def test_mcnamara_cube(self):
""" McNamara test on real cubes.
"""
dose = pt.DosCube()
dose.read(self.cube001)
let = pt.LETCube()
let.read(self.cube001)
v = pt.VdxCube(dose)
logger.info("Adding VDX from path " + self.vdx)
v.read(self.vdx)
# increasing LET should increase RBE
abx = 10.0 # alpha/beta ratio for x-rays [Gy]
rbe1 = rbe_mcnamara(dose.cube, let.cube, abx)
rbe2 = rbe_mcnamara(dose.cube, let.cube, 2.0)
self.assertTrue(np.all(rbe2 >= rbe1)) # RBE goes up as abx goes down.
def import_let(self, let_path):
"""
Import a let cube, add it to the list of loaded dos cubes.
"""
model = self.model # local object of plot_model
pm = self.model.plot # local object of plot_model
logger.debug("Open LETCube {:s}".format(let_path))
let = pt.LETCube()
let.read(let_path)
# update model
model.let.append(let)
pm.let = let # display new loaded cube immediately.
# add cube to the treeview
self.tree.update_tree()
self.plot.update_viewcanvas()
def load_data_cube(filename):
""" Loads either a Dos or LET-cube.
:params str filname: path to Dos or LET-cube.
:returns: a DosCube or LETCube object and a str containing the path to the basename.
"""
if not filename:
logger.warn("Empty data cube filename")
return None, None
logger.info("Reading " + filename)
d = None
basename_cube = None
# try to load LET cube
data_header, _ = pt.LETCube.parse_path(filename)
if data_header is not None:
basename_cube = os.path.splitext(data_header)[0]
d = pt.LETCube()
# try to load DOS cube
data_header, _ = pt.DosCube.parse_path(filename)
if d is None and data_header is not None:
basename_cube = os.path.splitext(data_header)[0]
d = pt.DosCube()
if d is not None:
d.read(filename)
logger.info("Data cube shape" + str(d.cube.shape))
if isinstance(d, pt.DosCube):
d *= 0.1 # convert %% to %
dmax = d.cube.max()
dmin = d.cube.min()
logger.info("Data min, max values: {:g} {:g}".format(dmin, dmax))
if d is None:
logger.warn("Filename " + filename +
" is neither valid DOS neither LET cube")
return d, basename_cube
#
# You should have received a copy of the GNU General Public License
# along with PyTRiP98. If not, see <http://www.gnu.org/licenses/>.
#
"""
Simple example of how to do arithmetic on Cube objects in PyTRiP.
"""
import pytrip as pt
# sum two dose cubes, write result:
print("Two half boxes: out.dos")
d1 = pt.DosCube()
d2 = pt.DosCube()
d1.read("box052000.dos")
d2.read("box053000.dos")
d = (d1 + d2)
d.write("out.dos")
# print minium and maximum value found in cubes
print(d1.cube.min(), d1.cube.max())
print(d2.cube.min(), d2.cube.max())
# calculate new dose average LET cube
l1 = pt.LETCube()
l2 = pt.LETCube()
l1.read("box052000.dosemlet.dos")
l2.read("box053000.dosemlet.dos")
let = ((d1 * l1) + (d2 * l2)) / (d1 + d2)
let.write("out.dosemlet.dos")
def import_let_from_file(self, path):
logger.debug("Open LetCube {:s}".format(path))
cube = pt.LETCube()
cube.read(path)
self.set_let(cube)