def test_exec(self):
""" Prepare and execute a dry-run test using the Executer.
"""
logger.info("Test norun TRiP98 execution")
logger.debug("Load CtxCube {:s}".format(self.ctx_path))
c = pt.CtxCube()
c.read(self.ctx_path)
logger.debug("Load VdxCube {:s}".format(self.vdx_path))
v = pt.VdxCube(c)
v.read(self.vdx_path)
print(v.get_voi_names())
plan = pte.Plan(basename=self.patient_name)
self.assertIsNotNone(plan)
plan.ddd_dir = "~/TRiP98/base/DATA/DDD/12C/RF3MM/*"
plan.spc_dir = "~/TRiP98/base/DATA/SPC/12C/RF3MM/*"
plan.sis_path = "~/TRiP98/base/DATA/SIS/12C.sis"
plan.hlut_path = "~/TRiP98/base/DATA/HLUT/19990218.hlut"
plan.dedx_path = "~/TRiP98/base/DATA/DEDX/20040607.dedx"
plan.working_dir = "." # working dir must exist.
# add the target voi to the plan
plan.voi_target = v.get_voi_by_name('target')
plan.rifi = 3.0
plan.bolus = 0.0
plan.offh2o = 1.873
# create a field and add it to the plan
field = pte.Field()
self.assertIsNotNone(field)
field.basename = self.patient_name
field.gantry = 10.0
field.couch = 90.0 # degrees
field.fwhm = 4.0 # spot size in [mm]
field.projectile = 'C'
plan.fields.append(field)
# flags for what output should be generated
plan.want_phys_dose = True
plan.want_bio_dose = False
plan.want_dlet = True
plan.want_rst = False
t = pte.Execute(c, v)
self.assertIsNotNone(t)
t.trip_bin_path = self.trip_path
print(self.trip_path)
if os.name != 'nt': # skip running fake TRiP98 on Windows as it is not supported there
t.execute(
plan, False
) # setup and make a dry-run, since TRiP98 is not installed.
executer_str = str(t)
self.assertGreater(len(executer_str), 1)
def test_exec_parse(self):
"""
"""
logger.info("Test parsing '{:s}'".format(self.exec_path))
plan = pte.Plan()
plan.read_exec(self.exec_path)
print(plan)
for field in plan.fields:
print(field)
def new_plan(model):
"""
Creates a new instance of a plan, and adds it to model.
"""
logger.debug("new_plan()")
if not model.ctx:
logger.error("No CT data loaded.")
return
# setup a new tripexecuter.plan object
import pytrip.tripexecuter as pte
plan = pte.Plan(basename=model.ctx.basename)
# attach this plan to the list of plans in models.
model.plans.append(plan)
# open a dialog for the user to edit it
PlanController.edit_plan(model, plan)
model.plans.append(plan)
# Next we load the CT cube:
c = pt.CtxCube()
c.read(ctx_path)
# And load the contours
v = pt.VdxCube(c)
v.read(vdx_path)
# we may print all contours found in the Vdx file, if we want to
print(v.get_voi_names())
# Ok, we have the Contours and the CT cube ready. Next we must prepare a plan.
# We may choose any basename for the patient. All output files will be named using
# this basename.
plan = pte.Plan(basename=patient_name)
# We need to specify where the kernel files can be found. The location may depend on the ion we
# wnat to treat with. This example is for carbon ions:
plan.ddd_dir = "/home/bassler/TRiP98/base/DATA/DDD/12C/RF3MM/*"
plan.spc_dir = "/home/bassler/TRiP98/base/DATA/SPC/12C/RF3MM/*"
plan.sis_path = "/home/bassler/TRiP98/base/DATA/SIS/12C.sis"
plan.hlut_path = "/home/bassler/TRiP98/base/DATA/HLUT/19990218.hlut"
plan.dedx_path = "/home/bassler/TRiP98/base/DATA/DEDX/20040607.dedx"
plan.working_dir = "/home/bassler/test/" # working dir must exist.
# Set the plan target to the voi called "CTV"
plan.voi_target = v.get_voi_by_name('CTV')
# some optional parameters (if not set, they will all be zero by default)
plan.rifi = 3.0 # 3 mm ripple filter. (This is only for documentaiton, it will not affect the dose optimization.)
# We need to specify where the kernel files can be found. The location may depend on the ion we
# want to treat with. This example sets up a kernel model for C-12 ions with a 3 mm Ripple Filter.
mykernel = pte.KernelModel()
mykernel.projectile = pte.Projectile("C", a=12)
mykernel.ddd_path = trip_path + "/DATA/DDD/12C/RF3MM/*"
mykernel.spc_path = trip_path + "/DATA/SPC/12C/RF3MM/*"
mykernel.sis_path = trip_path + "/DATA/SIS/19981218.sis"
mykernel.rifi_thickness = 3.0 # 3 mm ripple filter. (Only for documentaiton, will not affect dose optimization.)
mykernel.rifi_name = "GSI_1D_3mm" # Additional free text for documentation.
mykernel.comment = "Carbon-12 ions with 3 mm 1D Ripple Filter"
# Ok, we have the Contours, the CT cube and dose kernels ready. Next we must prepare a plan.
# We may choose any basename for the patient. All output files will be named using
# this basename.
plan = pte.Plan(basename=patient_name, default_kernel=mykernel)
# Plan specific data:
plan.hlut_path = trip_path + "/DATA/HLUT/19990218.hlut" # Hounsfield lookup table location
plan.dedx_path = trip_path + "/DATA/DEDX/20000830.dedx" # Stopping power tables
plan.working_dir = wdir
# Set the plan target to the voi called "CTV"
plan.voi_target = v.get_voi_by_name('CTV')
# some optional plan specific parameters (if not set, they will all be zero by default)
plan.bolus = 0.0 # No bolus is applied here. Set this to some value, if you are to optimize very shallow tumours.
plan.offh2o = 1.873 # Some offset mimicing the monitoring ionization chambers and exit window of the beam nozzle.
# Next we need to specify at least one field, and add that field to the plan.
field = pte.Field(
# We need to specify where the kernel files can be found. The location may depend on the ion we
# want to treat with. This example sets up a kernel model for C-12 ions with a 3 mm Ripple Filter.
mykernel = pte.KernelModel()
mykernel.projectile = pte.Projectile("C", a=12)
mykernel.ddd_path = "/home/bassler/TRiP98/base/DATA/DDD/12C/RF3MM/*"
mykernel.spc_path = "/home/bassler/TRiP98/base/DATA/SPC/12C/RF3MM/*"
mykernel.sis_path = "/home/bassler/TRiP98/base/DATA/SIS/12C.sis"
mykernel.rifi_thickness = 3.0 # 3 mm ripple filter. (Only for documentaiton, will not affect dose optimization.)
mykernel.rifi_name = "GSI_1D_3mm" # Additional free text for documentation.
mykernel.comment = "Carbon-12 ions with 3 mm 1D Ripple Filter"
# Ok, we have the Contours, the CT cube and dose kernels ready. Next we must prepare a plan.
# We may choose any basename for the patient. All output files will be named using
# this basename.
plan = pte.Plan(basename=patient_name, kernels=(mykernel, ))
# Plan specific data:
plan.hlut_path = "/home/bassler/TRiP98/base/DATA/HLUT/19990218.hlut" # Hounsfield lookup table location
plan.dedx_path = "/home/bassler/TRiP98/base/DATA/DEDX/20040607.dedx" # Stopping power tables
plan.working_dir = "/home/bassler/test/" # working dir must exist.
# Set the plan target to the voi called "CTV"
plan.voi_target = v.get_voi_by_name('CTV')
# some optional plan specific parameters (if not set, they will all be zero by default)
plan.bolus = 0.0 # No bolus is applied here. Set this to some value, if you are to optimize very shallow tumours.
plan.offh2o = 1.873 # Some offset mimicing the monitoring ionization chambers and exit window of the beam nozzle.
# Next we need to specify at least one field, and add that field to the plan.
field = pte.Field(
