from __future__ import annotations
from abc import ABC
import numpy as np
from pydicom.dataset import Dataset, FileMetaDataset
from pydicom.uid import UID, generate_uid
from .layers import Layer
class Simulator(ABC):
"""Abstract class for an image simulator"""
pixel_size: float
shape: (int, int)
image: np.ndarray
def __init__(self, sid: float = 1500):
"""
Parameters
----------
sid
Source to image distance in mm.
"""
self.image = np.zeros(self.shape, np.uint16)
self.sid = sid
self.mag_factor = sid / 1000
def add_layer(self, layer: Layer) -> None:
"""Add a layer to the image"""
self.image = layer.apply(self.image, self.pixel_size, self.mag_factor)
def as_dicom(
self,
gantry_angle: float = 0.0,
coll_angle: float = 0.0,
table_angle: float = 0.0,
) -> Dataset:
"""Create and return a pydicom Dataset. I.e. create a pseudo-DICOM image."""
raise NotImplementedError(
"This method has not been implemented for this simulator. Overload the method of your simulator."
)
def generate_dicom(
self,
file_out_name: str,
gantry_angle: float = 0.0,
coll_angle: float = 0.0,
table_angle: float = 0.0,
) -> None:
ds = self.as_dicom(gantry_angle, coll_angle, table_angle)
ds.save_as(file_out_name, write_like_original=False)
[docs]
class AS500Image(Simulator):
"""Simulates an AS500 EPID image."""
pixel_size: float = 0.78125
shape: (int, int) = (384, 512)
[docs]
def as_dicom(
self,
gantry_angle: float = 0.0,
coll_angle: float = 0.0,
table_angle: float = 0.0,
) -> Dataset:
# make image look like an EPID with flipped data (dose->low)
flipped_image = -self.image + self.image.max() + self.image.min()
file_meta = FileMetaDataset()
# Main data elements
ds = Dataset()
ds.ImageType = ["DERIVED", "SECONDARY", "PORTAL"]
ds.SOPClassUID = UID("1.2.840.10008.5.1.4.1.1.481.1")
ds.SOPInstanceUID = generate_uid()
ds.SeriesInstanceUID = generate_uid()
ds.StudyDate = "20150212"
ds.ContentDate = "20150212"
ds.StudyTime = "124120"
ds.ContentTime = "124120"
ds.AccessionNumber = ""
ds.Modality = "RTIMAGE"
ds.ConversionType = "WSD"
ds.Manufacturer = "IMPAC Medical Systems, Inc."
ds.ReferringPhysicianName = ""
ds.StudyDescription = "QA"
ds.SeriesDescription = "D + Gantry_0"
ds.PhysiciansOfRecord = "Awesome Physician"
ds.OperatorsName = ""
ds.ManufacturerModelName = "MOSAIQ"
ds.PatientName = "Lutz^Test Tool"
ds.PatientID = "zzzBAC_Lutz"
ds.PatientBirthDate = ""
ds.SoftwareVersions = "2.41.01J0"
ds.StudyInstanceUID = "1.2.840.113854.141883099300381770008774160544352783139"
ds.SeriesInstanceUID = (
"1.2.840.113854.141883099300381770008774160544352783139.1"
)
ds.StudyID = "348469"
ds.SeriesNumber = "4597199"
ds.InstanceNumber = "0"
ds.PatientOrientation = ""
ds.PositionReferenceIndicator = ""
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
ds.Rows = self.image.shape[0]
ds.Columns = self.image.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.RTImageLabel = "D"
ds.RTImagePlane = "NORMAL"
ds.XRayImageReceptorAngle = "0.0"
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-200.70400, 150.52800]
ds.RadiationMachineSAD = "1000.0"
ds.RTImageSID = self.sid
ds.PrimaryDosimeterUnit = "MU"
ds.GantryAngle = str(gantry_angle)
ds.BeamLimitingDeviceAngle = str(coll_angle)
ds.PatientSupportAngle = str(table_angle)
ds.PixelData = flipped_image # XXX Array of 393216 bytes excluded
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
return ds
[docs]
class AS1000Image(Simulator):
"""Simulates an AS1000 EPID image."""
pixel_size: float = 0.390625
shape: (int, int) = (768, 1024)
[docs]
def as_dicom(
self,
gantry_angle: float = 0.0,
coll_angle: float = 0.0,
table_angle: float = 0.0,
) -> Dataset:
# make image look like an EPID with flipped data (dose->low)
flipped_image = -self.image + self.image.max() + self.image.min()
# File meta info data elements
file_meta = FileMetaDataset()
# Main data elements
ds = Dataset()
ds.ImageType = ["DERIVED", "SECONDARY", "PORTAL"]
ds.SOPClassUID = UID("1.2.840.10008.5.1.4.1.1.481.1")
ds.SOPInstanceUID = generate_uid()
ds.SeriesInstanceUID = generate_uid()
ds.StudyDate = "20140819"
ds.ContentDate = "20140819"
ds.StudyTime = "130944"
ds.ContentTime = "130944"
ds.AccessionNumber = ""
ds.Modality = "RTIMAGE"
ds.ConversionType = "WSD"
ds.Manufacturer = "IMPAC Medical Systems, Inc."
ds.ReferringPhysicianName = ""
ds.StudyDescription = "QA"
ds.SeriesDescription = "Q + Couch_270"
ds.PhysiciansOfRecord = "I am king"
ds.OperatorsName = ""
ds.ManufacturerModelName = "MOSAIQ"
ds.PatientName = "Albert Einstein"
ds.PatientID = "abc123"
ds.PatientBirthDate = ""
ds.SoftwareVersions = "2.41.01J0"
ds.StudyInstanceUID = "1.2.840.113854.323870129946883845737820671794195198978"
ds.SeriesInstanceUID = (
"1.2.840.113854.323870129946883845737820671794195198978.1"
)
ds.StudyID = "348469"
ds.SeriesNumber = "4290463"
ds.InstanceNumber = "0"
ds.PatientOrientation = ""
ds.PositionReferenceIndicator = ""
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME2"
ds.Rows = self.shape[0]
ds.Columns = self.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.RTImageLabel = "Q"
ds.RTImagePlane = "NORMAL"
ds.XRayImageReceptorAngle = "0.0"
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-200.70400, 150.523400]
ds.RadiationMachineSAD = "1000.0"
ds.RTImageSID = self.sid
ds.PrimaryDosimeterUnit = "MU"
ds.GantryAngle = str(gantry_angle)
ds.BeamLimitingDeviceAngle = str(coll_angle)
ds.PatientSupportAngle = str(table_angle)
ds.PixelData = flipped_image # XXX Array of 1572864 bytes excluded
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
return ds
[docs]
class AS1200Image(Simulator):
"""Simulates an AS1200 EPID image."""
pixel_size: float = 0.336
shape: (int, int) = (1280, 1280)
[docs]
def as_dicom(
self,
gantry_angle: float = 0.0,
coll_angle: float = 0.0,
table_angle: float = 0.0,
) -> Dataset:
file_meta = FileMetaDataset()
file_meta.FileMetaInformationGroupLength = 196
file_meta.FileMetaInformationVersion = b"\x00\x01"
file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.481.1"
file_meta.MediaStorageSOPInstanceUID = (
"1.2.246.352.64.1.5468686515961995030.4457606667843517571"
)
file_meta.TransferSyntaxUID = "1.2.840.10008.1.2"
file_meta.ImplementationClassUID = "1.2.246.352.70.2.1.120.1"
file_meta.ImplementationVersionName = "MergeCOM3_410"
# Main data elements
ds = Dataset()
ds.SpecificCharacterSet = "ISO_IR 100"
ds.ImageType = ["ORIGINAL", "PRIMARY", "PORTAL"]
ds.InstanceCreationDate = "20161230"
ds.InstanceCreationTime = "215510"
ds.SOPClassUID = UID("1.2.840.10008.5.1.4.1.1.481.1")
ds.SOPInstanceUID = generate_uid()
ds.SeriesInstanceUID = generate_uid()
ds.StudyDate = "20161230"
ds.ContentDate = "20161230"
ds.StudyTime = "215441.936"
ds.ContentTime = "215441.936"
ds.AccessionNumber = ""
ds.Modality = "RTIMAGE"
ds.ConversionType = ""
ds.Manufacturer = "Varian Medical Systems"
ds.ReferringPhysicianName = ""
ds.StationName = "NDS-WKS-SN9999"
ds.OperatorsName = "King Kong"
ds.ManufacturerModelName = "VMS.XI.Service"
ds.PatientName = "Grace Hopper"
ds.PatientID = "VMS.XI.Service"
ds.PatientBirthDate = "19000101"
ds.PatientBirthTime = "000000"
ds.PatientSex = ""
ds.SoftwareVersions = "2.5.13.2"
ds.StudyInstanceUID = "1.2.246.352.64.4.5644626269434644263.1905029945372990626"
ds.SeriesInstanceUID = (
"1.2.246.352.64.2.5508761605912087323.11665958260371685307"
)
ds.StudyID = "fdd794f2-8520-4c4a-aecc-e4446c1730ff"
ds.SeriesNumber = None
ds.AcquisitionNumber = "739774555"
ds.InstanceNumber = "1"
ds.PatientOrientation = ""
ds.FrameOfReferenceUID = (
"1.2.246.352.64.3.4714322356925391886.9391210174715030407"
)
ds.PositionReferenceIndicator = ""
ds.SamplesPerPixel = 1
ds.PhotometricInterpretation = "MONOCHROME1"
ds.PlanarConfiguration = 0
ds.Rows = self.shape[0]
ds.Columns = self.shape[1]
ds.BitsAllocated = 16
ds.BitsStored = 16
ds.HighBit = 15
ds.PixelRepresentation = 0
ds.WindowCenter = "32767.0"
ds.WindowWidth = "65535.0"
ds.RescaleIntercept = "0.0"
ds.RescaleSlope = "1.0"
ds.RescaleType = "US"
ds.RTImageLabel = "MV_180"
ds.RTImageDescription = ""
ds.ReportedValuesOrigin = "ACTUAL"
ds.RTImagePlane = "NORMAL"
ds.XRayImageReceptorTranslation = [0.00, 0.00, 1000 - self.sid]
ds.XRayImageReceptorAngle = "0.0"
ds.RTImageOrientation = [1, 0, 0, 0, -1, 0]
ds.ImagePlanePixelSpacing = [self.pixel_size, self.pixel_size]
ds.RTImagePosition = [-214.872, 214.872]
ds.RadiationMachineName = "TrueBeam from Hell"
ds.RadiationMachineSAD = "1000.0"
ds.RTImageSID = self.sid
ds.PrimaryDosimeterUnit = "MU"
ds.GantryAngle = str(gantry_angle)
ds.BeamLimitingDeviceAngle = str(coll_angle)
ds.PatientSupportAngle = str(table_angle)
ds.TableTopVerticalPosition = "-24.59382842824"
ds.TableTopLongitudinalPosition = "200.813502948597"
ds.TableTopLateralPosition = "3.00246706215532"
ds.PixelData = self.image # XXX Array of 3276800 bytes excluded
ds.file_meta = file_meta
ds.is_implicit_VR = True
ds.is_little_endian = True
return ds