dials.import_xds needs a better interface and documentation

[dagewa]

A user is having trouble with this. I looked, and now I am having trouble with it.

The documentation is minimal, consisting of a single usage string (or a "usage: usage:" string? So helpful, it was named twice):

usage: usage: dials.import_xds [options] (SPOT.XDS|INTEGRATE.HKL)

Things that work

• dials.import_xds $(dials.data get -q centroid_test_data) - creates xds_models.expt from INTEGRATE.HKL
• dials.import_xds $(dials.data get -q centroid_test_data) xds_file=INTEGRATE.HKL - creates xds_models.expt from INTEGRATE.HKL
• dials.import_xds $(dials.data get -q centroid_test_data)/SPOT.XDS method=reflections - creates spot_xds.refl from SPOT.XDS

Things that fail with tracebacks

• dials.import_xds $(dials.data get -q centroid_test_data) method=reflections
• dials.import_xds $(dials.data get -q centroid_test_data) xds_file=SPOT.XDS
• dials.import_xds $(dials.data get -q centroid_test_data)/SPOT.XDS
• ...

[dagewa]

BTW the user reports that doing things the other way round - that is spot-finding and indexing in DIALS, then exporting to XDS - works very well and has been helpful to work around dials.integrate memory errors...

[stale]

This issue has been automatically marked as stale because it has not had recent activity. The label will be removed automatically if any activity occurs. Thank you for your contributions.

[graeme-winter]

I also find this annoying, as noted I made a duplicte issue

[erikssod]

I had a play with this, and I could get the following to work:

$ dials.data get -q centroid_test_data
$ cd path/centroid_test_data
$ centroid_test_data]$ dials.import_xds .
--------------------------------------------------------------------------------
Read 1 experiments from ./INTEGRATE.HKL
--------------------------------------------------------------------------------
Experiment 0
  format: <class 'dxtbx.format.Format.Format'>
  type: <class 'dxtbx_imageset_ext.ImageSequence'>
  num images: 900
--------------------------------------------------------------------------------
Writing experiments to xds_models.expt

$ centroid_test_data]$ dials.import_xds INTEGRATE.HKL xds_models.expt method=reflections
The following parameters have been modified:

input {
  method = experiment *reflections
}

Read 174911 reflections from INTEGRATE.HKL file............................1.64s
Reindex matrix:
1 0 0
0 1 0
0 0 1
Reindexed 174911 reflections...............................................0.01s
Created table with 174911 reflections......................................0.18s
Saved reflection table to integrate_hkl.refl...............................0.04s

I had a look at why this assertion failed:
File "/usr/local/dials-v3-18-0/build/../modules/dials/src/dials/command_line/import_xds.py", line 448
And spotted that the importer expects an experiment arg as well as the INTEGRATE.HKL file.

Things still break when I try to do the same with master files; fist because of pathing issues, and if I force the expected path to exist, things still break with the reindex matrix.

So, progress?

--
edit:
I'm on
DIALS 3.18.0-gbecf27540-release
Python 3.10.13