sirepo-bluesky 0.3.0

Sirepo-Bluesky interface

Sirepo-Bluesky interface

• Free software: 3-clause BSD license

• Citation:

  Maksim S. Rakitin, Abigail Giles, Kaleb Swartz, Joshua Lynch, Paul Moeller, Robert Nagler, Daniel B. Allan, Thomas A. Caswell, Lutz Wiegart, Oleg Chubar, and Yonghua Du “Introduction of the Sirepo-Bluesky interface and its application to the optimization problems”, Proc. SPIE 11493, Advances in Computational Methods for X-Ray Optics V, 1149311 (21 August 2020); https://doi.org/10.1117/12.2569000

Purpose

An attempt to integrate Sirepo/SRW simulations with Bluesky/Ophyd.

Based on this Sirepo simulation that can be downloaded in the next section:

Prepare a local Sirepo server

• Install Sirepo using Vagrant/VirtualBox following the instructions (you will need to install VirtualBox and Vagrant)

• After the successful installation start the VM with vagrant up and ssh to it with vagrant ssh

• Run the following command to start Sirepo with the Bluesky interface (bluesky is a “secret” key used on both server and client sides, and the SIREPO_FEATURE_CONFIG_SIM_TYPES=srw part is optional if you run Sirepo directly on a Linux/Mac machine and only have SRW installed):

SIREPO_FEATURE_CONFIG_SIM_TYPES=srw SIREPO_AUTH_METHODS=bluesky:guest SIREPO_AUTH_BLUESKY_SECRET=bluesky sirepo service http

• In your browser, go to http://10.10.10.10:8000/srw, click the “Import” button in the right-upper corner and upload the archive with the simulation stored in this repo

• You should be redirected to the address like http://10.10.10.10:8000/srw#/source/IKROlKfR

• Grab the last 8 alphanumeric symbols (IKROlKfR), which represent a UID for the simulation we will be working with in the next section.

You can also consider running a Docker container:

mkdir -p $HOME/tmp/sirepo-docker-run
docker run -it --init --rm --name sirepo \
       -e SIREPO_AUTH_METHODS=bluesky:guest \
       -e SIREPO_AUTH_BLUESKY_SECRET=bluesky \
       -e SIREPO_SRDB_ROOT=/sirepo \
       -e SIREPO_COOKIE_IS_SECURE=false \
       -p 8000:8000 \
       -v $HOME/tmp/sirepo-docker-run:/sirepo \
       radiasoft/sirepo:beta bash -l -c "sirepo service http"

or with the convenience script:

bash scripts/start_docker.sh -it

Prepare Bluesky and trigger a simulated Sirepo detector

• (OPTIONAL) Make sure you have mongodb installed and the service is running (see local.yml for details)

• Create a conda environment:

conda create -n sirepo_bluesky -y -c conda-forge python=3.9 shadow3 srwpy
conda activate sirepo_bluesky
pip install sirepo-bluesky  # a package from PyPI

• Clone this repository to have access to the examples:

git clone https://github.com/NSLS-II/sirepo-bluesky/
cd sirepo-bluesky/

• Start ipython and run the following where sim_id is the UID for the simulation we are working with:

%run -i examples/prepare_det_env.py
import sirepo_bluesky.srw_detector as sd
import bluesky.plans as bp
# Note: replace '00000001' with the `sim_id` from your simulation
srw_det = sd.SirepoSRWDetector(sim_id='00000001', sim_type='srw',
                               sirepo_server='http://localhost:8000')
srw_det.select_optic('Aperture')
param1 = srw_det.create_parameter('horizontalSize')
param2 = srw_det.create_parameter('verticalSize')
srw_det.configuration_attrs = ['horizontal_extent', 'vertical_extent', 'shape']

RE(bp.grid_scan([srw_det],
                param1, 0, 1, 10,
                param2, 0, 1, 10,
                True))

You should get something like:

• Get the data:

hdr = db[-1]
imgs = list(hdr.data(f'{srw_det.name}_image'))
cfg = hdr.config_data(srw_det.name)['primary'][0]
hor_ext = cfg[f'{srw_det.name}_horizontal_extent']
vert_ext = cfg[f'{srw_det.name}_vertical_extent']
plt.imshow(imgs[21], aspect='equal', extent=(*hor_ext, *vert_ext))

You should get something like:

To view single-electron spectrum report (Hint: use a different sim_id, e.g. for the NSLS-II CHX beamline example):

%run -i examples/prepare_det_env.py
import sirepo_bluesky.srw_detector as sd
import bluesky.plans as bp
srw_det = sd.SirepoSRWDetector(sim_id='<sim_id>', source_simulation=True,
                               sirepo_server='http://localhost:8000')
srw_det.configuration_attrs = ['photon_energy', 'shape']

RE(bp.count([srw_det]))

hdr = db[-1]
cfg = hdr.config_data(srw_det.name)['primary'][0]
energies = cfg[f'{srw_det.name}_photon_energy']
spectrum, = hdr.data(f'{srw_det.name}_image')
plt.plot(energies, spectrum)

You should get something like:

Use a simulated Sirepo Flyer to run multiple simulations

• This section is based on the Young’s Double Slit Experiment Sirepo example that can be found in the wavefront propagation folder on the SRW simulations section

• Open the simulation and grab the new UID (the last 8 alphanumeric symbols)

• Start ipython and run the following:

%run -i examples/prepare_flyer_env.py
import bluesky.plans as bp
import sirepo_bluesky.sirepo_flyer as sf

• To create 5 different simulations that change 4 parameters at a time:

params_to_change = []
for i in range(1, 6):
    key1 = 'Aperture'
    parameters_update1 = {'horizontalSize': i * .1, 'verticalSize': (16 - i) * .1}
    key2 = 'Lens'
    parameters_update2 = {'horizontalFocalLength': i + 7}
    key3 = 'Obstacle'
    parameters_update3 = {'horizontalSize': 6 - i}
    params_to_change.append({key1: parameters_update1,
                             key2: parameters_update2,
                             key3: parameters_update3})

• Create the flyer and run a fly scan where sim_id is the UID of this simulation:

sirepo_flyer = sf.SirepoFlyer(sim_id='<sim_id>', server_name='http://10.10.10.10:8000',
                              root_dir=root_dir, params_to_change=params_to_change,
                              watch_name='W60')

RE(bp.fly([sirepo_flyer]))

• Access the data:

In[13]: hdr = db[-1]
        hdr.table(stream_name='sirepo_flyer')

Out[13]:
                              time                    sirepo_flyer_image  \
seq_num
1       2020-08-10 07:54:01.426501  ae51b7d7-1a0f-4613-9118-1626b4f89bf0
2       2020-08-10 07:54:01.426501  14183b1a-03f1-4333-a4a2-b9e16ccdbf29
3       2020-08-10 07:54:01.426501  2e372fb4-7fe3-47ce-acf8-9af3e2d1acad
4       2020-08-10 07:54:01.426501  7bea7ace-0be3-4b97-a936-f2cec48cb370
5       2020-08-10 07:54:01.426501  7e22377b-985c-49d9-aaf4-26c967b1bd22

        sirepo_flyer_shape  sirepo_flyer_mean  sirepo_flyer_photon_energy  \
seq_num
1               [250, 896]       3.677965e+13                      4240.0
2               [250, 546]       9.944933e+13                      4240.0
3               [250, 440]       1.492891e+14                      4240.0
4               [252, 308]       2.234285e+14                      4240.0
5               [252, 176]       3.885947e+14                      4240.0

                          sirepo_flyer_horizontal_extent  \
seq_num
1        [-0.0013627376425855513, 0.0013596958174904943]
2         [-0.001015813953488372, 0.0010120930232558139]
3        [-0.0009701657458563539, 0.0009701657458563542]
4        [-0.0008026143790849673, 0.0008026143790849673]
5        [-0.0005374045801526716, 0.0005312977099236639]

                             sirepo_flyer_vertical_extent  \
seq_num
1         [-0.000249500998003992, 0.00024750499001996017]
2         [-0.000249500998003992, 0.00024750499001996017]
3        [-0.00024650698602794426, 0.0002504990019960079]
4        [-0.0002485029940119762, 0.00025249500998003984]
5        [-0.00025149700598802393, 0.0002495009980039921]

                  sirepo_flyer_hash_value sirepo_flyer_status  \
seq_num
1        d5d6628d50bd65a329717e8ffb942224           completed
2        d6f8b77048fe6ad48e007cfb776528ad           completed
3        e5f914471d873f156c31815ab705575f           completed
4        bf507c942bb67c7191d16968de6ddd5b           completed
5        1775724d932efa3e0233781465a5a67b           completed

         sirepo_flyer_Aperture_horizontalSize  \
seq_num
1                                         0.1
2                                         0.2
3                                         0.3
4                                         0.4
5                                         0.5

         sirepo_flyer_Aperture_verticalSize  \
seq_num
1                                       1.5
2                                       1.4
3                                       1.3
4                                       1.2
5                                       1.1

         sirepo_flyer_Lens_horizontalFocalLength  \
seq_num
1                                              8
2                                              9
3                                             10
4                                             11
5                                             12

         sirepo_flyer_Obstacle_horizontalSize
seq_num
1                                           5
2                                           4
3                                           3
4                                           2
5                                           1