public async Task ImportAsync(DicomDataset dicom)
{
//var patient = ToPatient(dicom);
//var study = ToStudy(dicom);
//var series = ToSeries(dicom);
//var image = ToImage(dicom);
//image.ReferencedFileID = await _fileRepo.SaveAsync(dicom);
//series.ImageCollection.Add(image);
//study.SeriesCollection.Add(series);
//study.Paitent = patient;
//await _studyRepo.AddOrUpdateImageAsync(study);
string studyUID = dicom.GetSingleValue <string>(DicomTag.StudyInstanceUID);
DicomStudy study = await _studyRepo.GetAsync(studyUID);
// Create one study if the studyUID doesn't exist.
if (study is NotFoundStudy)
{
study = DicomStudy.CreateFromDicom(dicom);
}
else
{
study.AddImageItem(dicom);
}
}
public async Task <DicomStudy> Add(DicomStudy study)
{
var collection = _context.Studies;
await collection.InsertOneAsync(study).ConfigureAwait(false);
return(study);
}
private void WriteStudyObjectToDb(DicomStudy study, PatientInformation patient)
{
if (study != null && patient != null)
{
AppSingleton.DatabaseService.SaveStudy(study, patient);
}
}
/// <summary>
/// Read the structure set from a DICOM dataset.
/// </summary>
/// <param name="ds"></param>
/// <returns></returns>
public static RadiotherapyStruct Read(DicomDataset ds)
{
var patient = DicomPatient.Read(ds);
var study = DicomStudy.Read(ds);
var series = DicomRTSeries.Read(ds);
var equipment = DicomEquipment.Read(ds);
var structureSet = DicomRTStructureSet.Read(ds);
// DicomRTStructureSetROI.RoiNumber is the primary key. We try and locate the first observation and roiContour data for eaach
// RoiNumber encountered.
var structures = DicomRTStructureSetROI.Read(ds);
var contoursData = DicomRTContour.Read(ds);
var observations = DicomRTObservation.Read(ds);
var allContours = new List <RadiotherapyContour>();
foreach (var s in structures)
{
var roiContours = contoursData.FirstOrDefault(c => c.ReferencedRoiNumber == s.Key);
var roiObservation = observations.FirstOrDefault(o => o.ReferencedRoiNumber == s.Key);
// we insist both must exist
if (roiContours != null && roiObservation != null)
{
allContours.Add(new RadiotherapyContour(roiContours, s.Value, roiObservation));
}
}
return(new RadiotherapyStruct(structureSet, patient, equipment, study, series, allContours));
}
static async Task InsertStudyToDbAsync(DicomStudy study)
{
var client = new MongoClient(connUrl);
IMongoDatabase db = client.GetDatabase(dbName);
var collection = db.GetCollection <DicomStudy>(collectionName);
var findOnes = collection.Find(s => s.StudyUID == study.StudyUID);
if (findOnes.Any())
{
var one = findOnes.First();
foreach (var item in study.SeriesCollection)
{
if (one.SeriesCollection.Any(s => s.SeriesUID == item.SeriesUID) == false)
{
// one.SeriesCollection.Add(item);
}
}
await collection.ReplaceOneAsync(s => s.StudyUID == study.StudyUID, one);
}
else
{
await collection.InsertOneAsync(study);
}
}
public void SaveStudy(DicomStudy study, PatientInformation patient)
{
if (study == null)
{
throw new ArgumentNullException(nameof(study));
}
if (patient == null)
{
throw new ArgumentNullException(nameof(patient));
}
if (string.IsNullOrWhiteSpace(patient.PatientKey))
{
throw new ArgumentNullException("patient.PatientKey");
}
string strNow = DatabaseDateString(DateTime.Now);
var cmd = _conn.CreateCommand();
cmd.CommandText = "INSERT INTO Study(ID, StudyDate, StudyDescription, PatientID) VALUES (@ID, @studydate, @studydescription, @patientID)";
cmd.Prepare();
Guid studyID = Guid.NewGuid();
study.ID = studyID;
cmd.Parameters.AddWithValue("@ID", DatabaseGuidString(studyID));
cmd.Parameters.AddWithValue("@studydate", DatabaseDateString(GetDicomStudyDate(study)));
cmd.Parameters.AddWithValue("@studydescription", study.StudyDescription);
cmd.Parameters.AddWithValue("@patientID", patient.PatientKey);
cmd.ExecuteNonQuery();
}
/// <summary>
/// Called when we open an existing structure set. Note we preserve the SeriesUID and the Series Description. (this is arguable if it
/// did not originate from us)
/// </summary>
/// <param name="structureSet"></param>
/// <param name="patient"></param>
/// <param name="equipment"></param>
/// <param name="study"></param>
/// <param name="series"></param>
/// <param name="contours"></param>
public RadiotherapyStruct(
DicomRTStructureSet structureSet, DicomPatient patient, DicomEquipment equipment,
DicomStudy study, DicomRTSeries series, IList <RadiotherapyContour> contours)
{
RTSeries = series;
Patient = patient;
Equipment = equipment;
Study = study;
StructureSet = structureSet;
Contours = contours;
}
/// <summary>
/// Add or update an image record (contains in <see cref="DicomStudy"/>) to database.
/// </summary>
/// <param name="study"></param>
/// <returns></returns>
public async Task AddOrUpdateImageAsync(DicomStudy study)
{
// Check image record.
if (CheckImageLevel(study) == false)
{
return;
}
var collection = GetDbCollection();
await InsertImageAsync(study, collection);
}
public List <DicomSeries> RetrieveStudySeriesDetails(DicomStudy study)
{
if (study == null)
{
throw new ArgumentNullException(nameof(study));
}
List <DicomSeries> list = new List <DicomSeries>();
try
{
var cmd = _conn.CreateCommand();
cmd.CommandText =
@"SELECT ID, SeriesDate, SeriesDescription, StudyID, Thumbnail FROM Series WHERE StudyID=@studyID";
cmd.Prepare();
cmd.Parameters.AddWithValue("@studyID", study.ID.ToString());
var reader = cmd.ExecuteReader();
string ID;
string seriesDate;
string seriesDescription;
string studyID;
byte[] thumbnail;
while (reader.Read())
{
ID = GetColumnValue <string>(reader, "ID");
seriesDate = GetColumnValue <string>(reader, "SeriesDate");
seriesDescription = GetColumnValue <string>(reader, "SeriesDescription");
studyID = GetColumnValue <string>(reader, "StudyID");
thumbnail = GetColumnValue <byte[]>(reader, "Thumbnail");
var series = CreateSeries(ID, seriesDate, seriesDescription, study, thumbnail);
list.Add(series);
}
}
catch (Exception e)
{
System.Diagnostics.Debug.WriteLine(e.Message);
System.Diagnostics.Debug.Assert(false, e.Message);
}
return(list);
}
public void SaveSeries(DicomSeries series, DicomStudy study, PatientInformation patient, string studyFolderPath)
{
if (series == null)
{
throw new ArgumentNullException(nameof(series));
}
if (study == null)
{
throw new ArgumentNullException(nameof(study));
}
if (patient == null)
{
throw new ArgumentNullException(nameof(patient));
}
if (string.IsNullOrWhiteSpace(patient.PatientKey))
{
throw new ArgumentNullException("patient.PatientKey");
}
string strNow = DatabaseDateString(DateTime.Now);
var pngFileList =
System.IO.Directory.EnumerateFiles(studyFolderPath, series.SeriesFileName + "*.png").ToList();
string pngFile = pngFileList.Count == 1 ? pngFileList[0] : "";
byte[] thumbnail = Utilities.CreateThumbnailFromFile(pngFile, 64, 64);
var cmd = _conn.CreateCommand();
cmd.CommandText =
"INSERT INTO Series(ID, SeriesDate, SeriesDescription, StudyID, DrapeUsedAtCapture, Thumbnail) VALUES (@ID, @seriesdate, @seriesdescription, @studyID, @drapeusedatcapture, @thumbnail)";
cmd.Prepare();
Guid seriesID = Guid.NewGuid();
series.ID = seriesID;
cmd.Parameters.AddWithValue("@ID", DatabaseGuidString(series.ID));
cmd.Parameters.AddWithValue("@seriesdate", DatabaseDateString(ParseDicomDateToDateTime(series.SeriesDate)));
cmd.Parameters.AddWithValue("@seriesdescription", series.SeriesDescription);
cmd.Parameters.AddWithValue("@studyID", DatabaseGuidString(study.ID));
cmd.Parameters.AddWithValue("@drapeusedatcapture", series.DrapeUsedAtCapture ? 1 : 0);
cmd.Parameters.AddWithValue("@drapeusedatcapture", series.DrapeUsedAtCapture ? 1 : 0);
cmd.Parameters.Add("@thumbnail", DbType.Binary, 20).Value = thumbnail;
cmd.ExecuteNonQuery();
}
private async Task InsertImageAsync(DicomStudy study, IMongoCollection <DicomStudy> collection)
{
// Has study?
var findOnes = collection.Find(s => s.StudyUID == study.StudyUID);
if (findOnes.Any() == false)
{
await collection.InsertOneAsync(study);
return;
}
// Has series?
var one = findOnes.First();
var series = one.SeriesCollection.FirstOrDefault(s => s.SeriesUID == study.SeriesCollection.First().SeriesUID);
if (series == null)
{
var addSeries = Builders <DicomStudy> .Update.Push(s => s.SeriesCollection, study.SeriesCollection.FirstOrDefault());
await collection.UpdateOneAsync(s => s.StudyUID == study.StudyUID, addSeries);
return;
}
// Has image?
//var theImage = study.SeriesCollection.First().ImageCollection.FirstOrDefault();
//var image = series.ImageCollection.FirstOrDefault(img => img.SOPInstanceUID == theImage.SOPInstanceUID);
//if (image == null)
//{
// var filter = Builders<DicomStudy>.Filter.Where(s => s.StudyUID == study.StudyUID)
// & Builders<DicomStudy>.Filter.Where(d => d.SeriesCollection.Any(r => r.SeriesUID == series.SeriesUID));
// var updateSeries = Builders<DicomStudy>.Update.Push(s => s.SeriesCollection[-1].ImageCollection, theImage);
// await collection.UpdateOneAsync(filter, updateSeries);
// return;
//}
//// Need change image record?
//if (image.Equals(theImage) == false)
//{
// image.ImageNumber = theImage.ImageNumber;
// image.ReferencedFileID = theImage.ReferencedFileID;
// var imageFilter = Builders<DicomStudy>.Filter.Where(s => s.StudyUID == study.StudyUID)
// & Builders<DicomStudy>.Filter.Where(d => d.SeriesCollection.Any(r => r.SeriesUID == series.SeriesUID));
// var updateImage = Builders<DicomStudy>.Update.Set(ss => ss.SeriesCollection[-1].ImageCollection, series.ImageCollection);
// await collection.UpdateOneAsync(imageFilter, updateImage);
//}
}
/// <summary>
/// This method will split dicom file to series and add to study object
/// </summary>
/// <param name="study"></param>
/// <param name="dicomFile"></param>
private void FindMatchingSeriesOrSplit(List <DicomStudy> studies, DicomFile dicomFile)
{
var seriesInstanceUID = dicomFile.Dataset.Get <string>(DicomTag.SeriesInstanceUID);
var studyInstanceUID = dicomFile.Dataset.Get <string>(DicomTag.StudyInstanceUID);
bool matchingStudyFound = false;
//first add study to list
foreach (var study in studies)
{
//check if study is in list
if (study.StudyInstanceUid == studyInstanceUID)
{
matchingStudyFound = true;
bool matchingSeriesFound = false;
foreach (var series in study.Series)
{
if (series.SeriesInstanceUid == seriesInstanceUID)
{
matchingSeriesFound = true;
//if series found then add the dicomfile to instance
series.Instances.Add(dicomFile);
}
}
//add series if matching series not found
if (matchingSeriesFound == false)
{
DicomSeries dicomSeries = new DicomSeries(dicomFile);
study.Series.Add(dicomSeries);
}
}
}
//check if study is in list if not add new study and add the series and instance
if (matchingStudyFound == false)
{
DicomStudy dicomStudy = new DicomStudy(dicomFile);
DicomSeries dicomSeries = new DicomSeries(dicomFile);
dicomSeries.Instances.Add(dicomFile);
dicomStudy.Series.Add(dicomSeries);
studies.Add(dicomStudy);
}
}
/// <summary>
/// Serialize the structure set to a DICOM dataset.
/// </summary>
/// <param name="ds"></param>
/// <param name="s"></param>
public static void Write(DicomDataset ds, RadiotherapyStruct s)
{
DicomPatient.Write(ds, s.Patient);
DicomStudy.Write(ds, s.Study);
DicomRTSeries.Write(ds, s.RTSeries);
DicomEquipment.Write(ds, s.Equipment);
DicomRTStructureSet.Write(ds, s.StructureSet);
// For each ROI, gather the contours, observations and roi details into seperate arrays and serialize
var rois = s.Contours.Select(c => c.StructureSetRoi);
var contours = s.Contours.Select(c => c.DicomRtContour);
var observations = s.Contours.Select(c => c.DicomRtObservation);
DicomRTStructureSetROI.Write(ds, rois);
DicomRTContour.Write(ds, contours);
DicomRTObservation.Write(ds, observations);
}
private void WriteSeriesObjectToDb(DicomSeries series, DicomStudy study, PatientInformation patient, string studyFolderPath)
{
if (series != null && study != null && patient != null && !string.IsNullOrWhiteSpace(studyFolderPath))
{
AppSingleton.DatabaseService.SaveSeries(series, study, patient, studyFolderPath);
var seriesImageFiles =
System.IO.Directory.EnumerateFiles(studyFolderPath, series.SeriesFileName + "*.*");
foreach (string filename in seriesImageFiles)
{
if (filename.EndsWith(".txt") || filename.EndsWith(".png"))
{
continue;
}
AppSingleton.DatabaseService.SaveSeriesImageFile(series, studyFolderPath, filename);
}
}
}
private DateTime GetDicomStudyDate(DicomStudy study)
{
if (study == null)
{
throw new ArgumentNullException(nameof(study));
}
if (!string.IsNullOrWhiteSpace(study.StudyDateLongForm))
{
DateTime studyDate;
if (!DateTime.TryParse(study.StudyDateLongForm, out studyDate))
{
studyDate = ParseDicomDateToDateTime(study.StudyDate);
}
return(studyDate);
}
else
{
return(ParseDicomDateToDateTime(study.StudyDate));
}
}
private bool CheckImageLevel(DicomStudy study)
{
var theImage = study.SeriesCollection.FirstOrDefault()?.ImageCollection.FirstOrDefault();
return(theImage != null);
}
public async Task Update(DicomStudy study)
{
var collection = _context.Studies;
await collection.ReplaceOneAsync(s => s.StudyUID == study.StudyUID, study);
}
public DicomSeries CreateSeries(string ID, string seriesDate, string seriesDescription, DicomStudy study, byte[] thumbnail)
{
DateTime seriesDateTime;
DateTime.TryParse(seriesDate, out seriesDateTime);
var series = new DicomSeries(study.PatientID.ToString(), study, null)
{
ID = Guid.Parse(ID),
SeriesDate = seriesDateTime.ToShortDateString(),
SeriesTime = seriesDateTime.ToShortTimeString(),
SeriesDescription = seriesDescription,
};
series.DicomSeriesDescription.Thumbnail = Convert.ToBase64String(thumbnail);
return(series);
}
private static DicomStudy ToStudy(DicomDataset record)
{
// This cannot work.
return(DicomStudy.CreateFromDicom(record));
}
public async Task AddOrUpdateSeriesAsync(DicomStudy study)
{
await InsertStudyToDbAsync(study);
}