com.tomdoel.mpg2dcm.EndoscopicFileProcessor.java Source code

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Here is the source code for com.tomdoel.mpg2dcm.EndoscopicFileProcessor.java

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/**
 * mpg2dcm by Tom Doel
 *
 * http://github.com/tomdoel/mpg2dcm
 *
 * Distributed under the MIT License
 */

package com.tomdoel.mpg2dcm;

import org.apache.commons.io.FilenameUtils;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.xml.sax.SAXException;

import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import java.io.File;
import java.io.IOException;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.*;

/**
 * Parses an XML file describing an endoscopic capture that is arranged in a structured file hierarchy
 *
 * <p>Part of <a href="http://github.com/tomdoel/mpg2dcm">mpg2dcm</a>
 *
 * @author Tom Doel
 * @version 1.0
 */
public class EndoscopicFileProcessor {

    private final Attributes dicomAttributes;
    private final List<File> fullVideoFileNames = new ArrayList<File>();
    private final List<File> fullPictureFileNames = new ArrayList<File>();
    private final List<File> fullSoundFileNames = new ArrayList<File>();

    /**
     * Creates the EndoscopicFileProcessor that will parse the XML file
     * @param xmlFile the XML file to be processed
     * @throws ParserConfigurationException
     * @throws SAXException
     * @throws IOException
     */
    public EndoscopicFileProcessor(final File xmlFile)
            throws ParserConfigurationException, SAXException, IOException, ParseException {

        // Parse the XML file to get the tags and video filenames
        EndoscopicXmlParser parser = parseEndoscopicXmlFile(xmlFile);

        // Convert the tags to Dicom tags
        dicomAttributes = convertEndoscopicXmlToDicomAttributes(parser.getTagMap());

        // Get full paths for each video file
        final String path = FilenameUtils.getFullPath(xmlFile.getAbsolutePath());
        for (final String fileName : parser.getVideoFilenames()) {
            fullVideoFileNames.add(new File(path, fileName));
        }
        for (final String fileName : parser.getPictureFilenames()) {
            fullPictureFileNames.add(new File(path, fileName));
        }

        for (final String fileName : parser.getSoundFilenames()) {
            fullSoundFileNames.add(new File(path, fileName));
        }
    }

    /**
     * @return DICOM attributes created by parsing the XML tags
     */
    public Attributes getDicomAttributes() {
        return dicomAttributes;
    }

    /**
     * @return list of video files referenced in the XML file
     */
    public List<File> getVideoFileNames() {
        return fullVideoFileNames;
    }

    /**
     * @return list of picture files referenced in the XML file
     */
    public List<File> getPictureFileNames() {
        return fullPictureFileNames;
    }

    /**
     * @return list of video files referenced in the XML file
     */
    public List<File> getSoundFileNames() {
        return fullSoundFileNames;
    }

    private EndoscopicXmlParser parseEndoscopicXmlFile(final File xmlFile)
            throws IOException, SAXException, ParserConfigurationException {
        final SAXParserFactory factory = SAXParserFactory.newInstance();
        final SAXParser saxParser = factory.newSAXParser();
        final EndoscopicXmlParser parser = new EndoscopicXmlParser();
        saxParser.parse(xmlFile, parser);
        return parser;
    }

    private static Attributes convertEndoscopicXmlToDicomAttributes(final Map<String, String> tagMap)
            throws ParseException {
        final Attributes dicomAttributes = new Attributes();
        for (final Map.Entry<String, String> entry : tagMap.entrySet()) {
            final String key = entry.getKey();
            final String value = entry.getValue();

            if (key.equals("PatID")) {
                dicomAttributes.setString(Tag.PatientID, VR.LO, value);

            } else if (key.equals("PatName")) {
                dicomAttributes.setString(Tag.PatientName, VR.PN, value);

            } else if (key.equals("ProcedureDescription")) {
                dicomAttributes.setString(Tag.StudyDescription, VR.PN, value);

            } else if (key.equals("ProcedureID")) {
                dicomAttributes.setString(Tag.StudyID, VR.PN, value);

            } else if (key.equals("ReferringPhysician")) {
                dicomAttributes.setString(Tag.ReferringPhysicianName, VR.PN, value);

            } else if (key.equals("StudyInstanceUID")) {
                dicomAttributes.setString(Tag.StudyInstanceUID, VR.UI, value);

            } else if (key.equals("SeriesInstanceUID")) {
                dicomAttributes.setString(Tag.SeriesInstanceUID, VR.UI, value);

            } else if (key.equals("OtherPatientID")) {
                dicomAttributes.setString(Tag.OtherPatientIDs, VR.UI, value);

            } else if (key.equals("PATAccession")) {
                dicomAttributes.setString(Tag.AccessionNumber, VR.SH, value);

            } else if (key.equals("PATSex")) {
                dicomAttributes.setString(Tag.PatientSex, VR.CS, value);

            } else if (key.equals("PatBirth")) {
                final DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy", Locale.ENGLISH);
                final Date date = dateFormat.parse(value);
                dicomAttributes.setDate(Tag.PatientBirthDate, VR.DA, date);

            } else if (key.equals("ORDate")) {
                final DateFormat orDateFormat = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss", Locale.ENGLISH);
                final Date orDate = orDateFormat.parse(value);
                dicomAttributes.setDate(Tag.StudyDate, VR.DA, orDate);
                dicomAttributes.setDate(Tag.StudyTime, VR.DA, orDate);

            }
        }
        return dicomAttributes;
    }
}