protected override IEnumerable <fo.DicomDataset> DoFind
(
fo.DicomDataset request,
IQueryOptions options,
string queryLevel,
IEnumerable <IMatchingCondition> conditions
)
{
return(QueryDataAccess.Search(conditions, options, queryLevel));
}
public IMediaId Create
(
fo.DicomDataset dataset,
int frame,
string mediaType,
string transferSyntax
)
{
return(new DicomMediaId(dataset, frame, mediaType, transferSyntax));
}
protected override void Upload(fo.DicomDataset dicomObject, int frame, IStorageLocation storeLocation)
{
var frameIndex = frame - 1;
DicomPixelData pd = DicomPixelData.Create(dicomObject);
byte[] buffer = pd.GetFrame(frameIndex).Data;
storeLocation.Upload(buffer);
}
public IEnumerable <T> ProcessDataSet(fo.DicomDataset dataset)
{
BeginProcessingElements( );
foreach (var element in dataset)
{
ProcessElement(element);
}
return(EndProcessingElements());
}
public fo.DicomDataset Convert(string xmlDcm)
{
fo.DicomDataset ds = new fo.DicomDataset( );
XDocument document = XDocument.Parse(xmlDcm);
ReadChildren(ds, document.Root, 0);
fo.DicomFile df = new fo.DicomFile(ds);
return(ds);
}
private static void FillInstsanceLevel(fo.DicomDataset instanceDs)
{
instanceDs.Add <object>(fo.DicomTag.SpecificCharacterSet, null);
instanceDs.Add <object>(fo.DicomTag.SOPClassUID, null);
instanceDs.Add <object>(fo.DicomTag.SOPInstanceUID, null);
instanceDs.Add <object>(fo.DicomTag.InstanceNumber, null);
instanceDs.Add <object>(fo.DicomTag.Rows, null);
instanceDs.Add <object>(fo.DicomTag.Columns, null);
instanceDs.Add <object>(fo.DicomTag.BitsAllocated, null);
instanceDs.Add <object>(fo.DicomTag.NumberOfFrames, null);
}
private fo.DicomDataset GetReferencedInstsance(fo.DicomDataset ds)
{
var classUID = ds.Get <fo.DicomElement> (fo.DicomTag.SOPClassUID, null);
var sopUID = ds.Get <fo.DicomElement> (fo.DicomTag.SOPInstanceUID, null);
var dataset = new fo.DicomDataset( );
dataset.AddOrUpdate(classUID);
dataset.AddOrUpdate(sopUID);
return(dataset);
}
protected virtual IEnumerable <DicomDataset> QueryInstances(IStudyId studyId)
{
Dicom.DicomDataset ds = new Dicom.DicomDataset();
ds.Add(Dicom.DicomTag.StudyInstanceUID, studyId.StudyInstanceUID);
ds.Add(DicomTag.SeriesInstanceUID, "");
ds.Add(DicomTag.PatientID, "");
ds.Add(DicomTag.PatientName, "");
ds.Add(DicomTag.SeriesDescription, "");
ds.Add(DicomTag.SOPInstanceUID, "");
return(QueryService.FindObjectInstances(ds, GetQueryOptions(studyId)));
}
protected override void Upload(fo.DicomDataset dicomDataset, int frame, IStorageLocation location)
{
fo.DicomFile df = new fo.DicomFile(dicomDataset);
using (Stream stream = new MemoryStream())
{
df.Save(stream);
stream.Position = 0;
location.Upload(stream);
}
}
private IEnumerable <DicomDataset> QueryInstances(string studyInstanceUid)
{
Dicom.DicomDataset ds = new Dicom.DicomDataset();
ds.Add(Dicom.DicomTag.StudyInstanceUID, studyInstanceUid);
ds.Add(DicomTag.SeriesInstanceUID, "");
ds.Add(DicomTag.PatientID, "");
ds.Add(DicomTag.PatientName, "");
ds.Add(DicomTag.SeriesDescription, "");
ds.Add(DicomTag.SOPInstanceUID, "");
return(QueryService.FindObjectInstances(ds, new QueryOptions( )));
}
public ICollection <fo.DicomDataset> Find
(
fo.DicomDataset request,
IQueryOptions options,
string queryLevel
)
{
IEnumerable <IMatchingCondition> conditions = null;
conditions = BuildConditions(request);
return(DoFind(request, options, queryLevel, conditions));
}
private static void FillSeriesLevel(fo.DicomDataset seriesDs)
{
seriesDs.Add <object>(fo.DicomTag.SpecificCharacterSet, null);
seriesDs.Add <object>(fo.DicomTag.Modality, null);
seriesDs.Add <object>(fo.DicomTag.TimezoneOffsetFromUTC, null);
seriesDs.Add <object>(fo.DicomTag.SeriesDescription, null);
seriesDs.Add <object>(fo.DicomTag.RetrieveURI, null);
seriesDs.Add <object>(fo.DicomTag.SeriesInstanceUID, null);
seriesDs.Add <object>(fo.DicomTag.SeriesNumber, null);
seriesDs.Add <object>(fo.DicomTag.NumberOfSeriesRelatedInstances, null);
seriesDs.Add <object>(fo.DicomTag.PerformedProcedureStepStartDate, null);
seriesDs.Add <object>(fo.DicomTag.PerformedProcedureStepStartTime, null);
//seriesDs.Add<object>(fo.DicomTag.RequestAttributesSequence,null) ; //Not supported yet
}
public UncompressedPixelDataWrapper(fo.DicomDataset ds)
{
if (ds.InternalTransferSyntax.IsEncapsulated)
{
Dataset = ds.Clone(DicomTransferSyntax.ImplicitVRLittleEndian);
}
else
{
// pull uncompressed frame from source pixel data
Dataset = ds;
}
PixelData = DicomPixelData.Create(Dataset);
}
protected override fo.DicomDataset GetMediaDataset(fo.DicomDataset data, DicomMediaProperties mediaInfo)
{
//TODO: this is still not working with when images BPP are not compatible from one Transfer to the other (12/16-bit -> 8-bit)
if (!string.IsNullOrWhiteSpace(mediaInfo.TransferSyntax))
{
return(data.Clone(fo.DicomTransferSyntax.Parse(mediaInfo.TransferSyntax)));
}
else if (data.InternalTransferSyntax != fo.DicomTransferSyntax.JPEGProcess1)
{
return(data.Clone(fo.DicomTransferSyntax.JPEGProcess1));
}
return(base.GetMediaDataset(data, mediaInfo));
}
protected virtual void ReadDefaultVr
(
fo.DicomTag tag,
fo.DicomVR vr,
JsonTextReader reader,
fo.DicomDataset dataset,
int level
)
{
//if VR was the first property we already read the right thing above,
//otherwise we'll got it from the dictionary. Could it be defined after the value?
switch (vr.Code)
{
case fo.DicomVRCode.SQ:
{
ReadVr_SQ(reader, tag, dataset, level);
}
break;
case fo.DicomVRCode.PN:
{
ReadVr_PN(reader, tag, dataset);
}
break;
default:
{
List <string> values = new List <string> ( );
while (reader.Read( ) && reader.TokenType == JsonToken.StartArray)
{
while (reader.Read( ) && reader.TokenType != JsonToken.EndArray)
{
values.Add(System.Convert.ToString(reader.Value));
}
break;
}
if (tag == fo.DicomTag.TransferSyntaxUID)
{
TransferSyntaxUID = values.FirstOrDefault( );
}
dataset.AddOrUpdate <string> (vr, tag, values.ToArray( ));
}
break;
}
}
public DCloudCommandResult StoreDicom
(
fo.DicomDataset dataset,
InstanceMetadata metadata
)
{
IStoreCommand storeCommand = CommandFactory.CreateStoreCommand( );
StoreCommandData storeData = new StoreCommandData( )
{
Dataset = dataset, Metadata = metadata
};
return(storeCommand.Execute(storeData));
}
protected virtual void ReadDicomItem
(
JsonTextReader reader,
fo.DicomTag tag,
fo.DicomDataset dataset,
int level
)
{
var vr = tag.DictionaryEntry.ValueRepresentations.FirstOrDefault( );
while (reader.Read( ) && reader.TokenType == JsonToken.PropertyName)
{
string propertyValue = (string)reader.Value;
switch (propertyValue)
{
case JsonConstants.VrField:
{
reader.Read( );
vr = fo.DicomVR.Parse((string)reader.Value);
}
break;
case JsonConstants.ValueField:
{
ReadDefaultVr(tag, vr, reader, dataset, level);
}
break;
case JsonConstants.ELEMENT_BULKDATA:
{
ReadBulkData(tag, vr, reader, dataset, level);
}
break;
case JsonConstants.ELEMENT_INLINEBINARY:
{
ReadInlineBinary(tag, vr, reader, dataset, level);
}
break;
default:
{
reader.Skip( );
}
break;
}
}
}
public PagedResult <fo.DicomDataset> FindPaged
(
fo.DicomDataset request,
IQueryOptions options,
string queryLevel
)
{
IEnumerable <IMatchingCondition> conditions = null;
conditions = BuildConditions(request, new ConditionFactory( ));
return(DoFindPaged(request, options, queryLevel, conditions));
}
private void ReadDicomAttribute(fo.DicomDataset ds, XElement element, int level)
{
XAttribute vrNode;
fo.DicomTag tag;
fo.DicomDictionaryEntry dicEntry;
fo.DicomVR dicomVR;
vrNode = element.Attribute(Constants.ATTRIBUTE_VR);
tag = fo.DicomTag.Parse(element.Attribute(Constants.ATTRIBUTE_TAG).Value);
dicomVR = null;
//if ( tag.ToString ("J") == "00020010" )
//{
// ds.InternalTransferSyntax = ReadValue ( element ).FirstOrDefault ( ) ;
//}
if (vrNode != null && !string.IsNullOrEmpty(vrNode.Value))
{
dicomVR = fo.DicomVR.Parse(vrNode.Value);
}
if (tag.IsPrivate)
{
tag = ds.GetPrivateTag(tag);
if (null != vrNode)
{
dicomVR = fo.DicomVR.Parse(vrNode.Value);
}
}
if (null == dicomVR)
{
dicEntry = fo.DicomDictionary.Default[tag];
dicomVR = dicEntry.ValueRepresentations.FirstOrDefault( );
}
if (dicomVR == fo.DicomVR.SQ)
{
ReadSequence(ds, element, tag, level);
}
else
{
ReadElement(ds, element, tag, dicomVR, level);
}
}
//TODO: is this used? update with fo-dicom
public Stream Convert(fo.DicomDataset ds)
{
//fo.DicomDataset command = new fo.DicomDataset () ;
//command[fo.DicomTag.TransferSyntaxUid] = ds[fo.DicomTag.TransferSyntaxUid] ;
//DicomMessage message = new DicomMessage (command, ds) ;
//DicomPixelData pd = DicomPixelData.CreateFrom ( message ) ;
//string tempFile = System.IO.Path.GetTempFileName ( ) ;
//System.IO.File.WriteAllBytes ( tempFile, pd.GetFrame (0));
//return new DICOMcloud.Storage.TempStream (new TempFile(tempFile));
return(null);
}
protected override fo.DicomDataset GetMediaDataset(fo.DicomDataset data, DicomMediaProperties mediaInfo)
{
if (mediaInfo.MediaType != MediaType)
{
throw new InvalidOperationException(string.Format("Invalid media type. Supported media type is:{0} and provided media type is:{1}",
MediaType, mediaInfo.MediaType));
}
if (!string.IsNullOrWhiteSpace(mediaInfo.TransferSyntax))
{
return(data.Clone(fo.DicomTransferSyntax.Parse(mediaInfo.TransferSyntax)));
}
return(base.GetMediaDataset(data, mediaInfo));
}
private void InsertDicomElement(fo.DicomDataset dicomRequest, string paramKey, string paramValue)
{
List <string> elements = new List <string>();
elements.AddRange(paramKey.Split('.'));
if (elements.Count > 1)
{
CreateSequence(elements, 0, dicomRequest, paramValue);
}
else
{
CreateElement(elements[0], dicomRequest, paramValue);
}
}
protected virtual void ReadChildren(JsonTextReader reader, fo.DicomDataset dataset, int level)
{
while (reader.Read( ) && reader.TokenType == JsonToken.PropertyName)
{
var tag = fo.DicomTag.Parse((string)reader.Value);
if (reader.Read( ) && reader.TokenType == JsonToken.StartObject)
{
ReadDicomItem(reader, tag, dataset, level);
}
}
if (reader.TokenType != JsonToken.EndObject)
{
throw new JsonReaderException("Malformed DICOM json");
}
}
public DicomMediaId
(
fo.DicomDataset dataset,
int frame,
string mediaType,
string transferSyntax
)
{
var dicomObject = new ObjectId( )
{
StudyInstanceUID = dataset.GetValueOrDefault(fo.DicomTag.StudyInstanceUID, 0, ""),
SeriesInstanceUID = dataset.GetValueOrDefault(fo.DicomTag.SeriesInstanceUID, 0, ""),
SOPInstanceUID = dataset.GetValueOrDefault(fo.DicomTag.SOPInstanceUID, 0, ""),
Frame = frame
};
Init(dicomObject, mediaType, transferSyntax);
}
protected override void Upload(fo.DicomDataset dicomDataset, int frame, IStorageLocation storeLocation)
{
var uncompressedData = new UncompressedPixelDataWrapper(dicomDataset);
var buffer = uncompressedData.PixelData.GetFrame(frame - 1);
var data = new byte[0];
try
{
//TODO: check fo-dicom, dicom file with no data will throw an exception althoug
//it is wrapped with a RangeByteBuffer but Internal is EmptyBuffer
//only way to find out is to ignore exception
data = buffer.Data;
}
catch {}
storeLocation.Upload(data);
}
private fo.DicomDataset GetTemplateDataset( )
{
var ds = new fo.DicomDataset( );
ds.Add(fo.DicomTag.PatientID, "test-pid");
ds.Add(fo.DicomTag.PatientName, "test^patient name");
ds.Add(fo.DicomTag.StudyInstanceUID, Study1UID);
ds.Add(fo.DicomTag.StudyID, "test-studyid");
ds.Add(fo.DicomTag.SeriesInstanceUID, Series1UID);
ds.Add(fo.DicomTag.SeriesNumber, 1);
ds.Add(fo.DicomTag.Modality, "XA");
ds.Add(fo.DicomTag.SOPInstanceUID, Instance1UID);
ds.Add(fo.DicomTag.SOPClassUID, "test.instance.class.uid");
ds.Add(fo.DicomTag.InstanceNumber, 1);
return(ds);
}
private void FillDataset(Dicom.DicomDataset dataset)
{
//type 1 attributes.
dataset.Add(DicomTag.SOPClassUID, DicomUID.SecondaryCaptureImageStorage);
dataset.Add(DicomTag.StudyInstanceUID, GenerateUid());
dataset.Add(DicomTag.SeriesInstanceUID, GenerateUid());
dataset.Add(DicomTag.SOPInstanceUID, GenerateUid());
//type 2 attributes
dataset.Add(DicomTag.PatientID, "12345");
dataset.Add(DicomTag.PatientName, PatientName);
dataset.Add(DicomTag.PatientBirthDate, PatientDateOfBirth);
switch (patientSex)
{
case Sex.Male:
dataset.Add(DicomTag.PatientSex, "M");
break;
case Sex.Female:
dataset.Add(DicomTag.PatientSex, "F");
break;
case Sex.Other:
dataset.Add(DicomTag.PatientSex, "O");
break;
default:
break;
}
dataset.Add(DicomTag.StudyDate, examinationDate);
dataset.Add(DicomTag.StudyTime, examinationDate);
dataset.Add(DicomTag.AccessionNumber, string.Empty);
dataset.Add(DicomTag.ReferringPhysicianName, string.Empty);
dataset.Add(DicomTag.StudyID, "1");
dataset.Add(DicomTag.SeriesNumber, "1");
dataset.Add(DicomTag.ModalitiesInStudy, "CR");
dataset.Add(DicomTag.Modality, "CR");
dataset.Add(DicomTag.NumberOfStudyRelatedInstances, "1");
dataset.Add(DicomTag.NumberOfStudyRelatedSeries, "1");
dataset.Add(DicomTag.NumberOfSeriesRelatedInstances, "1");
dataset.Add(DicomTag.PatientOrientation, "F/A");
dataset.Add(DicomTag.ImageLaterality, "U");
dataset.Add(DicomTag.StudyDescription, Comment);
}
//TODO: update this to return a type showing what objects got deleted e.g. IObjectId[]
//the "reuest" dataset is assumed to have the Object ID values. However,
//an extended implementation might send a query dataset and this method will query the DB and generate multiple Object IDs
//Example: the request dataset has a date range, wild-card or SOP Class UID...
public DCloudCommandResult Delete
(
fo.DicomDataset request,
ObjectQueryLevel level
)
{
DCloudCommandResult deleteResult = null;
IDeleteCommand deleteCommand = CommandFactory.CreateDeleteCommand( );
DeleteCommandData deleteData = new DeleteCommandData( )
{
Instances = new List <ObjectId> ( )
{
new ObjectId(request)
},
DeleteLevel = level
};
return(deleteResult = deleteCommand.Execute(deleteData));
}
protected virtual IEnumerable <IMatchingCondition> BuildConditions
(
fo.DicomDataset request
)
{
ConditionFactory condFactory = new ConditionFactory( );
IEnumerable <IMatchingCondition> conditions;
condFactory.BeginProcessingElements( );
foreach (var element in request)
{
condFactory.ProcessElement(element);
}
conditions = condFactory.EndProcessingElements( );
return(conditions);
}
protected override void Upload
(
fo.DicomDataset dicomObject,
int frame,
IStorageLocation storeLocation,
DicomMediaProperties mediaProperties
)
{
var frameIndex = frame - 1;
var dicomImage = new DicomImage(dicomObject, frameIndex);
var bitmap = dicomImage.RenderImage(frameIndex).AsBitmap();
var stream = new MemoryStream( );
bitmap.Save(stream, System.Drawing.Imaging.ImageFormat.Jpeg);
stream.Position = 0;
storeLocation.Upload(stream, MediaType);
}