def read_bin_file(file_name):
""" read sinogram from binary file
Return sinogram np.array produced by reading an Accuray sinogram
BIN file with the provided file name.
Parameters
----------
file_name : str
long file name of csv file
Returns
-------
sinogram : np.array
Notes
-----
BIN files are sinograms stored in binary format used in
Tomotherapy calibration plans.
"""
leaf_open_times = np.fromfile(file_name, dtype=float, count=-1, sep="")
num_leaves = 64
num_projections = int(len(leaf_open_times) / num_leaves)
sinogram = np.reshape(leaf_open_times, (num_projections, num_leaves))
return sinogram
def reduce_expanded_mask(expanded_mask, img_size, expansion):
return np.mean(
np.mean(
np.reshape(expanded_mask, (img_size, expansion, img_size, expansion)),
axis=1,
),
axis=2,
)
def get_interpolated_dose(coords_grid, dose_interpolation):
coords_grid_ij_indexing = np.array([
np.ravel(coords_grid[:, :, 1]),
np.ravel(coords_grid[:, :, 0]),
np.ravel(coords_grid[:, :, 2]),
]).T
interpolated_dose = dose_interpolation(coords_grid_ij_indexing)
coords_dim = np.shape(coords_grid)
interpolated_dose = np.reshape(interpolated_dose,
(coords_dim[0], coords_dim[1]))
return interpolated_dose
def gamma_filter_brute_force(axes_reference,
dose_reference,
axes_evaluation,
dose_evaluation,
distance_mm_threshold,
dose_threshold,
lower_dose_cutoff=0,
**_):
xx_ref, yy_ref, zz_ref = np.meshgrid(*axes_reference, indexing="ij")
gamma_array = np.ones_like(dose_evaluation).astype(np.float) * np.nan
mesh_index = np.meshgrid(
*[np.arange(len(coord_eval)) for coord_eval in axes_evaluation])
eval_index = np.reshape(np.array(mesh_index), (3, -1))
run_index = np.arange(np.shape(eval_index)[1])
np.random.shuffle(run_index)
sys.stdout.write(" ")
for counter, point_index in enumerate(run_index):
i, j, k = eval_index[:, point_index]
eval_x = axes_evaluation[0][i]
eval_y = axes_evaluation[1][j]
eval_z = axes_evaluation[2][k]
if dose_evaluation[i, j, k] < lower_dose_cutoff:
continue
distance = np.sqrt((xx_ref - eval_x)**2 + (yy_ref - eval_y)**2 +
(zz_ref - eval_z)**2)
dose_diff = dose_evaluation[i, j, k] - dose_reference
gamma = np.min(
np.sqrt((dose_diff / dose_threshold)**2 +
(distance / distance_mm_threshold)**2))
gamma_array[i, j, k] = gamma
if counter // 30 == counter / 30:
percent_pass = str(
np.round(calculate_pass_rate(gamma_array), decimals=1))
sys.stdout.write(
"\rPercent Pass: {0}% | Percent Complete: {1:.2f}%".format(
percent_pass, counter / np.shape(eval_index)[1] * 100))
sys.stdout.flush()
return calculate_pass_rate(gamma_array)
def create_point_combination(coords):
mesh_index = np.meshgrid(*coords)
point_combination = np.reshape(np.array(mesh_index), (3, -1))
return point_combination
def gamma_shell(
axes_reference,
dose_reference,
axes_evaluation,
dose_evaluation,
dose_percent_threshold,
distance_mm_threshold,
lower_percent_dose_cutoff=20,
interp_fraction=10,
max_gamma=None,
local_gamma=False,
global_normalisation=None,
skip_once_passed=False,
random_subset=None,
ram_available=DEFAULT_RAM,
quiet=False,
):
"""Compare two dose grids with the gamma index.
It computes 1, 2, or 3 dimensional gamma with arbitrary gird sizes while
interpolating on the fly. This function makes use of some of the ideas
presented within <http://dx.doi.org/10.1118/1.2721657>.
Parameters
----------
axes_reference : tuple
The reference coordinates.
dose_reference : np.array
The reference dose grid. Each point in the reference grid becomes the
centre of a Gamma ellipsoid. For each point of the reference, nearby
evaluation points are searched at increasing distances.
axes_evaluation : tuple
The evaluation coordinates.
dose_evaluation : np.array
The evaluation dose grid. Evaluation here is defined as the grid which
is interpolated and searched over at increasing distances away from
each reference point.
dose_percent_threshold : float
The percent dose threshold
distance_mm_threshold : float
The gamma distance threshold. Units must
match of the coordinates given.
lower_percent_dose_cutoff : float, optional
The percent lower dose cutoff below which gamma will not be calculated.
This is only applied to the reference grid.
interp_fraction : float, optional
The fraction which gamma distance threshold is divided into for
interpolation. Defaults to 10 as recommended within
<http://dx.doi.org/10.1118/1.2721657>. If a 3 mm distance threshold is chosen
this default value would mean that the evaluation grid is interpolated at
a step size of 0.3 mm.
max_gamma : float, optional
The maximum gamma searched for. This can be used to speed up
calculation, once a search distance is reached that would give gamma
values larger than this parameter, the search stops. Defaults to :obj:`np.inf`
local_gamma
Designates local gamma should be used instead of global. Defaults to
False.
global_normalisation : float, optional
The dose normalisation value that the percent inputs calculate from.
Defaults to the maximum value of :obj:`dose_reference`.
random_subset : int, optional
Used to only calculate a random subset of the reference grid. The
number chosen is how many random points to calculate.
ram_available : int, optional
The number of bytes of RAM available for use by this function. Defaults
to 0.8 times your total RAM as determined by psutil.
quiet : bool, optional
Used to quiet informational printing during function usage. Defaults to
False.
Returns
-------
gamma
The array of gamma values the same shape as that
given by the reference coordinates and dose.
"""
if max_gamma is None:
max_gamma = np.inf
options = GammaInternalFixedOptions.from_user_inputs(
axes_reference,
dose_reference,
axes_evaluation,
dose_evaluation,
dose_percent_threshold,
distance_mm_threshold,
lower_percent_dose_cutoff,
interp_fraction,
max_gamma,
local_gamma,
global_normalisation,
skip_once_passed,
random_subset,
ram_available,
quiet,
)
if not options.quiet:
if options.local_gamma:
print("Calcing using local normalisation point for gamma")
else:
print("Calcing using global normalisation point for gamma")
print("Global normalisation set to {}".format(
options.global_normalisation))
print("Global dose threshold set to {} ({}% of normalisation)".format(
options.global_dose_threshold, options.dose_percent_threshold))
print("Distance threshold set to {}".format(
options.distance_mm_threshold))
print("Lower dose cutoff set to {} ({}% of normalisation)".format(
options.lower_dose_cutoff, lower_percent_dose_cutoff))
print("")
current_gamma = gamma_loop(options)
gamma = {}
for i, dose_threshold in enumerate(options.dose_percent_threshold):
for j, distance_threshold in enumerate(options.distance_mm_threshold):
key = (dose_threshold, distance_threshold)
gamma_temp = current_gamma[:, i, j]
gamma_temp = np.reshape(gamma_temp, np.shape(dose_reference))
gamma_temp[np.isinf(gamma_temp)] = np.nan
with np.errstate(invalid="ignore"):
gamma_greater_than_ref = gamma_temp > max_gamma
gamma_temp[gamma_greater_than_ref] = max_gamma
gamma[key] = gamma_temp
if not options.quiet:
print("\nComplete!")
if len(gamma.keys()) == 1:
gamma = next(iter(gamma.values()))
return gamma