standardize export & restore of diffractometer configuration #279

prjemian · 2023-10-26T17:52:40Z

close Store operational information locally for use outside of bluesky #256

prjemian · 2023-10-26T22:12:02Z

@mrakitin @klauer This is ready for review. It's a major part of the coming v1.1 release.

docs/source/configuration.rst

padraic-shafer

TODO (for me, tomorrow):

Review 'hkl/configuration.py'
Review 'tests/conftest.py'
Review 'tests/test_configuration.py'

hkl/util.py

hkl/tests/test_tardis.py

padraic-shafer

This is a really useful feature, and nicely done. I left some comments and suggestions, but none of them are fatal.

hkl/tests/test_configuration.py

hkl/configuration.py

hkl/tests/test_configuration.py

prjemian · 2023-11-01T20:31:15Z

In discussion, @rodolakis is concerned that the constraints should not be restored. At least, it should be optional whether to restore the constraints since there may be hardware limitations for improper settings, or users may fail to achieve a solution for given $(hkl)$.

prjemian · 2023-11-01T20:34:33Z

While a nice thing to have, the $U$ matrix is not an absolute requirement. This could be moved to optional.

mrakitin

This is a very nice addition and great test coverage!
I added a few non-blocking comments.

docs/source/configuration.rst

mrakitin · 2023-10-31T20:58:10Z

hkl/sample.py

-        return dict(
-            reflection=dict(h=h, k=k, l=l),
-            flag=refl.flag_get(),
-            wavelength=geom.wavelength_get(1),
-            position={k: v for k, v in zip(geom.axis_names_get(), geom.axis_values_get(1))},
-            orientation_reflection=refl in self._orientation_reflections,
-        )
+        return {
+            "reflection": {"h": h, "k": k, "l": l},
+            "flag": refl.flag_get(),  # not used by hklpy
+            "wavelength": geom.wavelength_get(1),
+            "position": dict(zip(geom.axis_names_get(), geom.axis_values_get(1))),
+            "orientation_reflection": refl in self._orientation_reflections,
+        }


Why did not dict work?

pylint (use-dict-literal - R1735)

dict(zip(geom.axis_names_get(), geom.axis_values_get(1))) was still used, not sure if there is a huge benefit, but it's OK.

Right. That was the form suggested, rather than a dict comprehension. Go figure.

Pylint flagged the simpler dict(a=1, b="two") style for replacement with {"a": 1, "b": "two"}. Looks cumbersome to me and adds invisible benefit for such small dictionaries. But it makes pylint happy.

docs/source/configuration.rst

mrakitin · 2023-11-01T23:53:24Z

hkl/tests/data/e4c-config.json

I wonder if we need to add this file and other non-Python files to https://github.com/bluesky/hklpy/blob/main/MANIFEST.in.

Also, why not to reuse docs/source/_static/e4c-config.json?

2146ed2. Unit test is in-source.

hkl/util.py

mrakitin · 2023-11-01T23:59:31Z

hkl/tests/test_configuration.py

+
+    before.pop("datetime")
+    after.pop("datetime")
+    assert before == after, "should be same configuration"


We found it useful to use https://pypi.org/project/dictdiffer/ to compare large/nested dictionaries. It may be useful here as well.

hkl/configuration.py

mrakitin · 2023-11-02T00:45:29Z

hkl/configuration.py

+    """
+
+    def __init__(self, diffractometer):
+        from .diffract import Diffractometer


Why not import it on the top of the file?

Avoid potential for circular import.

hkl/configuration.py

Co-authored-by: Max Rakitin <mrakitin@users.noreply.github.com>

… into 256-orientation-dict

Co-authored-by: Max Rakitin <mrakitin@users.noreply.github.com>

mrakitin

Looks good to me!

strempfer · 2023-11-07T13:41:31Z

In [61]: config.restore(pathlib.Path("fourc-config.json"), clear=True)

In [62]: list_reflections(True)
Sample: main

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   2  0  0      37.000    0.000   90.000   71.500   first        
 1   0  4  0      60.000   30.000   90.000    0.000   second       
============================================================================
Sample: EuAl4

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   0  4  0      60.000   30.000   90.000    0.000   first        
 1   2  0  0      37.000    0.000   90.000   71.500   second       
============================================================================

In [63]: config.restore(pathlib.Path("fourc-config.json"), clear=False)

In [64]: list_reflections(True)
Sample: main

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   2  0  0      37.000    0.000   90.000   71.500   first        
 1   0  4  0      60.000   30.000   90.000    0.000   second       
============================================================================
Sample: EuAl4

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   0  4  0      60.000   30.000   90.000    0.000 
 1   2  0  0      37.000    0.000   90.000   71.500 
 2   2  0  0      37.000    0.000   90.000   71.500 
 3   0  4  0      60.000   30.000   90.000    0.000 
 4   0  4  0      60.000   30.000   90.000    0.000   first        
 5   2  0  0      37.000    0.000   90.000   71.500   second       
============================================================================

It looks like when clear=False, it reads reflections from 'main' also into the following sample.

prjemian · 2023-11-07T13:54:01Z

Sounds like a bug. Thanks for the report!

prjemian added 5 commits October 26, 2023 09:21

MNT #256 make this more obvious

c3b5c1a

TST #256 define some common test components

f8ce51d

TST #256 apply common structures

16d2bc8

ENH #256 new configuration export/restore

7a3398e

TST #256 test new code

78868f5

prjemian added the enhancement label Oct 26, 2023

prjemian added this to the v1.1 milestone Oct 26, 2023

prjemian self-assigned this Oct 26, 2023

prjemian added 5 commits October 26, 2023 14:26

ENH #256 Simplify for high-symmetry crystals

83390be

TST #256 was failing locally

d9a56a4

MNT #256 add datetime to configuration

c3b559e

TST #256 don't compare datetime keys

42c63ea

DOC #256

b9ae623

prjemian requested review from klauer and mrakitin October 26, 2023 22:11

prjemian marked this pull request as ready for review October 26, 2023 22:11

prjemian added 5 commits October 26, 2023 17:19

DOC #256 ctach up on the history

5e34515

DOC #256 one more catch-up

133644c

Merge branch 'main' into 256-orientation-dict

d337770

DOC #256 sort

1a1f94d

MNT #256 do not sort the keys in the YAML output

aec2fc0

prjemian requested a review from padraic-shafer October 26, 2023 22:43

padraic-shafer reviewed Oct 27, 2023

View reviewed changes

docs/source/configuration.rst Outdated Show resolved Hide resolved

padraic-shafer reviewed Oct 27, 2023

View reviewed changes

docs/source/configuration.rst Outdated Show resolved Hide resolved

padraic-shafer reviewed Oct 27, 2023

View reviewed changes

docs/source/configuration.rst Outdated Show resolved Hide resolved

padraic-shafer reviewed Oct 27, 2023

View reviewed changes

hkl/util.py Outdated Show resolved Hide resolved

hkl/tests/test_tardis.py Outdated Show resolved Hide resolved

hkl/tests/test_tardis.py Outdated Show resolved Hide resolved

hkl/tests/test_tardis.py Outdated Show resolved Hide resolved

padraic-shafer approved these changes Oct 27, 2023

View reviewed changes

ENH #256 add export to file as pathlib object

d041400

prjemian mentioned this pull request Nov 1, 2023

Add a SPEC-like subscriber that saves orientation automatically #247

Open

prjemian added 5 commits November 1, 2023 15:52

MNT #256 U matrix is not required

8eef8af

MNT #256 restore_constraints is an option

473f61f

MNT #256 update config file examples

8550a0f

TST #256 restore_constraints should be a bool

fe85c87

STY #256

aed169b

mrakitin reviewed Nov 2, 2023

View reviewed changes

prjemian and others added 12 commits November 1, 2023 20:43

Update docs/source/configuration.rst

0b23c5f

Co-authored-by: Max Rakitin <mrakitin@users.noreply.github.com>

DOC #256 code-block

6f33391

Merge branch '256-orientation-dict' of https://github.com/bluesky/hklpy…

131dd97

… into 256-orientation-dict

PKG #256

2146ed2

Update hkl/configuration.py

7438781

Co-authored-by: Max Rakitin <mrakitin@users.noreply.github.com>

DOC #256 attribute doc syntax

e07ff12

MNT #256 indent=2 default

b2036cc

DOC #256 LaTeX syntax

07de552

DOC #256 note

fea4f1a

DOC #256 reST syntax

8e30eeb

DOC #256

371f723

DOC #256

82eb9b5

mrakitin approved these changes Nov 2, 2023

View reviewed changes

prjemian merged commit e7abba8 into main Nov 2, 2023
8 checks passed

prjemian deleted the 256-orientation-dict branch November 2, 2023 14:02

prjemian mentioned this pull request Nov 8, 2023

BUG: restore(clear=False) reflections added to other samples #289

Closed

prjemian mentioned this pull request Nov 22, 2023

Save/restore information between sessions BCDA-APS/apstools#820

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

standardize export & restore of diffractometer configuration #279

standardize export & restore of diffractometer configuration #279

prjemian commented Oct 26, 2023

prjemian commented Oct 26, 2023 •

edited

Loading

padraic-shafer left a comment

padraic-shafer left a comment

prjemian commented Nov 1, 2023

prjemian commented Nov 1, 2023

mrakitin left a comment

mrakitin Oct 31, 2023

prjemian Nov 2, 2023

mrakitin Nov 2, 2023

prjemian Nov 2, 2023

prjemian Nov 2, 2023

mrakitin Nov 1, 2023

mrakitin Nov 1, 2023

prjemian Nov 2, 2023

mrakitin Nov 1, 2023

mrakitin Nov 2, 2023

prjemian Nov 2, 2023

mrakitin left a comment

strempfer commented Nov 7, 2023

prjemian commented Nov 7, 2023

standardize export & restore of diffractometer configuration #279

standardize export & restore of diffractometer configuration #279

Conversation

prjemian commented Oct 26, 2023

prjemian commented Oct 26, 2023 • edited Loading

padraic-shafer left a comment

Choose a reason for hiding this comment

padraic-shafer left a comment

Choose a reason for hiding this comment

prjemian commented Nov 1, 2023

prjemian commented Nov 1, 2023

mrakitin left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

mrakitin left a comment

Choose a reason for hiding this comment

strempfer commented Nov 7, 2023

prjemian commented Nov 7, 2023

prjemian commented Oct 26, 2023 •

edited

Loading