def mk_dcm(dcm_path, slice_data, meta):
file_meta = pydicom.Dataset()
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
file_meta.MediaStorageSOPClassUID = 'Secondary Capture Image Storage'
file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
file_meta.ImplementationClassUID = '1.3.6.1.4.1.9590.100.1.0.100.4.0'
ds = pydicom.FileDataset(dcm_path, {},
file_meta=file_meta,
preamble=b'\0' * 128)
ds.Modality = 'WSD'
ds.ContentDate = str(datetime.date.today()).replace('-', '')
ds.ContentTime = str(time.time()) #milliseconds since the epoch
ds.StudyInstanceUID = '1.3.6.1.4.1.9590.100.1.1.124313977412360175234271287472804872093'
ds.SeriesInstanceUID = '1.3.6.1.4.1.9590.100.1.1.369231118011061003403421859172643143649'
ds.SOPInstanceUID = '1.3.6.1.4.1.9590.100.1.1.111165684411017669021768385720736873780'
ds.SOPClassUID = 'Secondary Capture Image Storage'
ds.SecondaryCaptureDeviceManufctur = 'Python 3.6'
# TAGS NECESSARY TO CONTAIN IMAGE DATA:
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
ds.PixelRepresentation = 1
ds.HighBit = 15
ds.BitsStored = 16
ds.BitsAllocated = 16
ds.RescaleIntercept = 0
ds.RescaleSlope = 1
ds.WindowCenter = 80
ds.WindowWidth = 600
ds.Columns = slice_data.shape[0]
ds.Rows = slice_data.shape[1]
ds.PixelData = slice_data.tobytes()
[ds.add_new(k, 'LO', v) for k, v in meta.items()]
ds.save_as(dcm_path)
def gen_file(self, fn=None):
# print("Setting file meta information...")
# Populate required values for file meta information
file_meta = pydicom.Dataset()
file_meta.FileMetaInformationGroupLength = 60 # Will be rewritten but must exist
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
# Wants all of these to be legit:
# * (0002,0000) FileMetaInformationGroupLength, UL, 4
# * (0002,0001) FileMetaInformationVersion, OB, 2
# X * (0002,0002) MediaStorageSOPClassUID, UI, N
# X * (0002,0003) MediaStorageSOPInstanceUID, UI, N
# * (0002,0010) TransferSyntaxUID, UI, N
# X * (0002,0012) ImplementationClassUID, UI, N
ds = pydicom.FileDataset(fn,
self.as_pydicom_ds(),
file_meta=file_meta,
preamble=b"\0" * 128)
# print(ds)
with NamedTemporaryFile() as f:
ds.save_as(filename=f.name, write_like_original=True)
self.file = f.read()
def save(self) -> None:
"""
Save input data into DICOM file.
:return: None
"""
if not self.parseInput():
return
else:
filename = QtWidgets.QFileDialog.getSaveFileName(self, "Save DICOM", "../../..", "*.dcm")[0]
if filename == '':
return
else:
fm = pd.Dataset()
# CT Image Storage
fm.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.2"
fm.MediaStorageSOPInstanceUID = pd.uid.generate_uid()
fm.TransferSyntaxUID = pd.uid.ExplicitVRLittleEndian
fm.ImplementationClassUID = pd.uid.generate_uid()
ds = pd.FileDataset(None, {})
ds.file_meta = fm
# CT Image Storage
ds.SOPClassUID = "1.2.840.10008.5.1.4.1.1.2"
ds.SOPInstanceUID = pd.uid.generate_uid()
ds.ContentDate = f"{self.date_time.year:04}{self.date_time.month:02}{self.date_time.day:02}"
ds.ContentTime = f"{self.date_time.hour:02}{self.date_time.minute:02}{self.date_time.second:02}"
ds.StudyInstanceID = pd.uid.generate_uid()
ds.SeriesInstanceID = pd.uid.generate_uid()
ds.Modality = "CT"
ds.ConversionType = 'WSD' # workstation
ds.ImageType = r"ORIGINAL\PRIMARY\AXIAL"
ds.PatientName = self.input_data["PatientName"]
ds.PatientID = self.input_data["PatientID"]
ds.PatientSex = self.input_data["PatientSex"]
ds.ImageComments = self.input_data["ImageComments"]
ds.PixelData = self.img.astype(np.uint8).tobytes()
ds.Rows, ds.Columns = self.img.shape
ds.SamplesPerPixel = 1
ds.PixelRepresentation = 0
ds.PhotometricInterpretation = "MONOCHROME2"
ds.BitsAllocated, ds.BitsStored = 8, 8
ds.HighBit = 7
ds.is_little_endian = True
ds.is_implicit_VR = False
ds.save_as(f"{filename}.dcm", write_like_original=False)
self.close()
def write_dicom(output_name, data, image_number=0):
# Write the data to a dicom file.
# Dicom files are difficult to set up correctly, this file will likely
# crash when trying to open it using dcm2nii. However, if it is loaded in
# python (e.g., dicom.dcmread) then pixel_array contains the relevant
# voxel data
# Convert data from float to in
dataInts = data.astype(np.int16)
# Populate required values for file meta information
file_meta = dicom.Dataset()
file_meta.MediaStorageSOPClassUID = '1.2' # '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3"
file_meta.ImplementationClassUID = "1.2.3.4"
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
# Create the FileDataset
ds = dicom.FileDataset(output_name, {},
file_meta=file_meta,
preamble=b"\0" * 128)
# Set image dimensions
frames, rows, cols = dataInts.shape
ds.Rows = rows
ds.Columns = cols
ds.NumberOfFrames = frames
ds.SamplesPerPixel = 1
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.PixelRepresentation = 0
ds.InstanceNumber = image_number
ds.ImagePositionPatient = [0, 0, 0]
ds.ImageOrientationPatient = [.01, 0, 0, 0, 0, 0]
# Add the data elements -- not trying to set all required here. Check DICOM
# standard
ds.PatientName = "sim"
ds.PatientID = "sim"
# Set the transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set creation date/time
image_datetime = script_datetime + datetime.timedelta(seconds=image_number)
timeStr = image_datetime.strftime('%H%M%S')
ds.ContentDate = image_datetime.strftime('%Y%m%d')
ds.ContentTime = timeStr
# Add the data
ds.PixelData = dataInts.tobytes()
ds.save_as(output_name)
def validate_transfer_syntax_uid(data_set):
meta = pydicom.Dataset()
meta.ImplementationClassUID = pydicom.uid.generate_uid()
meta.TransferSyntaxUID = ImplicitVRLittleEndian
new_data_set = pydicom.FileDataset(filename_or_obj=None,
dataset=data_set,
is_little_endian=True,
file_meta=meta)
new_data_set.is_little_endian = True
new_data_set.is_implicit_VR = True
return new_data_set
def build(kwargs: dict = None) -> pydicom.FileDataset:
if kwargs is None:
kwargs = {}
validate_kwargs(kwargs)
file_meta = pydicom.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'
ds = pydicom.FileDataset('', {},
file_meta=file_meta,
preamble=b"\0" * 128)
# Add the data elements
ds.PatientName = 'Fake Name'
ds.PatientID = '123456'
# Set transfer syntax
ds.is_little_endian = True
ds.is_implicit_VR = True
# Set creation time
dt = datetime.datetime.now()
ds.ContentDate = dt.strftime('%Y%m%d')
ds.ContentTime = dt.strftime('%H%M%S.%f')
# Set transfer syntax
ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRBigEndian
ds.BitsAllocated = 8
ds.Rows = kwargs.get('Rows', 64)
ds.Columns = kwargs.get('Columns', 64)
ds.PixelRepresentation = 0
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME1'
ds.SeriesDescription = kwargs.get('SeriesDescription', '')
ds.ViewPosition = ''
np.random.seed(kwargs.get('seed', np.random.randint(0, 2**32 - 1)))
ds.PixelData = np.random.randint(0,
256,
size=(ds.Rows, ds.Columns),
dtype=np.uint8).reshape(-1)
return ds
def save_dicom(orgpath, npy, config, idx):
"""
Original code can be found in : https://github.com/jryoungw/DicomWrite/blob/master/write_dicom.py
Supported by Mingyu Kim
"""
dcm = pydicom.read_file(orgpath)
savepath = config.result_path + '/' + '/'.join(orgpath.split('/')[:-1])
os.makedirs(config.result_path + '/' + '/'.join(orgpath.split('/')[:-1]),
exist_ok=True)
ds = pydicom.FileDataset(config.result_path + '/' + '/'.join(orgpath.split('/')[:-1])+\
'/'+'{:05d}.dcm'.format(idx), {}, file_meta=pydicom.Dataset(), \
preamble=("\0"*128).encode())
ds.ImageType = dcm.ImageType
ds.SOPClassUID = dcm.SOPClassUID
ds.SOPInstanceUID = dcm.SOPInstanceUID
methods = [i for i in dcm.__dir__() if '_' not in i]
for m in methods:
try:
exec('ds.' + m + '=dcm.' + m)
except:
print('[*] ' + m + ' is not implemented')
try:
ds.RescaleIntercept = '-1024'
except:
pass
try:
ds.RescaleSlope = '1'
except:
pass
try:
ds.WindowCenterWidthExplanation = dcm.WindowCenterWidthExplanation
except:
pass
ds.is_little_endian = True
##################### If pixels are not written correctly, change this value to True #####################
ds.is_implicit_VR = False
##########################################################################################################
savepath = os.path.join(savepath, '{:05d}.dcm'.format(idx + 1))
ds.PixelData = npy.tostring()
ds.save_as(savepath)
def labelvol_to_rtstruct(roi_vol,
aff,
refdcm_file,
filename,
ordered_slices,
uid_base='1.2.826.0.1.3680043.9.7147.',
seriesDescription='test rois',
structureSetLabel='RTstruct',
structureSetName='my rois',
connect_holes=True,
roinames=None,
roidescriptions=None,
roigenerationalgs=None,
roi_colors=[['255', '0', '0'], ['0', '0', '255'],
['0', '255', '0'], ['255', '0', '255'],
['255', '255', '0'], ['0', '255', '255']],
tags_to_copy=[
'PatientName', 'PatientID', 'AccessionNumber',
'StudyID', 'StudyDescription', 'StudyDate',
'StudyTime', 'SeriesDate', 'SeriesTime'
],
tags_to_add=None):
"""Convert a 3D array with integer ROI label to RTstruct
Parameters
---------
roi_vol : 3d numpy integer array
in LPS orientation containing the ROI labels
0 is considered background
1 ... ROI-1
n ... ROI-n
aff : 2d 4x4 numpy array
affine matrix that maps from voxel to (RAS) world coordinates
refdcm_file : string or list
A single reference dicom file or a list of reference files (multiple CT slices)
From this file several dicom tags are copied (e.g. the FrameOfReferenceUID).
In case a list of files is given, the dicom tags are copied from the first file,
however all SOPInstanceUIDs are added to the ContourImageSequence (needed for some
RT systems)
filename : string
name of the output rtstruct file
uid_base : string, optional
uid base used to generate some dicom UID
seriesDescription : string, optional
dicom series description for the rtstruct series
structureSetLabel, structureSetName : string, optional
Label and Name of the structSet
connect_holes : bool, optional
whether to connect inner holes to their outer parents contour - default: True
this connection is needed to show holes correctly in MIM
roinames, roidescriptions, roigenerationalgs : lists, optional
containing strings for ROIName, ROIDescription and ROIGenerationAlgorithm
roi_colors: list of lists containing 3 integer strings (0 - 255), optional
used as ROI display colors
tags_to_copy: list of strings, list optional
extra dicom tags to copy from the refereced dicom file
tags_to_add: dictionary
with valid dicom tags to add in the header
"""
roinumbers = np.unique(roi_vol)
roinumbers = roinumbers[roinumbers > 0]
nrois = len(roinumbers)
if isinstance(refdcm_file, list):
refdcm = pydicom.read_file(refdcm_file[0])
else:
refdcm = pydicom.read_file(refdcm_file)
file_meta = pydicom.Dataset()
file_meta.ImplementationClassUID = uid_base + '1.1.1'
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid(
'1.2.840.10008.5.1.4.1.1.481.3.')
ds = pydicom.FileDataset(filename, {},
file_meta=file_meta,
preamble=b"\0" * 128)
ds.Modality = 'RTSTRUCT'
ds.SeriesDescription = seriesDescription
#--- copy dicom tags from reference dicom file
for tag in tags_to_copy:
if tag in refdcm:
setattr(ds, tag, refdcm.data_element(tag).value)
else:
warnings.warn(
tag + ' not in reference dicom file -> will not be written')
ds.StudyInstanceUID = refdcm.StudyInstanceUID
ds.SeriesInstanceUID = pydicom.uid.generate_uid(uid_base)
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
ds.SOPInstanceUID = pydicom.uid.generate_uid(uid_base)
ds.StructureSetLabel = structureSetLabel
ds.StructureSetName = structureSetName
dfr = pydicom.Dataset()
dfr.FrameOfReferenceUID = refdcm.FrameOfReferenceUID
ds.ReferencedFrameOfReferenceSequence = pydicom.Sequence([dfr])
if tags_to_add is not None:
for tag, value in tags_to_add.items():
setattr(ds, tag, value)
#######################################################################
#######################################################################
# write the ReferencedFrameOfReferenceSequence
contourImageSeq = pydicom.Sequence()
if isinstance(refdcm_file, list):
# in case we got all reference dicom files we add all SOPInstanceUIDs
# otherwise some RT planning systems refuse to read the RTstructs
for fname in refdcm_file:
with pydicom.read_file(fname) as tmpdcm:
tmp = pydicom.Dataset()
tmp.ReferencedSOPClassUID = tmpdcm.SOPClassUID
tmp.ReferencedSOPInstanceUID = tmpdcm.SOPInstanceUID
contourImageSeq.append(tmp)
else:
tmp = pydicom.Dataset()
tmp.ReferencedSOPClassUID = refdcm.SOPClassUID
tmp.ReferencedSOPInstanceUID = refdcm.SOPInstanceUID
contourImageSeq.append(tmp)
tmp2 = pydicom.Dataset()
tmp2.SeriesInstanceUID = refdcm.SeriesInstanceUID
tmp2.ContourImageSequence = contourImageSeq
tmp3 = pydicom.Dataset()
tmp3.ReferencedSOPClassUID = '1.2.840.10008.3.1.2.3.1'
# TODO SOP just copied from MIM rtstructs
tmp3.ReferencedSOPInstanceUID = refdcm.StudyInstanceUID
tmp3.RTReferencedSeriesSequence = pydicom.Sequence([tmp2])
tmp4 = pydicom.Dataset()
tmp4.FrameOfReferenceUID = refdcm.FrameOfReferenceUID
tmp4.RTReferencedStudySequence = pydicom.Sequence([tmp3])
ds.ReferencedFrameOfReferenceSequence = pydicom.Sequence([tmp4])
#######################################################################
#######################################################################
ds.StructureSetROISequence = pydicom.Sequence()
ds.ROIContourSequence = pydicom.Sequence()
if roinames is None: roinames = ['ROI-' + str(x) for x in roinumbers]
if roidescriptions is None:
roidescriptions = ['ROI-' + str(x) for x in roinumbers]
if roigenerationalgs is None:
roigenerationalgs = len(roinumbers) * ['MANUAL']
# loop over the ROIs
for iroi, roinumber in enumerate(roinumbers):
dssr = pydicom.Dataset()
dssr.ROINumber = roinumber
dssr.ROIName = roinames[iroi]
dssr.ROIDescription = roidescriptions[iroi]
dssr.ROIGenerationAlgorithm = roigenerationalgs[iroi]
dssr.ReferencedFrameOfReferenceUID = dfr.FrameOfReferenceUID
ds.StructureSetROISequence.append(dssr)
#######################################################################
#######################################################################
# write ROIContourSequence containing the actual 2D polygon points of the ROI
ds_contour = pydicom.Dataset()
ds_contour.ReferencedSOPClassUID = refdcm.SOPClassUID ###
# generate binary volume for the current ROI
bin_vol = (roi_vol == dssr.ROINumber).astype(int)
# find the bounding box in the last direction
ob_sls = find_objects(bin_vol)
z_start = min([x[2].start for x in ob_sls])
z_end = max([x[2].stop for x in ob_sls])
ds_roi_contour = pydicom.Dataset()
ds_roi_contour.ROIDisplayColor = roi_colors[iroi % len(roi_colors)]
ds_roi_contour.ReferencedROINumber = dssr.ROINumber
ds_roi_contour.ContourSequence = pydicom.Sequence()
# loop over the slices in the 2 direction to create 2D polygons
for sl in np.arange(z_start, z_end):
bin_slice = bin_vol[:, :, sl]
if bin_slice.max() > 0:
contours = binary_2d_image_to_contours(
bin_slice, connect_holes=connect_holes)
for ic in range(len(contours)):
npoints = contours[ic].shape[0]
contour = np.zeros((npoints, 3))
for ipoint in range(npoints):
contour[ipoint, :] = (aff @ np.concatenate(
(contours[ic][ipoint, :], [sl, 1])))[:-1]
dsci = pydicom.Dataset()
dsci.ReferencedSOPInstanceUID = ordered_slices[sl][0]
dsci.ContourGeometricType = 'CLOSED_PLANAR'
dsci.NumberOfContourPoints = contour.shape[0]
dsci.ContourImageSequence = pydicom.Sequence([ds_contour])
dsci.ContourData = contour.flatten().tolist()
# ContourImageSequence contains 1 element per 2D contour
ds_roi_contour.ContourSequence.append(dsci)
# has to contain one element per ROI
ds.ROIContourSequence.append(ds_roi_contour)
#######################################################################
#######################################################################
pydicom.filewriter.write_file(os.path.join('.', filename),
ds,
write_like_original=False)
return z_start, z_end
def __init__(self, fname, spotspecs=None, uid=None, verbose=False):
"""
Create a fake treatment plan DICOM file for unit testing. The spot
specs are a list of dictionaries, one dictionary per beam. Each beam
dictionary contains optional entries for gantry angle, patient support
angle and isocenter position and an obligatory list of "controlpoints".
A file with filename `fname` should not yet exist. A DICOM file with
name `fname` will be written by _test_plan_creator, and also be deleted
when the creator goes out of scope.
"""
assert (sys.version_info.major == 3)
self.verbose = verbose
assert (not os.path.exists(fname))
self.dcm_filename = fname
classUID = '1.2.840.10008.5.1.4.1.1.481.8' if uid is None else uid
instanceUID = pydicom.uid.generate_uid()
# File meta info data elements
file_meta = pydicom.Dataset()
file_meta.MediaStorageSOPClassUID = str(classUID)
file_meta.MediaStorageSOPInstanceUID = str(instanceUID)
file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
#FIXME: we probably need to apply for an official UID here
file_meta.ImplementationClassUID = '1.2.826.0.1.3680043.1.2.100.6.40.0.76'
file_meta.ImplementationVersionName = 'DicomObjects.NET'
self.ds = pydicom.FileDataset(self.dcm_filename, {},
file_meta=file_meta,
preamble=b"\0" * 128)
self.ds.SOPClassUID = classUID
self.ds.SOPInstanceUID = instanceUID
self.ds.PatientName = "unit test"
self.ds.PatientID = "42"
#print("trying to fix 'is_little_endian'")
if spotspecs:
self.ds.IonBeamSequence = pydicom.Sequence()
self.ds.NumberOfBeams = len(spotspecs)
for beamdata in spotspecs:
beam = pydicom.Dataset()
beam.BeamName = beamdata.get('Nm', 'noname')
beam.BeamNumber = beamdata.get('Nr', -1)
beam.NumberOfIonControlPoints = len(beamdata["controlpoints"])
beam.IonControlPointSequence = pydicom.Sequence()
for i, icpdata in enumerate(beamdata["controlpoints"]):
icp = pydicom.Dataset()
if i == 0:
if 'G' in beamdata:
icp.GantryAngle = beamdata['G']
if 'P' in beamdata:
icp.PatientSupportAngle = beamdata['P']
if "I" in beamdata:
icp.IsocenterPosition = list(
[str(v) for v in beamdata.get('I')])
else:
icp.IsocenterPosition = ""
icp.NominalBeamEnergy = icpdata.get('E', 100.)
if 'T' in icpdata:
icp.ScanSpotTuneID = icpdata['T']
#unfortunately, this does not work
icp.ScanSpotMetersetWeights = [
float(v) for v in icpdata['SSW']
]
icp.ScanSpotPositionMap = [
float(v) for v in np.array(icpdata['SSP']).flatten()
]
icp.NumberOfScanSpotPositions = int(
icpdata.get('NSSP',
len(icp.ScanSpotPositionMap) / 2))
beam.IonControlPointSequence.append(icp)
self.ds.IonBeamSequence.append(beam)
else:
self.ds.NumberOfBeams = 0
if verbose:
logger.info("number of beams is {}".format(self.ds.NumberOfBeams))
dt = datetime.datetime.now()
self.ds.ContentDate = dt.strftime('%Y%m%d')
timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
self.ds.ContentTime = timeStr
self.ds.is_little_endian = True
self.ds.is_implicit_VR = True
self.ds.fix_meta_info()
self.ds.save_as(self.dcm_filename)
if self.verbose:
logger.info("wrote dicom file {}".format(self.dcm_filename))
