/*
* ------------------------------------------------------------------------
*
* 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.List;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.defaultnodesettings.DialogComponentBoolean;
import org.knime.core.node.defaultnodesettings.DialogComponentNumber;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModelDouble;
import org.knime.core.node.defaultnodesettings.SettingsModelInteger;
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.KNIPRuntimeException;
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 net.imagej.ImgPlus;
import net.imglib2.Cursor;
import net.imglib2.FinalInterval;
import net.imglib2.img.Img;
import net.imglib2.img.ImgView;
import net.imglib2.type.numeric.RealType;
import net.imglib2.util.Intervals;
import net.imglib2.view.Views;
/**
* Automatically crops an image.
*
* @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 AutoCropNodeFactory<T extends RealType<T>> extends ValueToCellNodeFactory<ImgPlusValue<T>> {
private static SettingsModelBoolean createKeepWithinImgBordersModel() {
return new SettingsModelBoolean("keep_within_img_borders", true);
}
private static SettingsModelDouble createLowerPixelValueModel() {
return new SettingsModelDouble("lower_pixel_value", 0);
}
private static SettingsModelDimSelection createMarginDimSelectionModel() {
return new SettingsModelDimSelection("margin_dim_selection", "X", "Y");
}
private static SettingsModelInteger createMarginModel() {
return new SettingsModelInteger("margin", 0);
}
private static SettingsModelDouble createOutOfBoundsValueModel() {
return new SettingsModelDouble("out_of_bounds_value", 0);
}
private static SettingsModelDouble createUpperPixelValueModel() {
return new SettingsModelDouble("upper_pixel_value", 0);
}
/**
* {@inheritDoc}
*
* @deprecated
*/
@Deprecated
@Override
protected ValueToCellNodeDialog<ImgPlusValue<T>> createNodeDialog() {
return new ValueToCellNodeDialog<ImgPlusValue<T>>() {
@Override
public void addDialogComponents() {
addDialogComponent("Options", "Pixel values",
new DialogComponentNumber(createLowerPixelValueModel(), "Lower pixel value", 1.0));
addDialogComponent("Options", "Pixel values",
new DialogComponentNumber(createUpperPixelValueModel(), "Upper pixel value", 1.0));
addDialogComponent("Margin", "", new DialogComponentNumber(createMarginModel(),
"Margin", 1));
addDialogComponent("Margin", "", new DialogComponentDimSelection(createMarginDimSelectionModel(),
"Respected dimensions"));
final SettingsModelBoolean keepImgBorders = createKeepWithinImgBordersModel();
final SettingsModelDouble outOfBoundsVal = createOutOfBoundsValueModel();
keepImgBorders.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(final ChangeEvent arg0) {
outOfBoundsVal.setEnabled(!keepImgBorders.getBooleanValue());
}
});
addDialogComponent("Margin", "",
new DialogComponentBoolean(keepImgBorders, "Keep result within image borders"));
addDialogComponent("Margin", "", new DialogComponentNumber(outOfBoundsVal, "Out of bounds value", 1));
}
/**
* {@inheritDoc}
*/
@Override
protected String getDefaultSuffixForAppend() {
return "_autoCrop";
}
};
}
/**
* {@inheritDoc}
*/
@Override
public ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>> createNodeModel() {
return new ValueToCellNodeModel<ImgPlusValue<T>, ImgPlusCell<T>>() {
private ImgPlusCellFactory m_imgCellFactory;
private final SettingsModelBoolean m_smKeepWithinImgBorders = createKeepWithinImgBordersModel();
private final SettingsModelDouble m_smLowerPixelValue = createLowerPixelValueModel();
private final SettingsModelInteger m_smMargin = createMarginModel();
private final SettingsModelDimSelection m_smMarginDimSelection = createMarginDimSelectionModel();
private final SettingsModelDouble m_smOutOfBoundsValue = createOutOfBoundsValueModel();
private final SettingsModelDouble m_smUpperPixelValue = createUpperPixelValueModel();
@Override
protected void addSettingsModels(final List<SettingsModel> settingsModels) {
settingsModels.add(m_smMargin);
settingsModels.add(m_smLowerPixelValue);
settingsModels.add(m_smUpperPixelValue);
settingsModels.add(m_smKeepWithinImgBorders);
settingsModels.add(m_smOutOfBoundsValue);
settingsModels.add(m_smMarginDimSelection);
}
@Override
protected ImgPlusCell<T> compute(final ImgPlusValue<T> cellValue) throws Exception {
final ImgPlus<T> img = cellValue.getImgPlus();
final Cursor<T> cur = img.localizingCursor();
final long[] min = new long[img.numDimensions()];
img.max(min);
final long[] max = new long[img.numDimensions()];
img.min(max);
while (cur.hasNext()) {
cur.fwd();
if ((cur.get().getRealDouble() >= m_smLowerPixelValue.getDoubleValue())
&& (cur.get().getRealDouble() <= m_smUpperPixelValue.getDoubleValue())) {
for (int i = 0; i < img.numDimensions(); i++) {
min[i] = Math.min(min[i], cur.getIntPosition(i));
max[i] = Math.max(max[i], cur.getIntPosition(i));
}
}
}
// apply margins only to those dimension, which
// are selected
for (int i = 0; i < img.numDimensions(); i++) {
if (m_smMarginDimSelection.isSelectedDim(img.axis(i).type().getLabel())) {
min[i] -= m_smMargin.getIntValue();
max[i] += m_smMargin.getIntValue();
if (m_smKeepWithinImgBorders.getBooleanValue()) {
min[i] = Math.max(img.min(i), min[i]);
max[i] = Math.min(img.max(i), max[i]);
}
}
}
// crop
final FinalInterval interval = new FinalInterval(min, max);
for (int i = 0; i < max.length; i++) {
if (min[i] > max[i]) {
throw new KNIPRuntimeException("Illegal bounding box size. Most likely, the image didn't contain a pixel-value within the selected range.");
}
}
if (Intervals.numElements(interval) <= 0) {
throw new KNIPRuntimeException("Illegal bounding box size. Most likely, the image didn't contain a pixel-value within the selected range.");
}
Img<T> view;
if (m_smKeepWithinImgBorders.getBooleanValue()) {
view = ImgView.wrap(Views.interval(img, interval), img.factory());
} else {
final T val = img.firstElement().createVariable();
val.setReal(m_smOutOfBoundsValue.getDoubleValue());
view = ImgView.wrap(Views.interval(Views.extendValue(img, val), interval), img.factory());
}
return m_imgCellFactory.createCell(new ImgPlus<>(view, img));
}
/**
* {@inheritDoc}
*/
@Override
protected void prepareExecute(final ExecutionContext exec) {
m_imgCellFactory = new ImgPlusCellFactory(exec);
}
};
}
}