModelString("scaling", ImgConversionTypes.DIRECT.getLabel());
}
private static SettingsModelString createFactorySelectionModel() {
return new SettingsModelString("factoryselection", ImgFactoryTypes.SOURCE_FACTORY.toString());
}
private static SettingsModelString createTargetTypeModel() {
return new SettingsModelString("targetformat", NativeTypes.BYTETYPE.toString());
}
/**
* {@inheritDoc}
*/
@SuppressWarnings("deprecation")
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
/**
* {@inheritDoc}
*/
@Override
public void addDialogComponents() {
addDialogComponent("Options", "Target Type", new DialogComponentStringSelection(createTargetTypeModel(),
"Target type", EnumUtils.getStringListFromName(NativeTypes.values())));
addDialogComponent("Options", "Target Type", new DialogComponentStringSelection(
createConversionTypeModel(), "Conversion method", ImgConversionTypes.labelsAsStringArray()));
addDialogComponent("Options", "Factory Selection",
new DialogComponentStringSelection(createFactorySelectionModel(), "Factory Type",
EnumUtils.getStringListFromName(ImgFactoryTypes.values())));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_converted";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>>() {
private final SettingsModelString m_conversionType = createConversionTypeModel();
private final SettingsModelString m_factorySelection = createFactorySelectionModel();
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelString m_targetType = createTargetTypeModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_factorySelection);
settingsModels.add(m_conversionType);
settingsModels.add(m_targetType);
}
/**
* {@inheritDoc}
*
* @throws IllegalArgumentException
*/
@SuppressWarnings({"unchecked", "rawtypes"})
@Override
protected ImgPlusCell compute(final ImgPlusValue<T> cellValue) throws IOException {
final ImgPlus<T> img = cellValue.getImgPlus();
Img<? extends RealType> res = null;
final ImgConversionTypes mode = ImgConversionTypes.getByLabel(m_conversionType.getStringValue());
final ImgFactoryTypes facType = ImgFactoryTypes.valueOf(m_factorySelection.getStringValue());
switch (NativeTypes.valueOf(m_targetType.getStringValue().toUpperCase())) {
case BITTYPE:
res = convert(img, new BitType(), facType, mode);
break;
case BYTETYPE:
res = convert(img, new ByteType(), facType, mode);
break;
case DOUBLETYPE:
res = convert(img, new DoubleType(), facType, mode);
break;
case FLOATTYPE:
res = convert(img, new FloatType(), facType, mode);
break;
case INTTYPE:
res = convert(img, new IntType(), facType, mode);
break;
case LONGTYPE:
res = convert(img, new LongType(), facType, mode);
break;
case SHORTTYPE:
res = convert(img, new ShortType(), facType, mode);
break;
case UNSIGNED12BITTYPE:
res = convert(img, new Unsigned12BitType(), facType, mode);
break;
case UNSIGNEDBYTETYPE:
res = convert(img, new UnsignedByteType(), facType, mode);
break;
case UNSIGNEDINTTYPE:
res = convert(img, new UnsignedIntType(), facType, mode);
break;
case UNSIGNEDSHORTTYPE:
res = convert(img, new UnsignedShortType(), facType, mode);
break;
default:
throw new IllegalArgumentException("Unsupported conversion.");
}
final ImgPlus resImgPlus = new ImgPlus(res, img);
resImgPlus.setSource(img.getSource());
resImgPlus.setName(img.getName());
return m_imgCellFactory.createCell(resImgPlus);
}
@SuppressWarnings("unchecked")
public synchronized <O extends RealType<O> & NativeType<O>> Img<O>
convert(final Img<T> img, final O outType, final ImgFactoryTypes facType,
final ImgConversionTypes mode) {
return ImgView.<O> wrap(
new ConvertedRandomAccessibleInterval<T, O>(img,
new ImgConvert<T, O>(img.firstElement().createVariable(), outType, mode)
.createOp(img),
outType),
ImgFactoryTypes.<T> getImgFactory(facType, img));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
/**
* Converts complete images from one type into another TODO: Can now convert RandomAccessibleIntervals from one type
* into another.
*
* @author dietzc, University of Konstanz
* @deprecation will be replaced with ImageJ-Ops
*/
@Deprecated
public class ImgConvert<I extends RealType<I>, O extends RealType<O> & NativeType<O>> {
private final O m_outType;
private final I m_inType;
private final ImgConversionTypes m_conversionType;
/**
* For Compatability with previous API, this creates a default ImgFactory.
*
* @param inType
* @param outType
* @param type
* @deprecated Use the other constructor and specify a ImgFactory yourself.
*/
@Deprecated
public ImgConvert(final I inType, final O outType, final ImgConversionTypes type) {
m_outType = outType;
m_conversionType = type;
m_inType = inType;
}
public Convert<I, O> createOp(final RandomAccessibleInterval<I> img) {
final Iterable<I> iterImg = Views.iterable(img);
double factor;
ValuePair<I, I> oldMinMax;
Convert<I, O> convertOp = null;
switch (m_conversionType) {
case DIRECT:
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.DIRECT);
break;
case DIRECTCLIP:
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.DIRECTCLIP);
break;
case NORMALIZEDIRECT:
oldMinMax = Operations.compute(new MinMax<I>(), iterImg);
factor = Normalize.normalizationFactor(oldMinMax.a.getRealDouble(), oldMinMax.b.getRealDouble(),
m_inType.getMinValue(), m_inType.getMaxValue());
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.SCALE);
convertOp.setFactor(convertOp.getFactor() / factor);
convertOp.setInMin(0);
convertOp.setOutMin(0);
break;
case NORMALIZESCALE:
oldMinMax = Operations.compute(new MinMax<I>(), iterImg);
factor = Normalize.normalizationFactor(oldMinMax.a.getRealDouble(), oldMinMax.b.getRealDouble(),
m_inType.getMinValue(), m_inType.getMaxValue());
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.SCALE);
convertOp.setFactor(convertOp.getFactor() / factor);
convertOp.setInMin(oldMinMax.a.getRealDouble());
break;
case NORMALIZEDIRECTCLIP:
oldMinMax = Operations.compute(new MinMax<I>(), iterImg);
factor = Normalize.normalizationFactor(oldMinMax.a.getRealDouble(), oldMinMax.b.getRealDouble(),
m_inType.getMinValue(), m_inType.getMaxValue());
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.SCALECLIP);
convertOp.setFactor(convertOp.getFactor() / factor);
convertOp.setInMin(oldMinMax.a.getRealDouble());
break;
case SCALE:
convertOp = new Convert<I, O>(m_inType, m_outType, TypeConversionTypes.SCALE);
break;
default:
throw new IllegalArgumentException("Normalization type unknown");
}
return convertOp;
}
}
}