Polarisation / spin-echo tuning scans #200

jackbdoughty · 2025-05-15T13:28:37Z

Description of work

Minor refactoring/additions to devices/DAE area
- SimpleDae strategies now accept DAEs of type DAE rather than only SimpleDae. This is because some were needed by the new type of DAE being implemented.
- Implements a new type of DAE, DualRunDae, which requires a flipper device to be provided
  and will perform two runs, changing the flipper device at the start and in between runs.
- Creates two new types of reducers, one for normalising wavelength bounded spectra, and another which calculates polarisation and polarisation ratio given an up & down normalising wavelength bounded spectra. What this will give you is polarisation information per wavelength bound which is then plotted & fitted to.
- A function, polarising_dae which instantiates a DualRunDae suited for spin echo / polarisation, with the two new types of reducer. It will do the following each time it is triggered by the run engine:
```
1) change the state of the flipper (up)
2) start counting
3) do wavelength bounding & normalise 
4) change the state of the flipper (down)
5) start counting
6) do wavelength bounding & normalise 
7) calculate polarisation data
```
Addition to fitting area
- Introduces a ChainedLiveFit callback which handles a sequence of LiveFit instances where the parameters from each
  completed fit serve as the initial guess for the subsequent fit. By passing a set of mpl axes to it, it handles LiveFitPlots which point to the LiveFits. Only this should be subscribed, not any LiveFits/LiveFitPlots.
LARMOR inst script/plan
- A instrument script-like file that brings together the above additions into a spin-echo scan and autotuner, providing defaults and an interface for use on LARMOR.
- Larmor spin echo plan #213 larmor plans, not to be merged to be put in inst scripts
Unit tests & documentation

To test

run unit tests & check for good coverage
put dae into event sim mode, with spreadevents on (with lots of events), and have two blocks set up like the following img, and run a script that uses the top level plans. You may need to tweak certain defaults such as log file locations to get it to run. happy to help if can't sort out test setup
check that docs changes are verbose enough
probably best to squish to avoid having commits like "i <3 unit tests" and "remove a bit of code that idk where it came from?"
and "polarisation consolidation transformation"

Also note:

LARMOR: Magnet IOC Current IBEX#8766 issue created to patch larmor magnet ioc. Needed for this to be used on LARMOR
As part of the top level inst script/plan, we need to be able to make backups/restore backups/change dae settings which is covered by Plan wrappers for DAE setup changes with cleanup #164. A follow up ticket should be made & undertaken to account for this.

Initial commit

…Ticket_125

- realised that PolarisingDae should not be a type of SimpleDae - This meant that PolarisingDae could not use any of SimpleDae's controllers, waiters or reducers - As a result, centralised all controllers, waiters and reducers to a subdirectory of dae called strategies, whereby they all accept Dae rather than SimpleDae/PolarisingDae unless required to - Updated all references - May put something in architectural decisions

rerpha

some very initial thoughts

src/ibex_bluesky_core/utils.py

tests/callbacks/fitting/test_chained_fitting_callback.py

src/ibex_bluesky_core/devices/polarisingdae/__init__.py

rerpha · 2025-06-30T15:53:56Z

doc/devices/dae.md


 For complex use-cases, particularly those where the DAE may need to start and stop multiple 
-acquisitions per scan point (e.g. polarization measurements), [`SimpleDae`](ibex_bluesky_core.devices.simpledae.SimpleDae) is unlikely to be 
+acquisitions per scan point (e.g. Polarisation measurements), [`SimpleDae`](ibex_bluesky_core.devices.simpledae.SimpleDae) is unlikely to be 


I agree with this change.

doc/devices/dae.md

src/ibex_bluesky_core/callbacks/_fitting.py

rerpha · 2025-06-30T16:10:09Z

probably best to squish to avoid having commits like "i <3 unit tests" and "remove a bit of code that idk where it came from?"
and "polarisation consolidation transformation"

OK will squash and git commit --amend -m "initial commit"

rerpha · 2025-07-01T12:14:16Z

I get this after 2 points:

+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|   seq_num |       time |        bob | DAE-reducer-_wavelength_bands-0-polarisation | DAE-reducer-_wavelength_bands-1-polarisation | DAE-reducer-_wavelength_bands-0-polarisation_stddev | DAE-reducer-_wavelength_bands-1-polarisation_stddev |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|         1 | 13:11:11.8 |      0.000 |                                    -0.046238 |                                    -0.026738 |                                            0.057474 |                                            0.163024 |
|         2 | 13:11:26.0 |      1.111 |                                    -0.145277 |                                     0.079755 |                                            0.055797 |                                            0.178137 |
C:\Instrument\Apps\Python3\Lib\site-packages\uncertainties\core.py:1024: UserWarning: Using UFloat objects with std_dev==0 may give unexpected results.
  warn("Using UFloat objects with std_dev==0 may give unexpected results.")
|         3 | 13:11:40.5 |      2.222 |                                    -0.111412 |                                     0.222904 |                                            0.053564 |                                            0.154281 |
|         4 | 13:11:54.6 |      3.333 |                                    -0.004297 |                                     0.377670 |                                            0.060687 |                                            0.112492 |
|         5 | 13:12:08.9 |      4.444 |                                     0.064048 |                                    -0.012715 |                                            0.053104 |                                            0.151237 |
|         6 | 13:12:23.2 |      5.556 |                                     0.060740 |                                    -0.084991 |                                            0.058567 |                                            0.139122 |
|         7 | 13:12:37.5 |      6.667 |                                    -0.024282 |                                     0.211073 |                                            0.059050 |                                            0.164518 |
|         8 | 13:12:51.8 |      7.778 |                                    -0.098603 |                                     0.034672 |                                            0.057373 |                                            0.166516 |
|         9 | 13:13:06.5 |      8.889 |                                     0.042290 |                                     0.196634 |                                            0.056514 |                                            0.101424 |
|        10 | 13:13:20.7 |     10.000 |                                     0.044984 |                                     0.115505 |                                            0.053513 |                                            0.128628 |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
generator scan ['dfa177a4'] (scan num: 22)

also reproduceable in tests

src/ibex_bluesky_core/callbacks/_fitting.py

src/ibex_bluesky_core/devices/polarisingdae/__init__.py

src/ibex_bluesky_core/devices/polarisingdae/_spectra.py

jackbdoughty · 2025-07-02T11:55:26Z

I get this after 2 points:

+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|   seq_num |       time |        bob | DAE-reducer-_wavelength_bands-0-polarisation | DAE-reducer-_wavelength_bands-1-polarisation | DAE-reducer-_wavelength_bands-0-polarisation_stddev | DAE-reducer-_wavelength_bands-1-polarisation_stddev |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|         1 | 13:11:11.8 |      0.000 |                                    -0.046238 |                                    -0.026738 |                                            0.057474 |                                            0.163024 |
|         2 | 13:11:26.0 |      1.111 |                                    -0.145277 |                                     0.079755 |                                            0.055797 |                                            0.178137 |
C:\Instrument\Apps\Python3\Lib\site-packages\uncertainties\core.py:1024: UserWarning: Using UFloat objects with std_dev==0 may give unexpected results.
  warn("Using UFloat objects with std_dev==0 may give unexpected results.")
|         3 | 13:11:40.5 |      2.222 |                                    -0.111412 |                                     0.222904 |                                            0.053564 |                                            0.154281 |
|         4 | 13:11:54.6 |      3.333 |                                    -0.004297 |                                     0.377670 |                                            0.060687 |                                            0.112492 |
|         5 | 13:12:08.9 |      4.444 |                                     0.064048 |                                    -0.012715 |                                            0.053104 |                                            0.151237 |
|         6 | 13:12:23.2 |      5.556 |                                     0.060740 |                                    -0.084991 |                                            0.058567 |                                            0.139122 |
|         7 | 13:12:37.5 |      6.667 |                                    -0.024282 |                                     0.211073 |                                            0.059050 |                                            0.164518 |
|         8 | 13:12:51.8 |      7.778 |                                    -0.098603 |                                     0.034672 |                                            0.057373 |                                            0.166516 |
|         9 | 13:13:06.5 |      8.889 |                                     0.042290 |                                     0.196634 |                                            0.056514 |                                            0.101424 |
|        10 | 13:13:20.7 |     10.000 |                                     0.044984 |                                     0.115505 |                                            0.053513 |                                            0.128628 |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
generator scan ['dfa177a4'] (scan num: 22)

also reproduceable in tests

yes im really not sure about this, initially we thought it was to do with chainedlivefit, carrying over parameter uncertainties between fits but its something I've seen on other ibc branches too e.g momentum scan one we're working on atm, and after making the chainedlivefit fix, it didn't change this, might be good to have a chat about it..

rerpha · 2025-07-02T12:29:41Z

I get this after 2 points:

+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|   seq_num |       time |        bob | DAE-reducer-_wavelength_bands-0-polarisation | DAE-reducer-_wavelength_bands-1-polarisation | DAE-reducer-_wavelength_bands-0-polarisation_stddev | DAE-reducer-_wavelength_bands-1-polarisation_stddev |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
|         1 | 13:11:11.8 |      0.000 |                                    -0.046238 |                                    -0.026738 |                                            0.057474 |                                            0.163024 |
|         2 | 13:11:26.0 |      1.111 |                                    -0.145277 |                                     0.079755 |                                            0.055797 |                                            0.178137 |
C:\Instrument\Apps\Python3\Lib\site-packages\uncertainties\core.py:1024: UserWarning: Using UFloat objects with std_dev==0 may give unexpected results.
  warn("Using UFloat objects with std_dev==0 may give unexpected results.")
|         3 | 13:11:40.5 |      2.222 |                                    -0.111412 |                                     0.222904 |                                            0.053564 |                                            0.154281 |
|         4 | 13:11:54.6 |      3.333 |                                    -0.004297 |                                     0.377670 |                                            0.060687 |                                            0.112492 |
|         5 | 13:12:08.9 |      4.444 |                                     0.064048 |                                    -0.012715 |                                            0.053104 |                                            0.151237 |
|         6 | 13:12:23.2 |      5.556 |                                     0.060740 |                                    -0.084991 |                                            0.058567 |                                            0.139122 |
|         7 | 13:12:37.5 |      6.667 |                                    -0.024282 |                                     0.211073 |                                            0.059050 |                                            0.164518 |
|         8 | 13:12:51.8 |      7.778 |                                    -0.098603 |                                     0.034672 |                                            0.057373 |                                            0.166516 |
|         9 | 13:13:06.5 |      8.889 |                                     0.042290 |                                     0.196634 |                                            0.056514 |                                            0.101424 |
|        10 | 13:13:20.7 |     10.000 |                                     0.044984 |                                     0.115505 |                                            0.053513 |                                            0.128628 |
+-----------+------------+------------+----------------------------------------------+----------------------------------------------+-----------------------------------------------------+-----------------------------------------------------+
generator scan ['dfa177a4'] (scan num: 22)

also reproduceable in tests

yes im really not sure about this, initially we thought it was to do with chainedlivefit, carrying over parameter uncertainties between fits but its something I've seen on other ibc branches too e.g momentum scan one we're working on atm, and after making the chainedlivefit fix, it didn't change this, might be good to have a chat about it..

I get it on main - ignore it as a review comment on this PR

jackbdoughty added 20 commits May 2, 2025 13:37

start implementing PolarisingDae

39073dd

Initial commit

Merge remote-tracking branch 'origin/58_polarization_asymmetry' into …

1c240cd

…Ticket_125

add support for multiple wavelength bands

4b9a428

dae implemented pre test

ace2803

update flipper signal red

361b034

update flipper signal ref

f09fe6e

refactoring & fixes post test

5d77efe

refactoring

0096df7

polarising dae unit tests

8d82f8a

i <3 unit tests

f172c04

unit tests 4eva

a37539a

passing tests full coverage

59b5d47

unit tests refactoring

823d209

update docs

f6d824d

docstring improvement

71cdd84

docstring improvement

7321afc

removing unused imports

0202021

docs fix

c71f6b6

docs fix

8b8ccc2

docs fix

400b2e1

jackbdoughty added the bluesky-Semver-Minor New functionality / back-compatible changes label May 15, 2025

pull-request-size bot added the size/XXL label May 15, 2025

jackbdoughty added 8 commits May 15, 2025 14:46

ruff fixes

0ae86be

ruff fixes

aae36c5

ruff fixes

c646c76

ruff fixes

2fcde46

ruff fixes

70a6913

ruff fixes

2bddf69

circular import

4ac9d46

jackbdoughty added 2 commits June 20, 2025 16:54

refactoring

419f639

typing changes

fd9f2a8

jackbdoughty mentioned this pull request Jun 24, 2025

Polarisation / spin-echo tuning scans #125

Closed

jackbdoughty and others added 2 commits June 24, 2025 11:29

add comment to chainedlivefit

3e5ca92

Merge branch 'main' into Ticket_125

32edac4

jackbdoughty marked this pull request as ready for review June 26, 2025 10:46

jackbdoughty and others added 2 commits June 26, 2025 16:24

tiny description change

52c6d76

Merge branch 'main' into Ticket_125

7c19456

rerpha reviewed Jun 30, 2025

View reviewed changes

jackbdoughty and others added 4 commits July 1, 2025 09:26

Merge branch 'main' into Ticket_125

2ba27dd

requested changed

b8e00da

docs fix

8852fc0

docs fix again

8807bdb

rerpha reviewed Jul 1, 2025

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rerpha reviewed Jul 1, 2025

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src/ibex_bluesky_core/devices/polarisingdae/__init__.py Outdated Show resolved Hide resolved

rerpha reviewed Jul 1, 2025

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jackbdoughty and others added 5 commits July 2, 2025 12:59

remove show plot

eef347c

docs change

ff06540

Merge branch 'main' into Ticket_125

e48932b

fix merge

b454b5a

ruff pyright

40944ff

jackbdoughty added 2 commits July 2, 2025 14:20

change flipper to be generic

b61f1d7

flipper names

ff10f33

rerpha approved these changes Jul 2, 2025

View reviewed changes

rerpha merged commit 4f35fb9 into main Jul 2, 2025
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rerpha deleted the Ticket_125 branch July 2, 2025 13:36

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Polarisation / spin-echo tuning scans #200

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