Add probe to phil params and make probe in .expt human readable #654

toastisme · 2023-08-03T13:55:38Z

Adds Probe to phil params in beam.py
Changes the Probe in .expt files to be human readable.
Exposes empty PolychromaticBeam constructor at Python level
Few extra typehints

So now, can do from dxtbx.model.beam import Probe

Note the value is uninitialized!

>>> from dxtbx.model.beam import Beam >>> b=Beam() >>> b.get_probe() dxtbx_model_ext.Probe.xray

Now this works: >>> from dxtbx.model.beam import Beam >>> b=Beam() >>> b.get_probe() dxtbx_model_ext.Probe.xray >>> from dxtbx.model.beam import Probe >>> b.set_probe(Probe.neutron) >>> b.get_probe() dxtbx_model_ext.Probe.neutron

returned for each of the defined probe values

…thod

When setting panels by PHIL, merge multiple definitions first by id. This fixes cctbx#299.

Previously, a size (3,) array would have erroneously converted to a 0x3 length vec3. This is now explicitly forbidden; you must pass at least a (0, 3) multidimensional array. Fixes cctbx#439.

Partial support for Rigaku Oxford Diffraction format images. --------- Co-authored-by: Takanori Nakane <nakane.t@gmail.com> Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>

This was previously done implicitly, but only when dials_regression was present. This makes the test explicit, and works with dials-data (so that it will work on e.g. CI with restricted access to test cases).

Without this, slices sometimes needed to be indexed by their original image index, even inside the slice. The previous workaround in 67aab2 (cctbx#485) for negative offset was reacting to the erroneous behaviour introduced by including batch offsets in imagesequence slicing.

Without this, dxtbx did not work as a subdirectory in a larger CMakeLists project.

The E-32-0017 Eiger moved to P13 on 2021-5-22, where the goniometer axis no longer needs overriding. Check for that date in the MiniCBF, and check for the serial matching the date range. Co-authored-by: Christian Becke <christian.becke@fu-berlin.de> Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>

Add new Beam class "PolychromaticBeam" for polychromatic/multi-wavelength/wide bandpass experiments. --------- Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com> Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>

…anged Probe in .expt files to be human readable.

…ructor at the Python level. Fixed typo in Beam.from_dict.

codecov · 2023-08-03T14:04:51Z

Codecov Report

Merging #654 (dfdbc0a) into 575-beam-model-should-state-probe-type (1625cfa) will decrease coverage by 0.24%.
The diff coverage is 31.02%.

❗ Current head dfdbc0a differs from pull request most recent head 4312daf. Consider uploading reports for the commit 4312daf to get more accurate results

Additional details and impacted files

@@                            Coverage Diff                             @@
##           575-beam-model-should-state-probe-type     #654      +/-   ##
==========================================================================
- Coverage                                   39.39%   39.15%   -0.24%     
==========================================================================
  Files                                         178      179       +1     
  Lines                                       15519    15789     +270     
  Branches                                     2996     3053      +57     
==========================================================================
+ Hits                                         6113     6182      +69     
- Misses                                       8827     9026     +199     
- Partials                                      579      581       +2

dagewa

Thanks! The additions look good and I have confirmed that all tests pass with this and dials/dials#2482 in place. I aim to merge tomorrow.

dagewa · 2023-08-03T15:24:13Z

Well, can merge this one in now, and the PR into dxtbx tomorrow

dagewa and others added 27 commits July 21, 2023 15:36

Add a probe enum

c981f71

get_probe accessor

bae2822

probe-->Probe, and export to Python.

6eea2fd

So now, can do from dxtbx.model.beam import Probe

Export get_probe

eb22c37

Note the value is uninitialized!

Ensure probe_ is initialized. Now we get:

2b79fd8

>>> from dxtbx.model.beam import Beam >>> b=Beam() >>> b.get_probe() dxtbx_model_ext.Probe.xray

Add set_probe and export.

6979e25

Now this works: >>> from dxtbx.model.beam import Beam >>> b=Beam() >>> b.get_probe() dxtbx_model_ext.Probe.xray >>> from dxtbx.model.beam import Probe >>> b.set_probe(Probe.neutron) >>> b.get_probe() dxtbx_model_ext.Probe.neutron

Ensure probe is initialised by the other constructors too

e5c8839

Incorporate probe into equality and similarity checks

48c096d

Add get_probe_name method so that the NeXus probe name can be

899b166

returned for each of the defined probe values

Include the probe in to/from dict methods and pickle suite.

463391b

Add probe to make_polarized_beam, and fix longstanding bug in that me…

0b08c5d

…thod

Set electron probe for various 3D ED format classes

f5e5441

News

9f2400a

Rename newsfragments/xxx.feature to newsfragments/647.feature

823b075

Easier override of panel geometry (cctbx#644)

930be09

When setting panels by PHIL, merge multiple definitions first by id. This fixes cctbx#299.

Flumpy: Don't allow converting 1D vectors to vec2/3 (cctbx#648)

436a1b6

Previously, a size (3,) array would have erroneously converted to a 0x3 length vec3. This is now explicitly forbidden; you must pass at least a (0, 3) multidimensional array. Fixes cctbx#439.

FormatROD (cctbx#645)

180fac8

Partial support for Rigaku Oxford Diffraction format images. --------- Co-authored-by: Takanori Nakane <nakane.t@gmail.com> Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>

Check Registry against refl/expt files (cctbx#650)

e9b88d2

This was previously done implicitly, but only when dials_regression was present. This makes the test explicit, and works with dials-data (so that it will work on e.g. CI with restricted access to test cases).

MNT: Update CMake modules path relative to script

0a068b5

Without this, dxtbx did not work as a subdirectory in a larger CMakeLists project.

Merge branch 'main' into 575-beam-model-should-state-probe-type

3f1a106

Add probe to PolychromaticBeam

d2cf031

Fixes for tests

7f0e289

Added get_probe_from_name to Beam. Added Probe to beam_phil_scope. Ch…

1f3c257

…anged Probe in .expt files to be human readable.

Added more typehints for beam.py. Added empty PolychromaticBeam const…

4312daf

…ructor at the Python level. Fixed typo in Beam.from_dict.

toastisme mentioned this pull request Aug 3, 2023

Add probe type to the Beam model #647

Merged

toastisme requested a review from dagewa August 3, 2023 13:59

dagewa approved these changes Aug 3, 2023

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dagewa merged commit 35a312c into cctbx:575-beam-model-should-state-probe-type Aug 3, 2023
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Add probe to phil params and make probe in .expt human readable #654

Add probe to phil params and make probe in .expt human readable #654

toastisme commented Aug 3, 2023

codecov bot commented Aug 3, 2023

dagewa left a comment

dagewa commented Aug 3, 2023

Add probe to phil params and make probe in .expt human readable #654

Add probe to phil params and make probe in .expt human readable #654

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toastisme commented Aug 3, 2023

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dagewa commented Aug 3, 2023