/**
* 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.readfrominput;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.atomic.AtomicBoolean;
import org.knime.core.data.DataColumnSpec;
import org.knime.core.data.DataColumnSpecCreator;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.StringValue;
import org.knime.core.data.xml.XMLCell;
import org.knime.core.node.BufferedDataContainer;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.core.node.port.PortObjectSpec;
import org.knime.core.node.streamable.InputPortRole;
import org.knime.core.node.streamable.OutputPortRole;
import org.knime.core.node.streamable.PartitionInfo;
import org.knime.core.node.streamable.PortInput;
import org.knime.core.node.streamable.PortOutput;
import org.knime.core.node.streamable.RowInput;
import org.knime.core.node.streamable.RowOutput;
import org.knime.core.node.streamable.StreamableOperator;
import org.knime.knip.base.data.img.ImgPlusCell;
import org.knime.knip.base.node.NodeUtils;
import org.knime.knip.core.util.EnumUtils;
import org.knime.knip.io.nodes.imgreader2.AbstractImgReaderNodeModel;
import org.knime.knip.io.nodes.imgreader2.ColumnCreationMode;
import org.knime.knip.io.nodes.imgreader2.MetadataMode;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.img.cell.CellImgFactory;
import net.imglib2.img.planar.PlanarImgFactory;
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 class ImgReaderTableNodeModel<T extends RealType<T> & NativeType<T>> extends AbstractImgReaderNodeModel<T> {
private static final NodeLogger LOGGER = NodeLogger.getLogger(ImgReaderTableNodeModel.class);
/**
* @return Model to store the selected column in the optional input table
*/
public static SettingsModelString createFilenameColumnModel() {
return new SettingsModelString("filename_column", "");
}
public static SettingsModelString createColCreationModeModel() {
return new SettingsModelString("m_colCreationMode", ColumnCreationMode.NEW_TABLE.toString());
}
public static SettingsModelString createColSuffixNodeModel() {
return new SettingsModelString("m_colSuffix", "");
}
private final SettingsModelString m_filenameColumn = createFilenameColumnModel();
private final SettingsModelString m_colCreationMode = createColCreationModeModel();
private final SettingsModelString m_colSuffix = createColSuffixNodeModel();
public ImgReaderTableNodeModel() {
super(1, 1);
addSettingsModels(m_filenameColumn, m_colCreationMode, m_colSuffix);
}
@Override
protected DataTableSpec[] configure(DataTableSpec[] inSpecs) throws InvalidSettingsException {
int imgIdx = getPathColIdx(inSpecs[0]);
if (-1 == imgIdx) {
throw new InvalidSettingsException("A string column must be selected!");
}
return new DataTableSpec[] { getOutspec(inSpecs[0], imgIdx) };
}
@Override
protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec) throws Exception {
// boolean for exceptions and file format
final AtomicBoolean encounteredExceptions = new AtomicBoolean(false);
int imgIdx = getPathColIdx(inData[0].getDataTableSpec());
ReadImgTableFunction<T> rifp = createImgTableFunction(exec, inData[0].getDataTableSpec(),
Long.valueOf(inData[0].size()).intValue());
BufferedDataContainer bdc = exec.createDataContainer(getOutspec(inData[0].getDataTableSpec(), imgIdx));
Iterator<DataRow> iterator = inData[0].iterator();
while (iterator.hasNext()) {
rifp.apply(iterator.next()).forEachOrdered(dataRow -> {
if (dataRow.getSecond().isPresent()) {
encounteredExceptions.set(true);
LOGGER.warn("Encountered exception while reading image: " + dataRow.getFirst().getKey()
+ "! view log for more info.");
LOGGER.debug("Encountered exception while reading image:", dataRow.getSecond().get());
}
bdc.addRowToTable(dataRow.getFirst());
});
exec.checkCanceled();
}
// close img file sources
rifp.close();
bdc.close();
// data table for the table cell viewer
m_data = bdc.getTable();
if (encounteredExceptions.get()) {
setWarningMessage("Encountered errors during execution!");
}
return new BufferedDataTable[] { bdc.getTable() };
}
@Override
public StreamableOperator createStreamableOperator(final PartitionInfo partitionInfo,
final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
return new StreamableOperator() {
@Override
public void runFinal(PortInput[] inputs, PortOutput[] outputs, ExecutionContext exec) throws Exception {
RowInput in = (RowInput) inputs[0];
RowOutput out = (RowOutput) outputs[0];
// boolean for exceptions and file format
final AtomicBoolean encounteredExceptions = new AtomicBoolean(false);
ReadImgTableFunction<T> readImgFunction = createImgTableFunction(exec, in.getDataTableSpec(), 1);
DataRow row;
while ((row = in.poll()) != null) {
readImgFunction.apply(row).forEachOrdered(result -> {
if (result.getSecond().isPresent()) {
encounteredExceptions.set(true);
LOGGER.warn("Encountered exception while reading image: " + result.getFirst().getKey()
+ "! view log for more info.");
LOGGER.debug("Encountered exception while reading image:", result.getSecond().get());
}
try {
out.push(result.getFirst());
} catch (Exception exc) {
encounteredExceptions.set(true);
LOGGER.warn("Couldn't push row " + result.getFirst().getKey() + " into output stream.");
LOGGER.debug("Encountered exception when trying to push result: ", exc);
}
});
}
if (encounteredExceptions.get()) {
setWarningMessage("Encountered errors during execution!");
}
in.close();
out.close();
readImgFunction.close();
}
};
}
@Override
public InputPortRole[] getInputPortRoles() {
return new InputPortRole[] { InputPortRole.DISTRIBUTED_STREAMABLE };
}
@Override
public OutputPortRole[] getOutputPortRoles() {
return new OutputPortRole[] { OutputPortRole.DISTRIBUTED };
}
private DataTableSpec getOutspec(DataTableSpec spec, int imgIdx) {
MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(), MetadataMode.values());
boolean readImage = (metadataMode == MetadataMode.NO_METADATA || metadataMode == MetadataMode.APPEND_METADATA)
? true : false;
boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
|| metadataMode == MetadataMode.METADATA_ONLY) ? true : false;
DataTableSpec outSpec;
// new table
ColumnCreationMode columnCreationMode = ColumnCreationMode.fromString(m_colCreationMode.getStringValue());
if (columnCreationMode == ColumnCreationMode.NEW_TABLE) {
DataColumnSpec imgSpec = new DataColumnSpecCreator("Image", ImgPlusCell.TYPE).createSpec();
DataColumnSpec omeSpec = new DataColumnSpecCreator("OME-XML Metadata", XMLCell.TYPE).createSpec();
if (readImage && readMetadata) {
outSpec = new DataTableSpec(imgSpec, omeSpec);
} else if (readImage) {
outSpec = new DataTableSpec(imgSpec);
} else {
outSpec = new DataTableSpec(omeSpec);
}
}
// append
else if (columnCreationMode == ColumnCreationMode.APPEND) {
DataColumnSpec imgSpec = new DataColumnSpecCreator(
DataTableSpec.getUniqueColumnName(spec, "Image" + m_colSuffix.getStringValue()), ImgPlusCell.TYPE)
.createSpec();
DataColumnSpec omeSpec = new DataColumnSpecCreator(
DataTableSpec.getUniqueColumnName(spec, "OME-XML Metadata" + m_colSuffix.getStringValue()),
XMLCell.TYPE).createSpec();
List<DataColumnSpec> list = new ArrayList<>();
for (int i = 0; i < spec.getNumColumns(); i++) {
list.add(spec.getColumnSpec(i));
}
if (readImage && readMetadata) {
list.add(imgSpec);
list.add(omeSpec);
} else if (readImage) {
list.add(imgSpec);
} else {
list.add(omeSpec);
}
outSpec = new DataTableSpec(list.toArray(new DataColumnSpec[list.size()]));
}
// replace
else if (columnCreationMode == ColumnCreationMode.REPLACE) {
DataColumnSpec imgSpec = new DataColumnSpecCreator(
DataTableSpec.getUniqueColumnName(spec, "Image" + m_colSuffix.getStringValue()), ImgPlusCell.TYPE)
.createSpec();
DataColumnSpec omeSpec = new DataColumnSpecCreator(
DataTableSpec.getUniqueColumnName(spec, "OME-XML Metadata" + m_colSuffix.getStringValue()),
XMLCell.TYPE).createSpec();
List<DataColumnSpec> list = new ArrayList<>();
for (int i = 0; i < spec.getNumColumns(); i++) {
list.add(spec.getColumnSpec(i));
}
if (readImage && readMetadata) {
list.set(imgIdx, imgSpec);
list.add(imgIdx + 1, omeSpec);
} else if (readImage) {
list.set(imgIdx, imgSpec);
} else {
list.set(imgIdx, omeSpec);
}
outSpec = new DataTableSpec(list.toArray(new DataColumnSpec[list.size()]));
} else {
throw new IllegalStateException("Support for the columncreation mode" + m_colCreationMode.getStringValue()
+ " is not implemented!");
}
return outSpec;
}
private int getPathColIdx(final DataTableSpec inSpec) throws InvalidSettingsException {
int imgColIndex = -1;
if (null == this.m_filenameColumn.getStringValue()) {
return imgColIndex;
}
imgColIndex = inSpec.findColumnIndex(this.m_filenameColumn.getStringValue());
if (-1 == imgColIndex) {
if ((imgColIndex = NodeUtils.autoOptionalColumnSelection(inSpec, this.m_filenameColumn,
StringValue.class)) >= 0) {
setWarningMessage("Auto-configure Image Column: " + this.m_filenameColumn.getStringValue());
} else {
throw new InvalidSettingsException("No column selected!");
}
}
return imgColIndex;
}
private ReadImgTableFunction<T> createImgTableFunction(ExecutionContext exec, DataTableSpec inSpec, int rowCount)
throws InvalidSettingsException {
int imgIdx = getPathColIdx(inSpec);
MetadataMode metadataMode = EnumUtils.valueForName(m_metadataModeModel.getStringValue(), MetadataMode.values());
boolean readImage = (metadataMode == MetadataMode.NO_METADATA || metadataMode == MetadataMode.APPEND_METADATA)
? true : false;
boolean readMetadata = (metadataMode == MetadataMode.APPEND_METADATA
|| metadataMode == MetadataMode.METADATA_ONLY) ? true : false;
// create ImgFactory
ImgFactory<T> imgFac;
if (m_imgFactory.getStringValue().equals(IMG_FACTORIES[1])) {
imgFac = new PlanarImgFactory<>();
} else if (m_imgFactory.getStringValue().equals(IMG_FACTORIES[2])) {
imgFac = new CellImgFactory<>();
} else {
imgFac = new ArrayImgFactory<>();
}
// series selection
int seriesSelectionFrom;
int seriesSelectionTo;
if (m_readAllSeries.getBooleanValue()) {
seriesSelectionFrom = -1;
seriesSelectionTo = -1;
} else {
seriesSelectionFrom = Double.valueOf(m_seriesRangeSelection.getMinRange()).intValue();
seriesSelectionTo = Double.valueOf(m_seriesRangeSelection.getMaxRange()).intValue();
}
// create image function
ReadImgTableFunction<T> rifp = new ReadImgTableFunction<>(exec, rowCount, m_planeSelect, readImage,
readMetadata, m_readAllMetaDataModel.getBooleanValue(), m_checkFileFormat.getBooleanValue(),
m_isGroupFiles.getBooleanValue(), seriesSelectionFrom, seriesSelectionTo, imgFac,
ColumnCreationMode.fromString(m_colCreationMode.getStringValue()), imgIdx,
m_pixelType.getStringValue());
return rifp;
}
}