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Exploit improved CCTBX 'counting_sorted' binning algorithm #1130

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merged 5 commits into from
Feb 5, 2020
Merged

Exploit improved CCTBX 'counting_sorted' binning algorithm #1130

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4f54b2b
New optional parameter reflections_per_bin in resolutionizer
rjgildea Jan 23, 2020
4a8d2ac
Better error handling for small n_ref
rjgildea Jan 28, 2020
56e67b4
Add a newsfragment
benjaminhwilliams Feb 3, 2020
d81be1f
Print more meaningful output if σ(CC) is undefined
benjaminhwilliams Feb 4, 2020
45f1565
Unicode makes our Python 2 build sad
benjaminhwilliams Feb 5, 2020
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17 changes: 13 additions & 4 deletions algorithms/symmetry/laue_group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,10 +131,14 @@ def _estimate_cc_sig_fac(self):
max_n_group = int(min(n_pairs / min_num_groups, 200)) # maximum number in group
min_n_group = int(min(5, max_n_group)) # minimum number in group

if (max_n_group - min_n_group) < 4:
self.cc_sig_fac = 0
return

mean_ccs = flex.double()
rms_ccs = flex.double()
ns = flex.double()
for n in range(min_n_group, max_n_group):
for n in range(min_n_group, max_n_group + 1):
ns.append(n)
ccs = flex.double()
for i in range(200):
Expand All @@ -149,8 +153,10 @@ def _estimate_cc_sig_fac(self):
y = rms_ccs
fit = flex.linear_regression(x, y)

assert fit.is_well_defined()
self.cc_sig_fac = fit.slope()
if fit.is_well_defined():
self.cc_sig_fac = fit.slope()
else:
self.cc_sig_fac = 0

def _estimate_cc_true(self):

Expand Down Expand Up @@ -262,7 +268,10 @@ def __str__(self):
"Estimated expectation value of true correlation coefficient E(CC) = %.3f"
% self.E_cc_true
)
output.append("Estimated sd(CC) = %.3f / sqrt(N)" % self.cc_sig_fac)
if self.cc_sig_fac:
output.append("Estimated sd(CC) = %.3f / sqrt(N)" % self.cc_sig_fac)
else:
output.append("Too few reflections to estimate sd(CC).")
output.append(
"Estimated E(CC) of true correlation coefficient from identity = %.3f"
% self.cc_true
Expand Down
1 change: 1 addition & 0 deletions newsfragments/1130.bugfix
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Fix an issue (#1097) whereby aggregating small numbers of reflections into resolution bins could sometimes result in empty bins and consequent errors.
6 changes: 5 additions & 1 deletion util/resolutionizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,9 +264,12 @@ def miller_array_from_mtz(unmerged_mtz, params):
.expert_level = 2
nbins = 100
.type = int
.help = "Number of resolution bins to use for estimation of resolution limit."
.help = "Maximum number of resolution bins to use for estimation of resolution limit."
.short_caption = "Number of resolution bins."
.expert_level = 1
reflections_per_bin = 10
.type = int
.help = "Minimum number of reflections per bin."
binning_method = *counting_sorted volume
.type = choice
.help = "Use equal-volume bins or bins with approximately equal numbers of reflections per bin."
Expand Down Expand Up @@ -374,6 +377,7 @@ def __init__(self, i_obs, params, batches=None, reference=None):
self._merging_statistics = iotbx.merging_statistics.dataset_statistics(
i_obs=i_obs,
n_bins=self._params.nbins,
reflections_per_bin=self._params.reflections_per_bin,
cc_one_half_significance_level=self._params.cc_half_significance_level,
cc_one_half_method=self._params.cc_half_method,
binning_method=self._params.binning_method,
Expand Down