def create_dicom_base(self):
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
if self.header_set is False:
raise InputError("Header not loaded")
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage
meta.MediaStorageSOPInstanceUID = "1.2.3"
meta.ImplementationClassUID = "1.2.3.4"
meta.TransferSyntaxUID = UID.ImplicitVRLittleEndian # Implicit VR Little Endian - Default Transfer Syntax
ds = FileDataset("file", {}, file_meta=meta, preamble=b"\0" * 128)
ds.PatientsName = self.patient_name
ds.PatientID = "123456"
ds.PatientsSex = '0'
ds.PatientsBirthDate = '19010101'
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.AccessionNumber = ''
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = '1.2.3' # !!!!!!!!
ds.SOPInstanceUID = '1.2.3' # !!!!!!!!!!
ds.StudyInstanceUID = '1.2.3' # !!!!!!!!!!
ds.FrameofReferenceUID = '1.2.3' # !!!!!!!!!
ds.StudyDate = '19010101' # !!!!!!!
ds.StudyTime = '000000' # !!!!!!!!!!
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.SamplesPerPixel = 1
ds.ImageOrientationPatient = ['1', '0', '0', '0', '1', '0']
ds.Rows = self.dimx
ds.Columns = self.dimy
ds.SliceThickness = str(self.slice_distance)
ds.PixelSpacing = [self.pixel_size, self.pixel_size]
return ds
def set_dose(self, dose):
try:
dose = float(dose)
if dose < 0:
raise Exception()
self.dose = dose
except Exception:
raise InputError("Dose should be a number larger or equal to 0")
def set_zsteps(self, zsteps):
try:
zsteps = float(zsteps)
if zsteps < 0:
raise Exception()
self.zsteps = zsteps
except Exception:
raise InputError("ZSteps should be larger 0")
def set_doseextension(self, doseextension):
try:
doseextension = float(doseextension)
if doseextension < 0:
raise Exception()
self.doseextension = doseextension
except Exception:
raise InputError("Doseextension should be larger 0")
def set_contourextension(self, contourextension):
try:
contourextension = float(contourextension)
if contourextension < 0:
raise Exception()
self.contourextension = contourextension
except Exception:
raise InputError("Contourextension should be larger 0")
def _read_trip_data_file(
self,
datafile_path,
header_path,
multiply_by_2=False): # TODO: could be made private? #126
"""Read TRiP98 formatted data.
If header file was not previously loaded, it will be attempted first.
Due to an issue in VIRTUOS, sometimes DosCube data have been reduced with a factor of 2.
Setting multiply_by_2 to True, will restore the true values, in this case.
:param datafile_path: Path to TRiP formatted data.
:param multiply_by_2: The data read will automatically be multiplied with a factor of 2.
"""
# fill header data if self.header is empty
if not self.header_set:
self._read_trip_header_file(header_path)
# raise exception if reading header failed
if not self.header_set:
raise InputError("Header file not loaded")
# preparation
data_dtype = np.dtype(self.format_str)
data_count = self.dimx * self.dimy * self.dimz
# load data from data file (gzipped or not)
logger.info("Opening file: " + datafile_path)
if datafile_path.endswith('.gz'):
import gzip
with gzip.open(datafile_path, "rb") as f:
s = f.read(data_dtype.itemsize * data_count)
cube = np.frombuffer(s, dtype=data_dtype, count=data_count)
else:
cube = np.fromfile(datafile_path, dtype=data_dtype)
if self.byte_order == "aix":
logger.info("AIX big-endian data.")
# byteswapping is not needed anymore, handled by "<" ">" in dtype
# sanity check
logger.info("Cube data points : {:d}".format(len(cube)))
if len(cube) != self.dimx * self.dimy * self.dimz:
logger.error("Header size and cube size dont match.")
logger.error("Cube data points : {:d}".format(len(cube)))
logger.error("Header says : {:d} = {:d} * {:d} * {:d}".format(
self.dimx * self.dimy * self.dimz, self.dimx, self.dimy,
self.dimz))
raise IOError("Header data and dose cube size are not consistent.")
cube = np.reshape(cube, (self.dimz, self.dimy, self.dimx))
if multiply_by_2:
logger.warning(
"Cube was previously rescaled to 50%. Now multiplying with 2.")
cube *= 2
self.cube = cube
def set_hu_value(self, value):
if len(value) is 0:
self.hu_value = None
return
try:
value = float(value)
self.hu_value = value
except Exception:
raise InputError("HU Value should be a number")
def set_max_dose_fraction(self, max_dose_fraction):
try:
max_dose_fraction = float(max_dose_fraction)
if max_dose_fraction < 0:
raise Exception()
self.max_dose_fraction = max_dose_fraction
except Exception:
raise InputError("Max dose fraction should be "
"a number between 0 and 1")
def create_dicom(self):
""" Creates a Dicom RT-Dose object from self.
This function can be used to convert a TRiP98 Dose file to Dicom format.
:returns: a Dicom RT-Dose object.
"""
if not _dicom_loaded:
raise ModuleNotLoadedError("Dicom")
if not self.header_set:
raise InputError("Header not loaded")
ds = self.create_dicom_base()
ds.Modality = 'RTDOSE'
ds.SamplesperPixel = 1
ds.BitsAllocated = self.num_bytes * 8
ds.BitsStored = self.num_bytes * 8
ds.AccessionNumber = ''
ds.SeriesDescription = 'RT Dose'
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL'
ds.DoseGridScaling = self.target_dose / 10**5
ds.DoseSummationType = 'PLAN'
ds.SliceThickness = ''
ds.InstanceCreationDate = '19010101'
ds.InstanceCreationTime = '000000'
ds.NumberOfFrames = len(self.cube)
ds.PixelRepresentation = 0
ds.StudyID = '1'
ds.SeriesNumber = 14
ds.GridFrameOffsetVector = [
x * self.slice_distance for x in range(self.dimz)
]
ds.InstanceNumber = ''
ds.NumberofFrames = len(self.cube)
ds.PositionReferenceIndicator = "RF"
ds.TissueHeterogeneityCorrection = ['IMAGE', 'ROI_OVERRIDE']
ds.ImagePositionPatient = [
"%.3f" % (self.xoffset * self.pixel_size),
"%.3f" % (self.yoffset * self.pixel_size),
"%.3f" % (self.slice_pos[0])
]
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
ds.SOPInstanceUID = '1.2.246.352.71.7.320687012.47206.20090603085223'
ds.SeriesInstanceUID = '1.2.246.352.71.2.320687012.28240.20090603082420'
# Bind to rtplan
rt_set = Dataset()
rt_set.RefdSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5'
rt_set.RefdSOPInstanceUID = '1.2.3'
ds.ReferencedRTPlans = Sequence([rt_set])
pixel_array = np.zeros((len(self.cube), ds.Rows, ds.Columns),
dtype=self.pydata_type)
pixel_array[:][:][:] = self.cube[:][:][:]
ds.PixelData = pixel_array.tostring()
return ds
def set_fwhm(self, fwhm):
try:
fwhm = float(fwhm)
if fwhm <= 0:
raise Exception()
self.fwhm = fwhm
except Exception:
raise InputError("Fwhm shoud be a number and larger than 0")
def set_rasterstep(self, a, b):
try:
a = float(a)
b = float(b)
if a < 0 or b < 0:
raise Exception()
self.rasterstep = [a, b]
except Exception:
raise InputError("Rastersteps should be " "larger than 0 and numbers")
def get_voi_by_name(self, name):
""" Returns a Voi object by its name.
:param str name: Name of voi to be returned.
:returns: the Voi which has exactly this name, else raise an Error.
"""
for voi in self.vois:
if voi.name.lower() == name.lower():
return voi
raise InputError("Voi doesn't exist")
def set_couch(self, angle):
if type(angle) is str and not len(angle):
angle = 0
try:
angle = (float(angle) + 360) % 360
if angle < 0 or angle > 360:
raise Exception()
self.couch = angle
except Exception:
raise InputError("Couch angle shoud be " "a number between 0 and 360")
def set_gantry(self, angle):
if type(angle) is str and not len(angle):
angle = 0
try:
angle = (float(angle) + 360) % 360
if angle < 0 or angle > 360:
raise Exception()
self.gantry = angle
except Exception:
raise InputError("Gantry angle shoud be a " "number between 0 and 360")
def read_dicom(self, dcm):
""" Imports the dose distribution from DICOM object.
:param DICOM dcm: a DICOM object
"""
if "rtdose" not in dcm:
raise InputError("Data doesn't contain dose information")
if self.header_set is False:
self._set_header_from_dicom(dcm)
self.cube = np.zeros((self.dimz, self.dimy, self.dimx))
for i, item in enumerate(dcm["rtdose"].pixel_array):
self.cube[i][:][:] = item
def set_target(self, target):
if len(target) is 0:
self.target = []
return
target = target.split(",")
if len(target) is 3:
try:
self.target = [float(target[0]), float(target[1]), float(target[2])]
return
except Exception:
# TODO fix that !
pass
raise InputError("Target should be empty " "or in the format x,y,z")
def read_dicom(self, data, structure_ids=None):
"""
Reads structures from a Dicom RTSS Object.
:param Dicom data: A Dicom RTSS object.
:param structure_ids: (TODO: undocumented)
"""
if "rtss" not in data:
raise InputError("Input is not a valid rtss structure")
dcm = data["rtss"]
self.version = "2.0"
for i, item in enumerate(dcm.ROIContours):
if structure_ids is None or item.RefdROINumber in structure_ids:
v = Voi(dcm.RTROIObservations[i].ROIObservationLabel.decode('iso-8859-1'), self.cube)
v.read_dicom(dcm.RTROIObservations[i], item)
self.add_voi(v)
self.cube.xoffset = 0
self.cube.yoffset = 0
self.cube.zoffset = 0
"""shift = min(self.cube.slice_pos)
def read_dicom(self, dcm):
""" Imports CT-images from Dicom object.
:param Dicom dcm: a Dicom object
"""
if "images" not in dcm:
raise InputError("Data doesn't contain ct data")
if not self.header_set:
self.read_dicom_header(dcm)
self.cube = np.zeros((self.dimz, self.dimy, self.dimx), dtype=np.int16)
intersect = float(dcm["images"][0].RescaleIntercept)
slope = float(dcm["images"][0].RescaleSlope)
for i in range(len(dcm["images"])):
data = np.array(dcm["images"][i].pixel_array) * slope + intersect
self.cube[i][:][:] = data
if self.slice_pos[1] < self.slice_pos[0]:
self.slice_pos.reverse()
self.zoffset = self.slice_pos[0]
self.cube = self.cube[::-1]
def set_projectile(self, projectile):
if projectile not in ['H', 'C', 'O', 'Ne']:
raise InputError("Projectile not allowed")
self.projectile = projectile
def split_plan(self, plan=None):
self.targets = []
self.oar_list = []
dose = 0
for voi in self.plan.get_vois():
if voi.is_oar():
self.oar_list.append(voi)
if voi.is_target():
self.targets.append(voi)
if voi.get_dose() > dose:
dose = voi.get_dose()
if not len(self.targets):
raise InputError("No targets")
if not len(self.plan.get_fields()):
raise InputError("No fields")
self.target_dose = dose
if plan is None:
plan = self.plan
proj = []
self.projectile_dose_level = {}
for field in plan.fields:
if field.get_projectile() not in proj:
proj.append(field.get_projectile())
self.projectile_dose_level[field.get_projectile()] = 0
if len(proj) > 1:
self.mult_proj = True
else:
self.mult_proj = False
if self.mult_proj:
self.projectiles = {}
for field in plan.fields:
if field.get_projectile() not in self.projectiles.keys():
self.projectiles[field.get_projectile()] = {
"target_dos": DosCube(self.images),
"fields": [field],
"name": field.get_projectile(),
"projectile": field.get_projectile()
}
else:
self.projectiles[field.get_projectile()]["fields"].append(
field)
self.target_dos = DosCube(self.images)
for i, voi in enumerate(self.targets):
temp = DosCube(self.images)
voi_dose_level = int(voi.get_dose() / dose * 1000)
temp.load_from_structure(voi.get_voi().get_voi_data(), 1)
for projectile, data in self.projectiles.items():
dose_percent = self.plan.get_dose_percent(projectile)
if not voi.get_dose_percent(projectile) is None:
dose_percent = voi.get_dose_percent(projectile)
proj_dose_lvl = int(voi.get_dose() / self.target_dose *
dose_percent * 10)
if self.projectile_dose_level[projectile] < proj_dose_lvl:
self.projectile_dose_level[projectile] = proj_dose_lvl
if proj_dose_lvl == 0:
proj_dose_lvl = -1
if i == 0:
data["target_dos"] = temp * proj_dose_lvl
else:
data["target_dos"].merge_zero(temp * proj_dose_lvl)
if i == 0:
self.target_dos = temp * voi_dose_level
else:
self.target_dos.merge_zero(temp * voi_dose_level)
for projectile, data in self.projectiles.items():
data["target_dos"].cube[data["target_dos"].cube == -1] = int(0)
self.plan.add_dose(data["target_dos"],
"target_%s" % projectile)
self.rest_dose = copy.deepcopy(self.target_dos)
def create_dicom(self):
""" Creates a DICOM RT-Dose object from self.
This function can be used to convert a TRiP98 Dose file to DICOM format.
:returns: a DICOM RT-Dose object.
"""
if not _dicom_loaded:
raise ModuleNotLoadedError("DICOM")
if not self.header_set:
raise InputError("Header not loaded")
ds = self.create_dicom_base()
ds.Modality = 'RTDOSE'
ds.SamplesPerPixel = 1
ds.BitsAllocated = self.num_bytes * 8
ds.BitsStored = self.num_bytes * 8
ds.AccessionNumber = ''
ds.SeriesDescription = 'RT Dose'
ds.DoseUnits = 'GY'
ds.DoseType = 'PHYSICAL'
ds.DoseGridScaling = self.target_dose / 10**5
ds.DoseSummationType = 'PLAN'
ds.SliceThickness = ''
ds.InstanceCreationDate = '19010101'
ds.InstanceCreationTime = '000000'
ds.NumberOfFrames = len(self.cube)
ds.PixelRepresentation = 0
ds.StudyID = '1'
ds.SeriesNumber = '14' # SeriesNumber tag 0x0020,0x0011 (type IS - Integer String)
ds.GridFrameOffsetVector = [
x * self.slice_distance for x in range(self.dimz)
]
ds.InstanceNumber = ''
ds.PositionReferenceIndicator = "RF"
ds.TissueHeterogeneityCorrection = ['IMAGE', 'ROI_OVERRIDE']
ds.ImagePositionPatient = [
"%.3f" % (self.xoffset * self.pixel_size),
"%.3f" % (self.yoffset * self.pixel_size),
"%.3f" % (self.slice_pos[0])
]
ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.481.2'
ds.SOPInstanceUID = '1.2.246.352.71.7.320687012.47206.20090603085223'
# Study Instance UID tag 0x0020,0x000D (type UI - Unique Identifier)
# self._dicom_study_instance_uid may be either set in __init__ when creating new object
# or set when import a DICOM file
# Study Instance UID for structures is the same as Study Instance UID for CTs
ds.StudyInstanceUID = self._dicom_study_instance_uid
# Series Instance UID tag 0x0020,0x000E (type UI - Unique Identifier)
# self._dose_dicom_series_instance_uid may be either set in __init__ when creating new object
# Series Instance UID might be different than Series Instance UID for CTs
ds.SeriesInstanceUID = self._dose_dicom_series_instance_uid
# Bind to rtplan
rt_set = Dataset()
rt_set.RefdSOPClassUID = '1.2.840.10008.5.1.4.1.1.481.5'
rt_set.RefdSOPInstanceUID = '1.2.3'
ds.ReferencedRTPlanSequence = Sequence([rt_set])
pixel_array = np.zeros((len(self.cube), ds.Rows, ds.Columns),
dtype=self.pydata_type)
pixel_array[:][:][:] = self.cube[:][:][:]
ds.PixelData = pixel_array.tostring()
return ds
def create_dicom_base(self):
if _dicom_loaded is False:
raise ModuleNotLoadedError("Dicom")
if self.header_set is False:
raise InputError("Header not loaded")
# TODO tags + code datatypes are described here:
# https://www.dabsoft.ch/dicom/6/6/#(0020,0012)
# datatype codes are described here:
# ftp://dicom.nema.org/medical/DICOM/2013/output/chtml/part05/sect_6.2.html
meta = Dataset()
meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2' # CT Image Storage
# Media Storage SOP Instance UID tag 0x0002,0x0003 (type UI - Unique Identifier)
meta.MediaStorageSOPInstanceUID = self._ct_sop_instance_uid
meta.ImplementationClassUID = "1.2.3.4"
meta.TransferSyntaxUID = UID.ImplicitVRLittleEndian # Implicit VR Little Endian - Default Transfer Syntax
ds = FileDataset("file", {}, file_meta=meta, preamble=b"\0" * 128)
ds.PatientsName = self.patient_name
if self.patient_id in (None, ''):
ds.PatientID = datetime.datetime.today().strftime('%Y%m%d-%H%M%S')
else:
ds.PatientID = self.patient_id # Patient ID tag 0x0010,0x0020 (type LO - Long String)
ds.PatientsSex = '' # Patient's Sex tag 0x0010,0x0040 (type CS - Code String)
# Enumerated Values: M = male F = female O = other.
ds.PatientsBirthDate = '19010101'
ds.SpecificCharacterSet = 'ISO_IR 100'
ds.AccessionNumber = ''
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.SOPClassUID = '1.2.3' # !!!!!!!!
# SOP Instance UID tag 0x0008,0x0018 (type UI - Unique Identifier)
ds.SOPInstanceUID = self._ct_sop_instance_uid
# Study Instance UID tag 0x0020,0x000D (type UI - Unique Identifier)
# self._dicom_study_instance_uid may be either set in __init__ when creating new object
# or set when import a DICOM file
# Study Instance UID for structures is the same as Study Instance UID for CTs
ds.StudyInstanceUID = self._dicom_study_instance_uid
# Series Instance UID tag 0x0020,0x000E (type UI - Unique Identifier)
# self._ct_dicom_series_instance_uid may be either set in __init__ when creating new object
# or set when import a DICOM file
# Series Instance UID for structures might be different than Series Instance UID for CTs
ds.SeriesInstanceUID = self._ct_dicom_series_instance_uid
# Study Instance UID tag 0x0020,0x000D (type UI - Unique Identifier)
ds.FrameofReferenceUID = '1.2.3' # !!!!!!!!!
ds.StudyDate = datetime.datetime.today().strftime('%Y%m%d')
ds.StudyTime = datetime.datetime.today().strftime('%H%M%S')
ds.PhotometricInterpretation = 'MONOCHROME2'
ds.SamplesPerPixel = 1
ds.ImageOrientationPatient = ['1', '0', '0', '0', '1', '0']
ds.Rows = self.dimx
ds.Columns = self.dimy
ds.SliceThickness = str(self.slice_distance)
ds.PixelSpacing = [self.pixel_size, self.pixel_size]
# Add eclipse friendly IDs
ds.StudyID = '1' # Study ID tag 0x0020,0x0010 (type SH - Short String)
ds.ReferringPhysiciansName = 'py^trip' # Referring Physician's Name tag 0x0008,0x0090 (type PN - Person Name)
ds.PositionReferenceIndicator = '' # Position Reference Indicator tag 0x0020,0x1040
ds.SeriesNumber = '1' # SeriesNumber tag 0x0020,0x0011 (type IS - Integer String)
return ds