<commit_before>#!/usr/bin/env python
#
# dials.command_line.check_indexing_symmetry.py
#
#  Copyright (C) 2015 Diamond Light Source
#
#  Author: <NAME>
#
#  This code is distributed under the BSD license, a copy of which is
#  included in the root directory of this package.

from __future__ import division

from libtbx.phil import command_line
import iotbx.phil
from cctbx import sgtbx
from dials.util.options import OptionParser
from dials.util.options import flatten_reflections, flatten_experiments

help_message = '''

This program can be used to (i) generate the symmetry from the experiment
and apply to the input reflections, and (ii) for each symop for that symmetry
attempt to calculate the CC on that operation within the strong spot list.

  dials.check_indexing_symmetry experiment.json indexed.pickle \
    [d_min=3.0] [d_max=10.0]

'''

phil_scope = iotbx.phil.parse("""
d_min = 0
  .type = float
  .help = "High resolution limit to use for analysis"
d_max = 0
  .type = float
  .help = "Low resolution limit to use for analysis"
symop_threshold = 0
  .type = float
  .help = "Threshold above which we consider a symmetry operator true."
grid_search_scope = 0<commit_msg>update help for dials.check_indexing_symmetry: closes #5<commit_after>#!/usr/bin/env python
#
# dials.command_line.check_indexing_symmetry.py
#
#  Copyright (C) 2015 Diamond Light Source
#
#  Author: <NAME>
#
#  This code is distributed under the BSD license, a copy of which is
#  included in the root directory of this package.

from __future__ import division

from libtbx.phil import command_line
import iotbx.phil
from cctbx import sgtbx
from dials.util.options import OptionParser
from dials.util.options import flatten_reflections, flatten_experiments

help_message = '''

This program can be used to analyse the correlation coefficients between
reflections related by the symmetry operators belonging to the space group of
the input experiment.json file. It can also check for misindexing of
the diffraction pattern, possibly as a result of an incorrect beam centre.

Examples::

  dials.check_indexing_symmetry experiment.json indexed.pickle \\
    grid_search_scope=1 symop_threshold=0.7

'''

phil_scope = iotbx.phil.parse("""
d_min = 0
  .type = float
  .help = "High resolution limit to use for analysis"
d_max = 0
  .type = float
  .help = "Low resolution limit to use for analysis"
symop_threshold = 0
  .type = float
  .help = "Threshold above which we consider a symmetry operator true."
grid_search_scope = 0
{'fraction_non_alphanumeric': 0.07043374452845205, 'fraction_numerical': 0.009948269001193792, 'mean_word_length': 4.406451612903226, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '236436', 'n_tokens_mistral': 795, 'n_tokens_neox': 757, 'n_words': 297}