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Unit cell tool #1192

Merged
merged 4 commits into from
Mar 24, 2020
Merged

Unit cell tool #1192

merged 4 commits into from
Mar 24, 2020

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dagewa
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@dagewa dagewa commented Mar 11, 2020

Here are a couple of changes to the unit cell tool of dials.image_viewer.

First, I renamed parameters here to be more consistent with other DIALS programs: spacegroupspace_group and unitcellunit_cell. I suspect this tool is not used much here (whereas it may get much more use in cctbx.image_viewer). Therefore I don't think this change affects many users' existing work patterns.

The second change introduces a new parameter, show_hkl. This can be used to filter the displayed rings to show only those corresponding to Miller indices in the supplied list. This is helpful because datasheets for diffraction standards usually list only the strongly diffracting rings: https://www.emsdiasum.com/microscopy/technical/datasheet/80044.aspx

With this change only the desired rings are displayed

dials.image_viewer imported.expt \
  calibrate_unit_cell.unit_cell=4.094,4.094,4.094,90,90,90 \
  calibrate_unit_cell.d_min=0.81 \
  show_hkl=1,1,1 show_hkl=2,0,0 show_hkl=2,2,0 \
  show_hkl=3,1,1 show_hkl=2,2,2 show_hkl=4,0,0 \
  show_hkl=3,3,1 show_hkl=4,2,0 show_hkl=4,2,2

Screenshot from 2020-03-11 15-34-27

which is considerably easier to interpret than viewing all rings up to the specified resolution limit

dials.image_viewer imported.expt \
  calibrate_unit_cell.unit_cell=4.094,4.094,4.094,90,90,90 \
  calibrate_unit_cell.d_min=0.81

Screenshot from 2020-03-11 15-34-31

@dagewa dagewa requested review from phyy-nx and rjgildea March 11, 2020 15:48
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@phyy-nx phyy-nx left a comment

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Yah we use the unit cell tool a lot at xfels to do silver behenate calibration of distance and beam center. However, a while ago I hardcoded the default unit cell parameters to silver behenate so I wouldn't have to type them on the command line :) So renaming these parameters slightly doesn't actually affect us much!

The show hkl list is nice. Thanks.

@dagewa dagewa merged commit 4b705a7 into master Mar 24, 2020
@Anthchirp Anthchirp deleted the unit-cell-tool branch August 30, 2020 22:12
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2 participants