/// <summary>
/// Converts a medical scan, and a set of binary masks, into a Dicom representation.
/// The returned set of Dicom files will have files for all slices of the scan, and an RtStruct
/// file containing the contours that were derived from the masks. The RtStruct file will be the first
/// entry in the returned list of Dicom files.
/// Use with extreme care - many Dicom elements have to be halluzinated here, and there's no
/// guarantee that the resulting Dicom will be usable beyond what is needed in InnerEye.
/// </summary>
/// <param name="scan">The medical scan.</param>
/// <param name="imageModality">The image modality through which the scan was acquired.</param>
/// <param name="contours">A list of contours for individual anatomical structures, alongside
/// name and rendering color.</param>
/// <param name="seriesDescription">The value to use as the Dicom series description.</param>
/// <param name="patientID">The patient ID that should be used in the Dicom files. If null,
/// a randomly generated patient ID will be used.</param>
/// <param name="studyInstanceID">The study ID that should be used in the Dicom files (DicomTag.StudyInstanceUID). If null,
/// a randomly generated study ID will be used.</param>
/// <param name="additionalDicomItems">Additional Dicom items that will be added to each of the slice datasets. This can
/// be used to pass in additional information like manufacturer.</param>
/// <returns></returns>
public static List <DicomFileAndPath> ScanAndContoursToDicom(Volume3D <short> scan,
ImageModality imageModality,
IReadOnlyList <ContourRenderingInformation> contours,
string seriesDescription = null,
string patientID = null,
string studyInstanceID = null,
DicomDataset additionalDicomItems = null)
{
// To create the Dicom identifiers, write the volume to a set of Dicom files first,
// then read back in.
// When working with MR scans from the CNN models, it is quite common to see scans that have a large deviation from
// the 1:1 aspect ratio. Relax that constraint a bit (default is 1.001)
var scanFiles = ScanToDicomInMemory(scan, imageModality, seriesDescription, patientID, studyInstanceID, additionalDicomItems);
var medicalVolume = MedicalVolumeFromDicom(scanFiles, maxPixelSizeRatioMR: 1.01);
var dicomIdentifiers = medicalVolume.Identifiers;
var volumeTransform = medicalVolume.Volume.Transform;
medicalVolume = null;
var rtFile = ContoursToDicomRtFile(contours, dicomIdentifiers, volumeTransform);
var dicomFiles = new List <DicomFileAndPath> {
rtFile
};
dicomFiles.AddRange(scanFiles);
return(dicomFiles);
}
/// <summary>
/// Saves a medical scan to a set of Dicom files. Each file is saved into a memory stream.
/// The returned Dicom files have the Path property set to {sliceIndex}.dcm.
/// Use with extreme care - many Dicom elements have to be halluzinated here, and there's no
/// guarantee that the resulting Dicom will be usable beyond what is needed in InnerEye.
/// </summary>
/// <param name="scan">The medical scan.</param>
/// <param name="imageModality">The image modality through which the scan was acquired.</param>
/// <param name="seriesDescription">The series description that should be used in the Dicom files.</param>
/// <param name="patientID">The patient ID that should be used in the Dicom files. If null,
/// a randomly generated patient ID will be used.</param>
/// <param name="studyInstanceID">The study ID that should be used in the Dicom files (DicomTag.StudyInstanceUID). If null,
/// a randomly generated study ID will be used.</param>
/// <param name="additionalDicomItems">Additional Dicom items that will be added to each of the slice datasets. This can
/// be used to pass in additional information like manufacturer.</param>
/// <returns></returns>
public static List <DicomFileAndPath> ScanToDicomInMemory(Volume3D <short> scan,
ImageModality imageModality,
string seriesDescription = null,
string patientID = null,
string studyInstanceID = null,
DicomDataset additionalDicomItems = null)
{
var scanAsDicomFiles = Convert(scan, imageModality, seriesDescription, patientID, studyInstanceID, additionalDicomItems).ToList();
var dicomFileAndPath = new List <DicomFileAndPath>();
for (var index = 0; index < scanAsDicomFiles.Count; index++)
{
var stream = new MemoryStream();
scanAsDicomFiles[index].Save(stream);
stream.Seek(0, SeekOrigin.Begin);
var dicomFile = DicomFileAndPath.SafeCreate(stream, $"{index}.dcm");
dicomFileAndPath.Add(dicomFile);
}
return(dicomFileAndPath);
}
/// <summary>
/// Converts a volume 3D into a collection of Dicom files (split by slice on the primary plane).
/// This code writes the patient position as HFS (this might not be correct but was needed at some point to view the output).
///
/// Note: This code has not been tested with MR data. It also assumes the Photometric Interpretation to be MONOCHROME2.
/// Use with extreme care - many Dicom elements have to be halluzinated here, and there's no
/// guarantee that the resulting Dicom will be usable beyond what is needed in InnerEye.
/// </summary>
/// <param name="volume">The volume to convert.</param>
/// <param name="modality">The image modality.</param>
/// <param name="seriesDescription">The value to use as the Dicom series description.</param>
/// <param name="patientID">The patient ID that should be used in the Dicom files. If null,
/// a randomly generated patient ID will be used.</param>
/// <param name="studyInstanceID">The study ID that should be used in the Dicom files (DicomTag.StudyInstanceUID). If null,
/// a randomly generated study ID will be used.</param>
/// <param name="additionalDicomItems">Additional Dicom items that will be added to each of the slice datasets. This can
/// be used to pass in additional information like manufacturer.</param>
/// <returns>The collection of Dicom files that represents the Dicom image series.</returns>
public static IEnumerable <DicomFile> Convert(Volume3D <short> volume,
ImageModality modality,
string seriesDescription = null,
string patientID = null,
string studyInstanceID = null,
DicomDataset additionalDicomItems = null)
{
seriesDescription = seriesDescription ?? string.Empty;
patientID = CreateUidIfEmpty(patientID);
studyInstanceID = CreateUidIfEmpty(studyInstanceID);
if (!IsValidDicomLongString(seriesDescription))
{
throw new ArgumentException("The series description is not a valid Dicom Long String.", nameof(seriesDescription));
}
if (!IsValidDicomLongString(patientID))
{
throw new ArgumentException("The patient ID is not a valid Dicom Long String.", nameof(patientID));
}
if (!IsValidDicomLongString(studyInstanceID))
{
throw new ArgumentException("The study instance ID is not a valid Dicom Long String.", nameof(studyInstanceID));
}
var spacingZ = volume.SpacingZ;
var imageOrientationPatient = new decimal[6];
var directionColumn1 = volume.Direction.Column(0);
var directionColumn2 = volume.Direction.Column(1);
imageOrientationPatient[0] = (decimal)directionColumn1.X;
imageOrientationPatient[1] = (decimal)directionColumn1.Y;
imageOrientationPatient[2] = (decimal)directionColumn1.Z;
imageOrientationPatient[3] = (decimal)directionColumn2.X;
imageOrientationPatient[4] = (decimal)directionColumn2.Y;
imageOrientationPatient[5] = (decimal)directionColumn2.Z;
var frameOfReferenceUID = CreateUID().UID;
var seriesUID = CreateUID().UID;
var sopInstanceUIDs = new DicomUID[volume.DimZ];
// DicomUID.Generate() is not thread safe. We must create unique DicomUID's single threaded.
// https://github.com/fo-dicom/fo-dicom/issues/546
for (var i = 0; i < sopInstanceUIDs.Length; i++)
{
sopInstanceUIDs[i] = CreateUID();
}
var results = new DicomFile[volume.DimZ];
Parallel.For(0, volume.DimZ, i =>
{
var sliceLocation = (i * spacingZ) + volume.Origin.Z;
var imagePositionPatient = volume.Transform.DataToDicom.Transform(new Point3D(0, 0, i));
var dataset = new DicomDataset()
{
{ DicomTag.ImageType, new[] { "DERIVED", "PRIMARY", "AXIAL" } },
{ DicomTag.PatientPosition, "HFS" },
{ new DicomOtherWord(DicomTag.PixelData, new MemoryByteBuffer(ExtractSliceAsByteArray(volume, i))) },
{ new DicomUniqueIdentifier(DicomTag.SOPInstanceUID, sopInstanceUIDs[i]) },
{ new DicomUniqueIdentifier(DicomTag.SeriesInstanceUID, seriesUID) },
{ new DicomUniqueIdentifier(DicomTag.PatientID, patientID) },
{ new DicomUniqueIdentifier(DicomTag.StudyInstanceUID, studyInstanceID) },
{ new DicomUniqueIdentifier(DicomTag.FrameOfReferenceUID, frameOfReferenceUID) },
{ new DicomLongString(DicomTag.SeriesDescription, seriesDescription) },
{ new DicomUnsignedShort(DicomTag.Columns, (ushort)volume.DimX) },
{ new DicomUnsignedShort(DicomTag.Rows, (ushort)volume.DimY) },
{ new DicomDecimalString(DicomTag.PixelSpacing, (decimal)volume.SpacingY, (decimal)volume.SpacingX) }, // Note: Spacing X & Y are not the expected way around
{ new DicomDecimalString(DicomTag.ImagePositionPatient, (decimal)imagePositionPatient.X, (decimal)imagePositionPatient.Y, (decimal)imagePositionPatient.Z) },
{ new DicomDecimalString(DicomTag.ImageOrientationPatient, imageOrientationPatient) },
{ new DicomDecimalString(DicomTag.SliceLocation, (decimal)sliceLocation) },
{ new DicomUnsignedShort(DicomTag.SamplesPerPixel, DicomSeriesInformationValidator.ExpectedSamplesPerPixel) },
{ new DicomUnsignedShort(DicomTag.PixelRepresentation, 1) },
{ new DicomUnsignedShort(DicomTag.BitsStored, DicomSeriesInformationValidator.ExpectedBitsAllocated) },
{ new DicomUnsignedShort(DicomTag.BitsAllocated, DicomSeriesInformationValidator.ExpectedBitsAllocated) },
{ new DicomUnsignedShort(DicomTag.HighBit, DicomSeriesInformationValidator.ExpectedBitsAllocated - 1) },
{ new DicomCodeString(DicomTag.PhotometricInterpretation, DicomSeriesInformationValidator.ExpectedPhotometricInterpretation) }
};
if (modality == ImageModality.CT)
{
dataset.Add(DicomTag.SOPClassUID, DicomUID.CTImageStorage);
dataset.Add(DicomTag.Modality, ImageModality.CT.ToString());
dataset.Add(new DicomItem[]
{
new DicomDecimalString(DicomTag.RescaleIntercept, 0),
new DicomDecimalString(DicomTag.RescaleSlope, 1),
});
}
else if (modality == ImageModality.MR)
{
dataset.Add(DicomTag.SOPClassUID, DicomUID.MRImageStorage);
dataset.Add(DicomTag.Modality, ImageModality.MR.ToString());
}
if (additionalDicomItems != null)
{
foreach (var item in additionalDicomItems.Clone())
{
if (!dataset.Contains(item.Tag))
{
dataset.Add(item);
}
}
}
results[i] = new DicomFile(dataset);
});
return(results);
}
