def display_file_info(file_name, parent=None):
from iotbx import reflection_file_editor
from iotbx import file_reader
from iotbx import data_plots
hkl_in = file_reader.any_file(file_name, force_type="hkl")
hkl_in.check_file_type("hkl")
labels = []
tables = []
stats = []
arrays_and_flags = hkl_in.file_server.get_r_free_flags(
file_name=hkl_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True,
)
for array, test_flag_value in arrays_and_flags:
labels.append(array.info().label_string())
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=array, test_flag_value=test_flag_value
)
table = data_plots.table_data(
title="Distribution of R-free test set",
column_labels=["Reflection #", "Fraction counted"],
graph_names=["Fraction free vs. resolution"],
graph_labels=[["Reflection #", "ntest/total"]],
graph_columns=[[0, 1]],
data=[accu.reflection_counts, accu.free_fractions],
)
tables.append(table)
stats.append(
group_args(
n_free=n_free,
n_all=array.indices().size(),
percent_free=n_free / array.indices().size(),
completeness=array.completeness(),
)
)
if len(labels) == 0:
raise Sorry("No recognizable R-free flags found in this file.")
frame = wx.Frame(parent, -1, "R-free flags info", style=wx.DEFAULT_FRAME_STYLE)
szr = wx.BoxSizer(wx.VERTICAL)
frame.SetSizer(szr)
panel = RfreeInspector(frame, -1)
panel.set_data(
file_name=file_name,
labels=labels,
tables=tables,
stats=stats,
flags_and_values=[(a.data(), f) for (a, f) in arrays_and_flags],
)
szr.Add(panel, 1, wx.ALL | wx.EXPAND)
szr.Fit(panel)
frame.Fit()
frame.Show()
def display_file_info(file_name, parent=None):
from iotbx import reflection_file_editor
from iotbx import file_reader
from iotbx import data_plots
hkl_in = file_reader.any_file(file_name, force_type="hkl")
hkl_in.check_file_type("hkl")
labels = []
tables = []
stats = []
arrays_and_flags = hkl_in.file_server.get_r_free_flags(
file_name=hkl_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True)
for array, test_flag_value in arrays_and_flags:
labels.append(array.info().label_string())
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=array, test_flag_value=test_flag_value)
table = data_plots.table_data(
title="Distribution of R-free test set",
column_labels=["Reflection #", "Fraction counted"],
graph_names=["Fraction free vs. resolution"],
graph_labels=[["Reflection #", "ntest/total"]],
graph_columns=[[0, 1]],
data=[accu.reflection_counts, accu.free_fractions])
tables.append(table)
stats.append(
group_args(n_free=n_free,
n_all=array.indices().size(),
percent_free=n_free / array.indices().size(),
completeness=array.completeness()))
if (len(labels) == 0):
raise Sorry("No recognizable R-free flags found in this file.")
frame = wx.Frame(parent,
-1,
"R-free flags info",
style=wx.DEFAULT_FRAME_STYLE)
szr = wx.BoxSizer(wx.VERTICAL)
frame.SetSizer(szr)
panel = RfreeInspector(frame, -1)
panel.set_data(file_name=file_name,
labels=labels,
tables=tables,
stats=stats,
flags_and_values=[(a.data(), f)
for (a, f) in arrays_and_flags])
szr.Add(panel, 1, wx.ALL | wx.EXPAND)
szr.Fit(panel)
frame.Fit()
frame.Show()
def run(args=(), params=None, out=None):
if (out is None):
out = sys.stdout
validate_params(params)
from iotbx import reflection_file_editor
from iotbx import reflection_file_utils
from iotbx import file_reader
data_in = file_reader.any_file(params.import_data.data_file,
force_type="hkl")
data_in.check_file_type("hkl")
miller_arrays = data_in.file_server.miller_arrays
new_arrays = []
labels = ["H","K","L"]
warnings = []
have_r_free = False
for array in miller_arrays :
if (reflection_file_editor.is_rfree_array(array, array.info())):
have_r_free = True
if (params.import_data.flags_file is not None):
raise Sorry("The data file (%s) already contains R-free flags." %
params.import_data.data_file)
if (array.is_xray_reconstructed_amplitude_array()):
if ("F(+)" in labels):
labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"])
else :
labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"])
else :
labels.extend(array.info().labels)
array = array.map_to_asu()
if (not array.is_unique_set_under_symmetry()):
array = array.merge_equivalents().array()
new_arrays.append(array)
complete_set = reflection_file_utils.make_joined_set(
new_arrays).complete_set()
if (not have_r_free):
if (params.import_data.flags_file is not None):
flags_in = file_reader.any_file(params.import_data.flags_file,
force_type="hkl")
flags_in.check_file_type("hkl")
flags_and_values = flags_in.file_server.get_r_free_flags(
file_name=flags_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True)
if (len(flags_and_values) == 0):
raise Sorry("No R-free flags were found in the file %s." %
params.import_data.flags_file)
elif (len(flags_and_values) > 1):
raise Sorry(("Multiple valid sets of R-free flags were found in the "+
"file %s. Please use the reflection file editor to select a "+
"single set of flags.") % params.import_data.flags_file)
old_flags, test_flag_value = flags_and_values[0]
labels.extend(old_flags.info().labels)
old_flags = old_flags.map_to_asu().merge_equivalents().array()
old_flags = old_flags.customized_copy(
data=old_flags.data()==test_flag_value)
missing_set = complete_set.lone_set(old_flags)
n_missing = missing_set.indices().size()
fraction_free = old_flags.data().count(True) / old_flags.data().size()
if (n_missing != 0):
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=old_flags,
test_flag_value=True)
min_bins = int(old_flags.indices().size() * 0.005)
if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins):
if (not params.import_data.ignore_shells):
raise Sorry(("The R-free flags in %s appear to have been "+
"assigned in thin resolution shells. PHENIX is unable to "+
"properly extend flags created in this manner. If you "+
"prefer to ignore this check and want to create new flags using "+
"random assignment, or if you think this message is in error, "+
"you can use the reflection file editor instead. "+
"(To view the distribution of R-free flags, click the "+
"toolbar button \"Other tools\" and select \"Inspect R-free "+
"flags\".)") % params.import_data.flags_file)
else :
print >> out, "WARNING: ignoring thin shells"
if (n_missing <= 20) : # XXX hack
from scitbx.array_family import flex
missing_flags = missing_set.array(data=flex.bool(n_missing, False))
else :
missing_flags = missing_set.generate_r_free_flags(
fraction_free=fraction_free,
max_free=None,
use_lattice_symmetry=True)
new_flags = old_flags.concatenate(other=missing_flags)
else :
new_flags = old_flags
new_arrays.append(new_flags)
mtz_out = new_arrays[0].as_mtz_dataset(
column_root_label="A")
for i, array in enumerate(new_arrays[1:]):
mtz_out.add_miller_array(
miller_array=array,
column_root_label="%s" % string.uppercase[i+1])
mtz_obj = mtz_out.mtz_object()
for i, column in enumerate(mtz_obj.columns()):
column.set_label(labels[i])
if (params.import_data.output_file is None):
base,ext = os.path.splitext(params.import_data.data_file)
params.import_data.output_file = base + "_flags.mtz"
mtz_obj.write(file_name=params.import_data.output_file)
print >> out, "Data and flags written to %s" % params.import_data.output_file
return params.import_data.output_file
def run (args=(), params=None, out=None) :
if (out is None) :
out = sys.stdout
validate_params(params)
from iotbx import reflection_file_editor
from iotbx import reflection_file_utils
from iotbx import file_reader
data_in = file_reader.any_file(params.import_data.data_file,
force_type="hkl")
data_in.check_file_type("hkl")
miller_arrays = data_in.file_server.miller_arrays
new_arrays = []
labels = ["H","K","L"]
warnings = []
have_r_free = False
for array in miller_arrays :
if (reflection_file_editor.is_rfree_array(array, array.info())) :
have_r_free = True
if (params.import_data.flags_file is not None) :
raise Sorry("The data file (%s) already contains R-free flags." %
params.import_data.data_file)
if (array.is_xray_reconstructed_amplitude_array()) :
if ("F(+)" in labels) :
labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"])
else :
labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"])
else :
labels.extend(array.info().labels)
array = array.map_to_asu()
if (not array.is_unique_set_under_symmetry()) :
array = array.merge_equivalents().array()
new_arrays.append(array)
complete_set = reflection_file_utils.make_joined_set(
new_arrays).complete_set()
if (not have_r_free) :
if (params.import_data.flags_file is not None) :
flags_in = file_reader.any_file(params.import_data.flags_file,
force_type="hkl")
flags_in.check_file_type("hkl")
flags_and_values = flags_in.file_server.get_r_free_flags(
file_name=flags_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True)
if (len(flags_and_values) == 0) :
raise Sorry("No R-free flags were found in the file %s." %
params.import_data.flags_file)
elif (len(flags_and_values) > 1) :
raise Sorry(("Multiple valid sets of R-free flags were found in the "+
"file %s. Please use the reflection file editor to select a "+
"single set of flags.") % params.import_data.flags_file)
old_flags, test_flag_value = flags_and_values[0]
labels.extend(old_flags.info().labels)
old_flags = old_flags.map_to_asu().merge_equivalents().array()
old_flags = old_flags.customized_copy(
data=old_flags.data()==test_flag_value)
missing_set = complete_set.lone_set(old_flags)
n_missing = missing_set.indices().size()
fraction_free = old_flags.data().count(True) / old_flags.data().size()
if (n_missing != 0) :
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=old_flags,
test_flag_value=True)
min_bins = int(old_flags.indices().size() * 0.005)
if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins) :
if (not params.import_data.ignore_shells) :
raise Sorry(("The R-free flags in %s appear to have been "+
"assigned in thin resolution shells. PHENIX is unable to "+
"properly extend flags created in this manner. If you "+
"prefer to ignore this check and want to create new flags using "+
"random assignment, or if you think this message is in error, "+
"you can use the reflection file editor instead. "+
"(To view the distribution of R-free flags, click the "+
"toolbar button \"Other tools\" and select \"Inspect R-free "+
"flags\".)") % params.import_data.flags_file)
else :
print >> out, "WARNING: ignoring thin shells"
if (n_missing <= 20) : # XXX hack
from scitbx.array_family import flex
missing_flags = missing_set.array(data=flex.bool(n_missing, False))
else :
missing_flags = missing_set.generate_r_free_flags(
fraction_free=fraction_free,
max_free=None,
use_lattice_symmetry=True)
new_flags = old_flags.concatenate(other=missing_flags)
else :
new_flags = old_flags
new_arrays.append(new_flags)
mtz_out = new_arrays[0].as_mtz_dataset(
column_root_label="A")
for i, array in enumerate(new_arrays[1:]) :
mtz_out.add_miller_array(
miller_array=array,
column_root_label="%s" % string.uppercase[i+1])
mtz_obj = mtz_out.mtz_object()
for i, column in enumerate(mtz_obj.columns()) :
column.set_label(labels[i])
if (params.import_data.output_file is None) :
base,ext = os.path.splitext(params.import_data.data_file)
params.import_data.output_file = base + "_flags.mtz"
mtz_obj.write(file_name=params.import_data.output_file)
print >> out, "Data and flags written to %s" % params.import_data.output_file
return params.import_data.output_file
