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"""Helper functions for test modules."""
from pydicom.dataset import Dataset, FileMetaDataset
from pydicom.sequence import Sequence
from pydicom.uid import generate_uid
import numpy
# Constants for helper methods below
SLICE_Z = [-20, -10, 0, 10, 20]
NUM_SLICES = len(SLICE_Z)
STUDY_iUID = generate_uid()
CT_SERIES_iUID = generate_uid()
CT_iUID = [generate_uid() for i in range(NUM_SLICES)]
DOSE_SERIES_iUID = generate_uid()
PLAN_SERIES_iUID = generate_uid()
PLAN_iUID = generate_uid()
SS_SERIES_iUID = generate_uid()
SS_iUID = generate_uid()
FoR_UID = generate_uid()
DOSE_iUID = generate_uid()
# Position, orientation
CT_ipp = [2, 12, -20]
CT_iop = [0, -1, 0, 1, 0, 0] # head-first decubitus left
DOSE_ipp = CT_ipp
DOSE_iop = CT_iop
RTStructureSetStorage = "1.2.840.10008.5.1.4.1.1.481.3"
CTImageStorage = "1.2.840.10008.5.1.4.1.1.2"
RTDoseStorage = "1.2.840.10008.5.1.4.1.1.481.2"
# Helper methods for testing DVH calc, particularly decubitus
def _basic_file_meta(class_UID):
"""Create basic file meta for DICOM dataset."""
# File meta info data elements
file_meta = FileMetaDataset()
file_meta.FileMetaInformationVersion = b'\x00\x01'
file_meta.MediaStorageSOPClassUID = class_UID
file_meta.MediaStorageSOPInstanceUID = generate_uid()
file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
return file_meta
def fake_rtdose():
"""Create a fake RT Dose DICOM dataset."""
# Main data elements
file_meta = _basic_file_meta(RTDoseStorage)
ds = Dataset()
ds.SOPClassUID = RTDoseStorage
ds.SOPInstanceUID = DOSE_iUID
ds.StudyDate = '20220101'
ds.Modality = 'RTDOSE'
ds.PatientName = 'Decubitus'
ds.PatientID = 'Decubitus'
ds.PatientBirthDate = '18000101'
ds.PatientSex = 'O'
ds.SliceThickness = None
ds.StudyInstanceUID = STUDY_iUID
ds.SeriesInstanceUID = DOSE_SERIES_iUID
ds.StudyID = 'none'
ds.SeriesNumber = 1
ds.ImagePositionPatient = DOSE_ipp
ds.ImageOrientationPatient = DOSE_iop
ds.FrameOfReferenceUID = FoR_UID
ds.PositionReferenceIndicator = ''
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.NumberOfFrames = 5
ds.FrameIncrementPointer = (0x3004, 0x000c) # GridFrameOffsetVector
ds.Rows = 7
ds.Columns = 8
ds.PixelSpacing = [1.0, 2.0] # (between rows, between cols)
ds.BitsAllocated = 32
ds.BitsStored = 32
ds.HighBit = 31
ds.PixelRepresentation = 0
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL'
ds.DoseSummationType = 'PLAN'
ds.GridFrameOffsetVector = [0.0, 10.0, 20.0, 30.0, 40.0]
# Referenced RT Plan Sequence
refd_rt_plan_sequence = Sequence()
ds.ReferencedRTPlanSequence = refd_rt_plan_sequence
# Referenced RT Plan Sequence: Referenced RT Plan 1
refd_rt_plan1 = Dataset()
refd_rt_plan1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5'
refd_rt_plan1.ReferencedSOPInstanceUID = PLAN_iUID
refd_rt_plan_sequence.append(refd_rt_plan1)
arr = numpy.zeros(
(ds.NumberOfFrames, ds.Rows, ds.Columns), dtype=numpy.uint32
)
ds.DoseGridScaling = 0.00001 # take to near integer cGy in range of < 100
# Add small amount so values stay above their int value when dose scaled
rounding_guard = 1
for zindex in range(len(arr)):
for row in range(len(arr[0])):
for col in range(len(arr[0][0])):
arr[zindex, row, col] = 1000 * (
zindex*10 + (row > 2)*row + (col > 2) * (col)
) + rounding_guard
# Three middle slices after above math:
# # Shown with location of contours:
# (3, 14.5), (7, 14.5), (7, 17.5), (3, 17.5) (2 voxels across x, 3 down y)
# 2 mm x 1 mm pixel, across (cols, X) center of pixels from 2 to 16
# down (rows, Y) centers from 12 to 18
# volume = (2*2) x (3*1) x (3*10) = 360 mm^3 = 0.36 cm^3
# X=2 4 6 8 10 12 14 16
# Y=12 [10, 10, 10, 13, 14, 15, 16, 17]
# [10, 10, 10, 13, 14, 15, 16, 17]
# [10, 10, 10, 13, 14, 15, 16, 17]
# |-------|
# 15 [13, 13, 13, 16, 17, 18, 19, 20]
# [14, 14, 14, 17, 18, 19, 20, 21]
# [15, 15, 15, 18, 19, 20, 21, 22]
# |-------|
# Y=18 [16, 16, 16, 19, 20, 21, 22, 23]
# X=2 4 6 8 10 12 14 16
# Y=12 [20, 20, 20, 23, 24, 25, 26, 27]
# [20, 20, 20, 23, 24, 25, 26, 27]
# [20, 20, 20, 23, 24, 25, 26, 27]
# |-------|
# [23, 23, 23, 26, 27, 28, 29, 30]
# [24, 24, 24, 27, 28, 29, 30, 31]
# [25, 25, 25, 28, 29, 30, 31, 32]
# |-------|
# Y=18 [26, 26, 26, 29, 30, 31, 32, 33]
# X=2 4 6 8 10 12 14 16
# Y=12 [30, 30, 30, 33, 34, 35, 36, 37]
# [30, 30, 30, 33, 34, 35, 36, 37]
# [30, 30, 30, 33, 34, 35, 36, 37]
# |-------|
# [33, 33, 33, 36, 37, 38, 39, 40]
# [34, 34, 34, 37, 38, 39, 40, 41]
# [35, 35, 35, 38, 39, 40, 41, 42]
# |-------|
# Y=18 [36, 36, 36, 39, 40, 41, 42, 43]
ds.PixelData = arr.tobytes()
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
return ds
def fake_ss():
"""Create a fake RT Structure Set DICOM dataset."""
file_meta = _basic_file_meta(RTStructureSetStorage)
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = 'ISO_IR 192'
ds.InstanceCreationDate = '20220101'
ds.SOPClassUID = RTStructureSetStorage
ds.SOPInstanceUID = SS_iUID
ds.StudyDate = '20220101'
ds.Modality = 'RTSTRUCT'
ds.PatientName = 'Decubitus'
ds.PatientID = 'Decubitus'
ds.PatientBirthDate = '18000101'
ds.PatientSex = 'O'
ds.StudyInstanceUID = STUDY_iUID
ds.SeriesInstanceUID = SS_SERIES_iUID
ds.StudyID = '1'
ds.SeriesNumber = '10'
ds.StructureSetLabel = 'CT_1'
ds.StructureSetDate = '20220101'
# Referenced Frame of Reference Sequence
refd_frame_of_ref_sequence = Sequence()
ds.ReferencedFrameOfReferenceSequence = refd_frame_of_ref_sequence
# Referenced Frame of Reference Sequence: Referenced Frame of Reference 1
refd_frame_of_ref1 = Dataset()
refd_frame_of_ref1.FrameOfReferenceUID = FoR_UID
# RT Referenced Study Sequence
rt_refd_study_sequence = Sequence()
refd_frame_of_ref1.RTReferencedStudySequence = rt_refd_study_sequence
# RT Referenced Study Sequence: RT Referenced Study 1
rt_refd_study1 = Dataset()
rt_refd_study1.ReferencedSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.3'
rt_refd_study1.ReferencedSOPInstanceUID = STUDY_iUID
# RT Referenced Series Sequence
rt_refd_series_sequence = Sequence()
rt_refd_study1.RTReferencedSeriesSequence = rt_refd_series_sequence
# RT Referenced Series Sequence: RT Referenced Series 1
rt_refd_series1 = Dataset()
rt_refd_series1.SeriesInstanceUID = CT_SERIES_iUID
# Contour Image Sequence
contour_image_sequence = Sequence()
rt_refd_series1.ContourImageSequence = contour_image_sequence
# Contour Image Sequence: Contour Image 1
contour_image1 = Dataset()
contour_image1.ReferencedSOPClassUID = CTImageStorage
contour_image1.ReferencedSOPInstanceUID = CT_iUID
contour_image_sequence.append(contour_image1)
rt_refd_series_sequence.append(rt_refd_series1)
rt_refd_study_sequence.append(rt_refd_study1)
refd_frame_of_ref_sequence.append(refd_frame_of_ref1)
# Structure Set ROI Sequence
structure_set_roi_sequence = Sequence()
ds.StructureSetROISequence = structure_set_roi_sequence
# Structure Set ROI Sequence: Structure Set ROI 1
structure_set_roi1 = Dataset()
structure_set_roi1.ROINumber = 1
structure_set_roi1.ReferencedFrameOfReferenceUID = FoR_UID
structure_set_roi1.ROIName = 'PTV'
structure_set_roi1.ROIGenerationAlgorithm = 'MANUAL'
structure_set_roi_sequence.append(structure_set_roi1)
# ROI Contour Sequence
# Contour Sequence
# Contour Image Sequence (optional, references the CT slices)
# Contour Geometric Type (e.g. CLOSED_PLANAR)
# Number of Contour Points
# Contour Data
# Referenced ROI Number
roi_contour_sequence = Sequence()
ds.ROIContourSequence = roi_contour_sequence
# ROI Contour Sequence: ROI Contour 1
roi_contour1 = Dataset()
roi_contour1.ROIDisplayColor = [255, 128, 0]
# Contour Sequence
contour_sequence = Sequence()
roi_contour1.ContourSequence = contour_sequence
for i in range(1, NUM_SLICES-1): # contours on all but first, last slice
contour = Dataset()
contour.ContourGeometricType = 'CLOSED_PLANAR'
z = SLICE_Z[i]
contour.ContourData = [3, 14.5, z, 7, 14.5, z, 7, 17.5, z, 3, 17.5, z]
contour.NumberOfContourPoints = len(contour.ContourData) / 3
contour_sequence.append(contour)
roi_contour1.ReferencedROINumber = 1
roi_contour_sequence.append(roi_contour1)
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
return ds
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