/*
* ------------------------------------------------------------------------
*
* 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.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
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.ValueToCellNodeDialog;
import org.knime.knip.base.node.ValueToCellNodeFactory;
import org.knime.knip.base.node.ValueToCellNodeModel;
import org.knime.knip.base.node.dialog.DialogComponentSubsetSelection;
import org.knime.knip.base.node.nodesettings.SettingsModelSubsetSelection;
import org.knime.knip.core.data.img.DefaultImgMetadata;
import net.imagej.ImgPlus;
import net.imagej.axis.CalibratedAxis;
import net.imagej.space.DefaultCalibratedSpace;
import net.imglib2.Interval;
import net.imglib2.IterableInterval;
import net.imglib2.img.Img;
import net.imglib2.ops.operation.Operations;
import net.imglib2.ops.operation.iterableinterval.unary.MergeIterableIntervals;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
/**
* ImgCropperNodeFactory
*
* @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>
*/
public class ImgCropperNodeFactory<T extends RealType<T> & NativeType<T>>
extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private static SettingsModelBoolean createAdjustDimModel() {
return new SettingsModelBoolean("cfg_adjust_dimensionality", true);
}
private static SettingsModelSubsetSelection createSubsetSelectionModel() {
return new SettingsModelSubsetSelection("cfg_subset_selection");
}
/**
* {@inheritDoc}
*/
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
addDialogComponent("Options", "Subset Selection",
new DialogComponentSubsetSelection(createSubsetSelectionModel(), true, true));
addDialogComponent("Options", "Options",
new DialogComponentBoolean(createAdjustDimModel(), "Adjust Dimensionality?"));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_cropped";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>>() {
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelBoolean m_smAdjustDimensionality = createAdjustDimModel();
private final SettingsModelSubsetSelection m_smSubsetSel = createSubsetSelectionModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_smSubsetSel);
settingsModels.add(m_smAdjustDimensionality);
}
@Override
protected ImgPlusCell<T> compute(final ImgPlusValue<T> cellValue) throws Exception {
if (m_smSubsetSel.isCompletelySelected()) {
return m_imgCellFactory.createCell(cellValue.getImgPlusCopy());
} else {
final ImgPlus<T> img = cellValue.getImgPlus();
final long[] dimensions = new long[img.numDimensions()];
img.dimensions(dimensions);
final Interval[] intervals = m_smSubsetSel.createSelectedIntervals(dimensions, img);
@SuppressWarnings("unchecked")
final IterableInterval<T>[] iis = new IterableInterval[intervals.length];
for (int i = 0; i < intervals.length; i++) {
iis[i] = Views.iterable(Views.interval(img, intervals[i]));
}
final MergeIterableIntervals<T> mergeOp =
new MergeIterableIntervals<T>(img.factory(), m_smAdjustDimensionality.getBooleanValue());
if ((iis.length == 1) && m_smAdjustDimensionality.getBooleanValue()) {
// special case handling if dim
// adjusting is active and no
// dims with
// size > 1 remain everything
// will be deleted else
boolean valid = false;
for (int i = 0; i < iis[0].numDimensions(); i++) {
if (iis[0].min(i) != iis[0].max(i)) {
valid = true;
}
}
if (!valid) {
throw new KNIPException(
"dimension adjusting reduced the image to nothing(no dimension with size > 1 exists)",
new IllegalArgumentException("no dimensions left"));
}
}
final Img<T> res = Operations.compute(mergeOp, iis);
final List<CalibratedAxis> validAxes = new ArrayList<CalibratedAxis>();
for (int d = 0; d < img.numDimensions(); d++) {
if (!mergeOp.getInvalidDims().contains(d)) {
validAxes.add(cellValue.getMetadata().axis(d).copy());
}
}
final DefaultImgMetadata metadata =
new DefaultImgMetadata(new DefaultCalibratedSpace(validAxes), img, img, img);
metadata.setSource(img.getSource());
metadata.setName(img.getName());
return m_imgCellFactory.createCell(new ImgPlus<T>(res, metadata));
}
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}