sirepo-bluesky 0.0.2

Sirepo-Bluesky interface

Sirepo-Bluesky interface

• Free software: 3-clause BSD license

• Documentation: https://NSLS-II.github.io/sirepo-bluesky.

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 --rm -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 /home/vagrant/.pyenv/shims/sirepo service http

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:

git clone https://github.com/NSLS-II/sirepo-bluesky/
cd sirepo-bluesky/
conda create -n sirepo_bluesky python=3.7 -y
conda activate sirepo_bluesky
pip install -e .

• 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.sirepo_detector as sd
import bluesky.plans as bp
sirepo_det = sd.SirepoDetector(sim_id='<sim_id>', reg=db.reg)
sirepo_det.select_optic('Aperture')
param1 = sirepo_det.create_parameter('horizontalSize')
param2 = sirepo_det.create_parameter('verticalSize')
sirepo_det.read_attrs = ['image', 'mean', 'photon_energy']
sirepo_det.configuration_attrs = ['horizontal_extent',
                                  'vertical_extent',
                                  'shape']

RE(bp.grid_scan([sirepo_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('sirepo_det_image'))
cfg = hdr.config_data('sirepo_det')['primary'][0]
hor_ext = cfg['{}_horizontal_extent'.format(sirepo_det.name)]
vert_ext = cfg['{}_vertical_extent'.format(sirepo_det.name)]
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.sirepo_detector as sd
import bluesky.plans as bp
sirepo_det = sd.SirepoDetector(sim_id='<sim_id>', reg=db.reg, source_simulation=True)
sirepo_det.read_attrs = ['image', 'mean', 'photon_energy']
sirepo_det.configuration_attrs = ['horizontal_extent',
                                  'vertical_extent',
                                  'shape']

RE(bp.count([sirepo_det]))

hdr = db[-1]
imgs = list(hdr.data('sirepo_det_image'))
plt.plot(imgs[-1])

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:

hdr = db[-1]
hdr.table(stream_name="sirepo_flyer")

Databroker will return the following information: