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 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
def import_dos(self, dos_path):
"""
Import a dos 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 DosCube {:s}".format(dos_path))
dos = pt.DosCube()
dos.read(dos_path)
# update model
model.dos.append(dos)
pm.dos = dos # display new loaded cube immediately.
# add cube to the treeview
self.tree.update_tree()
self.plot.update_viewcanvas()
# PyTRiP98 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# 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")
def import_dose_from_file(self, path):
logger.debug("Open DosCube {:s}".format(path))
cube = pt.DosCube()
cube.read(path)
self.set_dose(cube)
def main(args=sys.argv[1:]):
""" Main function for dvhplot.py
"""
# parse arguments
parser = argparse.ArgumentParser()
parser.add_argument(
"cube",
help="Path to input cube. May also be a .dos or dosemlet.dos cube",
type=str)
parser.add_argument("vdx",
help="Path to .vdx file holding the structures",
type=str)
parser.add_argument(
"rois",
nargs="?",
help=
"Comma-seperated list for ROIs to be analyzed. If not set, print list.",
type=str,
default=None)
parser.add_argument("-d",
"--dose",
type=float,
dest='dose',
metavar='dose',
help="Taget dose in [Gy]",
default=-1.0)
parser.add_argument("-o",
"--output",
type=str,
dest='output',
metavar='filename',
help="Don't open GUI, save to filename instead.",
default=None)
parser.add_argument("-l",
"--legend",
dest='legend',
default=False,
action='store_true',
help="Print legend box")
parser.add_argument("-v",
"--verbosity",
action='count',
help="increase output verbosity",
default=0)
parser.add_argument('-V',
'--version',
action='version',
version=pt.__version__)
parsed_args = parser.parse_args(args)
if parsed_args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
elif parsed_args.verbosity > 1:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig()
path_cube = parsed_args.cube
path_vdx = parsed_args.vdx
rois_arg = parsed_args.rois
dose = parsed_args.dose
legend = parsed_args.legend
outfile = parsed_args.output
# there are some cases when this script is run on systems without DISPLAY variable being set
# in such case matplotlib backend has to be explicitly specified
# despite the fact interleaving imports with code lines is discouraged, we do it here
# as it depends on the users options
if outfile:
matplotlib.use('Agg')
import matplotlib.pyplot as plt
d = pt.DosCube()
d.read(path_cube)
v = pt.VdxCube(d)
v.read(path_vdx)
vois = v.get_voi_names()
if not rois_arg:
print("Available ROIs:")
for voi in vois:
print("'{:s}'".format(voi))
return
rois = rois_arg.split(",")
if d.type == 'DOS':
if dose < 0.0:
plt.xlabel("Dose [%]")
else:
plt.xlabel("Dose [Gy]")
elif d.type == 'LET':
plt.xlabel("LET [keV/um]")
else:
plt.xlabel("") # unknown data cube
for roi in rois:
logger.info("Processing ROI '{:s}'...".format(roi))
voi = v.get_voi_by_name(roi)
x, y = volume_histogram(d.cube, voi)
if d.type == 'DOS':
if dose < 0.0:
x = x * 0.1
else:
x = x * 0.001 * dose
plt.plot(x, y, label=roi)
plt.ylabel("Volume [%]")
plt.grid(True)
if legend:
plt.legend()
if outfile:
plt.savefig(outfile)
else:
plt.show()
def main(args=sys.argv[1:]):
""" Main function for dvhplot.py
"""
# parse arguments
parser = argparse.ArgumentParser()
parser.add_argument("cube", help="path to input cube. May also be a .dos or dosemlet.dos cube", type=str)
parser.add_argument("vdx", help="path to .vdx file holding the structures", type=str)
parser.add_argument("rois", nargs="?", help="comma-seperated list for ROIs to be analyzed. If not set, print list.",
type=str, default=None)
parser.add_argument("-d", "--dose", type=float, dest='dose', metavar='dose',
help="target dose in [Gy] (if target_dose is unavailable in cube)", default=None)
parser.add_argument("-o", "--output", type=str, dest='output', metavar='filename',
help="don't open GUI, save figure to <filename> instead.", default=None)
parser.add_argument("-t", "--tofile", type=str, dest='tofile', metavar='filename',
help="save histogram data to <filename>.", default=None)
parser.add_argument("-l", "--legend", dest='legend', default=False, action='store_true',
help="print legend box")
parser.add_argument("-v", "--verbosity", action='count', help="increase output verbosity", default=0)
parser.add_argument('-V', '--version', action='version', version=pt.__version__)
parsed_args = parser.parse_args(args)
if parsed_args.verbosity == 1:
logging.basicConfig(level=logging.INFO)
elif parsed_args.verbosity > 1:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig()
path_cube = parsed_args.cube
path_vdx = parsed_args.vdx
rois_arg = parsed_args.rois
dose = parsed_args.dose
legend = parsed_args.legend
outfile = parsed_args.output
tofile = parsed_args.tofile
# there are some cases when this script is run on systems without DISPLAY variable being set
# in such case matplotlib backend has to be explicitly specified
# despite the fact interleaving imports with code lines is discouraged, we do it here
# as it depends on the users options
if outfile:
matplotlib.use('Agg')
import matplotlib.pyplot as plt
d = pt.DosCube()
d.read(path_cube)
v = pt.VdxCube(d)
v.read(path_vdx)
vois = v.voi_names()
if not rois_arg:
print("Available ROIs:")
for voi in vois:
print("'{:s}'".format(voi))
return
rois = rois_arg.split(",")
for roi in rois:
voi = v.get_voi_by_name(roi)
vh = VolHist(d, voi, target_dose=dose)
plt.xlabel(vh.xlabel)
plt.ylabel(vh.ylabel)
plt.plot(vh.x, vh.y, label=vh.name)
plt.ylabel("Volume [%]")
plt.grid(True)
if legend:
plt.legend()
if tofile:
logger.info("Write {}".format(tofile))
f = open(tofile, "w+")
for _x, _y in zip(vh.x, vh.y):
f.write("{:.3f} {:.3f}\n".format(_x, _y))
f.close()
if outfile:
plt.savefig(outfile)
else:
plt.show()