def apply_to_map(self, map_manager):
assert map_manager is not None
# Apply to a map_manager that is similar to the one used to generate
# this around_model object
assert map_manager.crystal_symmetry().is_similar_symmetry(
self.original_crystal_symmetry)
ma1 = map_manager.map_data().accessor()
ma2 = self.original_accessor
assert ma1.all() == ma2.all()
assert ma1.origin() == ma2.origin()
assert ma1.focus() == ma2.focus()
map_data = map_manager.map_data()
# Check if map is all valid
bounds_info = get_bounds_of_valid_region(
map_data=map_data,
gridding_first=self.gridding_first,
gridding_last=self.gridding_last)
if self.wrapping or bounds_info.inside_allowed_bounds:
# Just copy everything
map_box = maptbx.copy(map_data, self.gridding_first,
self.gridding_last)
# Note: map_box gridding is self.gridding_first to self.gridding_last
else: # Need to copy and then zero outside of defined region
map_box = copy_and_zero_map_outside_bounds(map_data=map_data,
bounds_info=bounds_info)
# Now reshape map_box to put origin at (0,0,0)
map_box.reshape(flex.grid(self.box_all))
# Create new map_manager object:
# Use original values for:
# unit_cell_grid (gridding of original full unit cell)
# unit_cell_crystal_symmetry (symmetry of original full unit cell)
# input_file_name
# Use new (boxed) values for:
# map_data
# crystal_symmetry (symmetry of the part of the map that is present)
# Update:
# origin_shift_grid_units (position in the original map of the
# (0,0,0) grid point in map_box)
# labels (add label specifying boxing operation)
#
# New origin_shift_grid_units:
origin_shift_grid_units = [
self.gridding_first[i] + map_manager.origin_shift_grid_units[i]
for i in range(3)
]
# New labels:
new_label = "Boxed %s to %s %s" % (str(tuple(
self.gridding_first)), str(tuple(
self.gridding_last)), self.basis_for_boxing_string)
# Set up new map_manager.
# NOTE: origin_shift_grid_units is required as bounds have changed
new_map_manager = map_manager.customized_copy(
map_data=map_box, origin_shift_grid_units=origin_shift_grid_units)
# Add the label
new_map_manager.add_label(new_label)
return new_map_manager
def apply_to_map(self, map_manager):
'''
Apply boxing to a map_manager that is similar to the one used to generate
this around_model object
Also apply to its ncs_object, if any
'''
assert isinstance(map_manager, iotbx.map_manager.map_manager)
# This one should just have similar unit_cell_crystal_symmetry
# crystal_symmetry should match self.map_crystal_symmetry_at_initialization
assert map_manager.unit_cell_crystal_symmetry().is_similar_symmetry(
self._map_manager.unit_cell_crystal_symmetry())
assert map_manager.crystal_symmetry().is_similar_symmetry(
self.map_crystal_symmetry_at_initialization)
ma1 = map_manager.map_data().accessor()
ma2 = self.accessor_at_initialization
assert ma1.all() == ma2.all()
assert ma1.origin() == ma2.origin()
assert ma1.focus() == ma2.focus()
map_data = map_manager.map_data()
# Check if map is all valid
bounds_info = get_bounds_of_valid_region(map_data, self.gridding_first,
self.gridding_last)
# Allow override of wrapping
if isinstance(self._force_wrapping, bool):
wrapping = self._force_wrapping
else:
# Get wrapping from map_manager. If it is not defined and
# bounds are outside allowed, try to get the wrapping
wrapping = map_manager.wrapping()
if wrapping or bounds_info.inside_allowed_bounds:
# Just copy everything
map_box = maptbx.copy(map_data, self.gridding_first,
self.gridding_last)
# Note: map_box gridding is self.gridding_first to self.gridding_last
elif not bounds_info.some_valid_points:
# No valid points, Just copy everything and zero
map_box = maptbx.copy(map_data, self.gridding_first,
self.gridding_last)
map_box = map_box * 0.
self._warning_message += "\nWARNING: boxed map is entirely outside map"+\
" and wrapping=%s\n...setting all values to zero" %(wrapping)
else: # Need to copy and then zero outside of defined region
map_box = copy_and_zero_map_outside_bounds(map_data, bounds_info)
self._warning_message += \
"\nWARNING: boxed map goes outside original map"+\
" and wrapping=%s\n...setting unknown values to zero" %(wrapping)
# Now reshape map_box to put origin at (0, 0, 0)
map_box.reshape(flex.grid(self.box_all))
# Create new map_manager object:
# Use original values for:
# unit_cell_grid (gridding of original full unit cell)
# unit_cell_crystal_symmetry (symmetry of original full unit cell)
# input_file_name
# Use new (boxed) values for:
# map_data
# crystal_symmetry (symmetry of the part of the map that is present)
# Update:
# origin_shift_grid_units (position in the original map of the
# (0, 0, 0) grid point in map_box)
# labels (add label specifying boxing operation)
#
# New origin_shift_grid_units:
origin_shift_grid_units = [
self.gridding_first[i] + map_manager.origin_shift_grid_units[i]
for i in range(3)
]
# New labels:
new_label = "Boxed %s to %s %s" % (str(tuple(
self.gridding_first)), str(tuple(
self.gridding_last)), self.basis_for_boxing_string)
# Set up new map_manager. This will contain new data and not overwrite
# original
# NOTE: origin_shift_grid_units is required as bounds have changed
new_map_manager = map_manager.customized_copy(
map_data=map_box, origin_shift_grid_units=origin_shift_grid_units)
if self._force_wrapping:
# Set the wrapping of the new map if it is possible
if (self._force_wrapping and (new_map_manager.is_full_size())) or \
( (not self._force_wrapping) and (not new_map_manager.is_full_size())):
new_map_manager.set_wrapping(self._force_wrapping)
# Add the label
new_map_manager.add_label(new_label)
return new_map_manager