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SAXS/WAXS Analysis Workflows

Data analysis workflows for SAXS/WAXS

Clone repository and setup Python environment

git clone [email protected]:als-computing/SAXSWAXS_workflows.git
cd SAXSWAXS_workflows
python -m venv saxswaxs-workflows-env
source saxswaxs-workflows-env/bin/activate
pip install -r requirements.txt

The command source saxswaxs-workflows-env/bin/activate may need to be adapted for the specific operating system, see the venv documentation

Set up environment file with relevant paths

Create a file .env with the following content

TILED_URI="http://127.0.0.1:8888"
PREFECT_API_URL="http://127.0.0.1:4200/api"
TILED_API_KEY="<randomly generated key>"
PATH_TO_DATA="<path to folder that contains raw data>"
PATH_TO_PROCESSED_DATA="<path to folder where processed data can be written>"
PREFECT_WORK_DIR="<path to folder where this code resides>"

Prefect Server

In one terminal that has the environment activated start a prefect server

prefect server start

As instructed in the Prefect server startup prompt, make sure prefect is configured with the correct PREFECT_API_URL:

prefect config set PREFECT_API_URL=http://127.0.0.1:4200/api

Tiled server

Within the interface folder (the other repository /workflow-viz), follow the instructions to start a Tiled server, and a Tiled watch process that observes changes in a directory

First test

Adapt the parameters in the example in reduction.py to point to a dataset that is contained in the folder and run it

python saxswaxs-workflows/flows/reduction.py

Setup for beamtime

(Once we confirmed that the first part runs)

In another terminal, create work-pools:, the reduction-pool for reducing data, the fitting-pool for feature extraction, and the gpcam-pool for running gpCAM, and deploy all flows that are defined within prefect.yaml. For convinience, these steps are summarized in the script

./create_deployments.sh

Finally, start the workers with

prefect worker start --pool 'reduction-pool'

Copyright

MLExchange Copyright (c) 2023, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.

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