Create dicomdir file using dcm4che based on code from dcmdir command line tool

App.java

import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.UID;
import org.dcm4che3.data.VR;
import org.dcm4che3.io.DicomEncodingOptions;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.media.DicomDirReader;
import org.dcm4che3.media.DicomDirWriter;
import org.dcm4che3.media.RecordFactory;
import org.dcm4che3.media.RecordType;
import org.dcm4che3.tool.common.FilesetInfo;
import org.dcm4che3.util.UIDUtils;

import java.io.File;
import java.io.IOException;

/*
 * This Java source file was generated by the Gradle 'init' task.
 */
public class App {

    // The dicomdir_filename file to create
    File dicomdir_filename;
    // The directory containing the DCM files
    File dicom_dirname;

    DicomEncodingOptions encOpts = DicomEncodingOptions.DEFAULT;
    FilesetInfo fsInfo = new FilesetInfo();
    boolean checkDuplicate = false;
    RecordFactory recFact = new RecordFactory();

    DicomDirReader in;
    DicomDirWriter out;

    public App(String dicomdir_filename, String dicom_dirname) {
        this.dicomdir_filename = new File(dicomdir_filename);
        this.dicom_dirname = new File(dicom_dirname);
    }

    public static void main(String[] args) throws Exception {
        //System.out.println(new File(".").getAbsolutePath());

        App app = new App("DICOMDIR","DICOM");
        app.start();
    }

    public void start() throws IOException {
        create(this.dicomdir_filename);
        int num = 0;
        num = addReferenceTo(this.dicom_dirname);
        close();
    }

    protected void create(File file) throws IOException {
        DicomDirWriter.createEmptyDirectory(file,
                UIDUtils.createUIDIfNull(fsInfo.getFilesetUID()),
                fsInfo.getFilesetID(),
                fsInfo.getDescriptorFile(),
                fsInfo.getDescriptorFileCharset());
        in = out = DicomDirWriter.open(file);
        out.setEncodingOptions(encOpts);
    }

    protected int addReferenceTo(File f) throws IOException {
        int n = 0;
        if (f.isDirectory()) {
            for (String s : f.list())
                n += addReferenceTo(new File(f, s));
            return n;
        }
        // do not add reference to DICOMDIR
        if (f.equals(this.dicomdir_filename))
            return 0;

        Attributes fmi;
        Attributes dataset;
        DicomInputStream din = null;
        try {
            din = new DicomInputStream(f);
            din.setIncludeBulkData(DicomInputStream.IncludeBulkData.NO);
            fmi = din.readFileMetaInformation();
            dataset = din.readDataset(-1, Tag.PixelData);
        } catch (IOException e) {
            System.out.println("failed to parse image '" + f + "' - " + e.getMessage());
            return 0;
        } finally {
            if (din != null)
                try { din.close(); } catch (Exception ignore) {}
        }
        char prompt = '.';
        if (fmi == null) {
            fmi = dataset.createFileMetaInformation(UID.ImplicitVRLittleEndian);
            prompt = 'F';
        }
        String iuid = fmi.getString(Tag.MediaStorageSOPInstanceUID, null);
        if (iuid == null) {
            System.out.println("skip DICOM file '" + f + "' without SOP Instance UID (0008, 0018)");
            return 0;
        }

        return addRecords(dataset, n, out.toFileIDs(f), prompt, iuid, fmi);
    }

    private int addRecords(Attributes dataset, int num, String[] fileIDs, char prompt, String iuid, Attributes fmi)
            throws IOException {
        String pid = dataset.getString(Tag.PatientID, null);
        String styuid = dataset.getString(Tag.StudyInstanceUID, null);
        String seruid = dataset.getString(Tag.SeriesInstanceUID, null);

        if (styuid != null) {
            if (pid == null) {
                dataset.setString(Tag.PatientID, VR.LO, pid = styuid);
                prompt = prompt == 'F' ? 'P' : 'p';
            }
            Attributes patRec = in.findPatientRecord(pid);
            if (patRec == null) {
                patRec = recFact.createRecord(RecordType.PATIENT, null,
                        dataset, null, null);
                out.addRootDirectoryRecord(patRec);
                num++;
            }
            Attributes studyRec = in.findStudyRecord(patRec, styuid);
            if (studyRec == null) {
                studyRec = recFact.createRecord(RecordType.STUDY, null,
                        dataset, null, null);
                out.addLowerDirectoryRecord(patRec, studyRec);
                num++;
            }

            if (seruid != null) {
                Attributes seriesRec = in.findSeriesRecord(studyRec, seruid);
                if (seriesRec == null) {
                    seriesRec = recFact.createRecord(RecordType.SERIES, null,
                            dataset, null, null);
                    out.addLowerDirectoryRecord(studyRec, seriesRec);
                    num++;
                }

                if (iuid != null) {
                    Attributes instRec;
                    if (checkDuplicate) {
                        instRec = in.findLowerInstanceRecord(seriesRec, false, iuid);
                        if (instRec != null) {
                            System.out.print('-');
                            return 0;
                        }
                    }
                    instRec = recFact.createRecord(dataset, fmi, fileIDs);
                    out.addLowerDirectoryRecord(seriesRec, instRec);
                    num++;
                }
            }
        } else {
            if (iuid != null) {
                if (checkDuplicate) {
                    if (in.findRootInstanceRecord(false, iuid) != null) {
                        System.out.print('-');
                        return 0;
                    }
                }
                Attributes instRec = recFact.createRecord(dataset, fmi, fileIDs);
                out.addRootDirectoryRecord(instRec);
                prompt = prompt == 'F' ? 'R' : 'r';
                num++;
            }
        }
        System.out.print(prompt);
        return num;
    }

    protected void close() {
        if (in != null) {
            try {
                in.close();
            } catch (IOException ignore) {
            }
        }
        in = null;
        out = null;
    }
}