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)
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.)
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()
field.basename = patient_name # This name will be used for output filenames, if any field specific output is saved.
field.gantry = 10.0 # degrees
field.couch = 90.0 # degrees
field.fwhm = 4.0 # spot size in [mm]
field.projectile = 'C'
print(field) # We can print all parameters of this field, for checking.
plan.fields.append(
field) # attach field to plan. You may attach multiple fields.
# Next, set the flags for what output should be generated, when the plan has completed.
plan.want_phys_dose = True # We want a physical dose cube, "TST000000.dos"
plan.want_bio_dose = False # No biological cube (Dose * RBE)
plan.want_dlet = True # We want to have the dose-averaged LET cube
plan.want_rst = False # Print the raster scan files (.rst) for all fields.
my_plan.set_sis_file(sis_path)
# To enable remote access to trip, uncomment and eddit the following:
# my_plan.set_remote_state(True)
# my_plan.set_server("titan.phys.au.dk") # location of remote TRiP98 installation. Needs SSH access.
# my_plan.set_username("xxxxxxxxx")
# my_plan.set_password("xxxxxxxxx") # to login using SSH-keys, leave this commented out.
# add target VOI to the plan
my_plan.add_voi(target_voi)
my_plan.get_vois(
)[0].target = True # make TRiP98 aware of that this VOI is the target.
# Finally we need to add a field to the plan
# add default field, carbon ions
my_field = pte.Field("Field 1")
my_field.set_projectile(my_projectile) # set the projectile
my_field.set_couch(my_couch_angle)
my_field.set_gantry(my_gantry_angle)
my_plan.add_field(my_field)
# the next line is needed to correctly set offset between VOI and CT
ct_images = pt.CTImages(my_ctx)
# run TRiP98 optimisation
my_trip = pte.TripExecuter(ct_images.get_modified_images(my_plan))
# TRiP98 will then run the plan and generate the requested dose plan.
# The dose plan is stored in the working directory, and must then be loaded by the user for further processing.
# for local execution, we assume TRiP98 binary is present in PATH env. variable
my_trip.execute(my_plan)
# 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(
kernel=mykernel
) # The ion speicies is selected by passing the corresponding kernel to the field.
field.basename = patient_name # This name will be used for output filenames, if any field specific output is saved.
field.gantry = 10.0 # degrees
field.couch = 90.0 # degrees
field.fwhm = 4.0 # spot size in [mm]
print(field) # We can print all parameters of this field, for checking.
plan.fields.append(
field) # attach field to plan. You may attach multiple fields.
# Next, set the flags for what output should be generated, when the plan has completed.
plan.want_phys_dose = True # We want a physical dose cube, "TST000000.dos"
plan.want_bio_dose = False # No biological cube (Dose * RBE)
plan.want_dlet = True # We want to have the dose-averaged LET cube
plan.want_rst = False # Print the raster scan files (.rst) for all fields.