# Source code for skfmm.pfmm

```
from sys import float_info
import numpy as np
from .cfmm import cFastMarcher
FAR, NARROW, FROZEN, MASK = 0, 1, 2, 3
DISTANCE, TRAVEL_TIME, EXTENSION_VELOCITY = 0, 1, 2
def pre_process_args(phi, dx, narrow, periodic, ext_mask=None):
"""
get input data into the correct form for calling the c extension module
This wrapper allows for a little bit of flexibility in the input types
"""
if not isinstance(phi, np.ndarray):
phi = np.array(phi)
if type(dx) is float or type(dx) is int:
dx = [dx for x in range(phi.ndim)]
dx = np.array(dx)
if isinstance(phi, np.ma.MaskedArray):
flag = np.zeros(phi.shape, dtype=np.int)
flag[phi.mask] = MASK
phi = phi.data
else:
flag = np.zeros(phi.shape, dtype=np.int)
if ext_mask is None:
ext_mask = np.zeros(phi.shape, dtype=np.int)
periodic_data = 0
if isinstance(periodic, bool):
if periodic:
periodic_data = int(2**phi.ndim-1)
else:
if hasattr(periodic, "__len__") and len(periodic) == phi.ndim:
for i, value in enumerate(periodic):
if value:
periodic_data |= 1<<i
else:
raise ValueError("parameter \"periodic\" must be of type bool or sequence of type bool of length phi.ndim.")
if narrow < 0:
raise ValueError("parameter \"narrow\" must be greater than or equal to zero.")
return phi, dx, flag, ext_mask, periodic_data
def post_process_result(result):
"""
post-process results from the c module (add mask)
"""
if (result == float_info.max).any():
mask = (result == float_info.max)
result[mask] = 0
result = np.ma.MaskedArray(result, mask)
return result
[docs]def distance(phi, dx=1.0, self_test=False, order=2,
narrow=0.0, periodic=False):
"""Return the signed distance from the zero contour of the array phi.
Parameters
----------
phi : array-like
the zero contour of this array is the boundary location for
the distance calculation. Phi can of 1,2,3 or higher
dimension and can be a masked array.
dx : float or an array-like of len phi.ndim, optional
the cell length in each dimension.
self_test : bool, optional
if True consistency checks are made on the binary min
heap during the calculation. This is used in testing and
results in a slower calculation.
order : int, optional
order of computational stencil to use in updating points during
the fast marching method. Must be 1 or 2, the default is 2.
narrow : float, optional
narrow band half-width. If this optional argument is
specified the marching algorithm is limited to within a
given narrow band. If far-field points remain when this
condition is met a masked array is returned. The default
value is 0.0 which means no narrow band limit.
periodic : bool or an array-like of len phi.ndim, optional
specifies whether and in which directions periodic
boundary conditions are used. True sets periodic
boundary conditions in all directions. An array-like
(interpreted as True or False values) specifies the
absence or presence of periodic boundaries in
individual directions. The default value is False,
i.e., no periodic boundaries in any direction.
Returns
-------
d : an array the same shape as phi
contains the signed distance from the zero contour (zero level set)
of phi to each point in the array. The sign is specified by the sign
of phi at the given point.
"""
phi, dx, flag, ext_mask, periodic = \
pre_process_args(phi, dx, narrow, periodic)
d = cFastMarcher(phi, dx, flag, None, ext_mask,
int(self_test), DISTANCE, order, narrow, periodic)
d = post_process_result(d)
return d
[docs]def travel_time(phi, speed, dx=1.0, self_test=False, order=2,
narrow=0.0, periodic=False):
"""Return the travel from the zero contour of the array phi given the
scalar velocity field speed.
Parameters
----------
phi : array-like
the zero contour of this array is the boundary location for
the travel time calculation. Phi can of 1,2,3 or higher
dimension and can be a masked array.
speed : array-like, the same shape as phi
contains the speed of interface propagation at each point
in the domain.
dx : float or an array-like of len phi.ndim, optional
the cell length in each dimension.
self_test : bool, optional
if True consistency checks are made on the binary min
heap during the calculation. This is used in testing and
results in a slower calculation.
order : int, optional
order of computational stencil to use in updating points during
the fast marching method. Must be 1 or 2, the default is 2.
narrow : float, optional
narrow band half-width. If this optional argument is
specified the marching algorithm is limited to travel
times within a given value. If far-field points
remain when this condition is met a masked array is
returned. The default value is 0.0 which means no narrow
band limit.
periodic : bool or an array-like of len phi.ndim, optional
specifies whether and in which directions periodic
boundary conditions are used. True sets periodic
boundary conditions in all directions. An array-like
(interpreted as True or False values) specifies the
absence or presence of periodic boundaries in
individual directions. The default value is False,
i.e., no periodic boundaries in any direction.
Returns
-------
t : an array the same shape as phi
contains the travel time from the zero contour (zero level
set) of phi to each point in the array given the scalar
velocity field speed. If the input array speed has values less
than or equal to zero the return value will be a masked array.
"""
phi, dx, flag, ext_mask, periodic \
= pre_process_args(phi, dx, narrow, periodic)
t = cFastMarcher(phi, dx, flag, speed, ext_mask,
int(self_test), TRAVEL_TIME, order, narrow, periodic)
t = post_process_result(t)
return t
[docs]def extension_velocities(phi, speed, dx=1.0, self_test=False, order=2,
ext_mask=None, narrow=0.0, periodic=False):
"""Extend the velocities defined at the zero contour of phi, in the
normal direction, to the rest of the domain. Extend the velocities
such that grad f_ext dot grad d = 0 where where f_ext is the
extension velocity and d is the signed distance function.
Parameters
----------
phi : array-like
the zero contour of this array is the boundary location for
the travel time calculation. Phi can of 1,2,3 or higher
dimension and can be a masked array.
speed : array-like, the same shape as phi
contains the speed of interface propagation at each point
in the domain.
dx : float or an array-like of len phi.ndim, optional
the cell length in each dimension.
self_test : bool, optional
if True consistency checks are made on the binary min
heap during the calculation. This is used in testing and
results in a slower calculation.
order : int, optional
order of computational stencil to use in updating points during
the fast marching method. Must be 1 or 2, the default is 2.
ext_mask : array-like, the same shape as phi, optional
enables initial front values to be eliminated when
calculating the value at the interface before the
values are extended away from the interface.
narrow : float, optional
narrow band half-width. If this optional argument is
specified the marching algorithm is limited to within a
given narrow band. If far-field points remain when this
condition is met a masked arrays are returned. The default
value is 0.0 which means no narrow band limit.
periodic : bool or an array-like of len phi.ndim, optional
specifies whether and in which directions periodic
boundary conditions are used. True sets periodic
boundary conditions in all directions. An array-like
(interpreted as True or False values) specifies the
absence or presence of periodic boundaries in
individual directions. The default value is False,
i.e., no periodic boundaries in any direction.
Returns
-------
(d, f_ext) : tuple
a tuple containing the signed distance function d and the
extension velocities f_ext.
"""
phi, dx, flag, ext_mask, periodic = \
pre_process_args(phi, dx, narrow, periodic, ext_mask)
distance, f_ext = cFastMarcher(phi, dx, flag, speed, ext_mask,
int(self_test), EXTENSION_VELOCITY,
order, narrow, periodic)
distance = post_process_result(distance)
f_ext = post_process_result(f_ext)
return distance, f_ext
```