Encapsulate (save) PDF with FO-DICOM (into a DCM file)

encapsulate.cs

public static void Encapsulate( Patient patient, Study study, Institution institution, string directory, string filename, byte[] pdf )
{
  var name = new DicomPersonName( DicomTag.PatientName, patient.LastName, patient.FirstName,
    patient.MiddleName, patient.NamePrefix, patient.NameSuffix );
  var studyUID = new DicomUID( study.InstanceUID, "Study Instance UID", DicomUidType.SOPInstance );
  var company = Assembly.GetEntryAssembly().GetCustomAttribute<AssemblyCompanyAttribute>().Company;
  var product = Assembly.GetEntryAssembly().GetCustomAttribute<AssemblyProductAttribute>().Product;

  DicomDataset[] refItems = study.Series
      .SelectMany( s => s.Datasets )
      .Select( d => new DicomDataset
      {
          { DicomTag.ReferencedSOPClassUID, d.ClassUID },
          { DicomTag.ReferencedSOPInstanceUID, d.InstanceUID }
      } ).ToArray();

  var sourceInstances = new DicomSequence( DicomTag.SourceInstanceSequence, refItems );
  var conceptName = new DicomSequence( DicomTag.ConceptNameCodeSequence );

  var generator = new DicomUIDGenerator();
  var dataset = new DicomDataset
  {
      { DicomTag.SpecificCharacterSet, series.SpecificCharacterSet },
      { DicomTag.InstanceCreationDate, DateTime.Now },
      { DicomTag.InstanceCreationTime, DateTime.Now },
      { DicomTag.SOPClassUID, DicomUID.EncapsulatedPDFStorage },
      { DicomTag.SOPInstanceUID, generator.Generate() },
      { DicomTag.StudyDate, study.DateTime.Date },
      { DicomTag.ContentDate, DateTime.Now },
      { DicomTag.AcquisitionDateTime, DateTime.Now },
      { DicomTag.StudyTime, study.DateTime },
      { DicomTag.ContentTime, DateTime.Now },
      { DicomTag.AccessionNumber, study.AccessionNumber.ToString( CultureInfo.InvariantCulture ) },
      { DicomTag.Modality, "DOC" },
      { DicomTag.ConversionType, "WSD" },
      { DicomTag.ImageLaterality, planning.PatientSide },
      { DicomTag.Manufacturer, company },
      { DicomTag.ManufacturerModelName, product },
      { DicomTag.ReferringPhysicianName, (string)null },
      { DicomTag.PatientID, patient.ID },
      { DicomTag.PatientBirthDate, patient.BirthDate },
      { DicomTag.PatientSex, patient.Sex },
      { DicomTag.StudyInstanceUID, study.InstanceUID },
      { DicomTag.StudyDescription, study.Description },
      { DicomTag.SeriesInstanceUID, generator.Generate( studyUID ) },
      { DicomTag.SeriesDescription, $"{product} {planning.Description}" },
      { DicomTag.PerformingPhysicianName, Environment.UserName },
      { DicomTag.SeriesDate, DateTime.Now },
      { DicomTag.SeriesTime, DateTime.Now },
      { DicomTag.StudyID, study.ID },
      { DicomTag.SeriesNumber, planning.Series.OrderBy( s => s.Number ).Last().Number + 1 },
      { DicomTag.InstanceNumber, 1 },
      { DicomTag.BurnedInAnnotation, "YES" },
      { DicomTag.DocumentTitle, $"{product} Generated Document" },
      { DicomTag.VerificationFlag, "UNVERIFIED" },
      { DicomTag.MIMETypeOfEncapsulatedDocument, "application/pdf" },
      name,
      sourceInstances,
      conceptName,
      { DicomTag.EncapsulatedDocument, pdf }
  };

  dataset.Add( DicomTag.InstitutionName, institution.Name );
  dataset.Add( DicomTag.InstitutionAddress, institution.Address );
  dataset.Add( DicomTag.InstitutionalDepartmentName, institution.Department );

  var dicomFile = new DicomFile( dataset );
  using ( var file = new FileStream( Path.Combine( directory, filename ), FileMode.Create ) )
  {
      dicomFile.Save( file );
  }
}

Hi Alex,
thank you for that! Can you please share the complete code (with the implementations of Patient, Study and Institution classes)?
thanks

For those interested in a self-contained function creating an PDF Encapsulated Dicom file based on above you can use the following:

public void Encapsulate()
{
string dicom_file = @"C:\DicomFiles\Encapsulated.dcm";
string pdf_file = @"C:\DicomFiles\example.pdf";
byte[] pdf = System.IO.File.ReadAllBytes(pdf_file);

var studyUID = new DicomUID("1234", "Study Instance UID", DicomUidType.SOPInstance);                   
var generator = new DicomUIDGenerator();
var dataset = new DicomDataset
{
      { DicomTag.SpecificCharacterSet,  "ISO_IR 6" },
      { DicomTag.InstanceNumber, 1 },
      { DicomTag.InstanceCreationDate, DateTime.Now },
      { DicomTag.InstanceCreationTime, DateTime.Now },
      { DicomTag.SOPClassUID, DicomUID.EncapsulatedPDFStorage },
      { DicomTag.SOPInstanceUID, "" },
      { DicomTag.ContentDate, DateTime.Now },
      { DicomTag.ContentTime, DateTime.Now },
      { DicomTag.AcquisitionDateTime, DateTime.Now },                           
      { DicomTag.AccessionNumber, "1234"},
      { DicomTag.Modality, "DOC" },
      { DicomTag.ConversionType, "WSD" },
      { DicomTag.ImageLaterality, "" },
      { DicomTag.Manufacturer, "Manufacturer" },
      { DicomTag.ManufacturerModelName, "Product" },

      { DicomTag.ReferringPhysicianName, (string)null },
      { DicomTag.PerformingPhysicianName, "physician" }, 

      { DicomTag.PatientName, "Patient Name"},
      { DicomTag.PatientID, "" },
      { DicomTag.PatientBirthDate, "" },
      { DicomTag.PatientSex, "M" },
      { DicomTag.PatientAge, "" },
      { DicomTag.PatientWeight, "" },
      { DicomTag.PatientAddress, "" },

      { DicomTag.StudyID, "2345" },
      { DicomTag.StudyDate, "0095.07.24" },
      { DicomTag.StudyTime, "093900" },
      { DicomTag.StudyDescription, "" },

      { DicomTag.SeriesNumber, "1234" },
      { DicomTag.SeriesDate, DateTime.Now },
      { DicomTag.SeriesTime, DateTime.Now },
      { DicomTag.SeriesDescription, ""},
      { DicomTag.SeriesInstanceUID, generator.Generate( studyUID ) },    
   
      { DicomTag.BurnedInAnnotation, "YES" },
      { DicomTag.VerificationFlag, "VERIFIED" },
      { DicomTag.MIMETypeOfEncapsulatedDocument, "application/pdf" },         
      { DicomTag.EncapsulatedDocument, pdf }
};

DicomFile file = new DicomFile();           
file.Dataset.Add(dataset);
file.FileMetaInfo.TransferSyntax = DicomTransferSyntax.ImplicitVRLittleEndian; //Specify transfer syntax
file.Save(dicom_file);

}

this is SO awesome! Thanks all!

i notice that when i view the resulting DICOM file/image? with the PDF embedded (using MicroDICOM) i have to click on the PDF to open it in an external reader... will it also work like this if imported into Fuji or if viewed in something like Clear Canvas?

Hi Alex, Thanks for your reference I did pdf upload using this code its great, I have one another question, do you know how to create the KeyImages in dicom in the same way. it would be great if you can provide a sample like pdf upload

Thanks for the code.
I used it in my application with some modifications.
But when sending files to the DCM4CHEE-ARC server, I often received an error like Failure [0110: Processing failure] -> java.io.EOFException.
For a long time I could not understand why some files are sent successfully, while others return an error.
It turned out that the reason is in the length of the PDF file. If it is odd, the server does not accept it.
I solved it this way:

byte[] pdf = await File.ReadAllBytesAsync(pdfFilePath);
if (pdf.Length % 2 == 0)
{
    pdfDataset.Add(DicomTag.EncapsulatedDocument, pdf);
}
else
{
    byte[] pdfEven = new byte[pdf.Length + 1];
    for (int i = 0; i < pdf.Length; i++)
    {
        pdfEven[i] = pdf[i];
    }
    pdfEven[pdf.Length] = 0;

    pdfDataset.Add(DicomTag.EncapsulatedDocument, pdfEven);
}              

After this, all encapsulated PDFs are accepted without errors.

Best regards,
Alieksandr Kuznietsov

Association Abort [source: ServiceProvider; reason: InvalidPDUParameter] I get an error, what could be the cause? I get this error when sending to pacs server.