def load_let(self, path):
if hasattr(self, "letcube"):
if self.letcube is not None:
self.remove_let(self.letcube)
let = LETCube()
let.read(os.path.splitext(path)[0] + ".dos")
self.letcube = let
return let
def load_let(self, path):
""" Load and append a new LET cube from path to self.letcubes.
"""
let = LETCube()
let.read(os.path.splitext(path)[0] + ".dos")
# TODO: check if cube is already loaded, if so, dont load.
# UUID for LET cubes would be useful then?
self.letcubes.append(let)
def test_read(self):
l = LETCube()
l.read(self.let001)
v = create_sphere(l, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = l.calculate_lvh(v)
self.assertIsNotNone(result)
lvh, min_l, max_l, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(lvh.shape), 1)
self.assertEqual(lvh.shape[0], 3000)
self.assertEqual(min_l, 0.0)
self.assertEqual(max_l, 1.0)
self.assertGreater(l.get_max(), 30.0)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
l.write(outfile)
hed_file = outfile + LETCube.header_file_extension
dos_file = outfile + LETCube.data_file_extension
self.assertTrue(os.path.exists(hed_file))
self.assertTrue(os.path.exists(dos_file))
logger.info("Checking if output file " + hed_file + " is not empty")
self.assertGreater(os.path.getsize(hed_file), 1)
logger.info("Checking if output file " + dos_file + " is not empty")
self.assertGreater(os.path.getsize(dos_file), 1)
os.remove(hed_file)
os.remove(dos_file)
def _finish(self, plan):
""" return requested results, copy them back in to plan._working_dir
"""
for _file_name in plan._out_files:
_path = os.path.join(plan._temp_dir, _file_name)
# only copy files back, if we actually have been running TRiP
if self._norun:
logger.info("dummy run: would now copy {:s} to {:s}".format(
_path, plan._working_dir))
else:
logger.info("copy {:s} to {:s}".format(_path,
plan._working_dir))
shutil.copy(_path, plan._working_dir)
for _file_name in plan._out_files:
_path = os.path.join(plan._temp_dir, _file_name)
if ".phys.dos" in _file_name:
_ctx_cube = DosCube()
if not self._norun:
_ctx_cube.read(_path)
plan.dosecubes.append(_ctx_cube)
if ".bio.dos" in _file_name:
_ctx_cube = CtxCube()
if not self._norun:
_ctx_cube.read(_path)
plan.dosecubes.append(_ctx_cube)
if ".dosemlet.dos" in _file_name:
_let_cube = LETCube()
if not self._norun:
_let_cube.read(_path)
plan.letcubes.append(_let_cube)
if ".rst" in _file_name:
logger.warning(
"attaching fields to class not implemented yet {:s}".
format(_path))
# TODO
# need to access the RstClass here for each rst file. This will then need to be attached
# to the proper field in the list of fields.
if self._cleanup:
logger.debug("Delete {:s}".format(plan._temp_dir))
shutil.rmtree(plan._temp_dir)
def post_process(self):
phys_dose = None
bio_dose = None
dose_mean_let = None
temp_dos = None
for projectile in self.projectiles:
name = os.path.join(
self.path,
self.plan_name) + "_" + self.projectiles[projectile]["name"]
factor = float(self.projectile_dose_level[projectile]) / 1000
factor = 1
if os.path.exists(name +
".bio.dos") and self.plan.get_out_bio_dose():
path = os.path.join(name + ".bio.dos")
temp = DosCube()
temp.read(path)
temp *= factor
if self.mult_proj:
self.plan.add_dose(temp, "bio_%s" % projectile)
if bio_dose is None:
bio_dose = temp
else:
bio_dose += temp
if os.path.exists(name +
".phys.dos") and self.plan.get_out_phys_dose():
path = os.path.join(name + ".phys.dos")
temp_dos = DosCube()
temp_dos.read(path)
temp_dos *= factor
if self.mult_proj:
self.plan.add_dose(temp_dos, "phys_%s" % projectile)
if phys_dose is None:
phys_dose = temp_dos
else:
phys_dose += temp_dos
if os.path.exists(name + ".dosemlet.dos"
) and self.plan.get_out_dose_mean_let():
path = os.path.join(name + ".dosemlet.dos")
temp = LETCube()
temp.read(path)
if not self.mult_proj:
dose_mean_let = temp
else:
if dose_mean_let is None:
dose_mean_let = temp * temp_dos
else:
dose_mean_let = dose_mean_let + temp * temp_dos
out_path = os.path.join(self.path, self.plan_name)
if bio_dose is not None:
bio_dose.write(out_path + ".bio.dos")
if phys_dose is not None:
phys_dose.write(out_path + ".phys.dos")
if dose_mean_let is not None:
if self.mult_proj:
dose_mean_let /= phys_dose
dose_mean_let.write(out_path + ".hed")
def test_read(self):
let = LETCube()
let.read(self.let001)
v = create_sphere(let, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = let.calculate_lvh(v)
self.assertIsNotNone(result)
lvh, min_l, max_l, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(lvh.shape), 1)
self.assertEqual(lvh.shape[0], 3000)
self.assertEqual(min_l, 0.0)
self.assertEqual(max_l, 1.0)
self.assertGreater(let.get_max(), 30.0)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
let.write(outfile)
hed_file = outfile + LETCube.header_file_extension
dos_file = outfile + LETCube.data_file_extension
self.assertTrue(os.path.exists(hed_file))
self.assertTrue(os.path.exists(dos_file))
logger.info("Checking if output file " + hed_file + " is not empty")
self.assertGreater(os.path.getsize(hed_file), 1)
logger.info("Checking if output file " + dos_file + " is not empty")
self.assertGreater(os.path.getsize(dos_file), 1)
os.remove(hed_file)
os.remove(dos_file)