def __init__(self, boundary_radius=None, map_manager=None):
'''
Create a mask (map object) with values of 1 except at the map boundaries
This will not be a soft mask. To make it a soft mask, follow this with
soft_mask(soft_mask_radius = soft_mask_radius)
Parameters are:
boundary_radius: radius for masking
map_manager: source of information for n_real and crystal_symmetryi
. origin (0, 0, 0)
'''
assert boundary_radius is not None
assert (map_manager is not None)
n_real = map_manager.map_data().all()
self._crystal_symmetry = map_manager.crystal_symmetry()
from cctbx.maptbx.segment_and_split_map import get_zero_boundary_map
self._mask = get_zero_boundary_map(
map_data=map_manager.map_data(),
crystal_symmetry=self._crystal_symmetry,
radius=boundary_radius)
# Set up map_manager with this mask
self._map_manager = map_manager.customized_copy(map_data=self._mask)
self._map_manager.set_is_mask(True)
# Initialize soft mask
self._is_soft_mask = False
self._is_soft_mask_around_edges = False
def soft_mask_around_edges(self,
resolution = None,
soft_mask_radius = None, ):
'''
Create a new soft mask around the edges of box
Parameters:
resolution: Resolution to be used in smoothing
soft_mask_radius: Distance over which the edge mask affects the map
'''
# Checks:
assert resolution is not None
if soft_mask_radius is None:
soft_mask_radius = resolution
assert not self.is_soft_mask_around_edges() # do not do it twice
from cctbx.maptbx.segment_and_split_map import get_zero_boundary_map, \
smooth_mask_data
zero_boundary_map = get_zero_boundary_map(
map_data = self._map_manager.map_data(),
crystal_symmetry = self.box_crystal_symmetry,
radius = soft_mask_radius)
original_mask_data = zero_boundary_map.deep_copy()
self._mask= smooth_mask_data(mask_data = zero_boundary_map,
crystal_symmetry = self.box_crystal_symmetry,
rad_smooth = soft_mask_radius)
self._is_soft_mask_around_edges = True