def __init__(
self,
intensities,
anomalous=False,
n_resolution_bins=20,
xtriage_analyses=None,
run_xtriage_analysis=True,
):
self.n_bins = n_resolution_bins
self._xanalysis = xtriage_analyses
if anomalous:
intensities = intensities.as_anomalous_array()
intensities.setup_binner(n_bins=self.n_bins)
merged = intensities.merge_equivalents()
self.binner = intensities.binner()
self.merged_intensities = merged.array()
self.multiplicities = merged.redundancies().complete_array(
new_data_value=0)
if not self._xanalysis and run_xtriage_analysis:
# imports needed here or won't work, unsure why.
from mmtbx.scaling.xtriage import xtriage_analyses
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=intensities,
text_out="silent",
params=xtriage_params,
)
self._xanalysis = xanalysis
def xtriage_report(self):
xtriage_success = []
xtriage_warnings = []
xtriage_danger = []
s = StringIO()
pout = printed_output(out=s)
from mmtbx.scaling.xtriage import xtriage_analyses
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=self.intensities,
text_out=pout,
params=xtriage_params,
)
if self.report_dir is not None:
with open(os.path.join(self.report_dir, "xtriage.log"), "wb") as f:
f.write(s.getvalue())
xia2.Handlers.Files.FileHandler.record_log_file(
"Xtriage", os.path.join(self.report_dir, "xtriage.log"))
xs = StringIO()
xout = xtriage_output(xs)
xanalysis.show(out=xout)
xout.flush()
sub_header_to_out = xout._sub_header_to_out
issues = xanalysis.summarize_issues()
# issues.show()
for level, text, sub_header in issues._issues:
summary = sub_header_to_out.get(sub_header, StringIO()).getvalue()
d = {
"level": level,
"text": text,
"summary": summary,
"header": sub_header
}
if level == 0:
xtriage_success.append(d)
elif level == 1:
xtriage_warnings.append(d)
elif level == 2:
xtriage_danger.append(d)
self._xanalysis = xanalysis
return xtriage_success, xtriage_warnings, xtriage_danger
def xtriage_report(self):
xtriage_success = []
xtriage_warnings = []
xtriage_danger = []
s = StringIO()
pout = printed_output(out=s)
from mmtbx.scaling.xtriage import xtriage_analyses
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=self.intensities,
text_out=pout,
params=xtriage_params,
)
with open(os.path.join(self.report_dir, 'xtriage.log'), 'wb') as f:
f.write(s.getvalue())
xia2.Handlers.Files.FileHandler.record_log_file(
'Xtriage', os.path.join(self.report_dir, 'xtriage.log'))
xs = StringIO()
xout = xtriage_output(xs)
xanalysis.show(out=xout)
xout.flush()
sub_header_to_out = xout._sub_header_to_out
issues = xanalysis.summarize_issues()
#issues.show()
for level, text, sub_header in issues._issues:
summary = sub_header_to_out.get(sub_header, StringIO()).getvalue()
summary = summary.replace('<', '<').replace('>', '>')
d = {
'level': level,
'text': text,
'summary': summary,
'header': sub_header,
}
if level == 0: xtriage_success.append(d)
elif level == 1: xtriage_warnings.append(d)
elif level == 2: xtriage_danger.append(d)
self._xanalysis = xanalysis
return xtriage_success, xtriage_warnings, xtriage_danger
def __init__(
self,
intensities,
anomalous=False,
n_resolution_bins=20,
xtriage_analyses=None,
run_xtriage_analysis=True,
):
self.n_bins = n_resolution_bins
self._xanalysis = xtriage_analyses
if anomalous:
intensities = intensities.as_anomalous_array()
intensities.setup_binner(n_bins=self.n_bins)
merged = intensities.merge_equivalents()
self.binner = intensities.binner()
self.merged_intensities = merged.array()
self.multiplicities = merged.redundancies().complete_array(
new_data_value=0)
intensities.setup_binner_d_star_sq_step(auto_binning=True)
self.wilson_plot_result = intensities.wilson_plot(use_binning=True)
mr = matthews_rupp(intensities.crystal_symmetry(), out=StringIO())
self.n_residues = mr.n_residues
if not self._xanalysis and run_xtriage_analysis:
# imports needed here or won't work, unsure why.
from mmtbx.scaling.xtriage import master_params as xtriage_master_params
from mmtbx.scaling.xtriage import xtriage_analyses
xtriage_params = xtriage_master_params.fetch(sources=[]).extract()
xtriage_params.scaling.input.xray_data.skip_sanity_checks = True
try:
self._xanalysis = xtriage_analyses(
miller_obs=self.merged_intensities,
unmerged_obs=intensities,
text_out="silent",
params=xtriage_params,
)
except RuntimeError:
logger.warning("Xtriage analysis failed.", exc_info=True)
self._xanalysis = None