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dxtbx does not like files named *0000.cbf #133

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Anthchirp opened this issue Jan 28, 2020 · 1 comment
Closed

dxtbx does not like files named *0000.cbf #133

Anthchirp opened this issue Jan 28, 2020 · 1 comment
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@Anthchirp
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$ dials.find_spots 0001.cbf
DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
DIALS 2.1.1-gcdd629a7b-release
(...)
Found 0 strong pixels on image 1
(...)
Saved 0 reflections to strong.refl
Time Taken: 0.740225


$ cp 0001.cbf 0000.cbf


$ dials.find_spots 0000.cbf
DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
DIALS 2.1.1-gcdd629a7b-release
The following parameters have been modified:

input {
  experiments = <image files>
}

Setting spotfinder.filter.min_spot_size=3
Configuring spot finder from input parameters
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------


Finding spots in image 0 to 0...
Traceback (most recent call last):
  File "/dls_sw/apps/dials/dials-v2-1-1/build/../modules/dials/command_line/find_spots.py", line 196, in <module>
    script.run()
  File "/dls_sw/apps/dials/dials-v2-1-1/build/../modules/dials/command_line/find_spots.py", line 128, in run
    reflections = flex.reflection_table.from_observations(experiments, params)
  File "/dls_sw/apps/dials/dials-v2-1-1/modules/dials/array_family/flex.py", line 198, in from_observations
    return find_spots(experiments)
  File "/dls_sw/apps/dials/dials-v2-1-1/modules/dials/algorithms/spot_finding/finder.py", line 764, in __call__
    table, hot_mask = self._find_spots_in_imageset(imageset)
  File "/dls_sw/apps/dials/dials-v2-1-1/modules/dials/algorithms/spot_finding/finder.py", line 870, in _find_spots_in_imageset
    r, h = extract_spots(imageset[j0:j1])
  File "/dls_sw/apps/dials/dials-v2-1-1/modules/dxtbx/imageset.py", line 234, in __getitem__
    return self.partial_set(start - offset, stop - offset)
RuntimeError: Please report this error to [email protected]: dxtbx Internal Error: /dls_sw/apps/dials/dials-v2-1-1/modules/dxtbx/imageset.h(936): DXTBX_ASSERT(index < indices_.size()) failure.
@dagewa
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dagewa commented Jan 28, 2020

I note that the experiment apparently imports just fine and can be passed into dials.show or dials.image_viewer, but not dials.find_spots

@graeme-winter graeme-winter self-assigned this Feb 3, 2020
graeme-winter added a commit that referenced this issue Feb 3, 2020
If we are grabbing a single image respect the offset (i.e. don't just use
len(items) - fixes counting from 0 errors
graeme-winter added a commit to dials/dials that referenced this issue Feb 3, 2020
If shoebox starts at -1 will roll around before converting to float;

for cctbx/dxtbx#133
Anthchirp added a commit to dials/dials that referenced this issue Feb 3, 2020
Anthchirp pushed a commit to dials/dials that referenced this issue Feb 4, 2020
If shoebox starts at -1 will roll around before converting to float;

for cctbx/dxtbx#133
Anthchirp added a commit to dials/dials that referenced this issue Feb 10, 2020
* Make resolution estimation more stable in presence of ice and powder rings and with small molecule data (#1097)
* Fix spot finding and integration of files with index 0 (#1128, cctbx/dxtbx#133)
* Fix cutoff value on recent data files from DLS I03 (cctbx/dxtbx#136)
* Reduce memory usage when writing .refl files (#1115)
* `dials.integrate`: Fix broken memory check in cases of high multiplicity (#1121)
* `dials.symmetry`: Prevent failures when dealing with small numbers of reflections (#1130, cctbx/cctbx_project#435)
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