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Integrating a single image (numbered 0?) fails #1128

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graeme-winter opened this issue Feb 3, 2020 · 2 comments
Closed

Integrating a single image (numbered 0?) fails #1128

graeme-winter opened this issue Feb 3, 2020 · 2 comments

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@graeme-winter
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dials.import th_8_2_0000.cbf ; dials.find_spots imported.expt ; dials.index imported.expt strong.refl ; dials.integrate indexed*

=>

********************************************************************************
Warning: 9 reference spots were not matched to predictions
********************************************************************************

Using 388 / 391 reflections for sigma calculation
Calculating E.S.D Beam Divergence.
Calculating E.S.D Reflecting Range (mosaicity).
Traceback (most recent call last):
  File "/Users/graeme/svn/cctbx/build/../modules/dials/command_line/integrate.py", line 665, in <module>
    script.run()
  File "/Users/graeme/svn/cctbx/build/../modules/dials/command_line/integrate.py", line 334, in run
    experiments = ProfileModelFactory.create(params, experiments, reference)
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/factory.py", line 56, in create
    expr.scan,
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/gaussian_rs/model.py", line 228, in create
    params, reflections, crystal, beam, detector, goniometer, scan, profile
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/gaussian_rs/model.py", line 397, in create_from_reflections
    centroid_definition=params.gaussian_rs.centroid_definition,
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/gaussian_rs/calculator.py", line 579, in __init__
    algorithm=algorithm,
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/gaussian_rs/calculator.py", line 491, in __init__
    crystal, beam, detector, goniometer, scan, reflections
  File "/Users/graeme/svn/cctbx/modules/dials/algorithms/profile_model/gaussian_rs/calculator.py", line 330, in __init__
    "Something went wrong. Zero pixels selected for estimation of profile parameters."
RuntimeError: Please report this error to dials-support@lists.sourceforge.net: Something went wrong. Zero pixels selected for estimation of profile parameters.
@graeme-winter
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Yes, it does not work when image is numbered 0 🙄 - the same image numbered 1 works fine.

@graeme-winter
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Turns out the mask values are all invalid? 🤔

Anthchirp pushed a commit that referenced this issue Feb 4, 2020
@graeme-winter @Anthchirp
Use signed int here
f6f3e7d 
Fixes #1128

The type matters here - if z0 is -ve and z == 0 it unrolled to 1.84467e19
which made for some very weird behaviour (all reflections masked as overlaps)
@Anthchirp Anthchirp mentioned this issue Feb 5, 2020
Merged
Anthchirp added a commit that referenced this issue Feb 10, 2020
@Anthchirp
DIALS 2.1.3
2af47a5 
* 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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@graeme-winter