Website page for AutoMFX projects: VonHamos, EXAFS, Sim_EXAFS, Ondulator Pointing by MartinaDelGaudio · Pull Request #10 · lcls-mlcv/lcls-mlcv.github.io

MartinaDelGaudio · 2026-03-08T22:47:47Z

Creating a pull request to merge changes in the website by Martina and Amine

Added description of Xopt as the core optimization engine for automation efforts.

Expanded project goal section to detail the automation framework and its components.

Added an image to enhance the documentation of the automation framework.

Add documentation for EXAFS Scan Controller project, detailing its goals, functionalities, core components, accomplishments, limitations, and usage examples.

Added subprojects section and listing for AutoMFX projects.

Removed an error from file path for image

Image path + subproject fix

Updated image path for EXAFS project documentation.

Updated project title and improved section headings for clarity.

Updated project description and sections for clarity and detail.

Fixed formatting issue in the simulation documentation.

Removed unnecessary details from the project description.

Added documentation for the Von Hamos project, detailing its goals, functionalities, and workflows.

Updated project details and images for the MFX beamline automation project.

…utomfx-amine-martin

fredericpoitevin

Thanks @MartinaDelGaudio this is really great! Let's iterate a little bit over my comments, we're close!

fredericpoitevin · 2026-03-09T15:51:44Z

+### Xopt
+
+Xopt is the core optimization engine driving our group’s automation efforts in beamline alignment. It is a flexible, open-source Python framework designed for high-level optimization across simulations, experiments, and control systems. It allows users to define input variables, objectives and constraints through a simple “VOCS” interface, then select from advanced algorithmic generators (e.g., evolutionary, Bayesian, multi-objective, multi-fidelity) to drive optimization with minimal boilerplate.
+
+<p align="center">
+<img width="629" height="267" alt="xopt_diagram" src="/assets/img/xopt_diagram.png" />
+</p>


Add link to Xopt GitHub.

fredericpoitevin · 2026-03-09T15:54:54Z

+
+### Automation loop
+
+EXAFS scans require stepping photon energy while maintaining throughput and stability. This module runs that workflow by coupling **DCCM energy moves** (the primary scan axis) with **undulator K stepping** to keep the source tuned, and optional per-point optimization and tracking. It can align the **vernier** by maximizing intensity, apply **transfocator** focus configurations from a tracking map, track the **FEE spectrometer** (and optionally its camera), and manage the full **LCLS-II DAQ** lifecycle (configure → run → pause/resume when needed → stop). A flux threshold can be enforced to automatically pause DAQ if the beam drops and resume when it recovers.


Clarify what is meant by "track the FEE spectrometer (and optionally its camera)".

Added 2 lines, check if it's okay now

fredericpoitevin · 2026-03-09T15:56:41Z

+
+### Limitations
+
+Element edge metadata (foil/threshold energies) is currently hard-coded to a small set of transition metals, so adding new elements requires extending those tables. Focus tracking depends on precomputed tracking data. Vernier alignment is robust but can add overhead because it is scan-based rather than model-predicted. A few hardware interactions use shell calls and fixed PV names, which is less portable than fully device-native control. Finally, `long_escan` is intentionally feature-rich and therefore large, making it a good operational entry point but a natural target for refactoring and unit tests.


I would add that one of the lessons learned from beamtime is that the transfocator focus tracking capability needs to be improved as the stage motion was lagging behind. Also more work is necessary to ensure pointing remains optimal throughout the scan.

Done, maybe @amine-lamouchi wants to check on this

fredericpoitevin · 2026-03-09T15:57:58Z

I would merge the content of this file into the EXAFS.md file. Also, simulation.md could be understood as more general than just for EXAFS, we might want to keep it if we'd like to say more about the MFX Digital Twin?

Should I create 2 subpages in autoMFX: one for "real" experiments (name of the section open to suggestions) and one with Digital Twin; then, in the first section I put what is currently EXAFS and VonHamos, and in the digital twin we will put the various simulated parts, including exafs sim? Or do you prefer if every section will have its own "real device" part and simulated part? So, EXAFS will have 2 subsections, one for real and one for simulated, and same for vonhamos etc..?

Also, added a placeholder for undulator pointing for @amine-lamouchi to fill

fredericpoitevin · 2026-03-09T15:59:06Z

Can we change the title from "Von Hamos" to "Von Hamos Spectrometer"?

fredericpoitevin · 2026-03-09T16:01:16Z

+- **energy scans** by stepping crystal rotation,
+- **multi-crystal acquisition** where all six analyzers collect in parallel and spectra are combined downstream.
+
+Helper utilities like `optimize_crystal()`, `set_all_crystals()`, and position reporting functions provide quick “one-call” operations during shifts and alignment.


It would be great if we could expand on the alignment automation aspect of the project.

Done, maybe @amine-lamouchi wants to add more

fredericpoitevin · 2026-03-09T16:01:37Z

Let's have Leland review this fantasatic figure!

fredericpoitevin · 2026-03-09T16:02:24Z

I realize that this wasn't used: would we want to fix it and include it?

do you want me to try to fix it? Or you like the vonhamos_new.png in place of this? Or vonhamos_new.png + improved version of this?

fredericpoitevin · 2026-03-09T16:02:33Z

fredericpoitevin · 2026-03-09T16:02:55Z

@@ -3,8 +3,54 @@ layout: projects
 title: autoMFX
 description: Automation of the MFX beamline at LCLS
 img: assets/img/projects/automfx.jpg


We have better pictures now, could we replace that one?

Updated with the exafs image

Clarified the functionality of the automation loop in EXAFS scans, including tracking of the FEE spectrometer and its camera

Expanded limitations section to include focus tracking synchronization issues and pointing stability challenges during beamtime.

Added disclaimer about the iterative approach.

Added a second project goal for simulation and detailed the features of Sim-EXAFS, including its components and strengths.

Added initial content for Undulator Pointing project documentation.

Updated image reference to cropped version.

Expanded on typical workflows and added details about alignment automation features, including automated array initialization, closed-loop optimization, deterministic verification, and state reporting.

amine-lamouchi and others added 30 commits November 10, 2025 14:12

updated automfx.md with Xopt details

a624522

Added description of Xopt as the core optimization engine for automation efforts.

first draft of introduction

70f8683

Expanded project goal section to detail the automation framework and its components.

uploading image of MFX instrument

8559ea3

adding mfx instrument image

a2b570e

Added an image to enhance the documentation of the automation framework.

adding image of EXAFS workflow

e05ba2c

Create documentation for EXAFS Scan Controller

328374d

Add documentation for EXAFS Scan Controller project, detailing its goals, functionalities, core components, accomplishments, limitations, and usage examples.

small change to exafs title

8f237b3

Enhance automfx.md with subprojects information - first try

aa5794f

Added subprojects section and listing for AutoMFX projects.

clean exafs.md

d218040

another small change to exafs.md

049b408

Removed an error from file path for image

another minor change to exafs.md

0aba534

Image path + subproject fix

Fix image path in EXAFS project markdown

ebf2cdc

Updated image path for EXAFS project documentation.

adding image for EXAFS simulated

48b45ff

adding simulation subproject (first try)

3efde88

Add 'simulation' to subprojects list

c757769

Change title case from 'Simulation' to 'simulation'

b2a5bc1

Update subproject name from 'simulation' to 'Sim-EXAFS'

7574c5f

Revise simulation project title and headings

8baf25f

Updated project title and improved section headings for clarity.

Revise simulation.md for Sim-EXAFS project

10b2639

Updated project description and sections for clarity and detail.

minor changings to simulation.md

dbd4624

Correct device registry description formatting

c9496e6

Fixed formatting issue in the simulation documentation.

Update project description for Sim-EXAFS

c056232

Removed unnecessary details from the project description.

adding vonhamos png image

a1b34a8

Create documentation for Von Hamos project

3763f0b

Added documentation for the Von Hamos project, detailing its goals, functionalities, and workflows.

Add 'Von Hamos' to subprojects list

624d540

Update image format for Von Hamos project

3fe12c6

uploading new mfx instrument images

34069ff

Revise MFX project description and images

be5b31e

Updated project details and images for the MFX beamline automation project.

adding vonhamos image new

2786d95

updating image of vonhamos in projects

fd0037b

MartinaDelGaudio added 3 commits March 8, 2026 16:06

Fix prettier formatting and replace external xopt image with local copy

eee30f6

Fixing broken links:Merge remote-tracking branch 'origin/main' into a…

daad97c

…utomfx-amine-martin

Merge origin/main and fix prettier formatting

ae931fd

fredericpoitevin requested changes Mar 9, 2026

View reviewed changes

MartinaDelGaudio and others added 16 commits March 9, 2026 16:15

Enhance EXAFS automation loop description

97a4ed8

Clarified the functionality of the automation loop in EXAFS scans, including tracking of the FEE spectrometer and its camera

Update limitations section in exafs.md

e779743

Expanded limitations section to include focus tracking synchronization issues and pointing stability challenges during beamtime.

Update title of Von Hamos project

1d9456f

Add disclaimer for deterministic positioning module

5d8e62e

Added disclaimer about the iterative approach.

Expand exafs with content of simulation.md

10d4424

Added a second project goal for simulation and detailed the features of Sim-EXAFS, including its components and strengths.

Change headings from H3 to H2 in exafs.md

0d78d47

Update subproject name for clarity

bce5d2d

Create undulator_pointing.md for project details

b363b4b

Added initial content for Undulator Pointing project documentation.

Update subprojects list in automfx.md

a556ab8

added a cropped version of vonhamos image

130c2f8

Change image to cropped version for Von Hamos project

4945e6d

Updated image reference to cropped version.

Enhance documentation on workflows and automation features

56366d8

Expanded on typical workflows and added details about alignment automation features, including automated array initialization, closed-loop optimization, deterministic verification, and state reporting.

Improved description

8f106dd

Changed description a bit

8c5866c

Update project image for autoMFX

896ae8a

wip

feeaeac


		### Automation loop

		EXAFS scans require stepping photon energy while maintaining throughput and stability. This module runs that workflow by coupling DCCM energy moves (the primary scan axis) with undulator K stepping to keep the source tuned, and optional per-point optimization and tracking. It can align the vernier by maximizing intensity, apply transfocator focus configurations from a tracking map, track the FEE spectrometer (and optionally its camera), and manage the full LCLS-II DAQ lifecycle (configure → run → pause/resume when needed → stop). A flux threshold can be enforced to automatically pause DAQ if the beam drops and resume when it recovers.


		### Limitations

		Element edge metadata (foil/threshold energies) is currently hard-coded to a small set of transition metals, so adding new elements requires extending those tables. Focus tracking depends on precomputed tracking data. Vernier alignment is robust but can add overhead because it is scan-based rather than model-predicted. A few hardware interactions use shell calls and fixed PV names, which is less portable than fully device-native control. Finally, `long_escan` is intentionally feature-rich and therefore large, making it a good operational entry point but a natural target for refactoring and unit tests.

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MartinaDelGaudio commented Mar 8, 2026

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