/*
* ------------------------------------------------------------------------
*
* 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.imgwriter2;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Collection;
import org.apache.commons.io.FileUtils;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.StringValue;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
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.SettingsModelColumnName;
import org.knime.core.node.defaultnodesettings.SettingsModelInteger;
import org.knime.core.node.defaultnodesettings.SettingsModelString;
import org.knime.core.node.port.PortObjectSpec;
import org.knime.core.node.streamable.DataTableRowInput;
import org.knime.core.node.streamable.InputPortRole;
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.StreamableOperator;
import org.knime.core.node.util.CheckUtils;
import org.knime.core.util.FileUtil;
import org.knime.knip.base.data.img.ImgPlusValue;
import org.knime.knip.base.node.NodeUtils;
import org.knime.knip.core.util.MinimaUtils;
import io.scif.FormatException;
import net.imagej.ImgPlus;
import net.imglib2.type.numeric.RealType;
/**
*
*
* @param <T>
* image type
* @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>
*
*/
public class ImgWriter2NodeModel<T extends RealType<T>> extends NodeModel {
private static final NodeLogger LOGGER = NodeLogger.getLogger(ImgWriter2NodeModel.class);
/*
* SETTING MODELS
*/
private final SettingsModelString m_imgColumn = ImgWriter2SettingsModels.createImgColumnModel();
private final SettingsModelColumnName m_filenameColumn = ImgWriter2SettingsModels.createFileNameColumnModel();
/*
* Custom filename options.
*/
private final SettingsModelBoolean m_customNameOption = ImgWriter2SettingsModels.createUseCustomFileNameModel();
private final SettingsModelString m_customFileName = ImgWriter2SettingsModels.createCustomFileNameModel();
/*
* Output options.
*/
private final SettingsModelBoolean m_overwrite = ImgWriter2SettingsModels.createOverwriteModel();
private final SettingsModelBoolean m_forceMkdir = ImgWriter2SettingsModels.createForceDirCreationModel();
private final SettingsModelString m_directory = ImgWriter2SettingsModels.createDirectoryModel();
private SettingsModelBoolean m_useAbsolutePaths = ImgWriter2SettingsModels.createAbsolutePathsModel();
private final SettingsModelString m_format = ImgWriter2SettingsModels.createFormatModel();
private final SettingsModelString m_compression = ImgWriter2SettingsModels.createCompressionModel();
private final SettingsModelInteger m_frameRate = ImgWriter2SettingsModels.createFrameRateModel();
private SettingsModelBoolean m_writeSequentially = ImgWriter2SettingsModels.createWriteSequentiallyModel();
/*
* MAPPING SETTINGS MODELS.
*/
private final SettingsModelString m_tMapping = ImgWriter2SettingsModels.createTimeMappingModel();
private final SettingsModelString m_cMapping = ImgWriter2SettingsModels.createChannelMappingModel();
private final SettingsModelString m_zMapping = ImgWriter2SettingsModels.createZMappingModel();
private final Collection<SettingsModel> m_settingsCollection;
/**
* One input one output.
*
*/
public ImgWriter2NodeModel() {
super(1, 0);
// for state consistency:
m_customFileName.setEnabled(false);
m_settingsCollection = new ArrayList<SettingsModel>();
m_settingsCollection.add(m_directory);
m_settingsCollection.add(m_filenameColumn);
m_settingsCollection.add(m_imgColumn);
m_settingsCollection.add(m_format);
m_settingsCollection.add(m_compression);
m_settingsCollection.add(m_overwrite);
m_settingsCollection.add(m_zMapping);
m_settingsCollection.add(m_cMapping);
m_settingsCollection.add(m_tMapping);
m_settingsCollection.add(m_frameRate);
m_settingsCollection.add(m_forceMkdir);
m_settingsCollection.add(m_customNameOption);
m_settingsCollection.add(m_customFileName);
}
/**
* {@inheritDoc}
*/
@Override
protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
// check if dimension mapping is valid
checkDimensionMapping();
// check if configured filename column is still available
String imgNamColumn = m_filenameColumn.getStringValue();
// not a newly created node
if (imgNamColumn != null && !imgNamColumn.equals("") && !inSpecs[0].containsName(imgNamColumn)) {
throw new InvalidSettingsException("The configured Filename column: '" + m_filenameColumn.getStringValue()
+ "' is no longer avaiable!");
}
// check img column
String imgColumn = m_imgColumn.getStringValue();
if (imgColumn.equals("")) { // newly created node
if ((NodeUtils.autoOptionalColumnSelection(inSpecs[0], m_imgColumn, ImgPlusValue.class)) >= 0) {
setWarningMessage("Auto-configure Image Column: " + m_imgColumn.getStringValue());
} else {
throw new InvalidSettingsException("No Image column avaiable!");
}
} else if (!inSpecs[0].containsName(imgColumn)) {
throw new InvalidSettingsException("The configured Filename column: '" + m_filenameColumn.getStringValue()
+ "' is no longer avaiable!");
}
return null;
}
/**
* Checks that the dimension mappings, making sure no dimensions are mapped
* to the same label.
*
* @throws InvalidSettingsException
* when dimensions are mapped to the same labels.
*/
private void checkDimensionMapping() throws InvalidSettingsException {
if (m_zMapping.getStringValue().equals(m_cMapping.getStringValue())
|| m_zMapping.getStringValue().equals(m_tMapping.getStringValue())
|| m_cMapping.getStringValue().equals(m_tMapping.getStringValue())) {
throw new InvalidSettingsException("Dimensions must not be mapped to the same label!");
}
}
/**
* {@inheritDoc}
*/
@Override
protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
throws Exception {
run(new DataTableRowInput(inData[0]), exec, inData[0].size(), inData[0].getDataTableSpec());
return null;
}
protected void run(final RowInput inData, final ExecutionContext exec, final long size, final DataTableSpec spec)
throws InvalidSettingsException, IOException, URISyntaxException, MalformedURLException, FormatException,
CanceledExecutionException, InvalidPathException, InterruptedException {
checkDimensionMapping();
String directory = null;
// only initialize output directory when needed
if (!m_useAbsolutePaths.getBooleanValue()) {
Path folderPath = createOutputPath();
directory = folderPath.toString();
if (!directory.endsWith("/")) { // fix directory path
directory += "/";
}
}
// loop constants
final boolean overwrite = m_overwrite.getBooleanValue();
final boolean useCustomName = m_customNameOption.getBooleanValue();
final boolean useAbsolutPaths = m_useAbsolutePaths.getBooleanValue();
final boolean forceMkdir = m_forceMkdir.getBooleanValue();
final String customName = m_customFileName.getStringValue();
final int nameColIndex = spec.findColumnIndex(m_filenameColumn.getStringValue());
final int imgColIndex = spec.findColumnIndex(m_imgColumn.getStringValue());
final String format = m_format.getStringValue();
final String compression = m_compression.getStringValue();
/* File name number magic */
// get number of digits needed for padding
final int digits;
if (size == -1) {
// very magic
digits = (int) 7;
} else {
digits = (int) Math.log10(size) + 1;
}
final String digitStringFormat = "%0" + digits + "d";
int imgCount = 0;
// loop variables
ImgPlus<T> img;
String outfile;
boolean error = false;
final ImgWriter2 writer = new ImgWriter2().setWriteSequantially(m_writeSequentially.getBooleanValue())
.setFramesPerSecond(m_frameRate.getIntValue());
DataRow row;
while ((row = inData.poll()) != null) {
// set the filename
if (useAbsolutPaths) {
if (nameColIndex == -1) {
outfile = row.getKey().getString();
} else {
outfile = ((StringValue) row.getCell(nameColIndex)).getStringValue();
}
} else if (useCustomName) {
outfile = directory + customName + String.format(digitStringFormat, imgCount);
} else if (nameColIndex == -1) {
outfile = directory + row.getKey().getString();
} else { // file name column configured
try {
outfile = directory + ((StringValue) row.getCell(nameColIndex)).getStringValue();
} catch (ClassCastException e1) {
throw new IllegalArgumentException("Missing value in the filename column in row: " + row.getKey());
}
}
outfile += "." + writer.getSuffix(format);
// handle file location
final File f = FileUtil.resolveToPath(FileUtil.toURL(outfile)).toFile();
if (f.exists()) {
if (overwrite) {
LOGGER.warn("The file " + outfile + " already exits and will be OVERWRITTEN.");
f.delete();
} else {
throw new InvalidSettingsException(
"The file " + outfile + " exits and must not be overwritten due to user settings.");
}
// filename contained path to non existent directory
} else if (!f.getParentFile().exists()) {
if (forceMkdir) {
LOGGER.info("Creating directory: " + f.getParentFile().getPath());
FileUtils.forceMkdir(f.getParentFile());
} else {
throw new InvalidSettingsException("Output directory " + f.getParentFile().getPath()
+ " doesn't exist, you can force the creation" + " in the node settings.");
}
}
try {
img = MinimaUtils.getZeroMinImgPlus(((ImgPlusValue<T>) row.getCell(imgColIndex)).getImgPlus());
} catch (ClassCastException e) {
throw new IllegalArgumentException("Missing value in the img column in row: " + row.getKey());
}
// create dimensions mapping
final int[] map = createDimMapping(img);
try {
writer.writeImage(img, FileUtil.resolveToPath(FileUtil.toURL(outfile)).toString(), format, compression,
map);
} catch (final FormatException | IOException e) {
LOGGER.error("Error while writing image " + outfile + " : " + e.getMessage(), e);
error = true;
} catch (final UnsupportedOperationException e) {
LOGGER.error("Error while writing image " + outfile + " : "
+ "Check the filename for illegal characters! " + e.getMessage(), e);
error = true;
}
exec.setProgress((double) imgCount / size);
exec.checkCanceled();
imgCount++;
}
if (error) {
setWarningMessage("Some errors occured during the writing process!");
}
}
/**
* Creates and checks the output folder.
*
* @return the Path of the output folder.
* @throws InvalidSettingsException
* @throws IOException
* @throws URISyntaxException
* @throws MalformedURLException
*/
private Path createOutputPath()
throws InvalidSettingsException, IOException, URISyntaxException, MalformedURLException {
// check and locate target folder
try {
CheckUtils.checkDestinationDirectory(m_directory.getStringValue());
} catch (InvalidSettingsException e) {
// allow creation of nonexistent directories if set in the options.
if (e.getMessage().endsWith("does not exist")) {
if (!m_forceMkdir.getBooleanValue()) { // option not set
throw new InvalidSettingsException("Output directory doesn't exist, "
+ "you can force the creation in the" + " node settings.");
}
} else {
// don't hide other exceptions
throw e;
}
}
Path folderPath = FileUtil.resolveToPath(FileUtil.toURL(m_directory.getStringValue()));
if (folderPath == null) {
throw new InvalidSettingsException("Could not locate:" + m_directory.getStringValue()
+ ", are you trying to write to an non local directory?");
}
// handle target folder
final File folderFile = folderPath.toFile();
if (!folderFile.exists()) { // create nonexistent folders must be set to
// reach this point!.
try {
LOGGER.info("Creating directory: " + m_directory.getStringValue());
FileUtils.forceMkdir(folderFile);
} catch (final IOException e1) {
LOGGER.error("Selected Path " + folderPath + " is not a directory");
throw new IOException("Directory unreachable or file exists with the same name");
}
}
return folderPath;
}
/**
* Creates the dimension mapping for the given Img.
*
* @param img
* the image
* @return the dimension mapping
*/
private int[] createDimMapping(ImgPlus<T> img) {
final int[] map = new int[] { -1, -1, -1 };
for (int d = 2; d < img.numDimensions(); d++) {
if (img.axis(d).type().getLabel().equals(m_zMapping.getStringValue())) {
map[0] = d - 2;
}
if (img.axis(d).type().getLabel().equals(m_cMapping.getStringValue())) {
map[1] = d - 2;
}
if (img.axis(d).type().getLabel().equals(m_tMapping.getStringValue())) {
map[2] = d - 2;
}
}
return map;
}
/**
* {@inheritDoc}
*/
@Override
protected void loadInternals(final File nodeInternDir, final ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
//
}
/**
* {@inheritDoc}
*/
@Override
protected void reset() {
//
}
/**
* {@inheritDoc}
*/
@Override
protected void saveInternals(final File nodeInternDir, final ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
//
}
/**
* {@inheritDoc}
*/
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
for (final SettingsModel sm : m_settingsCollection) {
sm.saveSettingsTo(settings);
}
try {
// new in 1.4.0
m_useAbsolutePaths.saveSettingsTo(settings);
} catch (Exception e) {
//
}
}
/**
* {@inheritDoc}
*/
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
for (final SettingsModel sm : m_settingsCollection) {
sm.validateSettings(settings);
}
try {
// new in 1.4.0
m_useAbsolutePaths.validateSettings(settings);
} catch (Exception e) {
//
}
}
@Override
public StreamableOperator createStreamableOperator(PartitionInfo partitionInfo, PortObjectSpec[] inSpecs)
throws InvalidSettingsException {
return new StreamableOperator() {
@Override
public void runFinal(PortInput[] inputs, PortOutput[] outputs, ExecutionContext exec) throws Exception {
run(((RowInput) inputs[0]), exec, -1, (DataTableSpec) inSpecs[0]);
}
};
}
@Override
public InputPortRole[] getInputPortRoles() {
return new InputPortRole[] { InputPortRole.DISTRIBUTED_STREAMABLE };
}
/**
* {@inheritDoc}
*/
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
for (final SettingsModel sm : m_settingsCollection) {
sm.loadSettingsFrom(settings);
}
try {
// new in 1.4.0
m_useAbsolutePaths.loadSettingsFrom(settings);
} catch (Exception e) {
//
}
}
}