def test_dicom_plan(self):
c = DosCube()
c.read(self.cube000)
dp = c.create_dicom_plan()
self.assertIsNotNone(dp)
d = c.create_dicom()
self.assertIsNotNone(d)
def test_write_dicom(self):
c = DosCube()
c.read(self.cube000)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
self.assertTrue(os.path.exists(os.path.join(outdir, "rtdose.dcm")))
self.assertTrue(os.path.exists(os.path.join(outdir, "rtplan.dcm")))
self.assertGreater(os.path.getsize(os.path.join(outdir, "rtdose.dcm")), 0)
self.assertGreater(os.path.getsize(os.path.join(outdir, "rtplan.dcm")), 0)
shutil.rmtree(outdir)
def analyse_cube(self):
keys = self.projectiles.keys()
p1 = self.projectiles[keys[0]]
p2 = self.projectiles[keys[1]]
cube1 = p1["target_dos"]
cube2 = p2["target_dos"]
if not self.cube_in_other_cube(cube1, cube2):
temp = p1
p1 = p2
p2 = temp
cube1 = p1["target_dos"]
cube2 = p2["target_dos"]
self.execute_order = [keys[0], keys[1]]
self.split_proj_key = keys[1]
else:
self.execute_order = [keys[1], keys[0]]
self.split_proj_key = keys[0]
target_cube = copy.deepcopy(cube1)
shadow_cubes = []
for i, field in enumerate(p1["fields"]):
d = DosCube(cube1)
basis = get_basis_from_angles(field.get_gantry(),
field.get_couch())
basis = basis[0]
basis = np.array([
basis[0] / cube1.pixel_size, basis[1] / cube1.pixel_size,
basis[2] / cube1.slice_distance
])
basis /= np.max(np.abs(basis))
d.cube = pytriplib.create_field_shadow(
cube1.cube, cube2.cube, np.array(basis, dtype=np.double))
target_cube -= d
shadow_cubes.append(d)
target_cube.cube[target_cube.cube < 0] = 0
cube2.cube = cube2.cube + target_cube.cube
# ~ cube2.cube = pytriplib.extend_cube(cube2.cube)
cube1.cube = cube1.cube - target_cube.cube
if len(p1["fields"]) == 2:
a = self.execute_order.pop(1)
b = self.projectile_dose_level[a]
self.execute_order.append(a + str(1))
self.execute_order.append(a + str(2))
self.projectile_dose_level[a + str(1)] = b
self.projectile_dose_level[a + str(2)] = b
def test_read(self):
c = DosCube()
c.read(self.cube000)
self.assertEqual(c.cube.shape[0], 300)
self.assertEqual(c.cube.shape[1], 512)
self.assertEqual(c.cube.shape[2], 512)
# test method from C extension
dose_center = pytriplib.calculate_dose_center(np.array(c.cube))
self.assertEqual(dose_center.shape[0], 3)
self.assertGreater(dose_center[0], 0.0)
self.assertGreater(dose_center[1], 0.0)
self.assertGreater(dose_center[2], 0.0)
def test_read(self):
c = DosCube()
c.read(self.cube000)
self.assertEqual(c.cube.shape[0], 300)
self.assertEqual(c.cube.shape[1], 512)
self.assertEqual(c.cube.shape[2], 512)
# test method from C extension
dose_center = pytriplib.calculate_dose_center(np.array(c.cube))
self.assertEqual(dose_center.shape[0], 3)
self.assertGreater(dose_center[0], 0.0)
self.assertGreater(dose_center[1], 0.0)
self.assertGreater(dose_center[2], 0.0)
def calculate_rest_dose(self, proj):
self.rest_dose = copy.deepcopy(self.target_dos)
for k, projectile in self.projectiles.items():
if k == proj:
continue
name = os.path.join(self.path,
self.plan_name) + "_" + projectile["name"]
path = os.path.join(name + ".phys.dos")
if os.path.exists(path):
temp = DosCube()
temp.read(path)
temp = temp
self.rest_dose.cube = self.rest_dose.cube - temp.cube
def test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
x, y = volume_histogram(c.cube, v)
self.assertIsNotNone(x)
self.assertIsNotNone(y)
logger.info("Calculating DVH simple for entire cube")
x, y = volume_histogram(c.cube)
self.assertIsNotNone(x)
self.assertIsNotNone(y)
def test_dvh(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = c.calculate_dvh(v)
self.assertIsNotNone(result)
dvh, min_dose, max_dose, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(dvh.shape), 2)
self.assertEqual(dvh.shape[1], 2)
self.assertEqual(dvh.shape[0], 1500)
self.assertEqual(min_dose, 0.0)
self.assertEqual(max_dose, 0.001)
def test_dvh(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH")
result = c.calculate_dvh(v)
self.assertIsNotNone(result)
dvh, min_dose, max_dose, mean, area = result
self.assertGreater(area, 2.0)
self.assertEqual(len(dvh.shape), 2)
self.assertEqual(dvh.shape[1], 2)
self.assertEqual(dvh.shape[0], 1500)
self.assertEqual(min_dose, 0.0)
self.assertEqual(max_dose, 0.001)
def get_voi_cube(self):
"""
This method returns a DosCube object with value 1000 in each voxel within the Voi and zeros elsewhere.
It can be used as a mask, for selecting certain voxels.
The function may take some time to execute the first invocation, but is faster for subsequent calls,
due to caching.
:returns: a DosCube object which holds the value 1000 in those voxels which are inside the Voi.
"""
if hasattr(self, "voi_cube"): # caching: checks if class has voi_cube attribute
# TODO: add parameter as argument to this function. Note, this needs to be compatible with
# caching the cube. E.g. the method might be called twice with different arguments.
return self.voi_cube
self.voi_cube = DosCube(self.cube)
self.voi_cube.load_from_structure(self, 1000)
return self.voi_cube
def create_trip_exec_simple(self, no_output=False):
"""
Generates the .exec script and stores it into self.trip_exec.
"""
logger.info("Generating the trip_exec script...")
oar_list = self.oar_list
targets = self.targets
fields = self.plan.get_fields()
projectile = fields[0].get_projectile()
output = []
output.extend(self.create_exec_header())
output.extend(self.create_exec_load_data_files(projectile))
output.extend(self.create_exec_field(fields))
output.extend(self.create_exec_oar(oar_list))
dosecube = None
if len(targets) > 1:
dosecube = DosCube(self.images)
for i, voi in enumerate(targets):
temp = DosCube(self.images)
dose_level = int(voi.get_dose() / self.target_dose * 1000)
if dose_level == 0:
dose_level = -1
temp.load_from_structure(voi.get_voi().get_voi_data(),
dose_level)
if i == 0:
dosecube = temp * 1
else:
dosecube.merge_zero(temp)
dosecube.cube[dosecube.cube == -1] = int(0)
if not self.plan.get_target_dose_cube() is None:
dosecube = self.plan.get_target_dose_cube()
if dosecube is not None:
if not no_output:
dosecube.write(os.path.join(self.path, "target_dose.dos"))
output.extend(self.create_exec_plan(incube="target_dose"))
else:
output.extend(self.create_exec_plan())
if self.plan.get_optimize():
output.extend(self.create_exec_opt())
name = self.plan_name
output.extend(self.create_exec_output(name, fields))
out = "\n".join(output) + "\nexit\n"
self.trip_exec = out
def test_write(self):
c = DosCube()
c.read(self.cube000)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
c.write(outfile)
hed_file = outfile + DosCube.header_file_extension
dos_file = outfile + DosCube.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 test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
vh = VolHist(c, v)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
f1 = os.path.join(outdir, "foobar_1.dvh")
vh.write(f1, header=True)
self.assertTrue(os.path.exists(f1))
self.assertGreater(os.path.getsize(f1), 0)
f2 = os.path.join(outdir, "foobar_2.dvh")
vh.write(f2, header=False)
self.assertTrue(os.path.exists(f2))
self.assertGreater(os.path.getsize(f2), 0)
logger.info("Calculating DVH simple for entire cube")
vh = VolHist(c)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
f3 = os.path.join(outdir, "foobar_3.dvh")
vh.write(f3, header=True)
self.assertTrue(os.path.exists(f3))
self.assertGreater(os.path.getsize(f3), 0)
f4 = os.path.join(outdir, "foobar_4.dvh")
vh.write(f4, header=False)
self.assertTrue(os.path.exists(f4))
self.assertGreater(os.path.getsize(f4), 0)
shutil.rmtree(outdir)
def load_dose(self, path, _type, target_dose=0.0):
""" Load and append a new DosCube from path to self.doscubes.
"""
dos = DosCube()
dos.read(os.path.splitext(path)[0] + DosCube.data_file_extension)
dos._type = _type
dos.target_dose = target_dose
self.dosecubes.append(dos)
def test_dicom_plan(self):
c = DosCube()
c.read(self.cube000)
dp = c.create_dicom_plan()
self.assertIsNotNone(dp)
d = c.create_dicom()
self.assertIsNotNone(d)
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 test_write_dicom(self):
c = DosCube()
c.read(self.cube000)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
self.assertTrue(os.path.exists(os.path.join(outdir, "rtdose.dcm")))
self.assertTrue(os.path.exists(os.path.join(outdir, "rtplan.dcm")))
self.assertGreater(os.path.getsize(os.path.join(outdir, "rtdose.dcm")),
0)
self.assertGreater(os.path.getsize(os.path.join(outdir, "rtplan.dcm")),
0)
shutil.rmtree(outdir)
def test_write(self):
c = DosCube()
c.read(self.cube000)
fd, outfile = tempfile.mkstemp()
os.close(fd) # Windows needs it
os.remove(outfile) # we need only temp filename, not the file
c.write(outfile)
hed_file = outfile + ".hed"
dos_file = outfile + ".dos"
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 test_dvh_simple(self):
c = DosCube()
c.read(self.cube000)
v = create_sphere(c, name="sph", center=[10, 10, 10], radius=8)
self.assertIsNotNone(v)
logger.info("Calculating DVH simple")
vh = VolHist(c, v)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
outdir = tempfile.mkdtemp()
c.write_dicom(outdir)
f1 = os.path.join(outdir, "foobar_1.dvh")
vh.write(f1, header=True)
self.assertTrue(os.path.exists(f1))
self.assertGreater(os.path.getsize(f1), 0)
f2 = os.path.join(outdir, "foobar_2.dvh")
vh.write(f2, header=False)
self.assertTrue(os.path.exists(f2))
self.assertGreater(os.path.getsize(f2), 0)
logger.info("Calculating DVH simple for entire cube")
vh = VolHist(c)
self.assertIsNotNone(vh.x)
self.assertIsNotNone(vh.y)
f3 = os.path.join(outdir, "foobar_3.dvh")
vh.write(f3, header=True)
self.assertTrue(os.path.exists(f3))
self.assertGreater(os.path.getsize(f3), 0)
f4 = os.path.join(outdir, "foobar_4.dvh")
vh.write(f4, header=False)
self.assertTrue(os.path.exists(f4))
self.assertGreater(os.path.getsize(f4), 0)
shutil.rmtree(outdir)
class Voi:
"""
This is a class for handling volume of interests (VOIs). This class can e.g. be found inside the VdxCube object.
VOIs may for instance be organs (lung, eye...) or targets (PTV, GTV...), or any other volume of interest.
"""
sagital = 2 #: deprecated, backwards compability to pytripgui, do not use.
sagittal = 2 #: id for sagittal view
coronal = 1 #: id for coronal view
def __init__(self, name, cube=None):
self.cube = cube
self.name = name
self.is_concated = False
self.type = 90
self.slice_z = []
self.slices = {}
self.color = [0, 230, 0] # default colour
self.define_colors()
def create_copy(self, margin=0):
"""
Returns an independent copy of the Voi object
:param margin: (unused)
:returns: a deep copy of the Voi object
"""
voi = copy.deepcopy(self)
if not margin == 0:
pass
return voi
def get_voi_cube(self):
"""
This method returns a DosCube object with value 1000 in each voxel within the Voi and zeros elsewhere.
It can be used as a mask, for selecting certain voxels.
The function may take some time to execute the first invocation, but is faster for subsequent calls,
due to caching.
:returns: a DosCube object which holds the value 1000 in those voxels which are inside the Voi.
"""
if hasattr(self, "voi_cube"): # caching: checks if class has voi_cube attribute
# TODO: add parameter as argument to this function. Note, this needs to be compatible with
# caching the cube. E.g. the method might be called twice with different arguments.
return self.voi_cube
self.voi_cube = DosCube(self.cube)
self.voi_cube.load_from_structure(self, 1000)
return self.voi_cube
def add_slice(self, slice):
""" Add another slice to this VOI, and update self.slice_z table.
:param Slice slice: the Slice object to be appended.
"""
key = int(slice.get_position() * 100)
self.slice_z.append(key)
self.slices[key] = slice
def get_name(self):
"""
:returns: The name of this VOI.
"""
return self.name
def calculate_bad_angles(self, voi):
"""
(Not implemented.)
"""
pass
def concat_to_3d_polygon(self):
""" Concats all contours into a single contour, and writes all data points to sefl.polygon3d.
"""
self.concat_contour()
data = []
for slice in self.slices:
data.extend(self.slices[slice].contour[0].contour)
self.polygon3d = np.array(data)
def get_3d_polygon(self):
""" Returns a list of points rendering a 3D polygon of this VOI, which is stored in
sefl.polygon3d. If this attibute does not exist, create it.
"""
if not hasattr(self, "polygon3d"):
self.concat_to_3d_polygon()
return self.polygon3d
def create_point_tree(self):
"""
Concats all contours.
Writes a list of points into self.points describing this VOI.
"""
points = {}
self.concat_contour()
slice_keys = sorted(self.slices.keys())
for key in slice_keys:
contour = self.slices[key].contour[0].contour
p = {}
for x in contour:
p[x[0], x[1], x[2]] = []
points.update(p)
n_slice = len(slice_keys)
last_contour = None
for i, key in enumerate(slice_keys):
contour = self.slices[key].contour[0].contour
n_points = len(contour)
if i < n_slice - 1:
next_contour = self.slices[slice_keys[i + 1]].contour[0].contour
else:
next_contour = None
for j, point in enumerate(contour):
j2 = (j + 1) % (n_points - 2)
point2 = contour[j2]
points[(point[0], point[1], point[2])].append(point2)
points[(point2[0], point2[1], point2[2])].append(point)
if next_contour is not None:
point3 = pytrip.res.point.get_nearest_point(point, next_contour)
points[(point[0], point[1], point[2])].append(point3)
points[(point3[0], point3[1], point3[2])].append(point)
if last_contour is not None:
point4 = pytrip.res.point.get_nearest_point(point, last_contour)
if point4 not in points[(point[0], point[1], point[2])]:
points[(point[0], point[1], point[2])].append(point4)
points[(point4[0], point4[1], point4[2])].append(point)
last_contour = contour
self.points = points
def get_2d_projection_on_basis(self, basis, offset=None):
""" (TODO: Documentation)
"""
a = np.array(basis[0])
b = np.array(basis[1])
self.concat_contour()
bas = np.array([a, b])
data = self.get_3d_polygon()
product = np.dot(data, np.transpose(bas))
compare = self.cube.pixel_size
filtered = pytriplib.filter_points(product, compare / 2.0)
filtered = np.array(sorted(filtered, key=cmp_to_key(_voi_point_cmp)))
filtered = pytriplib.points_to_contour(filtered)
product = filtered
if offset is not None:
offset_proj = np.array([np.dot(offset, a), np.dot(offset, b)])
product = product[:] - offset_proj
return product
def get_2d_slice(self, plane, depth):
""" Gets a 2d Slice object from the contour in either sagittal or coronal plane.
Contours will be concated.
:param int plane: either self.sagittal or self.coronal
:param float depth: position of plane
:returns: a Slice object.
"""
self.concat_contour()
points1 = []
points2 = []
for key in sorted(self.slice_z):
slice = self.slices[key]
if plane is self.sagittal:
point = sorted(
pytriplib.slice_on_plane(np.array(slice.contour[0].contour), plane, depth), key=lambda x: x[1])
elif plane is self.coronal:
point = sorted(
pytriplib.slice_on_plane(np.array(slice.contour[0].contour), plane, depth), key=lambda x: x[0])
if len(point) > 0:
points2.append(point[-1])
if len(point) > 1:
points1.append(point[0])
s = None
if len(points1) > 0:
points1.extend(reversed(points2))
points1.append(points1[0])
s = Slice(cube=self.cube)
s.add_contour(Contour(points1))
return s
def define_colors(self):
""" Creates a list of default colours [R,G,B] in self.colours.
"""
self.colors = []
self.colors.append([0, 0, 255])
self.colors.append([0, 128, 0])
self.colors.append([0, 255, 0])
self.colors.append([255, 0, 0])
self.colors.append([0, 128, 128])
self.colors.append([255, 255, 0])
def calculate_center(self):
""" Calculates the center of gravity for the VOI.
:returns: A numpy array[x,y,z] with positions in [mm]
"""
if hasattr(self, "center_pos"):
return self.center_pos
self.concat_contour()
tot_volume = 0.0
center_pos = np.array([0.0, 0.0, 0.0])
for key in self.slices:
center, area = self.slices[key].calculate_center()
tot_volume += area
center_pos += area * center
self.center_pos = center_pos / tot_volume
return center_pos / tot_volume
def get_color(self, i=None):
"""
:param int i: selects a colour, default if None.
:returns: a [R,G,B] list.
"""
if i is None:
return self.color
return self.colors[i % len(self.colors)]
def set_color(self, color):
"""
:param [3*int]: set a color [R,G,B].
"""
self.color = color
def create_dicom_label(self):
""" Based on self.name and self.type, a Dicom ROI_LABEL is generated.
:returns: a Dicom ROI_LABEL
"""
roi_label = Dataset()
roi_label.ROIObservationLabel = self.name
roi_label.RTROIInterpretedType = self.get_roi_type_name(self.type)
return roi_label
def create_dicom_structure_roi(self):
""" Based on self.name, an empty Dicom ROI is generated.
:returns: a Dicom ROI.
"""
roi = Dataset()
roi.ROIName = self.name
return roi
def create_dicom_contour_data(self, i):
""" Based on self.slices, Dicom conours are generated for the Dicom ROI.
:returns: Dicom ROI_CONTOURS
"""
roi_contours = Dataset()
contours = []
for slice in self.slices.values():
contours.extend(slice.create_dicom_contours())
roi_contours.Contours = Sequence(contours)
roi_contours.ROIDisplayColor = self.get_color(i)
return roi_contours
def read_vdx_old(self, content, i):
""" Reads a single VOI from Voxelplan .vdx data from 'content', assuming a legacy .vdx format.
VDX format 1.2.
:params [str] content: list of lines with the .vdx content
:params int i: line number to the list.
:returns: current line number, after parsing the VOI.
"""
line = content[i]
items = line.split()
self.name = items[1]
self.type = int(items[3])
i += 1
while i < len(content):
line = content[i]
if re.match("voi", line) is not None:
break
if re.match("slice#", line) is not None:
s = Slice(cube=self.cube)
i = s.read_vdx_old(content, i)
if self.cube is not None:
for cont1 in s.contour:
for cont2 in cont1.contour:
cont2[2] = self.cube.slice_to_z(cont2[2]) # change from slice number to mm
if s.get_position() is None:
raise Exception("cannot calculate slice position")
# TODO investigate why 100 multiplier is needed
if self.cube is not None:
key = 100 * int((float(s.get_position()) - min(self.cube.slice_pos)))
else:
key = 100 * int(s.get_position())
self.slice_z.append(key)
self.slices[key] = s
if re.match("#TransversalObjects", line) is not None:
pass
# slices = int(line.split()[1]) # TODO holds information about number of skipped slices
i += 1
return i - 1
def read_vdx(self, content, i):
""" Reads a single VOI from Voxelplan .vdx data from 'content'.
Format 2.0
:params [str] content: list of lines with the .vdx content
:params int i: line number to the list.
:returns: current line number, after parsing the VOI.
"""
line = content[i]
self.name = ' '.join(line.split()[1:])
number_of_slices = 10000
i += 1
while i < len(content):
line = content[i]
if re.match("key", line) is not None:
self.key = line.split()[1]
elif re.match("type", line) is not None:
self.type = int(line.split()[1])
elif re.match("number_of_slices", line) is not None:
number_of_slices = int(line.split()[1])
elif re.match("slice", line) is not None:
s = Slice(cube=self.cube)
i = s.read_vdx(content, i)
if s.get_position() is None:
raise Exception("cannot calculate slice position")
if self.cube is None:
raise Exception("cube not loaded")
key = int((float(s.get_position()) - min(self.cube.slice_pos)) * 100)
self.slice_z.append(key)
self.slices[key] = s
elif re.match("voi", line) is not None:
break
elif len(self.slices) >= number_of_slices:
break
i += 1
return i - 1
def get_roi_type_number(self, type_name):
"""
:returns: 1 if GTV or CTV, else 0.
"""
if type_name == 'EXTERNAL':
return 0 # TODO: should be 10?
elif type_name == 'AVOIDANCE':
return 0
elif type_name == 'ORGAN':
return 0
elif type_name == 'GTV':
return 1
elif type_name == 'CTV':
return 1
else:
return 0
def get_roi_type_name(self, type_id):
"""
:returns: The type name of the ROI.
"""
if type_id == 10:
return "EXTERNAL"
elif type_id == 2:
return 'AVOIDANCE'
elif type_id == 1:
return 'CTV'
elif type_id == 0:
return 'other'
return ''
def read_dicom(self, info, data):
""" Reads a single ROI (= VOI) from a Dicom data set.
:param info: (not used)
:param Dicom data: Dicom ROI object which contains the contours.
"""
if "Contours" not in data.dir() and "ContourSequence" not in data.dir():
return
self.type = self.get_roi_type_number(np.typename)
self.color = data.ROIDisplayColor
if "Contours" in data.dir():
contours = data.Contours
else:
contours = data.ContourSequence
for i, contour in enumerate(contours):
key = int((float(contour.ContourData[2]) - min(self.cube.slice_pos)) * 100)
if key not in self.slices:
self.slices[key] = Slice(cube=self.cube)
self.slice_z.append(key)
self.slices[key].add_dicom_contour(contour)
def get_thickness(self):
"""
:returns: thickness of slice in [mm]. If there is only one slice, 3 mm is returned.
"""
if len(self.slice_z) <= 1:
return 3 # TODO: what is this? And shoudn't it be float?
return abs(float(self.slice_z[1]) - float(self.slice_z[0])) / 100
def to_voxel_string(self):
""" Creates the Voxelplan formatted text, which can be written into a .vdx file (format 2.0).
:returns: a str holding the all lines needed for a Voxelplan formatted file.
"""
if len(self.slices) is 0:
return ""
out = "\n"
out += "voi %s\n" % (self.name.replace(" ", "_"))
out += "key empty\n"
out += "type %s\n" % self.type
out += "\n"
out += "contours\n"
out += "reference_frame\n"
out += " origin 0.000 0.000 0.000\n"
out += " point_on_x_axis 1.000 0.000 0.000\n"
out += " point_on_y_axis 0.000 1.000 0.000\n"
out += " point_on_z_axis 0.000 0.000 1.000\n"
out += "number_of_slices %d\n" % self.number_of_slices()
out += "\n"
i = 0
thickness = self.get_thickness()
for k in self.slice_z:
sl = self.slices[k]
pos = sl.get_position()
out += "slice %d\n" % i
out += "slice_in_frame %.3f\n" % pos
out += "thickness %.3f reference " \
"start_pos %.3f stop_pos %.3f\n" % \
(thickness, pos - 0.5 * thickness, pos + 0.5 * thickness)
out += "number_of_contours %d\n" % \
self.slices[k].number_of_contours()
out += self.slices[k].to_voxel_string()
i += 1
return out
def get_row_intersections(self, pos):
""" (TODO: Documentation needed)
"""
slice = self.get_slice_at_pos(pos[2])
if slice is None:
return None
return np.sort(slice.get_intersections(pos))
def get_slice_at_pos(self, z):
""" Returns nearest VOI Slice at position z.
:param float z: position z in [mm]
:returns: a Slice object found at position z.
"""
thickness = self.get_thickness() / 2 * 100
for key in self.slices.keys():
key = key
low = z * 100 - thickness
high = z * 100 + thickness
if (low < key < 100 * z) or (high > key >= 100 * z):
return self.slices[key]
return None
def number_of_slices(self):
"""
:returns: number of slices covered by this VOI.
"""
return len(self.slices)
def concat_contour(self):
""" Concat all contours in all slices found in this VOI.
"""
if not self.is_concated:
for k in self.slices.keys():
self.slices[k].concat_contour()
self.is_concated = True
def get_min_max(self):
""" Set self.temp_min and self.temp_max if they dont exist.
:returns: minimum and maximum x y coordinates in Voi.
"""
temp_min, temp_max = None, None
if hasattr(self, "temp_min"):
return self.temp_min, self.temp_max
for key in self.slices:
if temp_min is None:
temp_min, temp_max = self.slices[key].get_min_max()
else:
min1, max1 = self.slices[key].get_min_max()
temp_min = pytrip.res.point.min_list(temp_min, min1)
temp_max = pytrip.res.point.max_list(temp_max, max1)
self.temp_min = temp_min
self.temp_max = temp_max
return temp_min, temp_max
def split_fields(self, proj):
if self.split_proj_key not in self.projectiles.keys():
return
name = os.path.join(
self.path, self.plan_name) + "_" + self.projectiles[proj]["name"]
path = os.path.join(name + ".phys.dos")
temp = DosCube()
temp.read(path)
temp.version = "2.0"
self.rest_dose = self.target_dos - temp
p = self.projectiles[self.split_proj_key]
p["target_dos"].cube = pytriplib.extend_cube(p["target_dos"].cube)
if len(p["fields"]) == 2:
temp.cube = (temp.cube < self.projectiles[proj]["target_dos"].cube) * \
self.projectiles[proj]["target_dos"].cube + \
(temp.cube > self.projectiles[proj]["target_dos"].cube) * temp.cube
dose = self.target_dos - temp
field1 = p["fields"][0]
field2 = p["fields"][1]
d1 = DosCube(temp)
d2 = DosCube(temp)
center = pytriplib.calculate_dose_center(p["target_dos"].cube)
dose.cube[dose.cube < 0] = 0
temp.cube *= self.target_dos.cube > 0
basis = get_basis_from_angles(field1.get_gantry(),
field1.get_couch())[0]
basis = np.array([
basis[0] / dose.pixel_size, basis[1] / dose.pixel_size,
basis[2] / dose.slice_distance
])
basis = basis / np.max(np.abs(basis)) * .5
d1.cube = pytriplib.create_field_shadow(
dose.cube, temp.cube, np.array(basis, dtype=np.double))
basis = get_basis_from_angles(field2.get_gantry(),
field2.get_couch())[0]
basis = np.array([
basis[0] / dose.pixel_size, basis[1] / dose.pixel_size,
basis[2] / dose.slice_distance
])
basis /= np.max(np.abs(basis))
d2.cube = pytriplib.create_field_shadow(
dose.cube, temp.cube, np.array(basis, dtype=np.double))
a = d2.cube > d1.cube
b = d2.cube < d1.cube
d2.cube = p["target_dos"].cube * a
d1.cube = p["target_dos"].cube * b
rest = p["target_dos"].cube * ((a + b) < 1)
b = pytriplib.split_by_plane(rest, center, basis)
d1.cube += b
d2.cube += rest - b
self.plan.add_dose(d1, "H1")
self.plan.add_dose(d2, "H2")
self.projectiles[field1.get_projectile() + str(1)] = {
"target_dos": d1,
"fields": [field1],
"name": field1.get_projectile() + str(1),
"projectile": field1.get_projectile()
}
self.projectiles[field2.get_projectile() + str(2)] = {
"target_dos": d2,
"fields": [field2],
"name": field2.get_projectile() + str(2),
"projectile": field2.get_projectile()
}
del self.projectiles[self.split_proj_key]
class TripExecuter(object):
def __init__(self, images, rbe=None):
logger.debug("Initializing TripExecuter()")
self.images = images
self.rbe = rbe
self.listeners = []
self.trip_bin_path = "TRiP98" # where TRiP98 is installed, if not accessible in /usr/local/bin or similar
self.logfile_stdout = "trip98.stdout"
self.logfile_stderr = "trip98.stderr"
self.rsakey_local_path = "~/.ssh/id_rsa"
self._runtrip = True # set this to False for a dry run without TRiP98 (for testing purposes)
self.remote_dir = "." # remote directory where all will be run
def delete_workspace(self):
shutil.rmtree(self.path)
def cube_in_other_cube(self, outer, inner):
m = np.max(inner.cube)
idx = np.where(inner.cube == m)
idx = [idx[0][0], idx[1][0], idx[2][0]]
a = outer.cube[idx[0], idx[1]]
b = inner.cube[idx[0], idx[1]]
res = a > b
if True in res[0:idx[2]] and True in res[idx[2]:-1]:
return True
return False
def analyse_cube(self):
keys = self.projectiles.keys()
p1 = self.projectiles[keys[0]]
p2 = self.projectiles[keys[1]]
cube1 = p1["target_dos"]
cube2 = p2["target_dos"]
if not self.cube_in_other_cube(cube1, cube2):
temp = p1
p1 = p2
p2 = temp
cube1 = p1["target_dos"]
cube2 = p2["target_dos"]
self.execute_order = [keys[0], keys[1]]
self.split_proj_key = keys[1]
else:
self.execute_order = [keys[1], keys[0]]
self.split_proj_key = keys[0]
target_cube = copy.deepcopy(cube1)
shadow_cubes = []
for i, field in enumerate(p1["fields"]):
d = DosCube(cube1)
basis = get_basis_from_angles(field.get_gantry(),
field.get_couch())
basis = basis[0]
basis = np.array([
basis[0] / cube1.pixel_size, basis[1] / cube1.pixel_size,
basis[2] / cube1.slice_distance
])
basis /= np.max(np.abs(basis))
d.cube = pytriplib.create_field_shadow(
cube1.cube, cube2.cube, np.array(basis, dtype=np.double))
target_cube -= d
shadow_cubes.append(d)
target_cube.cube[target_cube.cube < 0] = 0
cube2.cube = cube2.cube + target_cube.cube
# ~ cube2.cube = pytriplib.extend_cube(cube2.cube)
cube1.cube = cube1.cube - target_cube.cube
if len(p1["fields"]) == 2:
a = self.execute_order.pop(1)
b = self.projectile_dose_level[a]
self.execute_order.append(a + str(1))
self.execute_order.append(a + str(2))
self.projectile_dose_level[a + str(1)] = b
self.projectile_dose_level[a + str(2)] = b
def execute(self, plan, callback=None):
"""
Executes the plan object using TRiP98.
"""
self.plan = plan
self.callback = callback
self.ini_execute()
if not self.mult_proj:
self.execute_simple()
else:
self.execute_mult_proj()
if os.path.exists(
os.path.join(self.path, self.plan_name) +
".bio.dos") and self.plan.get_out_bio_dose():
self.plan.load_dose(
os.path.join(self.path, self.plan_name) + ".bio.dos", "bio",
self.target_dose)
if os.path.exists(
os.path.join(self.path, self.plan_name) +
".phys.dos") and self.plan.get_out_phys_dose():
self.plan.load_dose(
os.path.join(self.path, self.plan_name) + ".phys.dos", "phys",
self.target_dose)
if os.path.exists(
os.path.join(self.path, self.plan_name) +
".phys.dos") and self.plan.get_out_dose_mean_let():
self.plan.load_let(
os.path.join(self.path, self.plan_name) + ".dosemlet.dos")
self.finish()
def ini_execute(self):
self.split_plan(self.plan)
self.plan_name = self.plan.get_name().replace(" ", "_")
self.working_path = os.path.expandvars(self.plan.get_working_dir())
if not hasattr(self, "folder_name"):
self.folder_name = str(uuid.uuid4())
self.path = os.path.join(self.working_path, self.folder_name)
self.prepare_folder()
self.convert_files_to_voxelplan()
def execute_simple(self):
"""
Simple execution of TRiP, called by self.execute() when self.mult_proj is not set.
"""
logger.debug("In execute_simple mode")
self.create_trip_exec_simple()
self.run_trip()
def execute_mult_proj(self):
self.analyse_cube()
i = 3
for a in range(i):
for projectile in self.execute_order:
self.calculate_rest_dose(projectile)
if a == i - 1:
self.create_trip_exec_mult_proj(projectile, first=(a is 0))
else:
self.create_trip_exec_mult_proj(projectile,
last=False,
first=(a is 0))
self.run_trip()
self.split_fields(projectile)
self.post_process()
def create_trip_exec_simple(self, no_output=False):
"""
Generates the .exec script and stores it into self.trip_exec.
"""
logger.info("Generating the trip_exec script...")
oar_list = self.oar_list
targets = self.targets
fields = self.plan.get_fields()
projectile = fields[0].get_projectile()
output = []
output.extend(self.create_exec_header())
output.extend(self.create_exec_load_data_files(projectile))
output.extend(self.create_exec_field(fields))
output.extend(self.create_exec_oar(oar_list))
dosecube = None
if len(targets) > 1:
dosecube = DosCube(self.images)
for i, voi in enumerate(targets):
temp = DosCube(self.images)
dose_level = int(voi.get_dose() / self.target_dose * 1000)
if dose_level == 0:
dose_level = -1
temp.load_from_structure(voi.get_voi().get_voi_data(),
dose_level)
if i == 0:
dosecube = temp * 1
else:
dosecube.merge_zero(temp)
dosecube.cube[dosecube.cube == -1] = int(0)
if not self.plan.get_target_dose_cube() is None:
dosecube = self.plan.get_target_dose_cube()
if dosecube is not None:
if not no_output:
dosecube.write(os.path.join(self.path, "target_dose.dos"))
output.extend(self.create_exec_plan(incube="target_dose"))
else:
output.extend(self.create_exec_plan())
if self.plan.get_optimize():
output.extend(self.create_exec_opt())
name = self.plan_name
output.extend(self.create_exec_output(name, fields))
out = "\n".join(output) + "\nexit\n"
self.trip_exec = out
def create_exec_output(self, name, fields, last=True):
output = []
window = self.plan.get_window()
window_str = ""
if len(window) is 6:
window_str = " window(%.2f,%.2f,%.2f,%.2f,%.2f,%.2f) " % (
window[0], window[1], window[2], window[3], window[4],
window[5])
if self.plan.get_out_phys_dose() is True:
output.append('dose "' + name + '." /calculate alg(' +
self.plan.get_dose_algorithm() + ')' + window_str +
' field(*) write')
if last:
if self.plan.get_out_bio_dose() is True:
output.append('dose "' + name + '." /calculate ' + window_str +
' bioalgorithm(' +
self.plan.get_bio_algorithm() +
') biological norbe write')
if self.plan.get_out_dose_mean_let() is True:
output.append('dose "' + name + '." /calculate ' + window_str +
' field(*) dosemeanlet write')
if self.plan.get_out_field() is True and self.plan.get_optimize(
) is True:
for i, field in enumerate(fields):
output.append(
'field %d /write file(%s.rst) reverseorder ' %
(i + 1, field.get_name()))
field.set_rasterfile(self.working_path + '//' +
self.folder_name + '//' +
field.get_name())
return output
def create_exec_plan(self, incube=""):
output = []
plan = "plan / dose(%.2f) " % self.target_dose
if not self.plan.get_target_tissue_type() == "":
plan += "target(%s) " % (self.plan.get_target_tissue_type())
if not self.plan.get_res_tissue_type() == "":
plan += "residual(%s) " % (self.plan.get_res_tissue_type())
if not incube == "":
plan += "incube(%s) " % incube
output.append(plan)
return output
def create_exec_opt(self):
output = []
opt = "opt / field(*) "
opt += self.plan.get_opt_method() + " "
opt += "iterations(" + str(self.plan.get_iterations()) + ") "
opt += "dosealgorithm(" + self.plan.get_dose_algorithm() + ") "
opt += "" + self.plan.get_opt_princip() + " "
opt += "geps(" + str(self.plan.get_geps()) + ") "
opt += "eps(" + str(self.plan.get_eps()) + ") "
opt += "optalgorithm(" + self.plan.get_opt_algorithm() + ") "
opt += "bioalgorithm(" + self.plan.get_bio_algorithm() + ") "
output.append(opt)
return output
def create_exec_header(self):
output = []
output.append("time / on")
output.append("sis * /delete")
output.append("hlut * /delete")
output.append("ddd * /delete")
output.append("dedx * /delete")
output.append('dedx "' + self.plan.dedx_file + '" / read')
output.append('hlut "' + self.plan.hlut_file + '" / read')
output.append("scancap / offh2o(1.709) rifi(3) bolus(0.000) "
"minparticles(5000) path(none)")
output.append("random 1000")
return output
def create_exec_load_data_files(self, projectile):
output = []
ddd_folder = self.plan.get_ddd_folder()
spc_folder = self.plan.get_spc_folder()
sis_file = self.plan.get_sis_file()
if len(ddd_folder) > 0:
output.append('ddd "%s/*" / read' % ddd_folder)
if len(spc_folder) > 0:
output.append('spc "%s/*" / read' % spc_folder)
if len(sis_file) > 0:
output.append('sis "%s" / read' % sis_file)
else:
output.append('sis / dummy')
if not (len(spc_folder) > 0 or len(ddd_folder) > 0):
if projectile == "C":
output.append('ddd "$TRIP98/DATA/DDD/12C/RF3MM/12C*" / read')
output.append('spc "$TRIP98/DATA/SPC/12C/RF3MM/12C*" / read')
elif projectile == "H":
output.append('ddd "$TRIP98/DATA/DDD/1H/RF3MM/1H*" / read')
output.append('spc "$TRIP98/DATA/SPC/1H/RF3MM/1H*" / read')
elif projectile == "O":
output.append('ddd "$TRIP98/DATA/DDD/16O/RF3MM/16O*" / read')
output.append('spc "$TRIP98/DATA/SPC/16O/RF3MM/16O*" / read')
elif projectile == "Ne":
output.append('ddd "$TRIP98/DATA/DDD/20Ne/RF3MM/20Ne*" / read')
output.append('spc "$TRIP98/DATA/SPC/20Ne/RF3MM/20Ne*" / read')
output.append("ct " + self.plan_name + " /read")
output.append("voi " + self.plan_name + " /read")
output.append("voi * /list")
if not self.plan.get_target_tissue_type() == "":
rbe = self.rbe.get_rbe_by_name(self.plan.get_target_tissue_type())
output.append("rbe '%s' /read" % (rbe.get_path()))
if not self.plan.get_res_tissue_type() == "" and \
not self.plan.get_res_tissue_type() \
== self.plan.get_target_tissue_type():
rbe = self.rbe.get_rbe_by_name(
self.plan.get_target_tissue_type())
output.append("rbe %s /read" % (rbe.get_path()))
return output
def create_exec_field(self, fields):
output = []
if self.plan.get_optimize():
for i, val in enumerate(fields):
field = "field " + str(i + 1) + " / new "
field += "fwhm(%d) " % (val.get_fwhm())
raster = val.get_rasterstep()
if not raster[0] is 0 and not raster[1] is 0:
field += "raster(%.2f,%.2f) " % (raster[0], raster[1])
gantry, couch = angles_to_trip(val.get_gantry(),
val.get_couch())
field += "couch(" + str(couch) + ") "
field += "gantry(" + str(gantry) + ") "
target = val.get_target()
if len(val.get_target()) is not 0:
field += "target(%.1f,%.1f,%.1f) " % (target[0], target[1],
target[2])
if val.get_doseextension() > 0.0001:
field += "doseext(" + str(val.get_doseextension()) + ") "
field += "contourext(" + str(val.get_contourextension()) + ") "
if val.get_zsteps() > 0.001:
field += "zsteps(" + str(val.get_zsteps()) + ") "
field += 'proj(' + val.get_projectile() + ')'
output.append(field)
else:
for i, val in enumerate(fields):
field = 'field 1 /read file(' + val.get_rasterfile() + '.rst)'
field += "fwhm(%d) " % (val.get_fwhm())
raster = val.get_rasterstep()
if not raster[0] is 0 and not raster[1] is 0:
field += "raster(%.2f,%.2f) " % (raster[0], raster[1])
gantry, couch = angles_to_trip(val.get_gantry(),
val.get_couch())
field += "couch(" + str(couch) + ") "
field += "gantry(" + str(gantry) + ") "
if len(val.get_target()) is not 0:
field += "target(" + val.get_target() + ") "
if val.get_doseextension() > 0.0001:
field += "doseext(" + str(val.get_doseextension()) + ") "
field += "contourext(" + str(val.get_contourextension()) + ") "
if val.get_zsteps() > 0.001:
field += "zsteps(" + str(val.get_zsteps()) + ") "
field += 'proj(' + val.get_projectile() + ')'
output.append(field)
return output
def create_exec_oar(self, oar_list):
output = []
for oar in oar_list:
output.append("voi " + oar.get_name().replace(" ", "_") +
" / maxdosefraction(" +
str(oar.get_max_dose_fraction()) + ") oarset")
return output
def split_fields(self, proj):
if self.split_proj_key not in self.projectiles.keys():
return
name = os.path.join(
self.path, self.plan_name) + "_" + self.projectiles[proj]["name"]
path = os.path.join(name + ".phys.dos")
temp = DosCube()
temp.read(path)
temp.version = "2.0"
self.rest_dose = self.target_dos - temp
p = self.projectiles[self.split_proj_key]
p["target_dos"].cube = pytriplib.extend_cube(p["target_dos"].cube)
if len(p["fields"]) == 2:
temp.cube = (temp.cube < self.projectiles[proj]["target_dos"].cube) * \
self.projectiles[proj]["target_dos"].cube + \
(temp.cube > self.projectiles[proj]["target_dos"].cube) * temp.cube
dose = self.target_dos - temp
field1 = p["fields"][0]
field2 = p["fields"][1]
d1 = DosCube(temp)
d2 = DosCube(temp)
center = pytriplib.calculate_dose_center(p["target_dos"].cube)
dose.cube[dose.cube < 0] = 0
temp.cube *= self.target_dos.cube > 0
basis = get_basis_from_angles(field1.get_gantry(),
field1.get_couch())[0]
basis = np.array([
basis[0] / dose.pixel_size, basis[1] / dose.pixel_size,
basis[2] / dose.slice_distance
])
basis = basis / np.max(np.abs(basis)) * .5
d1.cube = pytriplib.create_field_shadow(
dose.cube, temp.cube, np.array(basis, dtype=np.double))
basis = get_basis_from_angles(field2.get_gantry(),
field2.get_couch())[0]
basis = np.array([
basis[0] / dose.pixel_size, basis[1] / dose.pixel_size,
basis[2] / dose.slice_distance
])
basis /= np.max(np.abs(basis))
d2.cube = pytriplib.create_field_shadow(
dose.cube, temp.cube, np.array(basis, dtype=np.double))
a = d2.cube > d1.cube
b = d2.cube < d1.cube
d2.cube = p["target_dos"].cube * a
d1.cube = p["target_dos"].cube * b
rest = p["target_dos"].cube * ((a + b) < 1)
b = pytriplib.split_by_plane(rest, center, basis)
d1.cube += b
d2.cube += rest - b
self.plan.add_dose(d1, "H1")
self.plan.add_dose(d2, "H2")
self.projectiles[field1.get_projectile() + str(1)] = {
"target_dos": d1,
"fields": [field1],
"name": field1.get_projectile() + str(1),
"projectile": field1.get_projectile()
}
self.projectiles[field2.get_projectile() + str(2)] = {
"target_dos": d2,
"fields": [field2],
"name": field2.get_projectile() + str(2),
"projectile": field2.get_projectile()
}
del self.projectiles[self.split_proj_key]
def calculate_rest_dose(self, proj):
self.rest_dose = copy.deepcopy(self.target_dos)
for k, projectile in self.projectiles.items():
if k == proj:
continue
name = os.path.join(self.path,
self.plan_name) + "_" + projectile["name"]
path = os.path.join(name + ".phys.dos")
if os.path.exists(path):
temp = DosCube()
temp.read(path)
temp = temp
self.rest_dose.cube = self.rest_dose.cube - temp.cube
# ~ self.rest_dose.cube[self.rest_dose.cube<0] = 0
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 split_plan(self, plan=None):
self.targets = []
self.oar_list = []
dose = 0
for voi in self.plan.get_vois():
if voi.is_oar():
self.oar_list.append(voi)
if voi.is_target():
self.targets.append(voi)
if voi.get_dose() > dose:
dose = voi.get_dose()
if not len(self.targets):
raise InputError("No targets")
if not len(self.plan.get_fields()):
raise InputError("No fields")
self.target_dose = dose
if plan is None:
plan = self.plan
proj = []
self.projectile_dose_level = {}
for field in plan.fields:
if field.get_projectile() not in proj:
proj.append(field.get_projectile())
self.projectile_dose_level[field.get_projectile()] = 0
if len(proj) > 1:
self.mult_proj = True
else:
self.mult_proj = False
if self.mult_proj:
self.projectiles = {}
for field in plan.fields:
if field.get_projectile() not in self.projectiles.keys():
self.projectiles[field.get_projectile()] = {
"target_dos": DosCube(self.images),
"fields": [field],
"name": field.get_projectile(),
"projectile": field.get_projectile()
}
else:
self.projectiles[field.get_projectile()]["fields"].append(
field)
self.target_dos = DosCube(self.images)
for i, voi in enumerate(self.targets):
temp = DosCube(self.images)
voi_dose_level = int(voi.get_dose() / dose * 1000)
temp.load_from_structure(voi.get_voi().get_voi_data(), 1)
for projectile, data in self.projectiles.items():
dose_percent = self.plan.get_dose_percent(projectile)
if not voi.get_dose_percent(projectile) is None:
dose_percent = voi.get_dose_percent(projectile)
proj_dose_lvl = int(voi.get_dose() / self.target_dose *
dose_percent * 10)
if self.projectile_dose_level[projectile] < proj_dose_lvl:
self.projectile_dose_level[projectile] = proj_dose_lvl
if proj_dose_lvl == 0:
proj_dose_lvl = -1
if i == 0:
data["target_dos"] = temp * proj_dose_lvl
else:
data["target_dos"].merge_zero(temp * proj_dose_lvl)
if i == 0:
self.target_dos = temp * voi_dose_level
else:
self.target_dos.merge_zero(temp * voi_dose_level)
for projectile, data in self.projectiles.items():
data["target_dos"].cube[data["target_dos"].cube == -1] = int(0)
self.plan.add_dose(data["target_dos"],
"target_%s" % projectile)
self.rest_dose = copy.deepcopy(self.target_dos)
def add_log_listener(self, listener):
self.listeners.append(listener)
def log(self, txt):
txt = txt.replace("\n", "")
for l in self.listeners:
l.write(txt)
def prepare_folder(self):
self.filepath = self.path + self.plan_name
if os.path.exists(self.path):
pass
# shutil.rmtree(self.path)
else:
os.makedirs(self.path)
def run_trip(self):
if self.plan.remote:
self.run_trip_remote()
else:
self.run_trip_local()
def run_trip_remote(self):
logger.info("Run TRiP98 in REMOTE mode.")
# self.create_remote_run_file()
self.compress_files()
self.copy_files_to_server()
ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
# If no password is supplied, try to look for a private key
if self.plan.get_password() is "" or None:
rsa_keypath = os.path.expanduser(self.rsakey_local_path)
if not os.path.isfile(rsa_keypath):
# login with provided username + empty password
try:
ssh.connect(self.plan.get_server(),
username=self.plan.get_username(),
password="")
except:
logger.error("Cannot connect to " + self.plan.get_server())
logger.error("Check username, password or key in " +
self.rsakey_local_path)
raise
else:
# login with provided username + private key
rsa_key = paramiko.RSAKey.from_private_key_file(rsa_keypath)
try:
ssh.connect(self.plan.get_server(),
username=self.plan.get_username(),
pkey=rsa_key)
except:
logger.error("Cannot connect to " + self.plan.get_server())
logger.error("Check username and your key in " +
self.rsakey_local_path)
raise
else:
# login with provided username + password
ssh.connect(self.plan.get_server(),
username=self.plan.get_username(),
password=self.plan.get_password())
if not self._runtrip:
norun = "echo "
else:
norun = ""
path_tgz = os.path.join(
self.remote_dir,
"temp.tar.gz") # remote place where temp.tar.gz is stored
rrun_dir = os.path.join(self.remote_dir,
self.folder_name) # remote run dir
commands = [
"cd " + self.remote_dir + ";" + "tar -zxvf " + path_tgz,
"cd " + rrun_dir + ";" + norun + "bash -lc '" +
self.trip_bin_path + " < plan.exec '", "cd " + self.remote_dir +
";" + "tar -zcvf " + path_tgz + " " + rrun_dir,
"cd " + self.remote_dir + ";" + "rm -r " + rrun_dir
]
logger.debug("Write stdout and stderr to " +
os.path.join(self.working_path, self.folder_name))
fp_stdout = open(
os.path.join(self.working_path, self.folder_name,
self.logfile_stdout), "w")
fp_stderr = open(
os.path.join(self.working_path, self.folder_name,
self.logfile_stderr), "w")
for cmd in commands:
logger.debug("Execute on remote: " + cmd)
self.log(cmd)
stdin, stdout, stderr = ssh.exec_command(cmd)
answer_stdout = stdout.read()
answer_stderr = stderr.read()
logger.debug("Remote answer stdout:" + answer_stdout)
logger.debug("Remote answer stderr:" + answer_stderr)
fp_stdout.write(answer_stdout)
fp_stderr.write(answer_stderr)
self.log(answer_stdout)
ssh.close()
fp_stdout.close()
fp_stderr.close()
self.copy_back_from_server()
self.decompress_data()
def run_trip_local(self):
"""
Runs TRiP98 on local computer.
"""
logger.info("Run TRiP98 in LOCAL mode.")
logger.debug("Write stdout and stderr to " +
os.path.join(self.working_path, self.folder_name))
fp_stdout = open(
os.path.join(self.working_path, self.folder_name,
self.logfile_stdout), "w")
fp_stderr = open(
os.path.join(self.working_path, self.folder_name,
self.logfile_stderr), "w")
os.chdir("%s" % (self.path))
if not self._runtrip: # for testing
norun = "echo "
else:
norun = ""
p = Popen([norun + self.trip_bin_path], stdout=PIPE, stdin=PIPE)
p.stdin.write(self.trip_exec)
p.stdin.flush()
while (True):
retcode = p.poll() # returns None while subprocess is running
answer_stdout = p.stdout.readline()
answer_stderr = p.stderr.readline()
logger.debug("Remote answer stdout:" + answer_stdout)
logger.debug("Remote answer stderr:" + answer_stderr)
fp_stdout.write(answer_stdout)
fp_stderr.write(answer_stderr)
self.log(answer_stdout)
if retcode is not None: # runs until process stops
break # TODO: check return code
os.chdir("..")
fp_stdout.close()
fp_stderr.close()
def finish(self):
pass
def create_trip_exec_mult_proj(self,
projectile,
no_output=False,
last=True,
first=True):
fields = self.projectiles[projectile]["fields"]
oar_list = self.oar_list
output = []
output.extend(self.create_exec_header())
output.extend(
self.create_exec_load_data_files(
self.projectiles[projectile]["projectile"]))
output.extend(self.create_exec_field(fields))
output.extend(self.create_exec_oar(oar_list))
dosecube = copy.deepcopy(self.projectiles[projectile]["target_dos"])
if not no_output:
if hasattr(self, "rest_dose"):
dosecube.cube = np.array(
(self.rest_dose.cube >= dosecube.cube) * dosecube.cube +
(self.rest_dose.cube < dosecube.cube) *
self.rest_dose.cube,
dtype=np.int16)
dosecube.cube[dosecube.cube < 0] = 0
# ~ self.plan.add_dose(self.rest_dose,"rest")
if not first:
a = (self.rest_dose.cube -
dosecube.cube) * (dosecube.cube > 0)
dosecube.cube += a * dosecube.cube / 500
dosecube.write(
os.path.join(
self.path, "target_dose_%s.dos" %
self.projectiles[projectile]["name"]))
self.projectile_dose_level[projectile] = np.max(dosecube.cube)
output.extend(
self.create_exec_plan(incube="target_dose_%s" %
self.projectiles[projectile]["name"]))
if self.plan.get_optimize() is True:
output.extend(self.create_exec_opt())
name = self.plan_name + "_" + self.projectiles[projectile]["name"]
output.extend(self.create_exec_output(name, fields))
out = "\n".join(output) + "\nexit\n"
self.trip_exec = out
def convert_files_to_voxelplan(self):
out_path = os.path.join(self.path, self.plan_name)
ctx = self.images
ctx.patient_name = self.plan_name
ctx.write(os.path.join(out_path + ".ctx"))
structures = VdxCube("", ctx)
structures.version = "2.0"
liste = []
area = 0
for voi in self.plan.get_vois():
voxelplan_voi = voi.get_voi().get_voi_data()
if voi.is_target():
mn, mx = voxelplan_voi.get_min_max()
area_temp = (mx[0] - mn[0]) * (mx[1] - mn[1]) * (mx[2] - mn[2])
if area_temp > area:
area = area_temp
liste.insert(0, voxelplan_voi)
else:
liste.append(voxelplan_voi)
voxelplan_voi.type = '1'
else:
liste.append(voxelplan_voi)
voxelplan_voi.type = '0'
for voxelplan_voi in liste:
structures.add_voi(voxelplan_voi)
structures.write_to_trip(out_path + ".vdx")
def compress_files(self):
"""
Builds the tar.gz from what is found in self.path.
"""
logger.debug("Compressing files in " + self.path)
self.save_exec(
os.path.join(self.working_path, self.folder_name, "plan.exec"))
with tarfile.open(
os.path.join(self.working_path, self.folder_name + ".tar.gz"),
"w:gz") as tar:
tar.add(self.path, arcname=self.folder_name)
def set_plan(self, plan):
self.plan = plan
self.plan_name = self.plan.get_name().replace(" ", "_")
def save_exec(self, path):
"""
Writes the .exec script to disk.
"""
self.split_plan()
if self.mult_proj:
path1 = path.replace(".exec", "")
for projectile in self.projectiles:
self.create_trip_exec(projectile, True)
with open(path1 + "_" + projectile + ".exec", "wb+") as fp:
fp.write(self.trip_exec)
else:
with open(path, "wb+") as fp:
fp.write(self.trip_exec)
def save_data(self, path):
out_path = path
ctx = self.images
ctx.patient_name = self.plan_name
ctx.write(os.path.join(out_path + ".ctx"))
structures = VdxCube("", ctx)
structures.version = "2.0"
for voi in self.plan.get_vois():
voxelplan_voi = voi.get_voi().get_voi_data()
structures.add_voi(voxelplan_voi)
if voi.is_target():
voxelplan_voi.type = '1'
else:
voxelplan_voi.type = '0'
structures.write_to_trip(out_path + ".vdx")
def get_transport(self):
transport = paramiko.Transport((self.plan.get_server(), 22))
transport.connect(username=self.plan.get_username(),
password=self.plan.get_password())
return transport
def copy_files_to_server(self):
"""
Copies the generated tar.gz file to the remote server.
"""
logger.debug("Copy tar.gz to server:" + self.path + ".tar.gz -> " +
os.path.join(self.remote_dir, "temp.tar.gz"))
transport = self.get_transport()
sftp = paramiko.SFTPClient.from_transport(transport)
sftp.put(localpath=self.path + ".tar.gz",
remotepath=os.path.join(self.remote_dir, 'temp.tar.gz'))
sftp.close()
transport.close()
def run_ssh_command(self, cmd):
ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh.connect(self.plan.get_server(),
username=self.plan.get_username(),
password=self.plan.get_password())
self.parent.write_to_log("Run Trip\n")
stdin, stdout, stderr = ssh.exec_command(cmd)
ssh.close()
def copy_back_from_server(self):
transport = self.get_transport()
sftp = paramiko.SFTPClient.from_transport(transport)
sftp.get(os.path.join(self.remote_dir, 'temp.tar.gz'),
self.path + ".tar.gz")
sftp.close()
transport.close()
def decompress_data(self):
output_folder = self.path
if os.path.exists(output_folder):
shutil.rmtree(output_folder)
with tarfile.open(self.path + ".tar.gz", "r:gz") as tar:
tar.extractall(self.working_path)
def clean_up(self):
f = "%s" % (self.path + ".tar.gz")
if os.path.exists(f):
os.remove(f)
shutil.rmtree("%s" % self.path)
def visualize_data(self):
pass
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 split_plan(self, plan=None):
self.targets = []
self.oar_list = []
dose = 0
for voi in self.plan.get_vois():
if voi.is_oar():
self.oar_list.append(voi)
if voi.is_target():
self.targets.append(voi)
if voi.get_dose() > dose:
dose = voi.get_dose()
if not len(self.targets):
raise InputError("No targets")
if not len(self.plan.get_fields()):
raise InputError("No fields")
self.target_dose = dose
if plan is None:
plan = self.plan
proj = []
self.projectile_dose_level = {}
for field in plan.fields:
if field.get_projectile() not in proj:
proj.append(field.get_projectile())
self.projectile_dose_level[field.get_projectile()] = 0
if len(proj) > 1:
self.mult_proj = True
else:
self.mult_proj = False
if self.mult_proj:
self.projectiles = {}
for field in plan.fields:
if field.get_projectile() not in self.projectiles.keys():
self.projectiles[field.get_projectile()] = {
"target_dos": DosCube(self.images),
"fields": [field],
"name": field.get_projectile(),
"projectile": field.get_projectile()
}
else:
self.projectiles[field.get_projectile()]["fields"].append(
field)
self.target_dos = DosCube(self.images)
for i, voi in enumerate(self.targets):
temp = DosCube(self.images)
voi_dose_level = int(voi.get_dose() / dose * 1000)
temp.load_from_structure(voi.get_voi().get_voi_data(), 1)
for projectile, data in self.projectiles.items():
dose_percent = self.plan.get_dose_percent(projectile)
if not voi.get_dose_percent(projectile) is None:
dose_percent = voi.get_dose_percent(projectile)
proj_dose_lvl = int(voi.get_dose() / self.target_dose *
dose_percent * 10)
if self.projectile_dose_level[projectile] < proj_dose_lvl:
self.projectile_dose_level[projectile] = proj_dose_lvl
if proj_dose_lvl == 0:
proj_dose_lvl = -1
if i == 0:
data["target_dos"] = temp * proj_dose_lvl
else:
data["target_dos"].merge_zero(temp * proj_dose_lvl)
if i == 0:
self.target_dos = temp * voi_dose_level
else:
self.target_dos.merge_zero(temp * voi_dose_level)
for projectile, data in self.projectiles.items():
data["target_dos"].cube[data["target_dos"].cube == -1] = int(0)
self.plan.add_dose(data["target_dos"],
"target_%s" % projectile)
self.rest_dose = copy.deepcopy(self.target_dos)
def load_dose(self, path, t, target_dose=0.0):
dos = DosCube()
dos.read(os.path.splitext(path)[0] + ".dos")
d = DoseCube(dos, t)
d.set_dose(target_dose)
self.add_dose(d)