def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
output = plugin.dataOutput
reference = XSDataResCutoffResult.parseFile(
self.getReferenceDataOutputFile())
EDAssert.strAlmostEqual(output.marshal(), reference.marshal(),
"output looks good")
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
output = plugin.dataOutput
reference = XSDataResCutoffResult.parseFile(self.getReferenceDataOutputFile())
EDAssert.strAlmostEqual(output.marshal(),
reference.marshal(),
"output looks good")
def process(self, _edObject = None):
EDPlugin.process(self)
completeness_cutoff_param = self.dataInput.completeness_cutoff
if completeness_cutoff_param is None:
completeness_cutoff = 80
else:
completeness_cutoff = completeness_cutoff_param.value
isig_cutoff_param = self.dataInput.isig_cutoff
if isig_cutoff_param is None:
isig_cutoff = 3
else:
isig_cutoff = isig_cutoff_param.value
res_override = self.dataInput.res_override
bins = list()
# for the first iteration
# comment from max's code: "less stringent at low res"
local_completeness_cutoff = 70
# declared but not initialized in the perl code
prev_isig = prev_res = 0
# XXX: if res is still not defined at the end it is set to
# detector_max_res, which we should somehow defined (in the
# data model?) and used as the default value before we start
# the processing
for entry in self.dataInput.completeness_entries:
outer_res = entry.outer_res.value
outer_complete = entry.outer_complete.value
outer_rfactor = entry.outer_rfactor.value
outer_isig = entry.outer_isig.value
if outer_complete < local_completeness_cutoff or outer_isig < isig_cutoff or \
(res_override is not None and outer_res < res_override.value):
if outer_complete < completeness_cutoff:
EDVerbose.DEBUG('incomplete data (%s) in this shell' % outer_complete)
res = prev_res
else:
res = _calculate_res_from_bins(prev_isig, prev_res,
outer_isig, outer_res)
bins.append(outer_res)
#NOTE: get out of the loop, see the value of `skip` in
#max's code
break
else:
bins.append(outer_res)
prev_res, prev_isig = outer_res, outer_isig
# Now the implementation of what max does when he encouters
# the total values, which are conveniently already parsed in
# our case
if len(bins) < 2:
EDVerbose.DEBUG("No bins with I/sigma greater than %s" % isig_cutoff)
EDVerbose.DEBUG("""something could be wrong, or the completeness could be too low!
bravais lattice/SG could be incorrect or something more insidious like
incorrect parameters in XDS.INP like distance, X beam, Y beam, etc.
Stopping""")
self.setFailure()
return
if res_override is not None:
res = res_override.value
# remove last bin (see why w/ max)
retbins = [XSDataFloat(x) for x in bins[:-1]]
data_output = XSDataResCutoffResult()
data_output.res = XSDataFloat(res)
data_output.bins = retbins
totals = self.dataInput.total_completeness
data_output.total_complete = totals.outer_complete
data_output.total_rfactor = totals.outer_rfactor
data_output.total_isig = totals.outer_isig
self.dataOutput = data_output
def process(self, _edObject=None):
EDPlugin.process(self)
detector_max_res = self.dataInput.detector_max_res
if detector_max_res is not None:
detector_max_res = detector_max_res.value
completeness_cutoff_param = self.dataInput.completeness_cutoff
if completeness_cutoff_param is None:
completeness_cutoff = 80
else:
completeness_cutoff = completeness_cutoff_param.value
isig_cutoff_param = self.dataInput.isig_cutoff
if isig_cutoff_param is None:
isig_cutoff = 3
else:
isig_cutoff = isig_cutoff_param.value
res_override = self.dataInput.res_override
bins = list()
# for the first iteration
# comment from max's code: "less stringent at low res"
local_completeness_cutoff = 70
# declared but not initialized in the perl code
prev_isig = prev_res = 0
# XXX: if res is still not defined at the end it is set to
# detector_max_res, which we should somehow defined (in the
# data model?) and used as the default value before we start
# the processing
res = detector_max_res
for entry in self.dataInput.completeness_entries:
outer_res = entry.outer_res.value
outer_complete = entry.outer_complete.value
outer_rfactor = entry.outer_rfactor.value
outer_isig = entry.outer_isig.value
if outer_complete < local_completeness_cutoff or outer_isig < isig_cutoff or \
(res_override is not None and outer_res < res_override.value):
if outer_complete < completeness_cutoff:
EDVerbose.DEBUG('incomplete data (%s) in this shell' %
outer_complete)
res = prev_res
else:
res = _calculate_res_from_bins(prev_isig, prev_res,
outer_isig, outer_res,
isig_cutoff)
bins.append(outer_res)
#NOTE: get out of the loop, see the value of `skip` in
#max's code
break
else:
bins.append(outer_res)
prev_res, prev_isig = outer_res, outer_isig
# Now the implementation of what max does when he encouters
# the total values, which are conveniently already parsed in
# our case
if len(bins) < 2:
EDVerbose.DEBUG("No bins with I/sigma greater than %s" %
isig_cutoff)
EDVerbose.DEBUG(
"""something could be wrong, or the completeness could be too low!
bravais lattice/SG could be incorrect or something more insidious like
incorrect parameters in XDS.INP like distance, X beam, Y beam, etc.
Stopping""")
self.setFailure()
return
if res is None:
res = sorted(bins)[0]
if res_override is not None:
res = res_override.value
# remove last bin (see why w/ max)
retbins = [XSDataFloat(x) for x in bins[:-1]]
data_output = XSDataResCutoffResult()
data_output.res = XSDataFloat(res)
data_output.bins = retbins
totals = self.dataInput.total_completeness
data_output.total_complete = totals.outer_complete
data_output.total_rfactor = totals.outer_rfactor
data_output.total_isig = totals.outer_isig
self.dataOutput = data_output