def delivery_from_tel_plan_contents(tel_contents):
pattern = get_control_point_pattern()
all_controlpoint_results = re.findall(pattern, tel_contents)
mu = np.cumsum([float(result[3]) for result in all_controlpoint_results])
iec_gantry_angle = [float(result[1]) for result in all_controlpoint_results]
bipolar_gantry_angle = pymedphys._utilities.transforms.convert_IEC_angle_to_bipolar( # pylint: disable = protected-access
iec_gantry_angle
)
iec_coll_angle = [float(result[2]) for result in all_controlpoint_results]
bipolar_coll_angle = pymedphys._utilities.transforms.convert_IEC_angle_to_bipolar( # pylint: disable = protected-access
iec_coll_angle
)
mlcs = [convert_mlc_string(result[0]) for result in all_controlpoint_results]
jaw_gap = np.array([float(result[4]) for result in all_controlpoint_results])
jaw_field_centre = np.array(
[float(result[5]) for result in all_controlpoint_results]
)
jaw_a = jaw_field_centre + jaw_gap / 2
jaw_b = -(jaw_field_centre - jaw_gap / 2)
jaws = np.vstack([jaw_a, jaw_b]).T
return mu, bipolar_gantry_angle, bipolar_coll_angle, mlcs, jaws
def calculate_expanded_mask(contours, dcm_ct, expansion):
dx, dy, Cx, Cy, Ox, Oy = get_image_transformation_parameters(dcm_ct)
ct_size = np.shape(dcm_ct.pixel_array)
new_ct_size = np.array(ct_size) * expansion
expanded_mask = np.zeros(new_ct_size)
for xyz in contours:
x = np.array(xyz[0::3])
y = np.array(xyz[1::3])
z = xyz[2::3]
if len(set(z)) != 1:
raise ValueError("Expected only one z value for a given contour")
r = (((y - Cy) / dy * Oy)) * expansion + (expansion - 1) * 0.5
c = (((x - Cx) / dx * Ox)) * expansion + (expansion - 1) * 0.5
expanded_mask = np.logical_or(
expanded_mask,
skimage.draw.polygon2mask(new_ct_size, np.array(list(zip(r, c)))),
)
return expanded_mask
def from_lists(self, x, y, meta={}):
""" import x and y lists
Parameters
----------
x : list
List of float x values
y : list
List of float y values
meta : dict, optional
Returns
-------
Profile
Examples
--------
``profile = Profile().fron_lists(x_list,data_list)``
"""
self.x = np.array(x)
self.y = np.array(y)
self.__init__(x=x, y=y, meta=meta)
return Profile(x=x, y=y, meta=meta)
def random_uncompared_logfiles(index, config, compared_hashes):
index_set = set(index.keys())
comparison_set = set(compared_hashes)
not_yet_compared = np.array(list(index_set.difference(comparison_set)))
field_types = np.array(
[
index[file_hash]["delivery_details"]["field_type"]
for file_hash in not_yet_compared
]
)
file_hashes_vmat = not_yet_compared[field_types == "VMAT"]
vmat_filepaths = np.array(
[
os.path.join(
config["linac_logfile_data_directory"],
"indexed",
index[file_hash]["filepath"],
)
for file_hash in file_hashes_vmat
]
)
shuffle_index = np.arange(len(vmat_filepaths))
np.random.shuffle(shuffle_index)
return file_hashes_vmat[shuffle_index], vmat_filepaths[shuffle_index]
def visual_circle_and_ellipse(insert_x, insert_y, width, length,
circle_centre):
t = np.linspace(0, 2 * np.pi)
circle = {
"x": width / 2 * np.sin(t) + circle_centre[0],
"y": width / 2 * np.cos(t) + circle_centre[1],
}
x_shift, y_shift, rotation_angle = visual_alignment_of_equivalent_ellipse(
insert_x, insert_y, width, length, None)
rotation_matrix = np.array([
[np.cos(rotation_angle), -np.sin(rotation_angle)],
[np.sin(rotation_angle),
np.cos(rotation_angle)],
])
ellipse = np.array([length / 2 * np.sin(t), width / 2 * np.cos(t)]).T
rotated_ellipse = ellipse @ rotation_matrix
translated_ellipse = rotated_ellipse + np.array([y_shift, x_shift])
ellipse = {"x": translated_ellipse[:, 1], "y": translated_ellipse[:, 0]}
return circle, ellipse
def _matches_fraction(self,
dicom_dataset,
fraction_number,
gantry_tol=3,
meterset_tol=0.5):
filtered = self._filter_cps()
dicom_metersets = get_fraction_group_beam_sequence_and_meterset(
dicom_dataset, fraction_number)[1]
dicom_fraction = convert_to_one_fraction_group(dicom_dataset,
fraction_number)
gantry_angles = get_gantry_angles_from_dicom(dicom_fraction)
delivery_metersets = filtered._metersets( # pylint: disable = protected-access
gantry_angles, gantry_tol)
try:
maximmum_diff = np.max(
np.abs(
np.array(dicom_metersets) - np.array(delivery_metersets)))
except ValueError:
maximmum_diff = np.inf
return maximmum_diff <= meterset_tol
def dicom_dose_interpolate(interp_coords, dicom_dose_dataset):
"""Interpolates across a DICOM dose dataset.
Parameters
----------
interp_coords : tuple(z, y, x)
A tuple of coordinates in DICOM order, z axis first, then y, then x
where x, y, and z are DICOM axes.
dose : pydicom.Dataset
An RT DICOM Dose object
"""
interp_z = np.array(interp_coords[0], copy=False)[:, None, None]
interp_y = np.array(interp_coords[1], copy=False)[None, :, None]
interp_x = np.array(interp_coords[2], copy=False)[None, None, :]
coords, dicom_dose_dataset = zyx_and_dose_from_dataset(dicom_dose_dataset)
interpolation = scipy.interpolate.RegularGridInterpolator(
coords, dicom_dose_dataset)
try:
result = interpolation((interp_z, interp_y, interp_x))
except ValueError:
print(f"coords: {coords}")
raise
return result
def _fraction_number(self, dicom_template, gantry_tol=3, meterset_tol=0.5):
fractions = dicom_template.FractionGroupSequence
if len(fractions) == 1:
return fractions[0].FractionGroupNumber
fraction_numbers = [
fraction.FractionGroupNumber for fraction in fractions
]
fraction_matches = np.array([
self._matches_fraction(
dicom_template,
fraction_number,
gantry_tol=gantry_tol,
meterset_tol=meterset_tol,
) for fraction_number in fraction_numbers
])
if np.sum(fraction_matches) < 1:
raise ValueError(
"A fraction group was not able to be found with the metersets "
"and gantry angles defined by the tolerances provided. "
"Please manually define the fraction group number.")
if np.sum(fraction_matches) > 1:
raise ValueError(
"More than one fraction group was found that had metersets "
"and gantry angles within the tolerances provided. "
"Please manually define the fraction group number.")
fraction_number = np.array(fraction_numbers)[fraction_matches]
return fraction_number
def calculate_anti_aliased_mask(contours, dcm_ct, expansion=5):
transformation_params = get_image_transformation_parameters(dcm_ct)
dx, dy, Cx, Cy, Ox, Oy = transformation_params
x_grid, y_grid, ct_size = get_grid(
dcm_ct, transformation_params=transformation_params)
new_ct_size = np.array(ct_size) * expansion
expanded_mask = np.zeros(new_ct_size)
for xyz in contours:
x = np.array(xyz[0::3])
y = np.array(xyz[1::3])
z = xyz[2::3]
assert len(set(z)) == 1
r = (((y - Cy) / dy * Oy)) * expansion + (expansion - 1) * 0.5
c = (((x - Cx) / dx * Ox)) * expansion + (expansion - 1) * 0.5
expanded_mask = np.logical_or(
expanded_mask,
skimage.draw.polygon2mask(new_ct_size, np.array(list(zip(r, c)))),
)
mask = reduce_expanded_mask(expanded_mask, ct_size[0], expansion)
mask = 2 * mask - 1
return x_grid, y_grid, mask
def find_data_index(file_contents):
"""Searches through the mephysto file for where the BEGIN_DATA and END_DATA
appear. This region contains only the raw data in column format. Returns a
list of ranges which span each scan region.
"""
# Find the positions of BEGIN_DATA
# Demo of match -- https://regex101.com/r/lR4pS2/5
begin_data_index = np.array([
i for i, item in enumerate(file_contents)
if re.search(r"^\t\tBEGIN_DATA$", item)
]).astype(int)
# Find the positions of END_DATA
# Demo of match -- https://regex101.com/r/lR4pS2/6
end_data_index = np.array([
i for i, item in enumerate(file_contents)
if re.search(r"^\t\tEND_DATA$", item)
]).astype(int)
# Convert the indices into the range type allowing for easy looping
data_index = [
range(begin_data_index[i] + 1, end_data_index[i])
for i in range(len(begin_data_index))
]
return data_index
def find_scan_index(file_contents):
"""Searches through the mephysto file for where the BEGIN_SCAN and END_SCAN
appear. This region contains all of the information for a given scan within
the mephysto file. Returns a list of ranges which span each scan region.
"""
# Find the positions of all BEGIN_SCAN
# Demo of match -- https://regex101.com/r/lR4pS2/2
# Demo of ignoring "BEGIN_SCAN_DATA" -- https://regex101.com/r/lR4pS2/4
# Basic guide to regular expressions (regex):
# http://www.regular-expressions.info/quickstart.html
begin_scan_index = np.array([
i for i, item in enumerate(file_contents)
if re.search(r"^\tBEGIN_SCAN\s\s\d+$", item)
]).astype(int)
# Find the positions of all END_SCAN
# Regex demo here -- https://regex101.com/r/lR4pS2/3
end_scan_index = np.array([
i for i, item in enumerate(file_contents)
if re.search(r"^\tEND_SCAN\s\s\d+$", item)
]).astype(int)
# Convert the indices into the range type allowing for easy looping
scan_index = [
range(begin_scan_index[i] + 1, end_scan_index[i])
for i in range(len(begin_scan_index))
]
return scan_index
def calc_min_distance(cube_definition, contours):
vertices = cube_vertices(cube_definition)
vectors = cube_vectors(cube_definition)
unit_vectors = [vector / np.linalg.norm(vector) for vector in vectors]
plane_norms = np.array(
[
unit_vectors[1],
-unit_vectors[0],
-unit_vectors[1],
unit_vectors[0],
unit_vectors[2],
-unit_vectors[2],
]
)
plane_points = np.array(
[vertices[0], vertices[1], vertices[2], vertices[0], vertices[0], vertices[3]]
)
plane_origin_dist = -np.sum(plane_points * plane_norms, axis=1)
distance_to_planes = np.dot(plane_norms, contours) + plane_origin_dist[:, None]
min_dist_squared = np.min(distance_to_planes ** 2, axis=0)
return min_dist_squared
def __init__(self, x=np.array([]), y=np.array([]), meta={}):
""" create profile
Parameters
----------
x : np.array, optional
y : np.array, optional
meta : dict, optional
Notes
-----
Normally created empty, then filled using a method, which returns
a new Profile.
"""
self.x = np.array(x)
self.y = np.array(y)
self.meta = meta
if len(self.x) < 2:
self.interp = None
else:
self.interp = interpolate.interp1d(self.x,
self.y,
bounds_error=False,
fill_value=0.0)
def pull_coords_from_contour_sequence(contour_sequence):
contours_by_slice_raw = [item.ContourData for item in contour_sequence]
x = [np.array(item[0::3]) for item in contours_by_slice_raw]
y = [np.array(item[1::3]) for item in contours_by_slice_raw]
z = [np.array(item[2::3]) for item in contours_by_slice_raw]
return x, y, z
def field(x, y):
x = np.array(x, copy=False)
y = np.array(y, copy=False)
x_shifted = x - centre[0]
y_shifted = y - centre[1]
x_rotated, y_rotated = rotate_coords(x_shifted, y_shifted, theta)
return width_profile(x_rotated) * length_profile(y_rotated)
def create_dose_function(net_od, dose):
net_od = np.array(net_od, copy=False)
dose = np.array(dose, copy=False)
to_minimise = create_to_minimise(net_od, dose)
result = basinhopping(to_minimise, [np.max(dose) / np.max(net_od), 1, 1])
return create_cal_fit(*result.x)
def as_array(self, only_coords: bool = True):
"""Return the point as a numpy array."""
if only_coords:
return np.array([getattr(self, item) for item in self._coord_list])
else:
return np.array([
getattr(self, item) for item in self._attr_list
if (getattr(self, item) is not None)
])
def calculate_coordinates_shell_1d(distance):
"""Output the two points that are of the defined distance in one-dimension
"""
if distance == 0:
x_coords = np.array([0])
else:
x_coords = np.array([distance, -distance])
return (x_coords,)
def from_snc_profiler(self, file_name, axis):
""" import profile form SNC Profiler file
Parameters
----------
file_name : string
file name with path, .prs
axis : string
'tvs' or 'rad'
Returns
-------
Profile
Raises
------
TypeError
if axis invalid
"""
with open(file_name) as profiler_file:
munge = "\n".join(profiler_file.readlines())
munge = munge.replace("\t", "").replace(": ", ":")
munge = munge.replace(" Time:", "\nTime:") # BREAK 2-ITEM ROWS
munge = munge.replace(" Revision:", "\nRevision:")
munge = munge.replace("Energy:", "\nEnergy:")
munge = munge.replace("Dose:", "\nDose:")
munge = munge.replace("Collimator Angle:", "\nCollimator Angle:")
munge = munge.split("TYPE")[0].split("\n") # DISCARD NON-METADATA
munge = [i.split(":", 1) for i in munge if i and ":" in i]
munge = [i for i in munge if i[1]] # DISCARD EMPTY ITEMS
meta = dict(munge)
with open(file_name) as profiler_file:
for row in profiler_file.readlines():
if row[:11] == "Calibration" and "File" not in row:
calibs = np.array(row.split())[1:].astype(float)
elif row[:5] == "Data:":
counts = np.array(row.split()[5:145]).astype(float)
elif row[:15] == "Dose Per Count:":
dose_per_count = float(row.split()[-1])
dose = counts * dose_per_count * calibs
x_vals = [-11.2 + 0.4 * i for i in range(57)]
x_prof = list(zip(x_vals, dose[:57]))
y_vals = [-16.4 + 0.4 * i for i in range(83)]
y_prof = list(zip(y_vals, dose[57:]))
if axis == "tvs":
return Profile().from_tuples(x_prof, meta=meta)
elif axis == "rad":
return Profile().from_tuples(y_prof, meta=meta)
else:
raise TypeError("axis must be 'tvs' or 'rad'")
def calculate_deformability(x_test, y_test, x_data, y_data, z_data):
"""Return the result of the deformability test.
This function takes an array of test points and loops over
``_single_calculate_deformability``.
The deformability test applies a shift to the spline to determine whether
or not sufficient information for modelling is available. For further
details on the deformability test see the *Methods: Defining valid
prediction regions of the spline* section within
<http://dx.doi.org/10.1016/j.ejmp.2015.11.002>.
Parameters
----------
x_test : np.ndarray
The x coordinate of the point(s) to test
y_test : np.ndarray
The y coordinate of the point(s) to test
x_data : np.ndarray
The x coordinate of the model data to test
y_data : np.ndarray
The y coordinate of the model data to test
z_data : np.ndarray
The z coordinate of the model data to test
Returns
-------
deformability : float
The resulting deformability between 0 and 1
representing the ratio of deviation the spline model underwent at
the point in question by introducing an outlier at the point in
question.
"""
dim = np.shape(x_test)
if np.size(dim) == 0:
deformability = _single_calculate_deformability(
x_test, y_test, x_data, y_data, z_data)
elif np.size(dim) == 1:
deformability = np.array([
_single_calculate_deformability(x_test[i], y_test[i], x_data,
y_data, z_data)
for i in range(dim[0])
])
else:
deformability = np.array([[
_single_calculate_deformability(x_test[i, j], y_test[i, j], x_data,
y_data, z_data)
for j in range(dim[1])
] for i in range(dim[0])])
return deformability
def delivery_from_tel_plan_contents(tel_contents):
pattern = get_control_point_pattern()
all_controlpoint_results = re.findall(pattern, tel_contents)
mu = np.cumsum([float(result[4])
for result in all_controlpoint_results]).tolist()
iec_gantry_angle = [
float(result[2]) for result in all_controlpoint_results
]
bipolar_gantry_angle = pymedphys._utilities.transforms.convert_IEC_angle_to_bipolar( # pylint: disable = protected-access
iec_gantry_angle).tolist()
iec_coll_angle = [float(result[3]) for result in all_controlpoint_results]
bipolar_coll_angle = pymedphys._utilities.transforms.convert_IEC_angle_to_bipolar( # pylint: disable = protected-access
iec_coll_angle).tolist()
mlcs = [
convert_mlc_string(result[0]) for result in all_controlpoint_results
]
jaw_gap = np.array(
[float(result[5]) for result in all_controlpoint_results])
jaw_field_centre = np.array(
[float(result[6]) for result in all_controlpoint_results])
jaw_a = jaw_field_centre + jaw_gap / 2
jaw_b = -(jaw_field_centre - jaw_gap / 2)
jaws = np.vstack([jaw_a, jaw_b]).T.tolist()
for i in range(len(mu) - 1, -1, -1):
result = all_controlpoint_results[i]
if result[
1] == "2,2": # A nasty hack to attempt to find static fields
if i == 0:
mu = [0] + mu
else:
mu = mu[0:i] + [mu[i - 1]] + mu[i::]
bipolar_gantry_angle = (bipolar_gantry_angle[0:i] +
[bipolar_gantry_angle[i]] +
bipolar_gantry_angle[i::])
bipolar_coll_angle = (bipolar_coll_angle[0:i] +
[bipolar_coll_angle[i]] +
bipolar_coll_angle[i::])
mlcs = mlcs[0:i] + [mlcs[i]] + mlcs[i::]
jaws = jaws[0:i] + [jaws[i]] + jaws[i::]
elif result[1] != "1,1":
raise ValueError(
"Detection for static or dynamic control points has fallen down"
)
return mu, bipolar_gantry_angle, bipolar_coll_angle, mlcs, jaws
def test_if_in_range(point_test, point_start, point_end):
point_test = np.array(point_test)
point_start = np.array(point_start)
point_end = np.array(point_end)
vector = point_end - point_start
dot = np.dot(point_test, vector)
item = [dot, np.dot(vector, point_start), np.dot(vector, point_end)]
item.sort()
return item[1] == dot
def group_consecutive_logfiles(file_hashes, index):
times = np.array([index[key]["local_time"]
for key in file_hashes]).astype(np.datetime64)
sort_reference = np.argsort(times)
file_hashes = file_hashes[sort_reference]
times = times[sort_reference]
hours_4 = np.array(60 * 60 * 4).astype(np.timedelta64)
split_locations = np.where(np.diff(times) >= hours_4)[0] + 1
return np.split(file_hashes, split_locations)
def apply_transform(xx, yy, transform):
xx = np.array(xx, copy=False)
yy = np.array(yy, copy=False)
xx_flat = np.ravel(xx)
transformed = transform @ np.vstack(
[xx_flat, np.ravel(yy), np.ones_like(xx_flat)])
xx_transformed = transformed[0]
yy_transformed = transformed[1]
xx_transformed.shape = xx.shape
yy_transformed.shape = yy.shape
return xx_transformed, yy_transformed
def decode_msq_mlc(raw_bytes):
"""Convert MLCs from Mosaiq SQL byte format to cm floats.
"""
raw_bytes = mosaiq_mlc_missing_byte_workaround(raw_bytes)
length = check_all_items_equal_length(raw_bytes, "mlc bytes")
if length % 2 == 1:
raise ValueError(
"There should be an even number of bytes within an MLC record."
)
mlc_pos = (
np.array(
[
[
struct.unpack("<h", control_point[2 * i : 2 * i + 2])
for i in range(len(control_point) // 2)
]
for control_point in raw_bytes
]
)
/ 100
)
return mlc_pos
def batch_process(image_paths,
edge_lengths,
bb_diameter=8,
penumbra=2,
display_figure=True):
bb_centres = []
field_centres = []
field_rotations = []
for image_path in image_paths:
bb_centre, field_centre, field_rotation = iview_find_bb_and_field(
image_path,
edge_lengths,
bb_diameter=bb_diameter,
penumbra=penumbra,
display_figure=display_figure,
)
bb_centres.append(bb_centre)
field_centres.append(field_centre)
field_rotations.append(field_rotation)
if display_figure:
plt.show()
data = np.concatenate(
[bb_centres, field_centres,
np.array(field_rotations)[:, None]],
axis=1)
return pd.DataFrame(
data=data, columns=["BB x", "BB y", "Field x", "Field y", "Rotation"])
def get_dose_grid_structure_mask(structure_name, dcm_struct, dcm_dose):
x_dose, y_dose, z_dose = xyz_axes_from_dataset(dcm_dose)
xx_dose, yy_dose = np.meshgrid(x_dose, y_dose)
points = np.swapaxes(np.vstack([xx_dose.ravel(), yy_dose.ravel()]), 0, 1)
x_structure, y_structure, z_structure = pull_structure(
structure_name, dcm_struct)
structure_z_values = np.array([item[0] for item in z_structure])
mask = np.zeros((len(y_dose), len(x_dose), len(z_dose)), dtype=bool)
for z_val in structure_z_values:
structure_indices = _get_indices(z_structure, z_val)
for structure_index in structure_indices:
dose_index = int(np.where(z_dose == z_val)[0])
assert z_structure[structure_index][0] == z_dose[dose_index]
structure_polygon = matplotlib.path.Path([
(x_structure[structure_index][i],
y_structure[structure_index][i])
for i in range(len(x_structure[structure_index]))
])
mask[:, :, dose_index] = mask[:, :, dose_index] | (
structure_polygon.contains_points(points).reshape(
len(y_dose), len(x_dose)))
return mask
def _get_indices(z_list, z_val):
indices = np.array([item[0] for item in z_list])
# This will error if more than one contour exists on a given slice
desired_indices = np.where(indices == z_val)[0]
# Multiple contour sets per slice not yet implemented
return desired_indices
def find_consecutive_logfiles(field_id_key_map, field_id, filehash, index):
keys = np.array(field_id_key_map[field_id])
times = np.array([index[key]["local_time"] for key in keys]).astype(np.datetime64)
sort_reference = np.argsort(times)
keys = keys[sort_reference]
times = times[sort_reference]
hours_4 = np.array(60 * 60 * 4).astype(np.timedelta64)
delivery_time = np.array(index[filehash]["local_time"]).astype(np.datetime64)
within_4_hours_reference = np.abs(delivery_time - times) < hours_4
within_4_hours = keys[within_4_hours_reference].tolist()
return within_4_hours
def calc_mu_density_return_grid(
mu,
mlc,
jaw,
grid_resolution=__DEFAULT_GRID_RESOLUTION,
max_leaf_gap=__DEFAULT_MAX_LEAF_GAP,
leaf_pair_widths=__DEFAULT_LEAF_PAIR_WIDTHS,
min_step_per_pixel=__DEFAULT_MIN_STEP_PER_PIXEL,
):
"""DEPRECATED. This is a temporary helper function to provide the old
api.
"""
leaf_pair_widths = np.array(leaf_pair_widths)
mu_density = calc_mu_density(
mu,
mlc,
jaw,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths,
min_step_per_pixel=min_step_per_pixel,
)
full_grid = get_grid(max_leaf_gap, grid_resolution, leaf_pair_widths)
grid_xx, grid_yy = np.meshgrid(full_grid["mlc"], full_grid["jaw"])
return grid_xx, grid_yy, mu_density