def _write_dicom_file(np_slice: np.ndarray, header: pydicom.FileDataset,
file_path: str):
"""Replace data in header with 2D numpy array and write to `file_path`.
Args:
np_slice (np.ndarray): 2D slice to encode in dicom file.
header (pydicom.FileDataset): DICOM header.
file_path: File path to write to.
"""
# Deep copy required in case headers are shared.
header = copy.deepcopy(header)
expected_dimensions = header.Rows, header.Columns
assert (
np_slice.shape == expected_dimensions
), "In-plane dimension mismatch - expected shape {}, got {}".format(
str(expected_dimensions), str(np_slice.shape))
np_slice_bytes = np_slice.tobytes()
bit_depth = int(
len(np_slice_bytes) / (np_slice.shape[0] * np_slice.shape[1]) * 8)
if bit_depth != header.BitsAllocated:
np_slice = _update_np_dtype(np_slice, header.BitsAllocated)
np_slice_bytes = np_slice.tobytes()
bit_depth = int(
len(np_slice_bytes) / (np_slice.shape[0] * np_slice.shape[1]) * 8)
assert bit_depth == header.BitsAllocated, "Bit depth mismatch: Expected {:d} got {:d}".format(
header.BitsAllocated, bit_depth)
header.PixelData = np_slice_bytes
header.save_as(file_path)
def __write_dicom_file__(self, np_slice: np.ndarray,
header: pydicom.FileDataset, filepath: str):
"""
Replace data in header with 2D numpy array and write to filepath
:param np_slice: a 2D numpy array
:param header: a pydicom.FileDataset with fields populated
:param filepath: Filepath to write dicom to
"""
expected_dimensions = header.Rows, header.Columns
assert np_slice.shape == expected_dimensions, "In-plane dimension mismatch - expected shape %s, got %s" % (
str(expected_dimensions), str(np_slice.shape))
np_slice_bytes = np_slice.tobytes()
bit_depth = int(
len(np_slice_bytes) / (np_slice.shape[0] * np_slice.shape[1]) * 8)
if bit_depth != header.BitsAllocated:
np_slice = __update_np_dtype__(np_slice, header.BitsAllocated)
np_slice_bytes = np_slice.tobytes()
bit_depth = int(
len(np_slice_bytes) / (np_slice.shape[0] * np_slice.shape[1]) *
8)
assert bit_depth == header.BitsAllocated, "Bit depth mismatch: Expected %d got %d" % (
header.BitsAllocated, bit_depth)
header.PixelData = np_slice_bytes
header.save_as(filepath)
def create_dcm_file(self):
suffix = '.dcm'
filename_little_endian = tempfile.NamedTemporaryFile(
suffix=suffix).name
filename_big_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
print("Setting file meta information...")
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
print("Setting dataset values...")
ds = FileDataset(filename_little_endian, {},
file_meta=file_meta,
preamble=b"\0" * 128)
ds.PatientName = self.get_patient_name(
) + " " + self.get_patient_surname()
ds.PatientID = self.get_patient_id()
ds.PatientSex = self.get_patient_sex()
ds.PatientAge = self.get_patient_age()
ds.PatientWeight = self.get_patient_weight()
ds.ImageComment = self.get_patient_comment()
ds.PatientBirthDate = self.get_patient_birth()
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set creation date/time
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
ds.ContentTime = timeStr
ds.BitsAllocated = 16
ds.Rows = self.image.shape[0]
ds.Columns = self.image.shape[1]
ds.PixelRepresentation = 0
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
image = self.image
image *= 255
image = image.astype("uint16")
ds.PixelData = Image.fromarray(image).tobytes()
print("Writing test file", filename_little_endian)
ds.save_as(filename_little_endian)
print("File saved.")
ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRBigEndian
ds.is_little_endian = False
ds.is_implicit_VR = False
print("Writing test file as Big Endian Explicit VR",
filename_big_endian)
ds.save_as(filename_big_endian)
return ds
def createStructDS(self, planData, ImageInfoUIDs, setupPosition,
roiShiftVector):
print("Creating Data structure")
# create RS SOPInstanceUID
structSOPInstanceUID = pydicom.uid.generate_uid()
structSeriesInstanceUID = pydicom.uid.generate_uid()
# get image header info from ImageSet_0.ImageInfo
structFrameUID = ''
structStudyInstanceUID = ''
structSeriesUID = ''
structClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
if "ImageInfoList" in ImageInfoUIDs:
structFrameUID = ImageInfoUIDs.ImageInfoList[0].FrameUID
structStudyInstanceUID = ImageInfoUIDs.ImageInfoList[
0].StudyInstanceUID
structSeriesUID = ImageInfoUIDs.ImageInfoList[0].SeriesUID
# structClassUID = ImageInfoUIDs.ImageInfoList[0].ClassUID
# Populate required values for file meta information
file_meta = Dataset()
# RT Structure Set Storage
file_meta.MediaStorageSOPClassUID = structClassUID
file_meta.MediaStorageSOPInstanceUID = structSOPInstanceUID
structfilename = "RS." + structSOPInstanceUID + ".dcm"
# this value remains static since implementation for creating file is the same
file_meta.ImplementationClassUID = '1.2.826.0.1.3680043.8.498.75006884747854523615841001'
# Create the FileDataset instance (initially no data elements, but file_meta supplied)
ds = FileDataset(structfilename, {},
file_meta=file_meta,
preamble=b'\x00' * 128)
# print(file_meta.preamble)
# add info_data,basic patientinfo
# [0008,0005] - [0008,0018]
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.InstanceCreationDate = time.strftime("%Y%m%d")
ds.InstanceCreationTime = time.strftime("%H%M%S")
ds.SOPClassUID = structClassUID
ds.SOPInstanceUID = structSOPInstanceUID
ds.Modality = 'RTSTRUCT'
ds.AccessionNumber = ""
ds.Manufacturer = 'Pinnalce3' # from sample dicom file, maybe should change?
# not sure where to get information for this element can find this and read in from
ds.StationName = "adacp3u7"
# ds.ManufacturersModelName = 'Pinnacle3'
ds = self.modifyPatientInfo(ds, planData)
# [0008,1110]
ds.ReferencedStudySequence = Sequence()
ReferencedStudy1 = Dataset()
ds.ReferencedStudySequence.append(ReferencedStudy1)
# Study Component Management SOP Class (chosen from template)
ds.ReferencedStudySequence[
0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2'
ds.ReferencedStudySequence[
0].ReferencedSOPInstanceUID = structStudyInstanceUID
# ds.StudyInstanceUID = StudyInstanceUID
print("Setting structure file study instance: " +
str(structStudyInstanceUID))
# [0020,000d]
ds.StudyInstanceUID = structStudyInstanceUID
# [0020,000e]
ds.SeriesInstanceUID = structSeriesInstanceUID
# [3006,0010]
ds.ReferencedFrameOfReferenceSequence = Sequence()
ReferencedFrameofReference1 = Dataset()
ds.ReferencedFrameOfReferenceSequence.append(
ReferencedFrameofReference1)
ds.ReferencedFrameOfReferenceSequence[
0].FrameofReferenceUID = structFrameUID
# [3006,0012]
ds.ReferencedFrameOfReferenceSequence[
0].RTReferencedStudySequence = Sequence()
RTReferencedStudy1 = Dataset()
ds.ReferencedFrameOfReferenceSequence[
0].RTReferencedStudySequence.append(RTReferencedStudy1)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.2'
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].ReferencedSOPInstanceUID = structStudyInstanceUID
# ds.StudyInstanceUID = StudyInstanceUID
# [3006,0014]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence = Sequence()
RTReferencedSeries1 = Dataset()
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence.append(RTReferencedSeries1)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[
0].SeriesInstanceUID = structSeriesUID
# [3006,0016]
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence = Sequence()
# [fffe,e000]
for i, value in enumerate(ImageInfoUIDs.ImageInfoList, 1):
exec("ContourImage%d = Dataset()" % i)
exec(
"ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].ContourImageSequence.append(ContourImage%d)"
% i)
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence[
i - 1].ReferencedSOPClassUID = value.ClassUID
ds.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[
0].RTReferencedSeriesSequence[0].ContourImageSequence[
i - 1].ReferencedSOPInstanceUID = value.InstanceUID
# exec("del ContourImage%d" % i)
# [3006,0020]
roiListData = planData.planROIsRawData.roiList
ds.StructureSetROISequence = Sequence()
for i, value in enumerate(roiListData, 1):
exec("ROISet%d = Dataset()" % i)
exec("ds.StructureSetROISequence.append(ROISet%d)" % i)
ds.StructureSetROISequence[i - 1].ROIName = value.name
ds.StructureSetROISequence[i - 1].ROINumber = i
ds.StructureSetROISequence[
i - 1].ReferencedFrameOfReferenceUID = structFrameUID
if 'volume' in value:
ds.StructureSetROISequence[i - 1].ROIVolume = value.volume
ds.StructureSetROISequence[
i - 1].ROIGenerationAlgorithm = value.roiinterpretedtype
# [3006,0039]get each ROI
ds.ROIContourSequence = Sequence()
for i, value in enumerate(roiListData, 1):
exec("ContourSequence%d = Dataset()" % i)
exec("ds.ROIContourSequence.append(ContourSequence%d)" % i)
ds.ROIContourSequence[i - 1].ROIDisplayColor = [0, 255, 0]
ds.ROIContourSequence[i - 1].ReferencedROINumber = i
# get all curves in current ROI
ds.ROIContourSequence[i - 1].ContourSequence = Sequence()
planROIsCurvesList = value.num_curve
# get each ROI_Curvers
for j, data in enumerate(planROIsCurvesList, 1):
exec("CurvesPoint%d = Dataset()" % j)
exec(
"ds.ROIContourSequence[i - 1].ContourSequence.append(CurvesPoint%d)"
% j)
# [3006,0040]
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourImageSequence = Sequence()
coutourImage1 = Dataset()
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourImageSequence.append(coutourImage1)
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourImageSequence[
0].ReferencedSOPClassUID = structClassUID
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourImageSequence[
0].ReferencedSOPInstanceUID = self.getCTInstanceUID(
data.Points[0], setupPosition, ImageInfoUIDs)
# [3006,0042]
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourGeometricType = "CLOSED_PLANAR"
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].NumberOfContourPoints = data.num_points
# get each ROI_Curves_Points, using data.Points
ds.ROIContourSequence[i - 1].ContourSequence[
j - 1].ContourData = self.getContourCurvePoints(
data.Points, setupPosition, roiShiftVector)
# [3006,0080]
ds.RTROIObservationsSequence = Sequence()
for i, current_roi in enumerate(ds.StructureSetROISequence, 1):
exec("Observation%d = Dataset()" % i)
exec("ds.RTROIObservationsSequence.append(Observation%d)" % i)
ds.RTROIObservationsSequence[
i - 1].ObservationNumber = current_roi.ROINumber
ds.RTROIObservationsSequence[
i - 1].ReferencedROINumber = current_roi.ROINumber
ds.RTROIObservationsSequence[i - 1].RTROIInterpretedType = 'ORGAN'
ds.RTROIObservationsSequence[i - 1].ROIInterpreter = ""
# find out where to get if its been approved or not
ds.ApprovalStatus = 'UNAPPROVED'
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# # Create the FileDataset instance (initially no data elements, but file_meta supplied)
# structds = FileDataset(structfilename, {},
# file_meta=ds, preamble=b'\x00' * 128)
# structfilepath=outputfolder + patientfolder + "/" + structfilename
# structds.save_as("structfilepath")
# print("Structure file being saved\n")
ds.save_as(os.getenv('HOME') + '/PinnWork/' + structfilename)
#
# dcmds = pydicom.dcmread(ds)
# print(dcmds)
return ds