Repository : ssh://g18-sc-serv-04.diamond.ac.uk/dials
On branch : master
>---------------------------------------------------------------
commit 821cc450e40f4518e728537e643e957e2d0e2cd6
Author: dgwaterman <[log in to unmask]>
Date: Wed Jul 25 15:30:35 2018 +0100
Merge relevant squashed commits from trim-scan-edge-centroids branch.
This adds a new option to refinement, default trim_scan_edges=0.0,
which removes centroids within this angular width in degrees from
the edges of the scan before refinement. Tests in #457 show that
this might not improve results for processing small wedge datasets,
so the default behaviour is left unchanged.
>---------------------------------------------------------------
821cc450e40f4518e728537e643e957e2d0e2cd6
algorithms/refinement/refiner.py | 11 +++++++++
algorithms/refinement/reflection_manager.py | 35 ++++++++++++++++++++++++-----
2 files changed, 40 insertions(+), 6 deletions(-)
diff --git a/algorithms/refinement/refiner.py b/algorithms/refinement/refiner.py
index 06819de2..5449786a 100644
--- a/algorithms/refinement/refiner.py
+++ b/algorithms/refinement/refiner.py
@@ -390,6 +390,16 @@
.type = float(value_min = 0)
.expert_level = 1
+ trim_scan_edges = 0.0
+ .help = "Reflections within this value in degrees from the centre of the"
+ "first or last image of the scan will be removed before"
+ "refinement, unless doing so would result in too few remaining"
+ "reflections. Reflections that are truncated at the scan edges"
+ "have poorly-determined centroids and can bias the refined model"
+ "if they are included."
+ .type = float(value_min=0,value_max=1)
+ .expert_level = 1
+
block_width = 1.0
.help = "Width of a reflection 'block' (in degrees) determining how fine-"
"grained the model used for scan-varying prediction during"
@@ -1735,6 +1745,7 @@ def config_refman(params, reflections, experiments, do_stills, verbosity):
max_sample_size = options.maximum_sample_size,
min_sample_size = options.minimum_sample_size,
close_to_spindle_cutoff=options.close_to_spindle_cutoff,
+ trim_scan_edges=options.trim_scan_edges,
outlier_detector=outlier_detector,
weighting_strategy_override=weighting_strategy,
verbosity=verbosity)
diff --git a/algorithms/refinement/reflection_manager.py b/algorithms/refinement/reflection_manager.py
index e7675258..1a928979 100644
--- a/algorithms/refinement/reflection_manager.py
+++ b/algorithms/refinement/reflection_manager.py
@@ -159,6 +159,7 @@ def __init__(self, reflections,
max_sample_size=None,
min_sample_size=0,
close_to_spindle_cutoff=0.02,
+ trim_scan_edges=0.0,
outlier_detector=None,
weighting_strategy_override=None,
verbosity=0):
@@ -200,11 +201,12 @@ def __init__(self, reflections,
break
# set up the reflection inclusion criteria
- self._close_to_spindle_cutoff = close_to_spindle_cutoff #too close to spindle
- self._outlier_detector = outlier_detector #for outlier rejection
- self._nref_per_degree = nref_per_degree #random subsets
- self._max_sample_size = max_sample_size #sample size ceiling
- self._min_sample_size = min_sample_size #sample size floor
+ self._close_to_spindle_cutoff = close_to_spindle_cutoff # close to spindle
+ self._trim_scan_edges = DEG2RAD * trim_scan_edges # close to the scan edge
+ self._outlier_detector = outlier_detector # for outlier rejection
+ self._nref_per_degree = nref_per_degree # random subsets
+ self._max_sample_size = max_sample_size # sample size ceiling
+ self._min_sample_size = min_sample_size # sample size floor
# exclude reflections that fail some inclusion criteria
refs_to_keep = self._id_refs_to_keep(reflections)
@@ -350,8 +352,29 @@ def _id_refs_to_keep(self, obs_data):
raise Sorry("Experiment id {0} contains no reflections with valid "
"scan angles".format(iexp))
- # combine tests
+ # combine tests so far
to_update = passed1 & passed2
+
+ # third test: reject reflections close to the centres of the first and
+ # last images in the scan
+ if self._trim_scan_edges > 0.0:
+ edge1, edge2 = [e + 0.5 for e in exp.scan.get_image_range()]
+ edge1 = exp.scan.get_angle_from_image_index(edge1, deg=False)
+ edge1 += (self._trim_scan_edges)
+ edge2 = exp.scan.get_angle_from_image_index(edge2, deg=False)
+ edge2 -= (self._trim_scan_edges)
+ passed3 = ((edge1 <= phi) & (phi <= edge2))
+
+ # combine the last test only if there would be a reasonable number of
+ # reflections left for refinement
+ tmp = to_update
+ to_update = to_update & passed3
+ if to_update.count(True) < 40:
+ logger.warning("Too few reflections to trim centroids from the scan "
+ "edges. Resetting trim_scan_edges=0.0")
+ to_update = tmp
+
+ # make selection
to_keep.set_selected(sel, to_update)
inc = inc.select(to_keep)
########################################################################
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