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| # hyperion | ||
|  [](https://codecov.io/gh/DiamondLightSource/hyperion) | ||
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| Repository for the Hyperion project to implement Unattended Data Collections on the Diamond MX beamlines using the [BlueSky](https://nsls-ii.github.io/bluesky/) / Ophyd framework from BNL. | ||
| **The hyperion project has now been integrated into [mx-bluesky](https://github.com/DiamondLightSource/mx-bluesky/tree/main/src/mx_bluesky/hyperion). The reasoning for this can be found [here](https://github.com/DiamondLightSource/mx-bluesky/issues/169)** | ||
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| Currently the software is able to: | ||
| * Centre a sample, first using an optical camera, then using an xray grid scan. This centring is done at two orthogonal angles so that the sample is centred in 3D. | ||
| * Perform a rotation scan to take diffraction data of the sample | ||
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| Left to do is: | ||
| * Mount/unmount samples | ||
| * Set up the beamline to be in a standard state for collection | ||
| * Change energy of the beamline | ||
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| Development Installation | ||
| ================= | ||
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| This project supports only the most recent Python version for which our dependencies are available - currently Python 3.11. | ||
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| Run `./utility_scripts/dls_dev_env.sh` (This assumes you're on a DLS machine. If you are not, you should be able to just run a subset of this script) | ||
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| Note that because Hyperion makes heavy use of [Dodal](https://github.com/DiamondLightSource/dodal) this will also pull a local editable version of dodal to the parent folder of this repo. | ||
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| Controlling the Gridscan Externally (e.g. from GDA) | ||
| ===================== | ||
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| Starting the bluesky runner | ||
| ------------------------- | ||
| You can start the bluesky runner by running `run_hyperion.sh`. Note that this will fail on a developer machine unless you have a simulated beamline running, instead you should do `run_hyperion.sh --dev --skip-startup-connection`, which will give you a running instance (note that without hardware trying to run a plan on this will fail). The `--dev` flag ensures that logging will not be sent to the production Graylog. | ||
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| This script will determine whether you are on a beamline or a production machine based on the `BEAMLINE` environment variable. If on a beamline Hyperion will run with `INFO` level logging, sending its logs to both production graylog and to the beamline/log/bluesky/hyperion.log on the shared file system. | ||
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| If in a dev environment Hyperion will log to a local graylog instance instead and into a file at `./tmp/dev/hyperion.log`. A local instance of graylog will need to be running for this to work correctly. To set this up and run up the containers on your local machine run the `setup_graylog.sh` script. | ||
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| This uses the generic defaults for a local graylog instance. It can be accessed on `localhost:9000` where the username and password for the graylog portal are both admin. | ||
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| The hyperion python module can also be run directly without the startup script. It takes the same command line options, including: | ||
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| `INFO` level logging of the Bluesky event documents can be enabled with the flag | ||
| ``` | ||
| python -m hyperion --dev --verbose-event-logging | ||
| ``` | ||
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| Lastly, you can choose to skip running the hardware connection scripts on startup with the flag | ||
| ``` | ||
| python -m hyperion --skip-startup-connection | ||
| ``` | ||
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| Testing | ||
| -------------- | ||
| Unit tests can be run with `python -m pytest -m "not s03" --random-order`. To see log output from tests you can turn on logging with the `--logging` command line option and then use the `-s` command line option to print logs into the console. So to run the unit tests such that all logs are at printed to the terminal, you can use `python -m pytest -m "not s03" --random-order --logging -s`. Note that this will likely overrun your terminal buffer, so you can narrow the selection of tests with the `-k "<test name pattern>"` option. | ||
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| To be able to run the system tests, or a complete fake scan, we need the simulated S03 beamline. This can be found at: https://gitlab.diamond.ac.uk/controls/python3/s03_utils | ||
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| To fake interaction and processing with Zocalo, you can run `fake_zocalo/dls_start_fake_zocalo.sh`, and make sure to run `module load dials/latest` before starting hyperion (in the same terminal). | ||
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| Tracing | ||
| -------------- | ||
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| Tracing information (the time taken to complete different steps of experiments) is collected by an [OpenTelemetry](https://opentelemetry.io/) tracer, and currently we export this information to a local Jaeger monitor (if available). To see the tracing output, run the [Jaeger all-in-one container](https://www.jaegertracing.io/docs/1.6/getting-started/), and go to the web interface at http://localhost:16686. | ||
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| Starting a scan | ||
| -------------- | ||
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| To start a scan you can do the following: | ||
| ``` | ||
| curl -X PUT http://127.0.0.1:5005/flyscan_xray_centre/start --data-binary "@tests/test_data/parameter_json_files/test_parameters.json" -H "Content-Type: application/json" | ||
| ``` | ||
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| Getting the Runner Status | ||
| ------------------------ | ||
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| To get the status of the runner: | ||
| ``` | ||
| curl http://127.0.0.1:5005/status | ||
| ``` | ||
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| Stopping the Scan | ||
| ----------------- | ||
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| To stop a scan that is currently running: | ||
| ``` | ||
| curl -X PUT http://127.0.0.1:5005/stop | ||
| ``` | ||
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| Writing out `DEBUG` logs | ||
| ------------------------ | ||
| To make the app write the `DEBUG` level logs stored in the `CircularMemoryHandler`: | ||
| ``` | ||
| curl -X PUT http://127.0.0.1:5005/flush_debug_log | ||
| ``` |