/**
* 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.io.nodes.imgreader2;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.BufferedDataTableHolder;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.defaultnodesettings.SettingsModel;
import org.knime.core.node.defaultnodesettings.SettingsModelBoolean;
import org.knime.core.node.defaultnodesettings.SettingsModelDoubleRange;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.knip.base.node.nodesettings.SettingsModelSubsetSelection2;
import org.knime.knip.core.types.NativeTypes;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
/**
* This Node reads images.
*
* @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>
* @author <a href="mailto:gabriel.einsdorf@uni.kn"> Gabriel Einsdorf</a>
* @author <a href="mailto:danielseebacher@t-online.de">Daniel Seebacher,
* University of Konstanz.</a>
*/
public abstract class AbstractImgReaderNodeModel<T extends RealType<T> & NativeType<T>> extends NodeModel
implements BufferedDataTableHolder {
/**
* The available factory types available for selection.
*/
public static final String[] IMG_FACTORIES = new String[] { "Array Image Factory", "Planar Image Factory",
"Cell Image Factory" };
public static final String[] PIXEL_TYPES = { NativeTypes.BITTYPE.toString(), NativeTypes.BYTETYPE.toString(),
NativeTypes.DOUBLETYPE.toString(), NativeTypes.FLOATTYPE.toString(), NativeTypes.INTTYPE.toString(),
NativeTypes.LONGTYPE.toString(), NativeTypes.SHORTTYPE.toString(), NativeTypes.UNSIGNEDSHORTTYPE.toString(),
NativeTypes.UNSIGNED12BITTYPE.toString(), NativeTypes.UNSIGNEDINTTYPE.toString(),
NativeTypes.UNSIGNEDBYTETYPE.toString(), "< Automatic >" };
/* data table for the table cell viewer */
protected BufferedDataTable m_data;
/*
* **********************************************************************
* ************** SETTINGS MODELS CREATOR
**********************************************************************/
/**
* @return Model to store the check file format option.
*/
public static final SettingsModelBoolean createCheckFileFormatModel() {
return new SettingsModelBoolean("check_file_format", true);
}
// New in 1.0.2
public static final SettingsModelBoolean createIsGroupFilesModel() {
return new SettingsModelBoolean("group_files", true);
}
/**
* @return Model to store the OME_XML-metadata column option.
*/
public static final SettingsModelBoolean createAppendOmexmlColModel() {
return new SettingsModelBoolean("xmlcolumns", false);
}
/**
* @return Model for the settings holding selected image planes.
*/
public static final SettingsModelSubsetSelection2 createPlaneSelectionModel() {
return new SettingsModelSubsetSelection2("plane_selection");
}
/**
* @return Model to store whether all series should be read
*/
public static final SettingsModelBoolean createReadAllSeriesModel() {
return new SettingsModelBoolean("read_all_series", true);
}
// /**
// * @return Key to store the selected series
// */
// public static final SettingsModelIntegerBounded
// createSeriesSelectionModel() {
// return new SettingsModelIntegerBounded("series_selection", 0, 0, 1000);
// }
public static SettingsModelDoubleRange createSeriesSelectionRangeModel() {
return new SettingsModelDoubleRange("series_range_selection", 0, Short.MAX_VALUE);
}
/**
* @return Model to store the factory used to create the images
*/
public static SettingsModelString createImgFactoryModel() {
return new SettingsModelString("img_factory", IMG_FACTORIES[0]);
}
/**
* @return Model to store the metadata mode.
*/
public static SettingsModelString createMetaDataModeModel() {
return new SettingsModelString("metadata_mode", MetadataMode.NO_METADATA.toString());
}
/**
* @return Model to store whether to read all meta data or not.
*/
public static SettingsModelBoolean createReadAllMetaDataModel() {
return new SettingsModelBoolean("read_all_metadata", false);
}
public static SettingsModelString createPixelTypeModel() {
return new SettingsModelString("m_pixeltype", "< Automatic >");
}
/*
* **********************************************************************
* ************** SETTINGS MODELS
**********************************************************************/
protected final SettingsModelBoolean m_checkFileFormat = createCheckFileFormatModel();
// New in 1.0.2
protected final SettingsModelBoolean m_isGroupFiles = createIsGroupFilesModel();
protected final SettingsModelSubsetSelection2 m_planeSelect = createPlaneSelectionModel();
// new in 1.1
protected final SettingsModelString m_imgFactory = createImgFactoryModel();
protected final SettingsModelBoolean m_readAllSeries = createReadAllSeriesModel();
// protected final SettingsModelIntegerBounded m_seriesSelection =
// createSeriesSelectionModel();
protected final SettingsModelDoubleRange m_seriesRangeSelection = createSeriesSelectionRangeModel();
// new in 1.3
protected final SettingsModelString m_metadataModeModel = createMetaDataModeModel();
protected final SettingsModelBoolean m_readAllMetaDataModel = createReadAllMetaDataModel();
protected final SettingsModelString m_pixelType = createPixelTypeModel();
protected final List<SettingsModel> m_settingsCollection = new ArrayList<>();
/**
* Initializes the ImageReader
*/
public AbstractImgReaderNodeModel(int numInPorts, int numOutPorts) {
super(numInPorts, numOutPorts);
m_settingsCollection.add(m_checkFileFormat);
m_settingsCollection.add(m_isGroupFiles);
m_settingsCollection.add(m_planeSelect);
m_settingsCollection.add(m_imgFactory);
m_settingsCollection.add(m_readAllSeries);
// m_settingsCollection.add(m_seriesSelection);
m_settingsCollection.add(m_seriesRangeSelection);
m_settingsCollection.add(m_metadataModeModel);
m_settingsCollection.add(m_readAllMetaDataModel);
m_settingsCollection.add(m_pixelType);
// m_seriesSelection.setEnabled(false);
m_seriesRangeSelection.setEnabled(false);
}
protected void addSettingsModels(SettingsModel... additionalSettingModels) {
for (SettingsModel sm : additionalSettingModels) {
m_settingsCollection.add(sm);
}
}
/**
* {@inheritDoc}
*/
@Override
public BufferedDataTable[] getInternalTables() {
return new BufferedDataTable[] { m_data };
}
/**
* {@inheritDoc}
*/
@Override
protected void loadInternals(final File nodeInternDir, final ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
//
}
/**
* {@inheritDoc}
*/
@Override
public void reset() {
m_data = null;
}
/**
* {@inheritDoc}
*/
@Override
protected void saveInternals(final File nodeInternDir, final ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
//
}
/**
* {@inheritDoc}
*/
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
for (final SettingsModel sm : m_settingsCollection) {
sm.loadSettingsFrom(settings);
}
}
/**
* {@inheritDoc}
*/
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
for (final SettingsModel sm : m_settingsCollection) {
sm.saveSettingsTo(settings);
}
}
/**
* {@inheritDoc}
*/
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
for (final SettingsModel sm : m_settingsCollection) {
sm.validateSettings(settings);
}
}
// // Methods for the table cell view ////
/**
* {@inheritDoc}
*/
@Override
public void setInternalTables(final BufferedDataTable[] tables) {
m_data = tables[0];
}
}