diff --git a/docs/tutorials/flyscanning/basics.md b/docs/tutorials/flyscanning/basics.md index 627f754..77ab23d 100644 --- a/docs/tutorials/flyscanning/basics.md +++ b/docs/tutorials/flyscanning/basics.md @@ -13,4 +13,4 @@ kernelspec: # Flyscanning Basics -TODO +TODO \ No newline at end of file diff --git a/docs/tutorials/tiled_integration/main.md b/docs/tutorials/tiled_integration/main.md new file mode 100644 index 0000000..589f4e2 --- /dev/null +++ b/docs/tutorials/tiled_integration/main.md @@ -0,0 +1,152 @@ +--- +jupytext: + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.16.4 +kernelspec: + display_name: Python 3 (ipykernel) + language: python + name: python3 +--- + +# Saving Bluesky Data in Tiled + ++++ + +In the standard Bluesky data model, it is assumed that each data point produced during an experiment is emitted in a separate Event document. During the acquisition, such high granularity enables fast feedback and supports low-latency downstream agents (e.g. live plotting), however the naive storage of individual documents as records in a database or lines in a file is not optimized for the retrieval of blocks of data spanning multiple rows. Instead, the recently developed solution presented here parses the Event data into a tabular format during ingestion. + +This tutorial introduces TiledWriter -- a specialized callback in Bluesky designed to aggregate and store the incoming data in a way that would facilitate future random access. TiledWriter consumes Bluesky documents (all types of them) stores their contents at rest via API calls into a Tiled server. It transforms the data streams into a tabular form, suitable for the efficient retrieval of columns. + ++++ + +### Initial Set-Up + +```{code-cell} ipython3 +import bluesky.plans as bp +from ophyd.sim import det, motor +from bluesky.run_engine import RunEngine +from bluesky.callbacks.tiled_writer import TiledWriter +from tiled.client import from_uri +from pprint import pprint +``` + +```{code-cell} ipython3 +# Start a local Tiled server +# The following is equivalent to 'tiled server catalog --temp --api-key=secret' + +from tiled_server import TempTiledServer + +server = TempTiledServer(api_key='secret', dir_path='tiled_data') +tiled_uri = server.run() +``` + +```{code-cell} ipython3 +# Initialize a Tiled client + +client = from_uri(tiled_uri, api_key="secret") +client +``` + +```{code-cell} ipython3 +# Initialize RunEngine and subscribe it to TiledWriter + +RE = RunEngine({}) +tw = TiledWriter(client) +RE.subscribe(tw) + +# Keep the documents for monitoring/debug +docs = [] +RE.subscribe(lambda name, doc : docs.append( (name, doc) )) +``` + +### Running the Acquisition + +```{code-cell} ipython3 +# Run the acquisition +docs.clear() +scan_id, = RE(bp.scan([det], motor, -5, 5, 10)) +print(f"Finished aquisition: {scan_id=}") +``` + +Executing the above cell would have produced a stream of Bluesky documents, which have been saved and can be inspected in the `docs` list. Specifically, the Descriptor (`docs[1]`) contains specification of all available `data_keys` produced by the experinment (values of detector, `det`, `motor` and `motor_setpoint`). + +```{code-cell} ipython3 +# Data specification from the Descriptor document +stream_name = docs[1][1]['name'] +print(f"Stream name: {stream_name}\n") +print("Specifications of recorded data:") +pprint(docs[1][1]['data_keys']) +``` + +The actual data values, along with their corresponding timestamps, are emmitted via Event documents (`docs[2:-1]`) + +```{code-cell} ipython3 +# Example of Event documents +pprint(docs[2:4]) +``` + +### Accessing Data in Tiled + ++++ + +The data produced during the experiment has been ingested into Tiled and stored in a container under the correpoding scan uuid. + +NOTE: The internal structure of the Bluesky container is not finzalized yet and will change in the future releases. + +```{code-cell} ipython3 +bs_run = client[scan_id] +bs_stream = bs_run[stream_name] +event_data = bs_stream['internal/events'] +event_data +``` + +It can now be accessed as a usual `pandas.DataFrame`: + +```{code-cell} ipython3 +event_data.read() +``` + +### Reading Data Directly from File + +```{code-cell} ipython3 +import pandas as pd + +data_fpath = f'./tiled_data/data/{scan_id}/{stream_name}/internal/events/partition-0.csv' +df = pd.read_csv(data_fpath) +df +``` + +### Exploring the Tiled Catalog + +```{code-cell} ipython3 +import sqlite3 + +db_fpath = f'./tiled_data/catalog.db' +con = sqlite3.connect(db_fpath) +cur = con.cursor() +``` + +```{code-cell} ipython3 +res = cur.execute("SELECT name FROM sqlite_master WHERE type='table';") +res.fetchall() +``` + +```{code-cell} ipython3 +res = cur.execute("PRAGMA table_info('assets');") +res.fetchall() +``` + +```{code-cell} ipython3 +res = cur.execute("SELECT * FROM assets;") +res.fetchall() +``` + +```{code-cell} ipython3 + +``` + +```{code-cell} ipython3 + +``` diff --git a/docs/tutorials/tiled_integration/tiled_server.py b/docs/tutorials/tiled_integration/tiled_server.py new file mode 100644 index 0000000..9510168 --- /dev/null +++ b/docs/tutorials/tiled_integration/tiled_server.py @@ -0,0 +1,54 @@ +import contextlib +import threading +import time +import uvicorn +import tempfile +import pathlib + +from tiled.server.app import build_app +from tiled.catalog import from_uri as catalog_from_uri + + +class ThreadedServer(uvicorn.Server): + + def install_signal_handlers(self): + pass + + @contextlib.contextmanager + def run_in_thread(self): + thread = threading.Thread(target=self.run) + thread.start() + try: + # Wait for server to start up, or raise TimeoutError. + for _ in range(100): + time.sleep(0.1) + if self.started: + break + else: + raise TimeoutError("Server did not start in 10 seconds.") + host, port = self.servers[0].sockets[0].getsockname() + yield f"http://{host}:{port}" + finally: + self.should_exit = True + thread.join() + + +class TempTiledServer: + + def __init__(self, port=0, dir_path=None, api_key="secret"): + if dir_path is None: + dir_path = pathlib.Path(tempfile.TemporaryDirectory().name) + else: + dir_path = pathlib.Path(dir_path) + dir_path.mkdir(parents=True, exist_ok=True) + + self.catalog = catalog_from_uri( + dir_path / "catalog.db", + writable_storage=dir_path / "data", + init_if_not_exists=True, + ) + self.app = build_app(self.catalog, authentication={"single_user_api_key": api_key}) + self._cm = ThreadedServer(uvicorn.Config(self.app, port=port, loop="asyncio")).run_in_thread() + + def run(self): + return self._cm.__enter__() diff --git a/pixi.lock b/pixi.lock index b18cd42..5775422 100644 --- a/pixi.lock +++ b/pixi.lock @@ -10,210 +10,603 @@ environments: - 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