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ENH: Provide a pyFAI Geometry Optimization Task #59

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@LouConreux LouConreux commented Oct 16, 2024 •
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Description

This PR provides a geometry refinement task using pyFAI enhanced by Bayesian Optimization.

The code mainly originates from what has been developped in btx/feature_pyFAI.

Checklist

  • Implement task parameters OptimizePyFAIGeometryParameters
    • Write geom_opt.py under lute.io.models
    • Create TaskParameters object and define relevant parameters for input tasks
    • Add nested parameter section for Bayesian Optimization hyperparameter definition
  • Implement First-Party OptimizePyFAIGeometry task
    • Write geom_opt.py under lute.tasks
    • Implement OptimizePyFAIGeometry task according to btx/feature_pyFAI code
    • Check code for fetching geometry
      • CalibFileFinder needs to be pointed to a source: exhaustive list
    • Code for computing powder for workflow definition
      • Convert hdf5 to npy
    • Change LCLSGeom detector definition for Rayonix binning
    • Add relevant _report_to_executor prints
      • Check logger to omit pyFAI optimization infos
    • Find way to retrieve wavelength and calibrant info
  • Implement managed task PyFAIGeometryOptimizer
    • Use MPIExecutor

PR Type:

  • New feature/Enhancement

Address issues:

  • N/A

Testing

Using the configuration YAML below for mfxx49820 run 8

%YAML 1.3
---
title: "LUTE Task Configuration" # Include experiment description if desired
experiment: "mfxx49820"
run: 8
date: "2023/10/25"
lute_version: 0.1      # Do not be change unless need to force older version
task_timeout: 600
work_dir: "/sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux"
...
---
OptimizePyFAIGeometry:
  #exp: "mfxx49820"
  #run: 8
  det_type: "epix10k2M"
  in_file: "/sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux/geom/0-end.data"
  powder: "/sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux/powder/r0008_max.npy"
  calibrant: "AgBh"
  bo_params:
    bounds:
      dist: 0.2
      poni1: [-0.01, 0.01]
      poni2: [-0.01, 0.01]
    res: 0.0002
    #n_samples: 50
    #n_iterations: 50
    #prior: True
    #af: "ucb"
    #hyperparams:
      #beta: 1.96
      #epsilon: 0.01

SubmitSMD:
  # Command line arguments
  producer: "/sdf/data/lcls/ds/mfx/mfxx49820/scratch/dorlhiac/smalldata_tools/lcls1_producers/smd_producer.py"
  #run: 99
  experiment: "mfxx49820"
  #stn: 0
  directory: "/sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux/smd_output"
  #gather_interval: 25
  #norecorder: False
  #url: "https://pswww.slac.stanford.edu"
  #epicsAll: False
  #full: False
  #fullSum: False
  #default: true
  #image: False
  #tiff: False
  #centerpix: False
  #postRuntable: False
  #wait: False
  #xtcav: False
  #noarch: False
  # Producer variables. These are substituted into the producer to run specific
  # data reduction algorithms. Uncomment and modify as needed.
  # If you prefer to modify the producer file directly, leave commented.
  # Beginning with `getROIs`, you will need to modify the first entry to be a
  # detector. This detector MUST MATCH one of the detectors in `detnames`.
  # In the future this will be automated. If you have multiple detectors you can
  # add them with their own set of parameters.
  detnames: ["epix10k2M"]
  detSumAlgos:
    all:
      - "calib"
      - "calib_dropped"
      - "calib_dropped_square"
      - "calib_thresADU1"
    epix10k2M:
      - "calib_thresADU5"
      - "calib_max"
    Rayonix:
      - "calib_skipFirst_thresADU1"
      - "calib_skipFirst_max"
...

Nota Bene

Depending on the yaml bounds input, the geometry optimizer is scanning distances 100mm around a distance guess if bounds["dist"] is a float, or in between two bounds if bounds["dist"] is a tuple. If providing a distance guess, I recommend running the task with --ntasks=102 so that a 1mm step is used between scanned distances. If providing distance bounds, set --ntasks=N+2 where N is the desired distance step size.

Nota Bene Bene

This implementation depends on the the LouConreux fork of lute since in that version, MPI tasks are mapped by core using the special argument in lute.execution.executor in _submit_cmd: mpi_cmd: str = f"mpirun -np {nprocs} --map-by core"

Task can be run independently

/sdf/home/l/lconreux/lute/launch_scripts/submit_slurm.sh -t PyFAIGeometryOptimizer -c /sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux/yamls/mfxx49820_lute.yaml --partition=milano --ntasks=102 --account=lcls:mfxx49820

Task can be run in workflow

/sdf/home/l/lconreux/lute/launch_scripts/submit_launch_airflow.sh /sdf/home/l/lconreux/lute/launch_scripts/launch_airflow.py -w geom_opt_pyfai -c /sdf/data/lcls/ds/mfx/mfxx49820/scratch/lconreux/yamls/mfxx49820_lute.yaml -e mfxx49820 -r 8 --partition=milano --ntasks=102--account=lcls:mfxx49820--debug --test

Outputs

Geometry files are produced inside a directory defined as such in_file.replace('0-end.data', f'{run}-end.data).
Summary plots are saved in work_dir/figs/ and posted on eLog.
Logger writes the final geometry at the end of optimization.

Screenshots

bayes_opt_geom_mfxx49820_r0008

@fredericpoitevin fredericpoitevin mentioned this pull request Nov 14, 2024
Closed
LouConreux and others added 29 commits November 14, 2024 09:43
@LouConreux
[edit] Remove hot pixels + percentile(95)
4d675b6
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
82c6d42
@LouConreux
[edit] percentile 98
25bdb2e
@LouConreux
[edit] Change max rings to 10 instead of 5
c6672ee
@actions-user @github-actions
Auto-commit black formatting
780b880
@LouConreux
[edit] Set max_rings=5 but percentile(99)
8e00112
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
55774a3
@LouConreux
[edit] Max_rings=10 and percentile(99)
743a9b7
@LouConreux
[test] Only percentile(99)
6bced5d
@actions-user @github-actions
Auto-commit black formatting
4cb0757
@LouConreux
[test] max_rings=10
5edfaca
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
cc1143f
@LouConreux
[test] Add thresholding filter with thresh=1e4
d61026f
@LouConreux
[edit] Add max_rings and Imin as args
7043e12
@LouConreux
[edit] fix an omission
c7af138
@LouConreux
[edit] Preprocess powder + set up default Imin to 99-percentile
ac39a56
@LouConreux
[edit] remove powder[nice_pix]=0
7d31b64
@LouConreux
[edit] Fix display
763e2be
@actions-user @github-actions
Auto-commit black formatting
4f7f7ce
@LouConreux
[edit] Fix display
1e76b4f
@LouConreux
[edit] Fix merging display
f3c6395
@actions-user @github-actions
Auto-commit black formatting
a09efb6
@LouConreux
[edit] Fix plotting powder intensity colorbar scale
4547e14
@LouConreux
[edit] Fix merging plotting powder
08be9cd
@actions-user @github-actions
Auto-commit black formatting
e44ed18
@LouConreux
[edit] Set default max_rings to 10
f79df97
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
462ce7f
@LouConreux
[edit] Set vmin=np.percentile(powder, 25)
a98f152
@LouConreux
[edit] Compute a custom score for exploring large distance range
8367369
actions-user and others added 30 commits December 10, 2024 23:54
@actions-user @github-actions
Auto-commit black formatting
dddab65
@LouConreux
[edit] Try to compute detector edge resolution
a9ee817
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
a3c1578
@actions-user @github-actions
Auto-commit black formatting
1493b36
@LouConreux
[edit] Set Imin lower bound to 98
122f9ff
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
bdb65ee
@LouConreux
[edit] Set Imin lower bound to 99
5a4a1c7
@LouConreux
[edit] Set Imin lower bound to 99
5ea90a4
@LouConreux
[edit] Set Imin lower bound to 99
55380dd
@LouConreux
[edit] Set Imin lower bound to 99.5
1e2d8fe
@LouConreux
[edit] Set back to 95
a80de81
@LouConreux
[edit] Add refined dist to label
ee2ac0e
@actions-user @github-actions
Auto-commit black formatting
e8d6f7b
@LouConreux
[edit] Fix plots
336b054
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
4f4a5ff
@LouConreux
[edit] Fix output on eLog
2bd18cb
@LouConreux
[edit] Fix plot for Elog summary
9618b1d
@LouConreux
[edit] Include plots in the eLog summary
c6365e8
@actions-user @github-actions
Auto-commit black formatting
27ea664
@LouConreux
[edit] Set back to 98
dca2ccd
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
deef9f4
@LouConreux
[edit] Refine not on rotation first, only on dist cx cy, then finally…
5e9ac77 
… apply rotations
@actions-user @github-actions
Auto-commit black formatting
d12e239
@LouConreux
[edit] Set back to 95
f75e4a6
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
1a57e9e
@LouConreux
[edit] Set back normal
d868e57
@actions-user @github-actions
Auto-commit black formatting
5f90f33
@LouConreux
[edit] Set to 99
09b9ef6
@LouConreux
Merge branch 'dev' of https://github.com/LouConreux/lute into dev
a169ebb
@LouConreux
[edit] Set back to 95
90920fe
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