def OnSaveMaskParams(self, event):
from dials.util.masking import phil_scope
file_name = self.params.output.mask_params
with open(file_name, "w") as f:
print("Saving parameters to %s" % file_name)
phil_scope.fetch_diff(phil_scope.format(self.params.masking)).show(f)
def run(self):
import os
from xia2.Handlers.Streams import Debug
Debug.write("Running dials.generate_mask")
self.clear_command_line()
assert self._params is not None
from dials.util.masking import phil_scope
working_phil = phil_scope.format(self._params)
diff_phil = phil_scope.fetch_diff(source=working_phil)
phil_filename = os.path.join(
self.get_working_directory(), "%s_mask.phil" % self.get_xpid()
)
with open(phil_filename, "wb") as f:
f.write(diff_phil.as_str())
f.write(
os.linesep
) # temporarily required for https://github.com/dials/dials/issues/522
self.add_command_line(
'input.experiments="%s"' % self._input_experiments_filename
)
if self._output_mask_filename is None:
self._output_mask_filename = os.path.join(
self.get_working_directory(), "%s_pixels.mask" % self.get_xpid()
)
if self._output_experiments_filename is None:
self._output_experiments_filename = os.path.join(
self.get_working_directory(), "%s_masked.expt" % self.get_xpid()
)
self.add_command_line('output.mask="%s"' % self._output_mask_filename)
self.add_command_line(
'output.experiments="%s"' % self._output_experiments_filename
)
self.add_command_line(phil_filename)
self.start()
self.close_wait()
self.check_for_errors()
assert os.path.exists(
self._output_mask_filename
), self._output_mask_filename
assert os.path.exists(
self._output_experiments_filename
), self._output_experiments_filename
return self._output_experiments_filename, self._output_mask_filename