Also consult the wiki (https://github.com/fo-dicom/fo-dicom/wiki) for answers to common questions.
Why there code can be Gray or color when i only losing fill the Bits Allocated?
DicomDataset dataset = new DicomDataset();
dataset.Add(DicomTag.PhotometricInterpretation, PhotometricInterpretation.Rgb.Value);
dataset.Add(DicomTag.Rows, (ushort)bitmap.Height);
dataset.Add(DicomTag.Columns, (ushort)bitmap.Width);
dataset.Add(DicomTag.BitsAllocated, (ushort)8);
dataset.Add(DicomTag.SOPClassUID, "1.2.840.10008.5.1.4.1.1.2");
dataset.Add(DicomTag.SOPInstanceUID, "1.2.840.10008.5.1.4.1.1.2.20181120090837121314");
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
pixelData.BitsStored = 8;
//pixelData.BitsAllocated = 8;
pixelData.SamplesPerPixel = 3;
pixelData.HighBit = 7;
pixelData.PixelRepresentation = 0;
pixelData.PlanarConfiguration = 0;
pixelData.AddFrame(buffer);Bits Allocated is a mandatory tag, without this the size of the pixel data is not known, and most DICOM software will just not process such data. Bits Stored are the bits that are actually used opposed to the number of bits allocated in memory/on disk.
Sorry ,i do not understand why without Bits Allocated will make the size of pixel data unknow ?can not use bit stored to caic that?
Hello @ALL
I am creating dicom file from video. File was created successfully but it is not showing up in Osmisis web viewer or stone web viewer. Apart from that when i am uploading that created dicom file manually in orthanc server it is playing fine. So can any one tell me how i can get out from this problem i am attaching my code here. Please guys help me into this.
codeStringBuilder uid = new StringBuilder();
uid.Append("1.08.1982.10121984.2.0.07").Append(".z").Append(DateTime.UtcNow.Ticks);
ds.Add(DicomTag.SOPInstanceUID, DicomUID.Generate());
ds.Add(DicomTag.PatientName, patientDetailsModelForDicom.PatientName);
ds.Add(DicomTag.PatientSex, patientDetailsModelForDicom.Gender);
ds.Add(DicomTag.PatientBirthDate, patientDetailsModelForDicom.PatientBirthDate);
ds.Add(DicomTag.StudyDate, DateTime.Now);
ds.Add(DicomTag.StudyTime, DateTime.Now);
DicomPixelData pixelData = DicomPixelData.Create(ds, true);
pixelData.Width = Convert.ToUInt16(width);
pixelData.Height = Convert.ToUInt16(height);
pixelData.NumberOfFrames = frameCount;
pixelData.BitsStored = 8;
pixelData.SamplesPerPixel = 3;
pixelData.HighBit = 7;
pixelData.PixelRepresentation = 0;
pixelData.PlanarConfiguration = 0;
pixelData.PhotometricInterpretation = PhotometricInterpretation.YbrPartial420;
ds.AddOrUpdate(DicomTag.NumberOfFrames, frameCount);
ds.AddOrUpdate(DicomTag.Columns, pixelData.Width);
ds.AddOrUpdate(DicomTag.Rows, pixelData.Height);
ds.Add(DicomTag.SpecificCharacterSet, "ISO_IR 100");
ds.Add(DicomTag.ConversionType, "SI");
ds.AddOrUpdate(DicomTag.BitsAllocated, (ushort)8);
ds.AddOrUpdate(DicomTag.InstanceNumber, "1");
DicomDataset sqContent = new DicomDataset
{
{ DicomTag.Modality, "OT" },
{ DicomTag.ScheduledProcedureStepStartDate, DateTime.Now.Date }
}; //Content of the sequence
DicomSequence sq = new DicomSequence(DicomTag.ScheduledProcedureStepSequence, sqContent); // Create sequence, add content
ds.AddOrUpdate(sq);
byte[] videoBytes = File.ReadAllBytes(model.Files[0].FileName);
MemoryByteBuffer buffer = new MemoryByteBuffer(videoBytes);
pixelData.AddFrame(buffer);
DicomFile dicomfile = new DicomFile(ds);
// dicomfile.FileMetaInfo.TransferSyntax = DicomTransferSyntax.JPEGProcess1;
dicomfile.FileMetaInfo.TransferSyntax = DicomTransferSyntax.Lookup(DicomUID.MPEG4HP41);
// dicomfile.FileMetaInfo.TransferSyntax = DicomTransferSyntax.Lookup(DicomUID.MPEG2MPHL);
dicomfile.Save(fileName);
await client.AddRequestAsync(new DicomCStoreRequest(dicomfile));
await client.SendAsync();
This is perhaps a silly question: Has anyone managed to use fo-dicom to stream ultrasound image frames directly and in real-time?
I'm using 4.0.8 with WPF and can't seem to get things fast enough.
- fo-dicom seems to do a lot of byte array copying, and then I make it worse by copying a final time for WPF
- Efferent might be writing and reading to disk on every frame render
When I try and stream it's very bursty, presumably due to the high GC pressure and dependence on IO, even though the dicom files are in memory.
Is there anything obvious I might be missing? I'm just holding the dicom file in memory and calling RenderImage. I feel like I'm going to have to resort to writing some kind of run-ahead buffer.
1 reply
private static IEnumerable<DicomDataset> GetDicomInstances(DicomFile inputDicomFile)
{
var numberOfFrames = inputDicomFile.Dataset.GetValueOrDefault(DicomTag.NumberOfFrames, 0, 1);
if (numberOfFrames < 2)
{
yield break;
}
DicomPixelData multiFramePixelData = DicomPixelData.Create(inputDicomFile.Dataset);
for (var frameIndex = 0; frameIndex < numberOfFrames; frameIndex++)
{
var image = new DicomImage(inputDicomFile.Dataset, frameIndex);
var dataset = inputDicomFile.Dataset.Clone();
dataset.AddOrUpdate(DicomTag.SOPInstanceUID, DicomUIDGenerator.GenerateDerivedFromUUID());
dataset.AddOrUpdate(DicomTag.NumberOfFrames, 1);
dataset.AddOrUpdate(DicomTag.InstanceNumber, frameIndex + 1);
var frame = multiFramePixelData.GetFrame(frameIndex);
var framePixelData = DicomPixelData.Create(dataset, true);
framePixelData.AddFrame(frame);
yield return dataset;
}
}
OnCStoreRequest "thread-safe", or can we get multiple C-STORE requests in parallel? I'm doing some very quick work when the first instance of a study is received but I would like to confirm that the DICOM files come sequentially, one after another. Or is it possible that during one DICOM transfer association multiple C-STORE requests are being handled in parallel?
Again a C-FIND challenge paired with characters like "äüö" in the response.dataset. So this already describes my problem well. My response.Dataset contains the "?" character instead of the expected "Umlaute":
string patname = response.Dataset.GetSingleValueOrDefault(DicomTag.PatientName, string.Empty);
DicomPersonName person = new DicomPersonName(DicomTag.PatientName, DicomEncoding.GetEncoding("ISO_IR 100"), patname);
Either solution does not work. The response dataset does NOT contain the specificCharacterSet Tag. It comes from Conquest. But the strange thing is this: If i run the same query from the WeasisViewer against conquest, Weasis displays the patient name correctly.
My query is super simple "^". So that it does not contain the "äöü" in my C-FIND dataset nor a SpecialCharacterSet Tag.
What's it that i am doing wrong?
GrayscalePixelDataS16 (and all the pixel data implmentations?) seem to cast the final double value to int, which is equivalent to flooring the values.Does the spec specify somewhere that values should be floored not rounded to the nearest integer?
Looking at DCMTK source it appears to cast, which I believe is truncation in C++ as well, but I haven't been able to confirm.
Another reconciliation question, trying to ensure fo-dicom doesn't make changes simply by loading and saving (unless necessary).
I have an input file with a private tag of VR SQ using undefined length.
FO-DICOM ignores the setting for explicit sequence length on private tags. Is there a reason for this? I've been combing the standard but I don't see anything obvious, and this file is from a big vendor.
This decision seems to date back a very long way.
fo-dicom/fo-dicom@b2b9441
@gofal Guys, I want to add an MP4 file to dicom file and I think I must add my this MP4 file to the Pixel Data tag (7FE0,0010) . So My code is like this:
string mp4 = @"C:\Users\arya.m\Desktop\MP4Dicoms\test_720\20211108-064551.mp4";
var dataset = new DicomDataset();
var rows = 720;
var columns = 1280;
var numFrames = 1080;
dataset.Add(DicomTag.PhotometricInterpretation, PhotometricInterpretation.Rgb.Value); dataset.Add(DicomTag.Rows, (ushort)rows);
dataset.Add(DicomTag.Columns, (ushort)columns); dataset.AddOrUpdate(DicomTag.BitsAllocated, (ushort)8);
dataset.AddOrUpdate(DicomTag.TransferSyntaxUID, DicomTransferSyntax.MPEG4AVCH264HighProfileLevel41.UID.UID);
dataset.Add( DicomTag.SOPClassUID, "Video Photographic Image Storage");
dataset.Add(DicomTag.SOPInstanceUID, "1.3.51.5146.1682.20140505.1225531.197"); dataset.AddOrUpdate(DicomTag.PatientName, "Arya pic1");
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);And at this point I probably add my file to the tag pixeldata like this since I don't know how to write it:
pixelData.Dataset.Add( My mp4 file);
DicomFile dicomfile = new DicomFile(pixelData.Dataset); dicomfile.Save(dicom_mp4);Anyone can help me complete my code?
5 replies
Hi, I am trying to save(store) modality images. I did a bit of digging but I have not found a straight answer. I feel this is how it might work and would be happy if someone could confirmed it and fix any mistake in my understanding.
1) I think medical images are transferred using PACS. So, I probably have to implement PACS.
2) I found out there are 2 type of file operations Classical-Dicom(DIMSE) and DicomWeb(P3.18).
3) I thought both did the same thing. So, either implementation works but after reading a paper(http://otechimg.com/publications/pdf/dicomweb_white_paper.pdf) I thought maybe the Classical-DIMSE is for communicating with Modality and DimcomWeb is for
any online device(mobile) to access/store the Server image.
4) I still do not know wither the modality directly sends the iamges to server(I am guessing its PACS)「CT(C-STORE SCU)-＞PACS(C-STORE SCP)」. or it first sends to workstations and then sends to PACS「CT（C-STORE SCU）-> Workstation(C-STORE SCP)/Workstation(C-STORE SCU) -> PACS(C-STORE SCP)」.
PS: I kind of felt guilty asking this conceptual question here. But I do not know any Dicom group where I could ask questions related to dicom's concept. If someone knows kindly let me know.
Thank You.
First, it is not clear what do you want to do: where your images come from, and where do you want to save them? As for your questions:
1) medical images are transferred using the DICOM protocol; a PACS is an archive that stores DICOM images by implementing the SOP Classes needed for that (e.g. C-FIND SCP, C-MOVE SCP, ...) - in DICOM language, it is just a DICOM node
2, 3) You should not be concerned with DIMSE - this is the protocol uses for service implementations which you get by using frameworks like fo-dicom; DicomWeb is indeed a newer means to transfer DICOM over web - what you need depends on your actual use case
4) This depends on the clinical workflow; images are sent from the modality to one or more configured DICOM nodes. In many cases, the images are indeed sent to a PACS, often they are additionally or instead sent to some workstation that acts as a DICOM node, which may process them and could send them to a PACS afterwards; all this is a matter of configuration
When getting an image using the image.RenderImage().AsSharpImage() method, I get the following error: Decoding dataset with transfer syntax: JPEG 2000 Image Compression (Lossless Only) is not supported.
I only get this when running in an Ubuntu container. I don't have this error when running on Windows.
Any clue for a way around this?