Java tutorial
/* * ------------------------------------------------------------------------ * * 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 io.scif.FormatException; import java.io.File; import java.io.IOException; import java.net.MalformedURLException; import java.net.URISyntaxException; import java.nio.file.Path; import java.util.ArrayList; import java.util.Collection; import net.imagej.ImgPlus; import net.imglib2.type.numeric.RealType; 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.util.CheckUtils; import org.knime.core.util.FileUtil; import org.knime.knip.base.data.img.ImgPlusValue; import org.knime.knip.base.node.NodeUtils; /** * * * @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} */ @SuppressWarnings("unchecked") @Override protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception { 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 = inData[0].getDataTableSpec().findColumnIndex(m_filenameColumn.getStringValue()); final int imgColIndex = inData[0].getDataTableSpec().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 = (int) Math.log10(inData[0].getRowCount()) + 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()); for (DataRow row : inData[0]) { // set the filename if (useAbsolutPaths) { 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 = ((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 / inData[0].getRowCount()); exec.checkCanceled(); imgCount++; } if (error) { setWarningMessage("Some errors occured during the writing process!"); } return null; } /** * 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) { // } } /** * {@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) { // } } }