def run(self, args=None):
# Parse the command line
params, options = self.parser.parse_args(args, show_diff_phil=True)
if not params.rs_mapper.map_file:
raise RuntimeError("Please specify output map file (map_file=)")
else:
self.map_file = params.rs_mapper.map_file
# Ensure we have either a data block or an experiment list
self.experiments = flatten_experiments(params.input.experiments)
if len(self.experiments) != 1:
self.parser.print_help()
print("Please pass either an experiment list\n")
return
self.reverse_phi = params.rs_mapper.reverse_phi
self.grid_size = params.rs_mapper.grid_size
self.max_resolution = params.rs_mapper.max_resolution
self.ignore_mask = params.rs_mapper.ignore_mask
self.grid = flex.double(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0
)
self.counts = flex.int(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0
)
for experiment in self.experiments:
self.process_imageset(experiment.imageset)
recviewer.normalize_voxels(self.grid, self.counts)
# Let's use 1/(100A) as the unit so that the absolute numbers in the
# "cell dimensions" field of the ccp4 map are typical for normal
# MX maps. The values in 1/A would give the "cell dimensions" around
# or below 1 and some MX programs would not handle it well.
box_size = 100 * 2.0 / self.max_resolution
uc = uctbx.unit_cell((box_size, box_size, box_size, 90, 90, 90))
ccp4_map.write_ccp4_map(
self.map_file,
uc,
sgtbx.space_group("P1"),
(0, 0, 0),
self.grid.all(),
self.grid,
flex.std_string(["cctbx.miller.fft_map"]),
)
def run(self):
from dials.util.options import flatten_datablocks
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=True)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
elif len(datablocks) != 1:
raise RuntimeError('only 1 datablock can be processed at a time')
if not params.rs_mapper.map_file:
raise RuntimeError('Please specify output map file (map_file=)')
else:
self.map_file = params.rs_mapper.map_file
self.datablocks = flatten_datablocks(params.input.datablock)
if len(self.datablocks) == 0:
self.parser.print_help()
return
self.reverse_phi = params.rs_mapper.reverse_phi
self.grid_size = params.rs_mapper.grid_size
self.max_resolution = params.rs_mapper.max_resolution
self.grid = flex.double(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
self.cnts = flex.int(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
for datablock in self.datablocks:
for imageset in datablock.extract_imagesets():
self.process_imageset(imageset)
recviewer.normalize_voxels(self.grid, self.cnts)
# Let's use 1/(100A) as the unit so that the absolute numbers in the
# "cell dimensions" field of the ccp4 map are typical for normal
# MX maps. The values in 1/A would give the "cell dimensions" around
# or below 1 and some MX programs would not handle it well.
box_size = 100 * 2.0 / self.max_resolution
uc = uctbx.unit_cell((box_size, box_size, box_size, 90, 90, 90))
ccp4_map.write_ccp4_map(self.map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), self.grid.all(), self.grid,
flex.std_string(["cctbx.miller.fft_map"]))
def run(self):
from dials.util.command_line import Command
from dials.util.options import flatten_datablocks
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=True)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
elif len(datablocks) != 1:
raise RuntimeError("only 1 datablock can be processed at a time")
if not params.rs_mapper.map_file:
raise RuntimeError("Please specify output map file (map_file=)")
else:
self.map_file = params.rs_mapper.map_file
self.datablocks = flatten_datablocks(params.input.datablock)
if len(self.datablocks) == 0:
self.parser.print_help()
return
self.reverse_phi = params.rs_mapper.reverse_phi
self.grid_size = params.rs_mapper.grid_size
self.max_resolution = params.rs_mapper.max_resolution
self.grid = flex.double(flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
self.cnts = flex.int(flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
for datablock in self.datablocks:
for imageset in datablock.extract_imagesets():
self.process_imageset(imageset)
recviewer.normalize_voxels(self.grid, self.cnts)
uc = uctbx.unit_cell((self.grid_size, self.grid_size, self.grid_size, 90, 90, 90))
ccp4_map.write_ccp4_map(
self.map_file,
uc,
sgtbx.space_group("P1"),
(0, 0, 0),
self.grid.all(),
self.grid,
flex.std_string(["cctbx.miller.fft_map"]),
)
def run(self):
from dials.util.command_line import Command
from dials.util.options import flatten_datablocks
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=True)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
elif len(datablocks) != 1:
raise RuntimeError('only 1 datablock can be processed at a time')
if not params.rs_mapper.map_file:
raise RuntimeError('Please specify output map file (map_file=)')
else:
self.map_file = params.rs_mapper.map_file
self.datablocks = flatten_datablocks(params.input.datablock)
if len(self.datablocks) == 0:
self.parser.print_help()
return
self.reverse_phi = params.rs_mapper.reverse_phi
self.grid_size = params.rs_mapper.grid_size
self.max_resolution = params.rs_mapper.max_resolution
self.grid = flex.double(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
self.cnts = flex.int(
flex.grid(self.grid_size, self.grid_size, self.grid_size), 0)
for datablock in self.datablocks:
for imageset in datablock.extract_imagesets():
self.process_imageset(imageset)
recviewer.normalize_voxels(self.grid, self.cnts)
uc = uctbx.unit_cell(
(self.grid_size, self.grid_size, self.grid_size, 90, 90, 90))
ccp4_map.write_ccp4_map(self.map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), self.grid.all(), self.grid,
flex.std_string(["cctbx.miller.fft_map"]))