diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 00000000..84f6269c --- /dev/null +++ b/.codespellrc @@ -0,0 +1,18 @@ +[codespell] + +skip = node_modules, + *-lock.json, + *.git, + *.pyc, + __pycache__, + ./build, + ./dist, + ./apidocs, + ./openflexure, + ./htmlcov, + ./src/openflexure_microscope_server/static, + .venv, + *.egg-info, + report.xml + +regex = [a-zA-Z0-9\-'’]+ diff --git a/.gitignore b/.gitignore index 19581d57..b94a21d8 100644 --- a/.gitignore +++ b/.gitignore @@ -58,8 +58,8 @@ pytest_report.xml # Django stuff: *.log -# Sphinx documentation -docs/_build/ +# Documentation +apidocs # PyBuilder target/ diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 77c2143b..0a2f663e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -72,6 +72,13 @@ version-check: - tags - web +# A job to protect reviewers from Julian's terrible spelling. +spelling: + stage: analysis + extends: .python + script: + - codespell . + # Python static analysis with ruff ruff-lint: stage: analysis @@ -168,6 +175,31 @@ build: paths: - "src/openflexure_microscope_server/static/" +build-docs: + extends: .python + stage: build + script: + - | + pydoctor -W \ + --docformat restructuredtext \ + --project-name "OpenFlexure Microscope Server" \ + --project-version $CI_COMMIT_REF_NAME \ + --theme readthedocs \ + --html-viewsource-base https://gitlab.com/openflexure/openflexure-microscope-server/-/tree/$CI_COMMIT_SHA/ \ + src/openflexure_microscope_server + - echo "JOB_ID=$CI_JOB_ID" > build-docs.env + artifacts: + expire_in: 1 week + name: "${CI_PROJECT_NAME}-${CI_JOB_NAME}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_SHORT_SHA}-docs" + paths: + - apidocs + reports: + dotenv: build-docs.env + environment: + name: review/$CI_COMMIT_REF_SLUG + url: https://$CI_PROJECT_ROOT_NAMESPACE.gitlab.io/-/openflexure-microscope-server/-/jobs/$JOB_ID/artifacts/apidocs/index.html + + server_integration_tests: extends: .python stage: integration @@ -261,3 +293,17 @@ server_integration_tests: # only: # - tags # - web + +pages: + needs: + - job: build-docs + artifacts: true + stage: deploy + image: "alpine:latest" + script: + - mv apidocs public + artifacts: + paths: + - public + only: + - v3 diff --git a/CHANGELOG.md b/CHANGELOG.md index 9bfbc0cd..6147a9bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -83,7 +83,7 @@ The following merge requests have been merged into v3: * !286 Use same version number for server and webapp, add CI check * !285 Swapped the order of CSM so y axis is completed first * !283 Add scan directory to json config -* !287 Update depedencies and changelog prior to v3.0.0-alpha1 release +* !287 Update depedencies and changelog prior to v3.0.0-alpha1 release # [v2.11.0](https://gitlab.com/openflexure/openflexure-microscope-server/compare/v2.10.1...v2.11.0) (2022-08-08) ## New features diff --git a/README.md b/README.md index f88df89c..45469838 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ > ## This is the v3 development branch > We are no longer actively developing v2, but v3 is not yet released. -> v3 is not yet stable enough for wider public release. Deveopment snapshots are released from time to time. +> v3 is not yet stable enough for wider public release. Development snapshots are released from time to time. > If you want to use a development snapshot before we do a wider alpha release the best thing to do is get in contact on the [forum](https://openflexure.discourse.group/). If you want to look at the code for v2 you should look at the [master branch](https://gitlab.com/openflexure/openflexure-microscope-server/-/tree/master). diff --git a/check_version_sync.py b/check_version_sync.py index c47365d7..23c13b1b 100755 --- a/check_version_sync.py +++ b/check_version_sync.py @@ -1,9 +1,5 @@ #! /usr/bin/env python3 - -""" -A script to check that the npm version string matches the python -version string exactly. -""" +"""Check that the npm version string matches the Python version string exactly.""" import json import tomllib diff --git a/hardware-specific-tests/picamera2/test_acquisition.py b/hardware-specific-tests/picamera2/test_acquisition.py index 3d8ef5c0..b8e2fe88 100644 --- a/hardware-specific-tests/picamera2/test_acquisition.py +++ b/hardware-specific-tests/picamera2/test_acquisition.py @@ -1,3 +1,5 @@ +"""Test data collection from the Raspberry Picamera.""" + from fastapi.testclient import TestClient from PIL import Image import numpy as np @@ -11,10 +13,13 @@ from openflexure_microscope_server.things.camera.picamera import StreamingPiCame @fixture(scope="module") def client(): - """ - A pytest fixture that initialises a test client for the StreamingPiCamera2 Thing. - This fixture sets up a ThingServer, registers a StreamingPiCamera2 instance at the - "/camera/" endpoint, and provides a ThingClient for interacting with it during tests. + """Initialise a test client for the StreamingPiCamera2 Thing. + + This fixture: + + * Sets up a ThingServer, + * Registers a StreamingPiCamera2 instance at the "/camera/" endpoint + * Provides a ThingClient for interacting with it during tests. """ server = ThingServer() server.add_thing(StreamingPiCamera2(), "/camera/") @@ -24,16 +29,14 @@ def client(): def test_calibration(client): - """ - Check that full auto calibrate completes without an exception - """ + """Check that full auto calibrate completes without an exception.""" client.full_auto_calibrate() def test_jpeg_and_array(client): - """ - Check that grabbing a jpeg from the stream results in the same size - image as a array capture or a jpeg capture. + """Check that a jpeg grabbed from the stream is the same size as other captures. + + Compare it to an array capture and a jpeg capture. """ # Grab a jpeg from the stream blob = client.grab_jpeg() diff --git a/hardware-specific-tests/picamera2/test_exposure_time_drift.py b/hardware-specific-tests/picamera2/test_exposure_time_drift.py index 4e712e5e..8e566612 100644 --- a/hardware-specific-tests/picamera2/test_exposure_time_drift.py +++ b/hardware-specific-tests/picamera2/test_exposure_time_drift.py @@ -1,5 +1,4 @@ -""" -Check exposure times do not drift. +"""Check exposure times do not drift. This can get very tedious. Recommend running pytest with -s option to monitor progress. @@ -19,8 +18,7 @@ logging.basicConfig(level=logging.DEBUG) def _test_exposure_time_drift(desired_time): - """ - Capture 10 full resolution images and check that the exposure time remains constant + """Capture 10 full resolution images and check that the exposure time remains constant. This confirms that automatic exposure time adjustment is fully turned off """ @@ -64,8 +62,6 @@ def _test_exposure_time_drift(desired_time): def test_exposure_time_drift(): - """ - Performs the exposure time test for a range of exposure time values. - """ + """Performs the exposure time test for a range of exposure time values.""" for desired_time in [100, 1000, 10000]: _test_exposure_time_drift(desired_time) diff --git a/hardware-specific-tests/picamera2/test_sensor_mode.py b/hardware-specific-tests/picamera2/test_sensor_mode.py index fbc575d6..af875d9c 100644 --- a/hardware-specific-tests/picamera2/test_sensor_mode.py +++ b/hardware-specific-tests/picamera2/test_sensor_mode.py @@ -1,3 +1,5 @@ +"""Test changing and setting camerat modes on the Raspberry Picamera.""" + import logging from fastapi.testclient import TestClient @@ -12,9 +14,7 @@ logging.basicConfig(level=logging.DEBUG) def test_sensor_mode(): - """ - Test capturing raw arrays in two different sensor modes - """ + """Test capturing raw arrays in two different sensor modes.""" cam = StreamingPiCamera2() server = ThingServer() server.add_thing(cam, "/camera/") diff --git a/hardware-specific-tests/picamera2/test_tuning.py b/hardware-specific-tests/picamera2/test_tuning.py index a6fd9b76..35a67676 100644 --- a/hardware-specific-tests/picamera2/test_tuning.py +++ b/hardware-specific-tests/picamera2/test_tuning.py @@ -1,6 +1,4 @@ -""" -Tests that check that a tuning file can be reloaded -""" +"""Tests that check that a tuning file can be reloaded.""" import os @@ -16,17 +14,13 @@ MODEL = Picamera2.global_camera_info()[0]["Model"] def load_default_tuning(): - """ - Return the default tuning file for the connected camera. - """ + """Return the default tuning file for the connected camera.""" fname = f"{MODEL}.json" return Picamera2.load_tuning_file(fname) def generate_bad_tuning(): - """ - Return a tuning file with an invalid version number to force an error when loaded. - """ + """Return a tuning file with an invalid version number to force an error when loaded.""" default_tuning = load_default_tuning() bad_tuning = default_tuning.copy() bad_tuning["version"] = 999 @@ -34,8 +28,7 @@ def generate_bad_tuning(): def print_tuning(read_file: bool = False): - """ - Print the path of the default tuning file from the the environment variable. + """Print the path of the default tuning file from the the environment variable. :param read_file: Boolean, set true to also print the file contents. @@ -53,7 +46,8 @@ def print_tuning(read_file: bool = False): def _test_bad_tuning_after_good_tuning(configure: bool = False): - """ + """Test loading good, bad, then another good tuning files in sequence. + Load the default tuning file into the camera, re-load with a broken tuning file, check it errors. Finally check the default tuning file will load again afterwards. @@ -101,19 +95,35 @@ def _test_bad_tuning_after_good_tuning(configure: bool = False): @pytest.mark.filterwarnings("ignore: Exception ignored") def test_bad_tuning_after_good_tuning_noconfigure(): - _test_bad_tuning_after_good_tuning(False) + """First run setting good, then bad, then good tuning. + + create_preview_configuration() is NOT run on initial setup. + """ + _test_bad_tuning_after_good_tuning(configure=False) @pytest.mark.filterwarnings("ignore: Exception ignored") def test_bad_tuning_after_good_tuning_configure(): - _test_bad_tuning_after_good_tuning(True) + """Second run setting good, then bad, then good tuning. + + create_preview_configuration() is run on initial setup this time. + """ + _test_bad_tuning_after_good_tuning(configure=True) @pytest.mark.filterwarnings("ignore: Exception ignored") def test_bad_tuning_after_good_tuning_noconfigure2(): - _test_bad_tuning_after_good_tuning(False) + """3rd run setting good, then bad, then good tuning. + + create_preview_configuration() is NOT run on initial setup. + """ + _test_bad_tuning_after_good_tuning(configure=False) @pytest.mark.filterwarnings("ignore: Exception ignored") def test_bad_tuning_after_good_tuning_configure2(): - _test_bad_tuning_after_good_tuning(True) + """Final run setting good, then bad, then good tuning. + + create_preview_configuration() is run on initial setup again. + """ + _test_bad_tuning_after_good_tuning(configure=True) diff --git a/integration-tests/testfile.py b/integration-tests/testfile.py index 959e24cc..a61fdb64 100755 --- a/integration-tests/testfile.py +++ b/integration-tests/testfile.py @@ -1,11 +1,10 @@ #! /usr/bin/env python3 -"""This module fires up a server in a subprocess to allow for integration tests. +"""Start a server subprocess for integration tests. -These are separated from the unit tests to stop them artificially inflating the test -coverage. For now this file should be run directly not with a test framework. +These tests are separated from unit tests to avoid inflating test coverage. +For now, this file should be run directly rather than through a test framework. -These tests are designed to run on CI. They should work on Linux or WSL for local -debugging. +They are designed to run on CI and should work on Linux or WSL for local debugging. """ from typing import Optional @@ -31,7 +30,7 @@ SERVER_CMD: list[str] = [ def main() -> None: - """Set up the server, run basic checks, shutdown, check for graceful exit + """Set up the server, run basic checks, shutdown, check for graceful exit. The basic checks include checks that: - The server boots @@ -70,7 +69,7 @@ def main() -> None: def test_client_connection() -> None: - """Check a ThingClient can interact with the simulation microscope camera""" + """Check a ThingClient can interact with the simulation microscope camera.""" print("Connecting Python client to microscope, and capturing image") cam_client = lt.ThingClient.from_url("http://localhost:5000/camera/") img = Image.open(cam_client.grab_jpeg().open()) @@ -82,7 +81,7 @@ def test_client_connection() -> None: def subscribe_to_mjpeg_stream() -> subprocess.Popen: """Start a background process subscribed to the mjpeg stream. - :return: The Popen object for the ongoing process. + :returns: The Popen object for the ongoing process. :raises: RuntimeError if the stream is not still connected after 2s """ @@ -125,12 +124,11 @@ def set_up_working_dir() -> None: def start_server() -> subprocess.Popen: - """ - Start the server in a subprocess. + """Start the server in a subprocess. The server is started in a subprocess and all outputs are buffered. - :return: Popen object for the ongoing process + :returns: Popen object for the ongoing process """ process = subprocess.Popen( SERVER_CMD, @@ -156,7 +154,6 @@ def error_if_server_not_started( :raises RuntimeError: If the server is not running as expected. """ - confirmed_uvicorn_is_running = False t_start = time() @@ -181,7 +178,7 @@ def error_if_server_not_started( def check_for_graceful_shutdown(server_process: subprocess.Popen) -> None: - """Check the server shutdown gracefully + """Check the server shutdown gracefully. Check the subprocess is not running Check the logs have no errors @@ -204,7 +201,7 @@ def check_for_graceful_shutdown(server_process: subprocess.Popen) -> None: def read_process_buffers(process: subprocess.Popen) -> list[str]: - """Return STDOUT from a process""" + """Return STDOUT from a process.""" stdout = [] while line := process.stdout.readline(): diff --git a/pyproject.toml b/pyproject.toml index ba5bd0da..e45c6eaf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,8 @@ dev = [ "pytest-mock==3.14", "matplotlib~=3.10", "hypothesis", + "pydoctor~=25.4", + "codespell~=2.4", ] pi = [ "picamera2~=0.3.27", @@ -106,10 +108,10 @@ select = [ # "B", # Flake8 bugbear "A", # Flake8 builtins checker "C", # Flake8 comprehensions -# "FIX", #TODO/FIXME's in code. These should be added during develoment for ongoing tasks. +# "FIX", #TODO/FIXME's in code. These should be added during development for ongoing tasks. # If they are not fixed before merge they should be converted to GitLab issues # "LOG", # Flake8 logging issues (pedantic logger formatting issues can be added with "G") -# "T20", # Warns for print statments, production code should log +# "T20", # Warns for print statements, production code should log # "PT", # pytest linting "RET", # Consistent clear return statements "RSE", # Raise parentheses @@ -118,10 +120,19 @@ select = [ "C90", # McCabe complexity! "NPY", # Numpy linting "N", # PEP8 naming -# "D", # Docstring checks these may need to be added gradually + "D", # Docstring checks these may need to be added gradually "ERA001", # Commented out code! ] ignore = [ - "E501" # Ignore long lines for now + "E501", # Ignore long lines for now + "D203", # incompatible with D204 + "D213", # incompatible with D212 + "D400", # A stricter version of #415 that doesn't allow ! + # The checkers below should be turned on as they complain about missing docstrings. ] + +[tool.ruff.lint.pydocstyle] +# This lets the D401 checker understand that decorated thing properties and thing +# settings act like properties so should be documented as such. +property-decorators = ["labthings_fastapi.thing_property", "labthings_fastapi.thing_setting"] \ No newline at end of file diff --git a/ruff-increased-checking.toml b/ruff-increased-checking.toml index 5973655d..fd63f8fe 100644 --- a/ruff-increased-checking.toml +++ b/ruff-increased-checking.toml @@ -19,10 +19,10 @@ select = [ "B", # Flake8 bugbear "A", # Flake8 builtins checker "C", # Flake8 comprehensions - "FIX", #TODO/FIXME's in code. These should be added during develoment for ongoing tasks. + "FIX", #TODO/FIXME's in code. These should be added during development for ongoing tasks. # If they are not fixed before merge they should be converted to GitLab issues "LOG", # Flake8 logging issues (pedantic logger formatting issues can be added with "G") - "T20", # Warns for print statments, production code should log + "T20", # Warns for print statements, production code should log "PT", # pytest linting "RET", # Consistent clear return statements "RSE", # Raise parentheses diff --git a/scripts/zenodo/README.md b/scripts/zenodo/README.md index 6fbc93fd..7f708e99 100644 --- a/scripts/zenodo/README.md +++ b/scripts/zenodo/README.md @@ -1,5 +1,5 @@ # Zenodo archiving -This folder contains some scripts put together by Kaspar Bumke, and re-used by Richard, to upload the contents of the repository, together with any CI build artefacts, to Zenodo. The result is a link, taking you to a pre-populated upload on Zenodo that you can manually correct and upload. In order to customise it for a new project, there are a few steps you need, outlined below. +This folder contains some scripts put together by Kaspar Bumke, and reused by Richard, to upload the contents of the repository, together with any CI build artefacts, to Zenodo. The result is a link, taking you to a pre-populated upload on Zenodo that you can manually correct and upload. In order to customise it for a new project, there are a few steps you need, outlined below. ## Setting up archival * Copy this folder to `scripts/zenodo` in your repository. diff --git a/scripts/zenodo/upload_to_zenodo.py b/scripts/zenodo/upload_to_zenodo.py index 64eefdeb..309efec1 100644 --- a/scripts/zenodo/upload_to_zenodo.py +++ b/scripts/zenodo/upload_to_zenodo.py @@ -1,9 +1,11 @@ +"""A script for uploading data to Zenodo.""" + import os from argparse import ArgumentParser, Namespace from zenodo import Zenodo import yaml -# you have to explicitely set ZENODO_USE_SANDBOX=false to not use the +# You have to explicitly set ZENODO_USE_SANDBOX=false to not use the # sandbox, any other value or unset variable means this script will use # the sandbox zenodo site if "ZENODO_USE_SANDBOX" in os.environ: @@ -19,17 +21,19 @@ else: def parse_arguments() -> Namespace: + """Parse the commandline arguments and return a namespace containing the result.""" p = ArgumentParser(description="Upload data to Zenodo") p.add_argument("paths", help="Directories and files to upload to Zenodo", nargs="*") return p.parse_args() def script_directory(path): - """resolves path to directory of the current script""" + """Return path to directory of the current script.""" return os.path.join(os.path.dirname(os.path.realpath(__file__)), path) def get_meta(): + """Return the metadata in the script directory as a dictionary.""" with open(script_directory("metadata.yaml"), encoding="utf-8") as f: metadata = f.read() @@ -37,6 +41,10 @@ def get_meta(): def main(): + """Create the zenodo deposit and upload it to Zenodo. + + This is the main function called when the full script is run. + """ args = parse_arguments() metadata = get_meta() diff --git a/scripts/zenodo/zenodo.py b/scripts/zenodo/zenodo.py index 943a50df..fdf47777 100644 --- a/scripts/zenodo/zenodo.py +++ b/scripts/zenodo/zenodo.py @@ -1,9 +1,9 @@ -""" +"""A script for packaging data for Zenodo. + Copyright (c) 2020 Bath Open Instrumentation Group Adapted from: https://gitlab.com/schlauch/zenodo-api-test/ Copyright (c) 2018 German Aerospace Center (DLR). All rights reserved. SPDX-License-Identifier: MIT-DLR - """ import json @@ -13,7 +13,15 @@ import requests class Zenodo: + """A class that packages data for Zenodo.""" + def __init__(self, api_token, use_sandbox=True): + """Initialise the zenodo packager with the API token. + + :param api_token: Your Zenodo API key. + :param use_sandbox: True to pushing to ``sandbox.zenodo.org`` rather than + ``zenodo.org`` for testing. + """ self._api_token = api_token self._use_sandbox = use_sandbox if use_sandbox: @@ -22,8 +30,7 @@ class Zenodo: self.zenodo_url = "https://zenodo.org/api/deposit/depositions" def create_new_deposit(self): - """Creates a new (unpublished) Zenodo deposit and return its deposition ID.""" - + """Create a new (unpublished) Zenodo deposit and return its deposition ID.""" headers = {"Content-Type": "application/json"} r = requests.post( self.zenodo_url, @@ -36,8 +43,7 @@ class Zenodo: return r.json() def set_metadata(self, deposition_id, metadata): - """Sets the given metadata for the specified deposit.""" - + """Set the given metadata for the specified deposit.""" headers = {"Content-Type": "application/json"} r = requests.put( self.zenodo_url + "/{}".format(deposition_id), @@ -49,8 +55,7 @@ class Zenodo: print(r.json()) def upload_file(self, deposition_id, file_path): - """Uploads a new file for the given deposit.""" - + """Upload a new file for the given deposit.""" file_name = os.path.basename(file_path) data = {"filename": file_name} files = {"file": open(file_path, "rb")} @@ -64,8 +69,7 @@ class Zenodo: print(r.json()) def publish_deposit(self, deposition_id): - """Publishes the given deposit. BEWARE: It is now visible to all!!!""" - + """Publish the given deposit. BEWARE: It is now visible to all!!!""" r = requests.post( self.zenodo_url + "/{}/actions/publish".format(deposition_id), params={"access_token": self._api_token}, @@ -74,8 +78,7 @@ class Zenodo: print(r.json()) def create_new_version(self, deposition_id): - """Creates a new version of an already published deposit.""" - + """Create a new version of an already published deposit.""" r = requests.post( self.zenodo_url + "/{}/actions/newversion".format(deposition_id), params={"access_token": self._api_token}, @@ -85,8 +88,7 @@ class Zenodo: return os.path.basename(r.json()["links"]["latest_draft"]) def remove_all_files(self, deposition_id): - """Removes all uploaded files of a unpublished deposit.""" - + """Remove all uploaded files of a unpublished deposit.""" r = requests.get( self.zenodo_url + "/{}/files".format(deposition_id), params={"access_token": self._api_token}, diff --git a/src/openflexure_microscope_server/__init__.py b/src/openflexure_microscope_server/__init__.py index e69de29b..67e2757a 100644 --- a/src/openflexure_microscope_server/__init__.py +++ b/src/openflexure_microscope_server/__init__.py @@ -0,0 +1,17 @@ +"""The OpenFlexure Microscope Server Package. + +The OpenFlexure Microscope Server is a LabThings-FastAPI server. All hardware +interfaces, and almost all functionality exposed over HTTP is done using ``Things``. + +On the microscope the server is started by systemd. It can be controlled using commands +such as ``ofm restart``, ``ofm start``, and ``ofm stop``. + +The server can also be run in simulation mode from the terminal. In the root directory +of the repository the server can be started with run: + +.. code-block:: bash + + openflexure-microscope-server --fallback -c ./ofm_config_simulation.json + + +""" diff --git a/src/openflexure_microscope_server/logging.py b/src/openflexure_microscope_server/logging.py index 63832652..eb49f11f 100644 --- a/src/openflexure_microscope_server/logging.py +++ b/src/openflexure_microscope_server/logging.py @@ -1,3 +1,16 @@ +"""Configure logging for the OpenFlexure Server. + +A module containing a custom logging handler and helper function for +the OpenFlexure server. These handle formatting logs, ensuring that logs +are logged both to a file and to the terminal (see note below!). Functionality +is also provided for retrieving logs for to send over HTTP. + +Note that when running in production OpenFlexure Microscope the server is run via +``systemd``. As such, the logs that are sent to the terminal (STDERR) or any other +output to STDOUT/STDERR are captured by ``systemd``. These can be viewed by using +``journalctl`` or the ``ofm journal`` command. +""" + import logging from logging.handlers import RotatingFileHandler import os @@ -8,9 +21,17 @@ OFM_LOG_FILE = None def configure_logging(log_folder): + """Configure logging for the server while it is running. + + This modifies the root logger to have a rotating file handler and + adds a custom handler that prints and stores all records except + ``uvicorn.access`` logs. + + It is important not to let Uvicorn override these settings. + """ root_logger = logging.getLogger() root_logger.setLevel(logging.INFO) - # Explictly make OFM_LOG_FILE a global so it can be updated based on log settings + # Explicitly make OFM_LOG_FILE a global so it can be updated based on log settings global OFM_LOG_FILE OFM_LOG_FILE = os.path.join(log_folder, "openflexure_microscope.log") @@ -39,25 +60,24 @@ def configure_logging(log_folder): def retrieve_log() -> PlainTextResponse: - """ - Returns logs since we started running the server, up to a maximum of - 250 messages. This log is the one shown in the UI and on the logging page. + """Return logs since the server started, up to a maximum of 250 messages. - It does not include any of the `uvicorn.access` logs as these are emmitted + This log is the one shown in the UI and on the logging page. + + It does not include any of the ``uvicorn.access`` logs as these are emitted every time any API route is called. - All logs, including `uvicorn.access` are logged to the OFM_LOG_FILE (see above) - ths is the best place to get logs about crashes. + All logs, including ``uvicorn.access`` are logged to the OFM_LOG_FILE (see above) + this is the best place to get logs about crashes. """ return PlainTextResponse(OFM_HANDLER.log_history) def retrieve_log_from_file() -> PlainTextResponse: - """ - Returns the full log from the file for downloading. + """Return the full log from the file for downloading. Note this is read and then sent as otherwise it causes a RuntimeError if it - is written to while sending through FileResponse + is written to while sending through FileResponse. """ if OFM_LOG_FILE is None: raise RuntimeError( @@ -69,29 +89,33 @@ def retrieve_log_from_file() -> PlainTextResponse: class OFMHandler(logging.Handler): - """ - A child class of logging.Handler. This class handles storing the most recent - logs for access by the server. - """ + """A logging.Handler that stores the most recent logs for access by the server.""" def __init__(self, level=logging.INFO, max_logs=250): + """Initialise the handler with a set logging level and message buffer size. + + :param level: The level of logs captured. As standard logs of INFO and above + are captured. + :param max_logs: The maximum number of logs to hold in memory. This sets + how many can be returned over HTTP. + """ super().__init__(level=level) self._log = [] self._max_logs = max_logs def append_record(self, record): - """ - Use the built in formatter to format the record, then save - it to an array. Pop any in excess of the maximum number of logs + """Format message and append it to a list of records. + + The built in formatter is used to format the record. + + Any records in excess of the maximum number of logs are removed. """ self._log.append(self.format(record)) while len(self._log) > self._max_logs: self._log.pop(0) def emit(self, record): - """ - Emit will save the logged record to the log - """ + """Emit will save the logged record to the log.""" # Basic filter for now that simply stops uvicorn.access logs # These are the logs each time an API endpoint is accessed # This is only the log for the UI. @@ -109,9 +133,7 @@ class OFMHandler(logging.Handler): @property def log_history(self): - """ - Return the log history up to the maximum number of logs - """ + """Return the log history up to the maximum number of logs.""" return "\n".join(self._log) diff --git a/src/openflexure_microscope_server/scan_directories.py b/src/openflexure_microscope_server/scan_directories.py index 361abf40..0fa96b48 100644 --- a/src/openflexure_microscope_server/scan_directories.py +++ b/src/openflexure_microscope_server/scan_directories.py @@ -1,9 +1,4 @@ -""" -This submodule contains functionality for interacting with scan directories. - -Currently it handles scan getting information from a information from a scan directory, -eventually is should handle all the file system operation for smart_scan. -""" +"""Functionality to manage file system operations for scan directories.""" from typing import Optional import os @@ -21,11 +16,11 @@ IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpe?g$") class NotEnoughFreeSpaceError(IOError): - pass + """An exception raised if there is not enough free space on disk to scan.""" class ScanInfo(BaseModel): - """Summary information about a scan folder""" + """Summary information about a scan folder.""" name: str created: float @@ -36,35 +31,37 @@ class ScanInfo(BaseModel): class ScanDirectoryManager: - """ - A class for managing interactions with scan directories - """ + """A class for managing interactions with scan directories.""" _base_scan_dir: str def __init__(self, base_scan_dir: str): + """Initialise the scan directory manager. + + :param base_scan_dir: Path of the directory that holds all scans. + """ self._base_scan_dir = base_scan_dir if not os.path.exists(self._base_scan_dir): os.makedirs(self._base_scan_dir) @property def base_dir(self) -> str: - """The base directory scans are saved to""" + """The base directory scans are saved to.""" return self._base_scan_dir def exists(self, scan_name: str) -> bool: - """True if scan of this name exists on disk""" + """Return True if scan of this name exists on disk.""" return os.path.isdir(self.path_for(scan_name)) def path_for(self, scan_name: str) -> str: - """Return the path for a given scan name + """Return the path for a given scan name. Returns the path even if it doesn't exist """ return os.path.join(self._base_scan_dir, scan_name) def img_dir_for(self, scan_name: str) -> str: - """Return the path for the image dir for a given scan name + """Return the path for the image dir for a given scan name. Returns the path even if it doesn't exist """ @@ -73,7 +70,7 @@ class ScanDirectoryManager: def get_file_path_from( self, scan_name: str, filename: str, check_exists: bool = False ) -> Optional[str]: - """Return the full file path for the file within a scan directory + """Return the full file path for the file within a scan directory. If check_exists is True then None will be returned if the file does not exist. @@ -87,7 +84,7 @@ class ScanDirectoryManager: def get_file_path_from_img_dir( self, scan_name: str, filename: str, check_exists: bool = False ) -> Optional[str]: - """Return the full file path for the file within a scan directory + """Return the full file path for the file within a scan directory. If check_exists is True, None is returned if the file does not exist. If False then the path is returned anyway @@ -110,19 +107,18 @@ class ScanDirectoryManager: @property def all_scans(self) -> list[str]: - """Return a list of the scan names in the base directory""" + """Return a list of the scan names in the base directory.""" return [f.name for f in os.scandir(self._base_scan_dir) if f.is_dir()] def all_scans_info(self) -> list[ScanInfo]: - """Return a lists of ScanInfo objects for each scan""" - + """Return a lists of ScanInfo objects for each scan.""" all_info: list[ScanInfo] = [] for scan_name in self.all_scans: all_info.append(ScanDirectory(scan_name, self.base_dir).scan_info()) return all_info def _unique_scan_name(self, scan_name: str) -> str: - """Get the next unique scan name starting with the given name + """Get the next unique scan name starting with the given name. For more explanation on the scan naming see `new_scan_dir` """ @@ -151,9 +147,9 @@ class ScanDirectoryManager: return f"{scan_name}_{scan_num:0{SCAN_ZERO_PAD_DIGITS}d}" def new_scan_dir(self, scan_name: str) -> "ScanDirectory": - """Get a unique name for this scan and create a directory for it + """Get a unique name for this scan and create a directory for it. - The scan will be named `{scan_name}_0001` where the number is + The scan will be named ``{scan_name}_0001`` where the number is zero-padded to be SCAN_ZERO_PAD_DIGITS digits long (to allow correct sorting if the scans are ordered alphanumerically). @@ -161,7 +157,6 @@ class ScanDirectoryManager: Returns the a ScanDirectory object """ - # if no scan name is set set to "scan". This done here as empty strings # get passed in otherwise. if not scan_name: @@ -174,26 +169,25 @@ class ScanDirectoryManager: return ScanDirectory(full_scan_name, self.base_dir) def delete_scan(self, scan_name: str) -> None: - """Delete a scan""" + """Delete a scan.""" shutil.rmtree(self.path_for(scan_name)) def zip_scan(self, scan_name: str, final_version: bool = False) -> "ScanDirectory": - """Zips any images from the scan not yet zipped, return full path to zip + """Zips any images from the scan not yet zipped, return full path to zip. - `final_version` Set true to stitch all files not just the scan images + ``final_version`` Set true to stitch all files not just the scan images this should only be done at the end as it is not possible to update a file in a zip. """ return ScanDirectory(scan_name, self.base_dir).zip_files(final_version) def check_free_disk_space(self, min_space: int = 500000000) -> None: - """ - Raise an exception if there is not enough free disk space to continue scanning + """Raise an exception if there is not enough free disk space to continue scanning. :param min_space: the minimum space required in bytes. Default = 500,000,000 (500MB) - :raises: NotEnoughFreeSpaceError if the remaining storage is below min_space + :raises NotEnoughFreeSpaceError: if the remaining storage is below min_space """ disk_usage = shutil.disk_usage(self._base_scan_dir) if disk_usage.free < min_space: @@ -204,17 +198,17 @@ class ScanDirectoryManager: class ScanDirectory: - """A class for handling interactions with scan directories - - Initalisation parameters: - name: the name of the scan (the scan directory basename) - base_scan_dir: Path of the directory that holds all scans - """ + """A class for handling interactions with scan directories.""" _name: str _base_scan_dir: str def __init__(self, name: str, base_scan_dir: str): + """Initialise the scan directory. + + :param name: the name of the scan (the scan directory basename). + :param base_scan_dir: Path of the directory that holds all scans. + """ self._name = name self._base_scan_dir = base_scan_dir if not os.path.isdir(self.dir_path): @@ -224,19 +218,19 @@ class ScanDirectory: @property def name(self) -> str: - """The name of the scan""" + """The name of the scan.""" return self._name @property def dir_path(self) -> str: - """The full path to the scan directory""" + """The full path to the scan directory.""" return os.path.join(self._base_scan_dir, self._name) @property def images_dir(self) -> Optional[str]: - """ - The path to the images directory. None is returned if no images directory - was created + """The path to the images directory. + + None is returned if no images directory was created. """ im_path = os.path.join(self.dir_path, IMG_DIR_NAME) if os.path.isdir(im_path): @@ -245,27 +239,27 @@ class ScanDirectory: @property def created_time(self) -> float: - """The time the directory was created on disk""" + """The time the directory was created on disk.""" return os.path.getctime(self.dir_path) def get_scan_files(self): - """Return a list of the files in the images dir""" + """Return a list of the files in the images dir.""" if self.images_dir is None: return [] return os.listdir(self.images_dir) def _extract_scan_images(self, file_list: list[str]): - """Extract files which match the naming convention for scan images + """Extract files which match the naming convention for scan images. :param file_list: The list of files to search. Normally this would be - `self.get_scan_files()` + ``self.get_scan_files()`` :returns: The list of files that match the naming convention for scan images """ return [i for i in file_list if IMAGE_REGEX.search(i)] def _extract_final_stitches(self, file_list: list[str]): - """Extract files which match the naming convention for final stitches + """Extract files which match the naming convention for final stitches. :param file_list: The list of files to search. @@ -274,7 +268,7 @@ class ScanDirectory: return [i for i in file_list if STITCH_REGEX.search(i)] def _extract_dzi_files(self, file_list: list[str]): - """Extract files which match the naming convention for dzi_files + """Extract files which match the naming convention for dzi_files. :param file_list: The list of files to search. @@ -283,7 +277,7 @@ class ScanDirectory: return [i for i in file_list if i.endswith("dzi")] def get_final_stitch_name(self) -> Optional[str]: - """Return the filename for the final stitch (in the images dir) + """Return the filename for the final stitch (in the images dir). If no final stitch is found, return None """ @@ -293,12 +287,11 @@ class ScanDirectory: return stitches[0] def get_modified_time(self) -> float: - """Return the modified time of the directory""" + """Return the modified time of the directory.""" return max(os.stat(root).st_mtime for root, _, _ in os.walk(self.dir_path)) def scan_info(self) -> ScanInfo: - """Return the information for the scan directory as a ScanInfo object""" - + """Return the information for the scan directory as a ScanInfo object.""" scan_files = self.get_scan_files() scan_images = self._extract_scan_images(scan_files) stitches = self._extract_final_stitches(scan_files) @@ -336,13 +329,12 @@ class ScanDirectory: return files def zip_files(self, final_version: bool = False) -> str: - """Zips any images from the scan not yet zipped, return full path to zip + """Zips any images from the scan not yet zipped, return full path to zip. - `final_version` Set true to stitch all files not just the scan images + ``final_version`` Set true to stitch all files not just the scan images this should only be done at the end as it is not possible to update a file in a zip. """ - zip_fname = os.path.join(self.dir_path, "images.zip") if os.path.isfile(zip_fname): @@ -369,6 +361,6 @@ class ScanDirectory: def get_files_in_zip(zip_path): - """List the relative paths of all files and folders in the zip folder specified""" + """List the relative paths of all files and folders in the zip folder specified.""" scan_zip = zipfile.ZipFile(zip_path) return [os.path.normpath(i) for i in scan_zip.namelist()] diff --git a/src/openflexure_microscope_server/scan_planners.py b/src/openflexure_microscope_server/scan_planners.py index 32dea090..b30cacc7 100644 --- a/src/openflexure_microscope_server/scan_planners.py +++ b/src/openflexure_microscope_server/scan_planners.py @@ -1,5 +1,4 @@ -""" -This module contains functionality for planning a scan route +"""Functionality for planning scan routes. A scan route can be planned by a ScanPlanner class currently there is only one type the SmartSpiral. More can be added using by @@ -27,8 +26,11 @@ NEIGHBOUR_CUTOFF = 1.4 def enforce_xy_tuple(value: XYPos) -> XYPos: - """ - Used for enforcing that an input is a tuple and is the correct length + """Check input is a tuple and is of length 2. + + If possible it will coerce the value to a tuple. + + :raises ValueError: if the input cannot be coerced to a tuple of length 2. """ if not isinstance(value, (list, tuple)): raise ValueError("2 value tuple expected") @@ -40,8 +42,11 @@ def enforce_xy_tuple(value: XYPos) -> XYPos: def enforce_xyz_tuple(value: XYZPos) -> XYZPos: - """ - Used for enforcing that an input is a tuple and is the correct length + """Check input is a tuple and is of length 3. + + If possible it will coerce the value to a tuple. + + :raises ValueError: if the input cannot be coerced to a tuple of length 3. """ if not isinstance(value, (list, tuple)): raise ValueError("3 value tuple expected") @@ -53,40 +58,39 @@ def enforce_xyz_tuple(value: XYZPos) -> XYZPos: class ScanPlanner: - """ - A base class for a scan planner. + """A base class for a scan planner. This should never be used directly for a scan, it should be subclassed. Each subclass should implement at least the methods with NotImplementedError set: - * _parse() - to parse the planner_settings dictionary, saving values to class - variables - * _intial_location_list() - Sets the list of locations for the scan to follow - For a simple scan pattern this should be sufficent. For more complex ones that - dynanically adjust the path it is suggested to override `mark_location_visited()` - calling `super().mark_location_visited()` at the start of the method so that all + * ``_parse()`` - to parse the planner_settings dictionary, saving values to class + variables + * ``_initial_location_list()`` - Sets the list of locations for the scan to follow + + For a simple scan pattern this should be sufficient. For more complex ones that + dynamically adjust the path it is suggested to override ``mark_location_visited()`` + calling ``super().mark_location_visited()`` at the start of the method so that all locations are adjusted. - When subclassing be sure to use enforce_xy_tuple and enforce_xyz_tuple on any user - data before running + When subclassing be sure to use ``enforce_xy_tuple`` and ``enforce_xyz_tuple`` on + any user data before running. """ - def __init__(self, intial_position: XYPos, planner_settings: Optional[dict] = None): - """ - Set up lists for the path planning, and scan history. - """ - - self._initial_position = enforce_xy_tuple(intial_position) + def __init__( + self, initial_position: XYPos, planner_settings: Optional[dict] = None + ): + """Set up lists for the path planning, and scan history.""" + self._initial_position = enforce_xy_tuple(initial_position) self._parse(planner_settings) # The remaining (x,y) locations to scan # (This was `path` before refactoring from the long `sample_scan` code) - self._remaining_locations: XYPosList = self._intial_location_list() + self._remaining_locations: XYPosList = self._initial_location_list() # This holds a list of all (x,y,z) locations where images were taken - # this may not be equivalent to the x,y poistions ins self._path_history + # this may not be equivalent to the x,y positions ins self._path_history # if background detect is used # (This was not used in the `sample_scan` code) self._imaged_locations: XYZPosList = [] @@ -103,48 +107,37 @@ class ScanPlanner: @property def scan_complete(self) -> bool: - """ - Return True if there are no locations left to scan. - """ + """Return True if there are no locations left to scan.""" return not self._remaining_locations @property def remaining_locations(self) -> XYPosList: - """ - Property to access a copy of the remaining_locations - """ + """Property to access a copy of the remaining_locations.""" return copy(self._remaining_locations) @property def imaged_locations(self) -> XYZPosList: - """ - Property to access a copy of the imaged_locations - """ + """Property to access a copy of the imaged_locations.""" return copy(self._imaged_locations) @property def focused_locations(self) -> XYZPosList: - """ - Property to access a copy of the focused_locations - """ + """Property to access a copy of the focused_locations.""" return copy(self._focused_locations) @property def path_history(self) -> XYPosList: - """ - Property to access a copy of the path_history - """ + """Property to access a copy of the path_history.""" return copy(self._path_history) def _parse(self, planner_settings: Optional[dict] = None) -> None: - """ - Parse any settings sent to this planner and store them if needed. - """ + """Parse any settings sent to this planner and store them if needed.""" raise NotImplementedError("Did you call the ScanPlanner base class?") - def _intial_location_list(self) -> XYPosList: - """ - Called on initalisation. Sets the initial list of locations for this scan planner + def _initial_location_list(self) -> XYPosList: + """Set the initial list of locations for this scan planner. + + This is called on initialisation. For a simple grid scan/snake scan this would be all locations to move to. @@ -154,23 +147,17 @@ class ScanPlanner: raise NotImplementedError("Did you call the ScanPlanner base class?") def position_visited(self, position: XYPos) -> bool: - """ - Return True if input xy position has been visited before - """ + """Return True if input xy position has been visited before.""" # Ensure tuple for correct matching! return tuple(position) in self._path_history def position_planned(self, position: XYPos) -> bool: - """ - Return True if input xy position is planned - """ + """Return True if input xy position is planned.""" # Ensure tuple for correct matching! return tuple(position) in self._remaining_locations def get_next_location_and_z_estimate(self) -> tuple[XYPos, Optional[int]]: - """ - Return the next location to scan, and the estimated z-position - for this location. + """Return the next location to scan and its estimated z-position. Note z-position may be None! This indicates that the current z, position should be used. @@ -190,10 +177,12 @@ class ScanPlanner: return next_location, z def closest_focus_site(self, xy_pos: XYPos) -> Optional[XYZPos]: - """ - Return the xyz position of the closest site where focus was achieved - to the input xy_position, with the most recently taken image returned in - the case of a tie + """Return the xyz position of the closest site where focus was achieved. + + The most recently taken image is returned in the case of a tie. + + :param xy_pos: The xy_position which the returned position should be closest + to. Returns None if there if no focussed locations are present """ @@ -218,13 +207,13 @@ class ScanPlanner: def mark_location_visited( self, xyz_pos: XYZPos, imaged: bool, focused: bool ) -> None: - """ - Mark the location as visited + """Mark the location as visited. Args: xyz_pos: the x_y_z position imaged: true if an image was taken, false if not (due to background detect) focused: true if autofocus completed successfully + """ # ensure is tuple! xyz_pos = enforce_xyz_tuple(xyz_pos) @@ -246,14 +235,14 @@ class ScanPlanner: class SmartSpiral(ScanPlanner): - """ - This is a smart spiral scan that spirals out from the centre, but prioritises - short moves over rigidly sticking to minimising radius from the centre of the - scan. + """A scan planner that spirals outward from the centre, prioritising short moves. + + This planner spirals out from the centre, but prioritises short moves over rigidly + sticking to minimising radius from the centre of the scan. Each time and image is taken the four neighbouring images are added - to the list of poisitions to image (unless they are already listed or - tried). However if a location is not imaged due no sample being detected + to the list of positions to image (unless they are already listed or + tried). However, if a location is not imaged due no sample being detected then neibouring positions are not imaged. The next image taken is the closes to the centre (considering the largest @@ -266,14 +255,12 @@ class SmartSpiral(ScanPlanner): _dy: int = 0 def _parse(self, planner_settings: Optional[dict] = None) -> None: - """ - Parse SmartSpiral Settings. This should be a dictionary + """Parse SmartSpiral Settings dictionary. - "dx" - the movement size in x - "dy" - the movement size in y - "max_dist" - The maximum distance to a location can be from the centre. + * ``dx`` - the movement size in x + * ``dy`` - the movement size in y + * ``max_dist`` - The maximum distance to a location can be from the centre. """ - expected_keys = ["max_dist", "dx", "dy"] invalid_msg = "SmartSpiral requires a planner_settings dictionary with keys: " if not planner_settings: @@ -285,9 +272,10 @@ class SmartSpiral(ScanPlanner): self._dy = int(planner_settings["dy"]) self._max_dist = int(planner_settings["max_dist"]) - def _intial_location_list(self) -> XYPosList: - """ - Called on initalisation. Sets the initial list of locations for this scan planner + def _initial_location_list(self) -> XYPosList: + """Set the initial list of locations for this scan planner. + + This is salled on initialisation. For smart spiral this is just the first point """ @@ -296,13 +284,13 @@ class SmartSpiral(ScanPlanner): def mark_location_visited( self, xyz_pos: XYZPos, imaged: bool = True, focused: bool = True ) -> None: - """ - Mark the location as visited. Adjust extra positions accordingly + """Mark the location as visited. Adjust extra positions accordingly. Args: xyz_pos: the x_y_z position imaged: true if an image was taken, false if not (due to background detect) focused: true if autofocus completed successfully + """ # First call the base class to update the positions super().mark_location_visited(xyz_pos, imaged, focused) @@ -313,10 +301,14 @@ class SmartSpiral(ScanPlanner): self._re_sort_remaining_locations(xy_pos) def _add_surrounding_positions(self, xy_pos: XYPos) -> None: - """ - This adds the surrounding (4 point connectivity) positions - to the remaining locations if they are not too far away or - already planned or already visited + """Add the 4 surrounding positions to the list of remaining locations to visit. + + This adds the surrounding positions (with 4 point connectivity) to the + remaining locations list if they are not: + + * too far away + * already planned + * already visited """ new_positions = [ (xy_pos[0] - self._dx, xy_pos[1]), @@ -337,9 +329,7 @@ class SmartSpiral(ScanPlanner): self._remaining_locations.append(new_pos) def _re_sort_remaining_locations(self, current_pos: XYPos) -> None: - """ - Sort the remaining positions besed on the current location - """ + """Sort the remaining positions based on the current location.""" # Defined rather than use a lambda for readability def sort_key(pos): @@ -352,10 +342,10 @@ class SmartSpiral(ScanPlanner): self._remaining_locations.sort(key=sort_key) def get_next_location_and_z_estimate(self) -> tuple[XYPos, Optional[int]]: - """ - Return the next location to scan, and the estimated z-position - for this location. This overrides the default behaviour of ScanPlanner - to take the lowest value of nearest neighbours as this works best for smart stack + """Return the next location to scan and its estimated z-position. + + This overrides the default behaviour of ScanPlanner to take the lowest value of + nearest neighbours as this works best for smart stack. Note z-position may be None! This indicates that the current z position should be used. @@ -375,11 +365,12 @@ class SmartSpiral(ScanPlanner): return next_location, z def select_nearby_focus_site(self, xy_pos: XYPos) -> Optional[XYZPos]: - """ - Return the xyz position of the nearby site with the lowest z position. + """Return the xyz position of the nearby site with the lowest z position. + Lowest position is best, as starting too high causes smart stacking to autofocus and restart. Starting too low just requires extra movements in +z. - Nearby is defined as within NEIGHBOUR_CUTOFF times the distance to the closest neighbour. + Nearby is defined as within NEIGHBOUR_CUTOFF times the distance to the closest + neighbour. Returns None if there if no focused locations are present """ @@ -413,13 +404,11 @@ class SmartSpiral(ScanPlanner): starting_pos: XYPos | np.ndarray, ending_pos: XYPos | np.ndarray, ) -> float: - """ - Return the number of moves between two xy positions in the x or y direction - whichever is largest + """Return the larger of x moves or y moves between two xy positions. + + :param starting_pos: the position to measure from + :param ending_pos: the position to measure to - Args: - starting_pos: the position to measure from - ending_pos: the position to measure to """ move_size = np.array([self._dx, self._dy]) @@ -434,10 +423,9 @@ class SmartSpiral(ScanPlanner): def distance_between( current_pos: XYPos | np.ndarray, next_pos: XYPos | np.ndarray ) -> float: - """ - Calculate the distance between the two xy positions + """Calculate the distance between the two xy positions. - This was previously called `distance_to_site` + This was previously called ``distance_to_site`` """ next_pos = np.array(next_pos, dtype="float64") current_pos = np.array(current_pos, dtype="float64") diff --git a/src/openflexure_microscope_server/server/__init__.py b/src/openflexure_microscope_server/server/__init__.py index 7f54b05d..dc864e11 100644 --- a/src/openflexure_microscope_server/server/__init__.py +++ b/src/openflexure_microscope_server/server/__init__.py @@ -1,3 +1,5 @@ +"""A package responsible for, setup, booting, and shutting down the server.""" + from __future__ import annotations from typing import Optional, Callable @@ -14,11 +16,10 @@ from ..logging import configure_logging, retrieve_log, retrieve_log_from_file def set_shutdown_function(shutdown_function: Callable[[], None]): - """ - Ensure a function is called before the shutdown + """Ensure a function is called before the shutdown. This monkey patches the Uvicorn Server's handle_exit. This is needed because - the uvicorn `lifecycle` events and FastAPI `shutdown` events only fire once + the uvicorn ``lifecycle`` events and FastAPI ``shutdown`` events only fire once background tasks have completed. Without this the system exits cleanly only if no client is receiving a @@ -26,9 +27,8 @@ def set_shutdown_function(shutdown_function: Callable[[], None]): send streaming responses. :param shutdown_function: A callable with no arguments or outputs. This - should stop any async generators that may be sending to streaming responses. + should stop any async generators that may be sending to streaming responses. """ - original_handler = Server.handle_exit @wraps(Server.handle_exit) @@ -53,12 +53,10 @@ def customise_server( def _get_scans_dir(config: dict) -> Optional[str]: - """ - Read the config and return the scans directory. + """Read the config and return the scans directory. Return is None if there is no /smart_scan/ thing loaded. """ - if "/smart_scan/" in config["things"]: try: return config["things"]["/smart_scan/"]["kwargs"]["scans_folder"] @@ -69,7 +67,7 @@ def _get_scans_dir(config: dict) -> Optional[str]: def serve_from_cli(argv: Optional[list[str]] = None): - """Start the server from the command line""" + """Start the server from the command line.""" args = lt.cli.parse_args(argv) log_config = copy(uvicorn.config.LOGGING_CONFIG) diff --git a/src/openflexure_microscope_server/server/legacy_api.py b/src/openflexure_microscope_server/server/legacy_api.py index 5fd9a3e9..65be40d5 100644 --- a/src/openflexure_microscope_server/server/legacy_api.py +++ b/src/openflexure_microscope_server/server/legacy_api.py @@ -1,9 +1,12 @@ +"""Provide endpoints that mimic the v2 API for OpenFlexure Connect discoverability.""" + import labthings_fastapi as lt from fastapi import Response from socket import gethostname def add_v2_endpoints(thing_server: lt.ThingServer): + """Add the v2 API endpoints for OpenFlexure Connect discoverability.""" app = thing_server.app # TODO: update openflexure connect to make this unnecessary!! @@ -12,7 +15,10 @@ def add_v2_endpoints(thing_server: lt.ThingServer): # This is necessary until Connect is rebuilt. @app.get("/routes") def routes_stub() -> dict[str, dict]: - """A stub list of routes, used by OF Connect to identify the microscope""" + """Return a stub list of routes. + + This is used by OF Connect to identify the microscope. + """ fake_routes = [ "/api/v2/", "/api/v2/streams/snapshot", @@ -26,11 +32,11 @@ def add_v2_endpoints(thing_server: lt.ThingServer): @app.get("/api/v2/streams/snapshot") @app.head("/api/v2/streams/snapshot") async def thumbnail() -> JPEGResponse: - """A low-resolution snapshot, for compatibility with OF connect""" + """Return a low-resolution snapshot, for compatibility with OF connect.""" blob = await thing_server.things["/camera/"].lores_mjpeg_stream.grab_frame() return JPEGResponse(blob) @app.get("/api/v2/instrument/settings/name") def get_hostname() -> str: - """Get the hostname of the device, for compatibility with OF connect""" + """Get the hostname of the device, for compatibility with OF connect.""" return gethostname() diff --git a/src/openflexure_microscope_server/server/serve_static_files.py b/src/openflexure_microscope_server/server/serve_static_files.py index 123c6d3e..fc54d50c 100644 --- a/src/openflexure_microscope_server/server/serve_static_files.py +++ b/src/openflexure_microscope_server/server/serve_static_files.py @@ -1,3 +1,5 @@ +"""Add endpoints for static files to the underlying FastAPI server.""" + import os from typing import Optional @@ -9,9 +11,10 @@ THIS_DIR = os.path.dirname(os.path.abspath(__file__)) def add_static_file(app: FastAPI, fname: str, folder: str) -> None: - """Add a single file to the root of the FastAPI app - The file with name `fname` will be mounted at `/fname` - the - `folder` does not affect where it is mounted in the app. + """Add a single file to the root of the FastAPI app. + + The file with name ``fname`` will be mounted at ``/fname`` - the + ``folder`` does not affect where it is mounted in the app. app: The FastAPI app to add to, in this case the OpenFlexure server fname: the name of the file to add @@ -24,7 +27,7 @@ def add_static_file(app: FastAPI, fname: str, folder: str) -> None: def add_static_files(app: FastAPI, scans_folder: Optional[str]) -> None: - """Add the static files responsible for the webapp app to the FastAPI app + """Add the static files responsible for the webapp app to the FastAPI app. app: The FastAPI app to add to, in this case the OpenFlexure server """ diff --git a/src/openflexure_microscope_server/things/__init__.py b/src/openflexure_microscope_server/things/__init__.py index e69de29b..35b09029 100644 --- a/src/openflexure_microscope_server/things/__init__.py +++ b/src/openflexure_microscope_server/things/__init__.py @@ -0,0 +1,5 @@ +"""A package for all of the core LabThings-FastAPI Things shipped with the microscope. + +The microscope can be extended to be used with other hardware by creating a package +with other Things and including them in the LabThings-FastAPI config file. +""" diff --git a/src/openflexure_microscope_server/things/auto_recentre_stage.py b/src/openflexure_microscope_server/things/auto_recentre_stage.py index 28ca6936..c54270be 100644 --- a/src/openflexure_microscope_server/things/auto_recentre_stage.py +++ b/src/openflexure_microscope_server/things/auto_recentre_stage.py @@ -1,3 +1,5 @@ +"""Provide functionality for automatically recentring the Stage.""" + import numpy as np import logging @@ -14,6 +16,12 @@ AutofocusDep = lt.deps.direct_thing_client_dependency(AutofocusThing, "/autofocu class RecentringThing(lt.Thing): + """A Thing for recentring the stage by monitoring parasitic z motion of the stage. + + As the stage moves over a sphere-cap there is parasitic motion in z during xy + movement. The highest z position is the centre of motion. + """ + @lt.thing_action def recentre( self, @@ -22,7 +30,7 @@ class RecentringThing(lt.Thing): max_steps=15, lateral_distance=5000, ): - """Recentre the stage, based on the focal plane + """Recentre the stage, based on the focal plane. Autofocuses at multiple points around the sample to find the overall maximum (or minimum) height, which @@ -43,7 +51,6 @@ class RecentringThing(lt.Thing): much between these sites, making the procedure more sensitive to noise or a failed autofocus. """ - max_steps = 20 dx = lateral_distance diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py index 23766e72..3ec21a74 100644 --- a/src/openflexure_microscope_server/things/autofocus.py +++ b/src/openflexure_microscope_server/things/autofocus.py @@ -1,4 +1,4 @@ -"""OpenFlexure Microscope autofocus module +"""OpenFlexure Microscope autofocus module. This module defines a Thing that is responsible for using the stage and camera together to perform an autofocus routine. @@ -26,21 +26,7 @@ from .stage import StageDependency as Stage class StackParams: - """A class for holding for scan parameters - - All arguments are keyword only - - :param stack_dz: The number of motor steps between images - :param images_to_save: The number of images to save to disk - :param min_images_to_test: The minimum number of images in the stack before, the - stack is evaluated for focus. As more images are captured evaluation of the focus - is always evaluated with the same number of images. i.e. if min_images_to_test=9, - then 9 images are captured, if the stack is not well focused, a 10th image is - captured and images 2 to 10 are evaluated for focus - :param autofocus_dz: The number of steps in a full autofocus (when required) - :param images_dir: The directory to save images to disk - :param save_resolution: The resolution to save the captures to disk with - """ + """A class for holding for stack parameters, and returning computed ones.""" def __init__( self, @@ -52,6 +38,20 @@ class StackParams: images_dir: str, save_resolution: tuple[int, int], ) -> None: + """Initialise the parameters. All arguments are keyword only. + + :param stack_dz: The number of motor steps between images + :param images_to_save: The number of images to save to disk + :param min_images_to_test: The minimum number of images in the stack before, + the stack is evaluated for focus. As more images are captured evaluation + of the focus is always evaluated with the same number of images. i.e. if + ``min_images_to_test=9``, then 9 images are captured, if the stack is not + well focused, a 10th image is captured and images 2 to 10 are evaluated + for focus + :param autofocus_dz: The number of steps in a full autofocus (when required) + :param images_dir: The directory to save images to disk + :param save_resolution: The resolution to save the captures to disk with + """ if min_images_to_test < images_to_save: raise ValueError("Can't save more images than the minimum number tested") if min_images_to_test % 2 == 0 or min_images_to_test <= 0: @@ -97,19 +97,17 @@ class StackParams: @property def stack_z_range(self) -> int: - """The range of the z stack, in steps + """The range of the z stack, in steps. Note that this is the range of the minimum number of images captured, which is also the range of the images stored in memory that can be - saved.""" + saved. + """ return self.stack_dz * (self.min_images_to_test - 1) @property def steps_undershoot(self) -> int: - """ - The distance to deliberately undershoot the estimated optimal starting point - """ - + """The distance to deliberately undershoot the estimated optimal starting point.""" # Starting too low by "steps_undershoot" makes smart stacking faster. # Starting a stack too high requires it to move to the start, # autofocus and then re-stack. Starting slightly too low only @@ -118,14 +116,14 @@ class StackParams: @property def max_images_to_test(self) -> int: - """The maximum number of images that will be captured and tested in a stack + """The maximum number of images that will be captured and tested in a stack. This is 15 images more then the minimum number that are captured. """ return self.min_images_to_test + 15 def slice_to_save(self, sharpest_index): - """Return the slice of images to save given the index of the sharpest image""" + """Return the slice of images to save given the index of the sharpest image.""" images_each_side = (self.images_to_save - 1) // 2 return slice( max(sharpest_index - images_each_side, 0), @@ -135,9 +133,7 @@ class StackParams: @dataclass class CaptureInfo: - """ - The information from a capture in a z_stack - """ + """The information from a capture in a z_stack.""" buffer_id: int position: dict[str, int] @@ -145,7 +141,7 @@ class CaptureInfo: @property def filename(self) -> str: - """The filename for this image generated from the position""" + """The filename for this image generated from the position.""" return f"{self.position['x']}_{self.position['y']}_{self.position['z']}.jpeg" @@ -157,21 +153,20 @@ def _get_capture_by_id(captures: list[CaptureInfo], buffer_id: int) -> CaptureIn :returns: the CaptureInfo object of the capture with matching id - :raises: ValueError if buffer_id does not match the buffer_id of any captures + :raises ValueError: if buffer_id does not match the buffer_id of any captures """ return captures[_get_capture_index_by_id(captures, buffer_id)] def _get_capture_index_by_id(captures: list[CaptureInfo], buffer_id: int) -> int: - """Return the index of the capture with the matching id from a list of CaptureInfo - objects + """Return the index of the capture with the matching id. :param captures: A list of capture objects :param buffer_id: The buffer id of the image to return :returns: the list index of the capture with matching id - :raises: ValueError if buffer_id does not match the buffer_id of any captures + :raises ValueError: if buffer_id does not match the buffer_id of any captures """ ids = [capture.buffer_id for capture in captures] if buffer_id not in ids: @@ -180,6 +175,13 @@ def _get_capture_index_by_id(captures: list[CaptureInfo], buffer_id: int) -> int class SharpnessDataArrays(BaseModel): + """A BaseModel with the position and sharpness data from JPEGSharpnessMonitor. + + Each JPEG Size (representing a sharpness metric) has an associated timestamp, + as does each stage position. The stage positions need to be interpolated so + they correspond with the image timestamps. + """ + jpeg_times: NDArray jpeg_sizes: NDArray stage_times: NDArray @@ -187,7 +189,29 @@ class SharpnessDataArrays(BaseModel): class JPEGSharpnessMonitor: + """A class with direct access to the CameraThing for monitoring the MJPEG stream. + + The autofocus algorithm uses sharpness calculated from the file size of the + images in the MJPEG stream. This class monitors both the stage position and the + jpeg sharpness over time. + + The ``run`` context manager is used to start monitoring the camera stream. Position + monitoring happens during ``focus_rel``. Raw data can be retrieved with + ``data_dict`` and data with interpolated ``z`` positions can be retrieved with + move_data. + + A new JPEGSharpnessMonitor instance is created each time an action with the + SharpnessMonitorDep as an argument is called. + """ + def __init__(self, stage: Stage, camera: Camera, portal: lt.deps.BlockingPortal): + """Initialise a new JPEGSharpnessMonitor. The args are injected automatically. + + :param stage: A direct_thing_client dependency for the the microscope stage. + :param camera: A raw_thing_client depeendency for the camera. This is a raw + dependency as the underlying class needs to be + :param portal: The asyncio blocking portal for asynchronous task scheduling. + """ self.camera = camera self.stage = stage self.portal = portal @@ -200,7 +224,7 @@ class JPEGSharpnessMonitor: running = False async def monitor_sharpness(self): - """Start monitoring the frame sizes""" + """Start monitoring the frame sizes.""" self.running = True async for frame in self.camera.lores_mjpeg_stream.frame_async_generator(): self.jpeg_times.append(time.time()) @@ -210,7 +234,7 @@ class JPEGSharpnessMonitor: @contextmanager def run(self): - """Context manager, during which we will monitor sharpness from the camera""" + """Context manager, during which we will monitor sharpness from the camera.""" self.portal.start_task_soon(self.monitor_sharpness) try: yield @@ -218,6 +242,16 @@ class JPEGSharpnessMonitor: self.running = False def focus_rel(self, dz: int, **kwargs) -> tuple[int, int]: + """Move the stage by dz, monitoring the position over time. + + This performs exactly one move. Multiple calls of this method + will append to the internal position storage for more complex + autofocus procedures. + + This should be run from within the JPEGSharpnessMonitor.run + context manager so that sharpness data and timestamps are also + collected. + """ # Store the start time and position self.stage_times.append(time.time()) self.stage_positions.append(self.stage.position) @@ -238,7 +272,7 @@ class JPEGSharpnessMonitor: def move_data( self, istart: int, istop: Optional[int] = None ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: - """Extract sharpness as a function of (interpolated) z""" + """Extract sharpness as a function of (interpolated) z.""" if istop is None: istop = istart + 2 jpeg_times: np.ndarray = np.array(self.jpeg_times) @@ -266,7 +300,7 @@ class JPEGSharpnessMonitor: return jpeg_times, jpeg_zs, jpeg_sizes[start:stop] def sharpest_z_on_move(self, index: int) -> int: - """Return the z position of the sharpest image on a given move""" + """Return the z position of the sharpest image on a given move.""" _, jz, js = self.move_data(index) if len(js) == 0: raise ValueError( @@ -275,7 +309,7 @@ class JPEGSharpnessMonitor: return jz[np.argmax(js)] def data_dict(self) -> SharpnessDataArrays: - """Return the gathered data as a single convenient dictionary""" + """Return the gathered data as a single convenient dictionary.""" data = {} for k in ["jpeg_times", "jpeg_sizes", "stage_times", "stage_positions"]: data[k] = getattr(self, k) @@ -290,7 +324,8 @@ class AutofocusThing(lt.Thing): Actions here involve moving a stage in z, and using the camera to either capture images (generally, z-stacking) and measuring the sharpness of the - field of view to assess focus (autofocus and testing the success of a z-stack)""" + field of view to assess focus (autofocus and testing the success of a z-stack) + """ @lt.thing_action def fast_autofocus( @@ -299,7 +334,7 @@ class AutofocusThing(lt.Thing): dz: int = 2000, start: str = "centre", ) -> SharpnessDataArrays: - """Sweep the stage up and down, then move to the sharpest point + """Sweep the stage up and down, then move to the sharpest point. This method will will move down by dz/2, sweep up by dz, and then evaluate the position where the image was sharpest. We'll then move back down, and @@ -329,16 +364,16 @@ class AutofocusThing(lt.Thing): dz: Sequence[int], wait: float = 0, ) -> SharpnessDataArrays: - """Make a move (or a series of moves) and monitor sharpness + """Make a move (or a series of moves) and monitor sharpness. This method will will make a series of relative moves in z, and return the sharpness (JPEG size) vs time, along with timestamps for the moves. This can be used to calibrate autofocus. Each move is relative to the last one, i.e. we will finish at - `sum(dz)` relative to the starting position. + ``sum(dz)`` relative to the starting position. - If `wait` is specified, we will wait for that many seconds + If ``wait`` is specified, we will wait for that many seconds between moves. """ with sharpness_monitor.run(): @@ -358,9 +393,9 @@ class AutofocusThing(lt.Thing): ): """Repeatedly autofocus the stage until it looks focused. - This action will run the `fast_autofocus` action until it settles on a point + This action will run the ``fast_autofocus`` action until it settles on a point in the middle 3/5 of its range. Such logic can be helpful if the microscope - is close to focus, but not quite within `dz/2`. It will attempt to autofocus + is close to focus, but not quite within ``dz/2``. It will attempt to autofocus up to 10 times. """ repeat = True @@ -397,33 +432,34 @@ class AutofocusThing(lt.Thing): stack_images_to_save = lt.ThingSetting( initial_value=1, model=int, - description="""The number of images to save in a stack. - - Defaults to 1 unless you need to see either side of focus""", ) + """The number of images to save in a stack. + + Defaults to 1 unless you need to see either side of focus + """ stack_min_images_to_test = lt.ThingSetting( initial_value=9, model=int, - description="""The minimum number of images to capture in a stack. - - This many images are captures and tested for focus, if the focus - is not central enough more images may be captured. After new images - are captured the number sets the number of images used for checking - if focus is central. - - Defaults to 9 which balances reliability and speed - """, ) + """The minimum number of images to capture in a stack. - stack_dz = lt.ThingSetting( - initial_value=50, - model=int, - description="""Space in steps between images in a z-stack - Suggested is 50 for 60-100x - 100 for 40x - 200 for 20x""", - ) + This many images are captures and tested for focus, if the focus is not central + enough more images may be captured. After new images are captured the number sets + the number of images used for checking if focus is central. + + Defaults to 9 which balances reliability and speed/ + """ + + stack_dz = lt.ThingSetting(initial_value=50, model=int) + """Distance in steps between images in a z-stack. + + Suggested values: + + * 50 for 60-100x + * 100 for 40x + * 200 for 20x + """ @lt.thing_action def run_smart_stack( @@ -435,26 +471,30 @@ class AutofocusThing(lt.Thing): autofocus_dz: int, save_resolution: tuple[int, int], ) -> tuple[bool, int]: - """Run a smart stack, which captures images offset in z, testing - whether the sharpest image is towards the centre of the stack. - The sharpest image, and optionally images around the sharpest, - will be saved using their coordinates to images_dir + """Run a smart stack. + + A smart stack captures images offset in z, testing whether the sharpest image + is towards the centre of the stack. + + The sharpest image, and optionally images around the sharpest, will be saved + to the images_dir with their coordinates in the filename. :param cam: Camera Dependency supplied by LabThings dependency injection :param stage: Stage Dependency supplied by LabThings dependency injection :param sharpness_monitor: Sharpness Monitor Dependency (for focus detection) - supplied by LabThings dependency injection + supplied by LabThings dependency injection :param images_dir: the folder to save all images :param autofocus_dz: the range to autofocus over if a stack fails :param save_resolution: The resolution the images should be saved at, the - images will be resampled if this doesn't match the camera's capture resolution + images will be resampled if this doesn't match the camera's capture + resolution :returns: A tuple containing: - - A boolean, True if stack was successfully - - The z position of the sharpest image - """ + * A boolean, True if stack was successfully + * The z position of the sharpest image + """ # Set the variables to prevent changes from the GUI or other windows stack_parameters = StackParams( stack_dz=self.stack_dz, @@ -465,9 +505,9 @@ class AutofocusThing(lt.Thing): save_resolution=save_resolution, ) - trys = 0 + tries = 0 # Loop until a stack is successful - while trys < stack_parameters.max_attempts: + while tries < stack_parameters.max_attempts: success, captures, sharpest_id = self.z_stack( stack_parameters=stack_parameters, cam=cam, @@ -508,14 +548,13 @@ class AutofocusThing(lt.Thing): stage: Stage, sharpness_monitor: SharpnessMonitorDep, ) -> None: - """Return to the initial height of the current stack, and run - a looping autofocus. + """Return to the initial z position and run a looping autofocus. - Arguments: - initial_z_pos: The initial z positions of previous captures - autofocus_dz: the range in steps to autofocus - variables stage and sharpness_monitor are Thing dependencies passed through from - the calling action + :param initial_z_pos: The initial z positions of previous captures + :param autofocus_dz: the range in steps to autofocus + + ``stage`` and ``sharpness_monitor`` are Thing dependencies passed through + from the calling action. """ stage.move_absolute(z=initial_z_pos) self.looping_autofocus( @@ -531,17 +570,18 @@ class AutofocusThing(lt.Thing): stack_parameters: StackParams, cam: WrappedCamera, ) -> int: - """Save the required captures to disk. Will save the sharpest image, - and any images either side of focus. + """Save the required captures to disk. + + This will save the sharpest image, and optionally extra images either + side of focus (see ``stack_parameters.images_to_save``). + + :param sharpest_id: the buffer id index of the sharpest image + :param captures: a list of captures, including file name, image data and + metadata + :param stack_parameters: a StackParams object holding stack parameters + :param cam: is a Thing dependency passed through from the calling action - Arguments: - sharpest_id: the buffer id index of the sharpest image - captures: a list of captures, including file name, image data and metadata - stack_parameters: a StackParams object holding stack parameters - variables logger and capture are Thing dependencies passed through from the - calling action """ - sharpest_index = _get_capture_index_by_id(captures, sharpest_id) slice_to_save = stack_parameters.slice_to_save(sharpest_index) @@ -561,17 +601,22 @@ class AutofocusThing(lt.Thing): cam: WrappedCamera, stage: Stage, ) -> tuple[bool, list[CaptureInfo], Optional[int]]: - """Capture a series of images offset by stack_parameters.stack_dz, and test whether - the sharpest image is towards the centre of the stack. + """Capture a series of images checking that sharpest image central. + + The images are separated in z offset by stack_parameters.stack_dz, as they + are captured the last stack_parameters.min_images_to_test images are checked + to see if the sharpest image is central enough in the stack. If it is the stack + completes. :param stack_parameters: a StackParams object holding stack parameters :param cam: Camera Dependency to be passed through from the calling action :param stage: Stage Dependency to be passed through from the calling action :returns: A tuple of - - the stack result (True for successful stack, False for failed stack), - - a list of CaptureInfo objects, - - the buffer_id of the shapest image (or None if the stack failed) + + * the stack result (True for successful stack, False for failed stack), + * a list of CaptureInfo objects, + * the buffer_id of the sharpest image (or None if the stack failed). """ # Move down by the height of the z stack, plus an overshoot # Better to start too low and take too many images than too high and need to refocus @@ -628,11 +673,11 @@ class AutofocusThing(lt.Thing): :param cam: Camera Dependency to be passed through from the calling action :param stage: Stage Dependency to be passed through from the calling action - :buffer_max: The maximum number of images to tell the camera to keep in memory - for saving once the stack is complete + :param buffer_max: The maximum number of images to tell the camera to keep in memory + for saving once the stack is complete - :return: A CaptureInfo object containing the capture information including its - camera buffer_id needed for saving. + :returns: A CaptureInfo object containing the capture information including its + camera buffer_id needed for saving. """ stage_location = stage.position buffer_id = cam.capture_to_memory(buffer_max=buffer_max) @@ -645,18 +690,22 @@ class AutofocusThing(lt.Thing): def check_stack_result( self, captures: list[CaptureInfo] ) -> tuple[Literal["success", "continue", "restart"], int]: - """Test a list of captures, to decide whether the sharpest image from a - stack is centrally enough in the stack + """Check if the sharpest image in a list of captures is central enough. :param captures: a list of the capture objects to for testing if the - sharpeness has converged in the centre + sharpness has converged in the centre - :return: A tuple with two values: - - result - which is one of three literal values: - 'success' if the sharpest image is towards the centre - 'continue' if the sharpest image is in the final two images of the list - 'restart' if the sharpest image is in the first two images of the list - - capture_id - the buffer id of the sharpest image + :returns: A tuple with two values: + + * result - which is one of three literal values: + + * ``success`` if the sharpest image is towards the centre + * ``continue`` if the sharpest image is in the final two images of the + list + * ``restart`` if the sharpest image is in the first two images of the + list + + * capture_id - the buffer id of the sharpest image """ sharpest_index = np.argmax([capture.sharpness for capture in captures]) # The buffer id of the sharpest image diff --git a/src/openflexure_microscope_server/things/background_detect.py b/src/openflexure_microscope_server/things/background_detect.py index f27b9096..1c147093 100644 --- a/src/openflexure_microscope_server/things/background_detect.py +++ b/src/openflexure_microscope_server/things/background_detect.py @@ -1,3 +1,10 @@ +"""Provide functionality to detect if the camera is imaging sample or background. + +An example background image must be captured and analysed by BackgroundDetectThing, +information from this images is used to detect whether the current camera field of +view contains sample. +""" + from typing import Mapping, Optional import cv2 import numpy as np @@ -10,19 +17,31 @@ from .camera import CameraDependency as CamDep class ChannelDistributions(BaseModel): + """A BaseModel for storing the channel distribution of a background image.""" + means: list[float] + """The mean of each channel in the colourspace.""" standard_deviations: list[float] + """The standard deviation of each channel in the colourspace.""" colorspace: str = "LUV" + """The colourspace used.""" class BackgroundDetectThing(lt.Thing): + """Thing for setting a background image and detecting sample in the field of view. + + This uses an LUV colour space checking only the mean and standard deviation of the + UV channels. Over time different, selectable, background detection methods will be + added. + """ + # Requires a getter and a setter to support being a BaseModel but being # saved to file as a dict _background_distributions: Optional[ChannelDistributions] = None @lt.thing_setting def background_distributions(self) -> Optional[ChannelDistributions]: - """The statistics of the background image""" + """The statistics of the background image.""" bd = self._background_distributions if bd is None: return None @@ -46,19 +65,19 @@ class BackgroundDetectThing(lt.Thing): tolerance = lt.ThingSetting( initial_value=7.0, model=float, - description="How many standard deviations to allow for the background", ) + """How many standard deviations to allow for the background.""" fraction = lt.ThingSetting( initial_value=25.0, model=float, - description="How much of the image needs to be not background to label as sample", ) + """How much of the image needs to be not background to label as sample""" def background_mask(self, image: np.ndarray) -> np.ndarray: - """Calculate a binary image, showing whether each pixel is background + """Calculate a binary image, showing whether each pixel is background. - The image should be in LUV format, the ouput will be binary with the + The image should be in LUV format, the output will be binary with the same shape in the first two dimensions. """ d = self.background_distributions @@ -78,7 +97,7 @@ class BackgroundDetectThing(lt.Thing): @lt.thing_action def background_fraction(self, cam: CamDep) -> float: - """Determine what fraction of the current image is background + """Determine what fraction of the current image is background. This action will acquire a new image from the preview stream, then evaluate whether it is foreground or background, by comparing it @@ -96,7 +115,7 @@ class BackgroundDetectThing(lt.Thing): @lt.thing_action def image_is_sample(self, cam: CamDep) -> bool: - """Label the current image as either background or sample""" + """Label the current image as either background or sample.""" b_fraction = self.background_fraction(cam) fraction_threshold = self.fraction @@ -104,7 +123,7 @@ class BackgroundDetectThing(lt.Thing): @lt.thing_action def set_background(self, cam: CamDep): - """Grab an image, and use its statistics to set the background + """Grab an image, and use its statistics to set the background. This should be run when the microscope is looking at an empty region, and will calculate the mean and standard deviation of the pixel values @@ -135,6 +154,7 @@ class BackgroundDetectThing(lt.Thing): @property def thing_state(self) -> Mapping: + """Summary metadata describing the current state of the Thing.""" bd = self.background_distributions return { "background_distributions": bd.model_dump() if bd else None, diff --git a/src/openflexure_microscope_server/things/camera/__init__.py b/src/openflexure_microscope_server/things/camera/__init__.py index 3ac1a3b1..12301213 100644 --- a/src/openflexure_microscope_server/things/camera/__init__.py +++ b/src/openflexure_microscope_server/things/camera/__init__.py @@ -1,7 +1,7 @@ -"""OpenFlexure Microscope Camera +"""OpenFlexure Microscope Camera. This module defines the interface for cameras. Any compatible lt.Thing -should enabe the server to work. +should enable the server to work. See repository root for licensing information. """ @@ -19,39 +19,41 @@ from labthings_fastapi.types.numpy import NDArray class JPEGBlob(lt.blob.Blob): + """A class representing a JPEG image as a LabThings FastAPI Blob.""" + media_type: str = "image/jpeg" class PNGBlob(lt.blob.Blob): - """A class representing a PNG image as a LabThings FastAPI Blob""" + """A class representing a PNG image as a LabThings FastAPI Blob.""" media_type: str = "image/png" class ArrayModel(RootModel): - """A model for an array""" + """A model for an array.""" root: NDArray class CaptureError(RuntimeError): - """An error trying to capture from a CameraThing""" + """An error trying to capture from a CameraThing.""" class NoImageInMemoryError(RuntimeError): - """An error called if no image in in memory when an method is called to use that image""" + """An error called if no image is in memory when accessed.""" class CameraMemoryBuffer: - """ - A class that holds images in memory. The images are by default PIL images. + """A class that holds images in memory. The images are by default PIL images. - However subclasses of BaseCamera can use this class to store other object types + However subclasses of BaseCamera can use this class to store other object types. """ _storage: dict[int, tuple[Any, Optional[dict]]] def __init__(self): + """Create the buffer instance.""" # This dictionary is the main store for data. Dictionaries are ordered since # Python 3.6, so the order in the dictionary is the capture order self._storage = {} @@ -62,20 +64,19 @@ class CameraMemoryBuffer: def add_image( self, image: Any, metadata: Optional[dict] = None, buffer_max: int = 1 ) -> int: - """ - Add an image to the Memory buffer + """Add an image to the Memory buffer. This will add an image to the memory buffer. By default the buffer will be cleared. To allow saving multiple images the buffer_max must be set every time an image is added. :param image: The image to add. A PIL image is recommended, but cameras - can choose to use other formats + can choose to use other formats :param metadata: Optional, a dictionary of the image metadata. :param buffer_max: The maximum number of images that should be in the buffer - once this images is added. Default is 1. + once this images is added. Default is 1. - :return buffer_id: The id in the buffer for this image + :returns: The id in the buffer for this image """ self._latest_id += 1 self._create_space(buffer_max) @@ -85,8 +86,7 @@ class CameraMemoryBuffer: def get_image( self, buffer_id: Optional[int] = None, remove: bool = True ) -> tuple[Any, Optional[dict]]: - """ - Return the image with the given id. + """Return the image with the given id. If no id is given the most recent image is returned. However, the buffer is also cleared, otherwise it would be possible to accidentally @@ -94,9 +94,8 @@ class CameraMemoryBuffer: :param buffer_id: The buffer id of the image to retrieve :param remove: True (default) to remove this image from the buffer, False - to leave the image in the buffer. + to leave the image in the buffer. """ - # No id given if buffer_id is None: # Get the latest image and metadata tuple from storage @@ -118,17 +117,14 @@ class CameraMemoryBuffer: ) from e def clear(self): - """ - Clear all images from memory - """ + """Clear all images from memory.""" self._storage.clear() def _create_space(self, buffer_max: int) -> None: - """ - Create space to add an image. + """Create space to add an image. :param buffer_max: The maximum number of images that should be in the buffer - once another images is added. + once another images is added. """ # If only one image to be stored just clear the storage and return if buffer_max <= 1: @@ -147,37 +143,45 @@ class CameraMemoryBuffer: class BaseCamera(lt.Thing): - """The base class for all cameras. All cameras must directly inherit from this class""" + """The base class for all cameras. All cameras must directly inherit from this class. + + The connection to the camera hardware should be added to the ``__enter__`` method not + ``__init__`` method of the subclass. + """ mjpeg_stream = lt.outputs.MJPEGStreamDescriptor() lores_mjpeg_stream = lt.outputs.MJPEGStreamDescriptor() _memory_buffer = CameraMemoryBuffer() def __enter__(self) -> None: + """Open hardware connection when the Thing context manager is opened.""" raise NotImplementedError("CameraThings must define their own __enter__ method") def __exit__(self, _exc_type, _exc_value, _traceback) -> None: + """Close hardware connection when the Thing context manager is closed.""" raise NotImplementedError("CameraThings must define their own __exit__ method") @lt.thing_action def start_streaming( self, main_resolution: tuple[int, int], buffer_count: int ) -> None: - """Start (or stop and restart) the camera with the given resolution - for the main stream, and buffer_count number of images in the buffer""" + """Start (or stop and restart) the camera. + + :param main_resolution: the resolution to use for the main stream. + :param buffer_count: number of images in the stream buffer. + """ raise NotImplementedError( "CameraThings must define their own start_streaming method" ) def kill_mjpeg_streams(self): - """ - Kill the streams now as the server is shutting down. + """Kill the streams now as the server is shutting down. This is called when uvicorn gets the a shutdown signal. As this is called from the event loop it cannot interact with the our ThingProperties or run - `self.mjpeg_stream.stop()` as the portal cannot be called from this loop. + ``self.mjpeg_stream.stop()`` as the portal cannot be called from this loop. - Instead we just set the `_streaming` value to False. This stops the async frame + Instead we just set the ``_streaming`` value to False. This stops the async frame generator when the next frame notifies. """ if self.stream_active: @@ -186,7 +190,7 @@ class BaseCamera(lt.Thing): @lt.thing_property def stream_active(self) -> bool: - "Whether the MJPEG stream is active" + """Whether the MJPEG stream is active.""" raise NotImplementedError( "CameraThings must define their own stream_active method" ) @@ -197,6 +201,7 @@ class BaseCamera(lt.Thing): stream_name: Literal["main", "lores", "raw", "full"] = "main", wait: Optional[float] = 5, ) -> NDArray: + """Acquire one image from the camera and return as an array.""" raise NotImplementedError( "CameraThings must define their own capture_array method" ) @@ -208,7 +213,7 @@ class BaseCamera(lt.Thing): resolution: Literal["lores", "main", "full"] = "main", wait: Optional[float] = 5, ) -> JPEGBlob: - """Acquire one image from the camera and return as a JPEG blob""" + """Acquire one image from the camera and return as a JPEG blob.""" raise NotImplementedError( "CameraThings must define their own capture_jpeg method" ) @@ -219,9 +224,9 @@ class BaseCamera(lt.Thing): portal: lt.deps.BlockingPortal, stream_name: Literal["main", "lores"] = "main", ) -> JPEGBlob: - """Acquire one image from the preview stream and return as an array + """Acquire one image from the preview stream and return as an array. - This differs from `capture_jpeg` in that it does not pause the MJPEG + This differs from ``capture_jpeg`` in that it does not pause the MJPEG preview stream. Instead, we simply return the next frame from that stream (either "main" for the preview stream, or "lores" for the low resolution preview). No metadata is returned. @@ -238,7 +243,7 @@ class BaseCamera(lt.Thing): portal: lt.deps.BlockingPortal, stream_name: Literal["main", "lores"] = "main", ) -> int: - """Acquire one image from the preview stream and return its size""" + """Acquire one image from the preview stream and return its size.""" stream = ( self.lores_mjpeg_stream if stream_name == "lores" else self.mjpeg_stream ) @@ -250,7 +255,7 @@ class BaseCamera(lt.Thing): stream_name: Literal["main", "lores", "raw"], wait: Optional[float], ) -> None: - """Capture a PIL image from stream stream_name with timeout wait""" + """Capture a PIL image from stream stream_name with timeout wait.""" raise NotImplementedError( "CameraThings must define their own capture_image method" ) @@ -263,15 +268,15 @@ class BaseCamera(lt.Thing): metadata_getter: lt.deps.GetThingStates, save_resolution: Optional[Tuple[int, int]] = None, ) -> None: - """Capture an image and save it to disk + """Capture an image and save it to disk. :param jpeg_path: The path to save the file to :param logger: This should be injected automatically by Labthings FastAPI - when calling the action + when calling the action :param metadata_getter: This should be injected automatically by Labthings - FastAPI when calling the action + FastAPI when calling the action :param save_resolution: can be set to resize the image before saving. By - default this is None meaning that the image is saved at original resolution. + default this is None meaning that the image is saved at original resolution. """ image, metadata = self._robust_image_capture( metadata_getter, @@ -293,20 +298,19 @@ class BaseCamera(lt.Thing): metadata_getter: lt.deps.GetThingStates, buffer_max: int = 1, ) -> None: - """ - Capture an image to memory. This can be saved later with `save_from_memory` + """Capture an image to memory. This can be saved later with ``save_from_memory``. Note that only one image is held in memory so this will overwrite any image in memory. :param logger: This should be injected automatically by Labthings FastAPI - when calling the action + when calling the action :param metadata_getter: This should be injected automatically by Labthings - FastAPI when calling the action + FastAPI when calling the action :param buffer_max: The maximum number of images that should be in the buffer - once this images is added. Default is 1. + once this images is added. Default is 1. - :return: the buffer id of the image captured + :returns: the buffer id of the image captured """ image, metadata = self._robust_image_capture(metadata_getter, logger) return self._memory_buffer.add_image(image, metadata, buffer_max=buffer_max) @@ -319,16 +323,16 @@ class BaseCamera(lt.Thing): save_resolution: Optional[Tuple[int, int]] = None, buffer_id: Optional[int] = None, ) -> None: - """ - Save an image that has been captured to memory. + """Save an image that has been captured to memory. :param jpeg_path: The path to save the file to :param logger: This should be injected automatically by Labthings FastAPI - when calling the action + when calling the action :param save_resolution: can be set to resize the image before saving. By - default this is None meaning that the image is saved at original resolution. + default this is None meaning that the image is saved at original + resolution. :param buffer_id: The buffer id of the image to save, this was returned by - `capture_to_memory` + ``capture_to_memory`` """ image, metadata = self._memory_buffer.get_image(buffer_id) @@ -342,7 +346,7 @@ class BaseCamera(lt.Thing): @lt.thing_action def clear_buffers(self) -> None: - """Clear all images in memory""" + """Clear all images in memory.""" self._memory_buffer.clear() def _robust_image_capture( @@ -350,12 +354,14 @@ class BaseCamera(lt.Thing): metadata_getter: lt.deps.GetThingStates, logger: lt.deps.InvocationLogger, ) -> Image: - """Capture an image in memory and return it with metadata - CaptureError raised if the capture fails for any reason - returns tuple with PIL Image, and dict of metadata. + """Capture an image in memory and return it with metadata. This robust capturing method attempts to capture the image five times each time with a 5 second timeout set. + + :raises CaptureError: if the capture fails for any reason + + :returns: tuple with PIL Image, and dictionary of metadata. """ for capture_attempts in range(5): try: @@ -376,10 +382,14 @@ class BaseCamera(lt.Thing): logger: lt.deps.InvocationLogger, save_resolution: Optional[Tuple[int, int]] = None, ) -> None: - """Saving the captured image and metadata to disk - logger warning (via InvocationLogger) is raised if metadata is failed to be added - IOError is raised if the file cannot be saved - nothing is returned on success""" + """Save the captured image and metadata to disk. + + A warning (via InvocationLogger) is raised if metadata is failed to be added + + :raises IOError: if the file cannot be saved + + nothing is returned on success + """ if save_resolution is not None and image.size != save_resolution: image = image.resize(save_resolution, Image.BOX) try: diff --git a/src/openflexure_microscope_server/things/camera/opencv.py b/src/openflexure_microscope_server/things/camera/opencv.py index 66e0b050..a5604432 100644 --- a/src/openflexure_microscope_server/things/camera/opencv.py +++ b/src/openflexure_microscope_server/things/camera/opencv.py @@ -1,7 +1,7 @@ -"""OpenFlexure Microscope OpenCV Camera +"""OpenFlexure Microscope OpenCV Camera. This module defines a camera Thing that uses OpenCV's -`VideoCapture`. +``VideoCapture``. See repository root for licensing information. """ @@ -23,14 +23,19 @@ from . import BaseCamera, JPEGBlob class OpenCVCamera(BaseCamera): - """A Thing representing an OpenCV camera""" + """A Thing that provides and interface to an OpenCV Camera.""" def __init__(self, camera_index: int = 0): + """Iniatilise the thing storing the index of the camera to use. + + :param camera_index: The index of the camera to use for the microscope. + """ self.camera_index = camera_index self._capture_thread: Optional[Thread] = None self._capture_enabled = False def __enter__(self): + """Start the capture thread when the Thing context manager is opened.""" self.cap = cv2.VideoCapture(self.camera_index) self._capture_enabled = True self._capture_thread = Thread(target=self._capture_frames) @@ -38,6 +43,10 @@ class OpenCVCamera(BaseCamera): return self def __exit__(self, _exc_type, _exc_value, _traceback): + """Release the camera when the Thing context manager is closed. + + Before releasing the camera the capture thread is closed. + """ if self.stream_active: self._capture_enabled = False self._capture_thread.join() @@ -45,7 +54,7 @@ class OpenCVCamera(BaseCamera): @lt.thing_property def stream_active(self) -> bool: - "Whether the MJPEG stream is active" + """Whether the MJPEG stream is active.""" if self._capture_enabled and self._capture_thread: return self._capture_thread.is_alive() return False @@ -71,13 +80,13 @@ class OpenCVCamera(BaseCamera): self, resolution: Literal["main", "full"] = "full", ) -> NDArray: - """Acquire one image from the camera and return as an array + """Acquire one image from the camera and return as an array. This function will produce a nested list containing an uncompressed RGB image. It's likely to be highly inefficient - raw and/or uncompressed captures using binary image formats will be added in due course. """ - logging.warning(f"OpenCV camera doen't respect {resolution} setting") + logging.warning(f"OpenCV camera doesn't respect {resolution} setting") ret, frame = self.cap.read() if not ret: raise RuntimeError( @@ -91,11 +100,11 @@ class OpenCVCamera(BaseCamera): metadata_getter: lt.deps.GetThingStates, resolution: Literal["main", "full"] = "main", ) -> JPEGBlob: - """Acquire one image from the camera and return as a JPEG blob + """Acquire one image from the camera and return as a JPEG blob. This function will produce a JPEG image. """ - logging.warning(f"OpenCV camera doen't respect {resolution} setting") + logging.warning(f"OpenCV camera doesn't respect {resolution} setting") frame = self.capture_array() jpeg = cv2.imencode(".jpg", frame)[1].tobytes() exif_dict = { diff --git a/src/openflexure_microscope_server/things/camera/picamera.py b/src/openflexure_microscope_server/things/camera/picamera.py index 6ec2e862..0e3dd04f 100644 --- a/src/openflexure_microscope_server/things/camera/picamera.py +++ b/src/openflexure_microscope_server/things/camera/picamera.py @@ -1,5 +1,4 @@ -""" -This SubModule interacts with a Raspberry Pi camera using the Picamera2 library. +"""Submodule for interacting with a Raspberry Pi camera using the Picamera2 library. The Picamera2 library uses LibCamera as the underlying camera stack. This gives us some control of the GPU pipeline for the image. @@ -41,10 +40,10 @@ from . import BaseCamera, JPEGBlob, ArrayModel class PicameraStreamOutput(Output): - """An Output class that sends frames to a stream""" + """An Output class that sends frames to a stream.""" def __init__(self, stream: lt.outputs.MJPEGStream, portal: lt.deps.BlockingPortal): - """Create an output that puts frames in an MJPEGStream + """Create an output that puts frames in an MJPEGStream. We need to pass the stream object, and also the blocking portal, because new frame notifications happen in the anyio event loop and frames are @@ -58,14 +57,14 @@ class PicameraStreamOutput(Output): def outputframe( self, frame, _keyframe=True, _timestamp=None, _packet=None, _audio=False ): - """Add a frame to the stream's ringbuffer""" + """Add a frame to the stream's ringbuffer.""" self.stream.add_frame(frame, self.portal) class SensorMode(BaseModel): - """ - A Pydantic model holding all the information about a specific - sensor mode as reported by the PiCamera. + """A Pydantic model holding all the information about a specific sensor mode. + + This data is as reported by the PiCamera2 module. """ unpacked: str @@ -78,11 +77,11 @@ class SensorMode(BaseModel): class SensorModeSelector(BaseModel): - """ - A Pydantic model holding the two values needed to select a PiCamera - Sensor mode. The output size and the bit depth. + """A Pydantic model holding the two values needed to select a PiCamera Sensor mode. - This is a Pydantic modell so that it can be saved to the disk. + These values are the output size and the bit depth. + + This is a Pydantic model so that it can be saved to disk. """ output_size: tuple[int, int] @@ -90,14 +89,13 @@ class SensorModeSelector(BaseModel): class LensShading(BaseModel): - """ - A Pydantic model holding the lens shading tables. + """A Pydantic model holding the lens shading tables. PiCamera needs three numpy arrays for lens shading correction. Each array is (12, 16) in size. The arrays are luminance, red-difference chroma (Cr), and blue-difference chroma (Cb). - This is a Pydantic modell so that it can be saved to the disk. + This is a Pydantic model so that it can be saved to the disk. """ luminance: list[list[float]] @@ -106,9 +104,20 @@ class LensShading(BaseModel): class StreamingPiCamera2(BaseCamera): - """A Thing that represents an OpenCV camera""" + """A Thing that provides and interface to the Raspberry Pi Camera. + + Currently the Thing only supports the PiCamera v2 board. This needs + generalisation. + """ def __init__(self, camera_num: int = 0): + """Initialise the camera with the given camera number. + + This makes no connection to the camera (except to get the default tuning file). + + :param camera_num: The number of the camera. This should generally be left as 0 + as most Raspberry Pi boards only support 1 camera. + """ self._setting_save_in_progress = False self.camera_num = camera_num self.camera_configs: dict[str, dict] = {} @@ -130,22 +139,22 @@ class StreamingPiCamera2(BaseCamera): stream_resolution = lt.ThingProperty( tuple[int, int], initial_value=(820, 616), - description="Resolution to use for the MJPEG stream", ) + """Resolution to use for the MJPEG stream.""" mjpeg_bitrate = lt.ThingProperty( Optional[int], initial_value=100000000, - description="Bitrate for MJPEG stream (None for default)", ) + """Bitrate for MJPEG stream (None for default).""" stream_active = lt.ThingProperty( bool, initial_value=False, - description="Whether the MJPEG stream is active", observable=True, readonly=True, ) + """Whether the MJPEG stream is active.""" def save_settings(self): """Override save_settings to ensure that camera properties don't recurse. @@ -153,7 +162,7 @@ class StreamingPiCamera2(BaseCamera): This method is run by any Thing when a ThingSetting is saved. However, the method reads the thing_setting. As reading the thing setting talks to the camera and calls save_settings if the value is not as expected, this could - cause recursion. Aslo this means that saving one setting causes all others + cause recursion. Also this means that saving one setting causes all others to be read each time. """ try: @@ -168,6 +177,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_setting def analogue_gain(self) -> float: + """The Analogue gain applied by the camera sensor.""" if not self._setting_save_in_progress and self.streaming: with self._streaming_picamera() as cam: cam_value = cam.capture_metadata()["AnalogueGain"] @@ -187,6 +197,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_setting def colour_gains(self) -> tuple[float, float]: + """The red and blue colour gains, must be between 0.0 and 32.0.""" if not self._setting_save_in_progress and self.streaming: with self._streaming_picamera() as cam: cam_value = cam.capture_metadata()["ColourGains"] @@ -206,6 +217,11 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_setting def exposure_time(self) -> int: + """The camera exposure time in microseconds. + + When setting this property the camera will adjust the set value + to the nearest allowed value that is lower than the current setting. + """ if not self._setting_save_in_progress and self.streaming: with self._streaming_picamera() as cam: cam_value = cam.capture_metadata()["ExposureTime"] @@ -246,7 +262,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def sensor_modes(self) -> list[SensorMode]: - """All the available modes the current sensor supports""" + """All the available modes the current sensor supports.""" if not self._sensor_modes: with self._streaming_picamera() as cam: self._sensor_modes = cam.sensor_modes @@ -256,15 +272,14 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def sensor_mode(self) -> Optional[SensorModeSelector]: - """The intended sensor mode of the camera""" + """The intended sensor mode of the camera.""" if self._sensor_mode is None: return None return SensorModeSelector(**self._sensor_mode) @sensor_mode.setter def sensor_mode(self, new_mode: Optional[SensorModeSelector | dict]): - """Change the sensor mode used""" - + """Change the sensor mode used.""" if new_mode is None: self._sensor_mode = None elif isinstance(new_mode, SensorModeSelector): @@ -280,16 +295,17 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def sensor_resolution(self) -> Optional[tuple[int, int]]: - """The native resolution of the camera's sensor""" + """The native resolution of the camera's sensor.""" with self._streaming_picamera() as cam: return cam.sensor_resolution tuning = lt.ThingSetting(Optional[dict], None, readonly=True) + """The Raspberry PiCamera Tuning File JSON.""" def _initialise_picamera(self): - """Acquire the picamera device and store it as `self._picamera`. + """Acquire the picamera device and store it as ``self._picamera``. - This duplicates logic in `Picamera2.__init__` to provide a tuning file that + This duplicates logic in ``Picamera2.__init__`` to provide a tuning file that will be read when the camera system initialises. """ if self._picamera_lock is not None: @@ -319,6 +335,11 @@ class StreamingPiCamera2(BaseCamera): self._picamera_lock = RLock() def __enter__(self): + """Start streaming when the Thing context manager is opened. + + This opens the picamera connection, initialises the camera, sets the + sensor_modes property, and then starts the streams. + """ self._initialise_picamera() # populate sensor modes by reading the property self.sensor_modes @@ -327,21 +348,22 @@ class StreamingPiCamera2(BaseCamera): @property def streaming(self) -> bool: - """True if the camera is streaming""" + """True if the camera is streaming.""" return self._picamera is not None and self._picamera.started @contextmanager def _streaming_picamera(self, pause_stream=False) -> Iterator[Picamera2]: - """Lock access to picamera and return the underlying `Picamera2` instance. + """Lock access to picamera and return the underlying ``Picamera2`` instance. Optionally the stream can be paused to allow updating the camera settings. - :param pause_stream: If False the `Picamera2` instance is simply yielded. - If True: - * Stop the MJPEG Stream - * Yield the `Picamera2` instance for function calling the context manager to - make changes. - * On closing of the context manager the stream will restart. + :param pause_stream: If False the ``Picamera2`` instance is simply yielded. + If True: + + * Stop the MJPEG Stream + * Yield the ``Picamera2`` instance for function calling the context manager to + make changes. + * On closing of the context manager the stream will restart. """ already_streaming = self.stream_active with self._picamera_lock: @@ -354,7 +376,7 @@ class StreamingPiCamera2(BaseCamera): self.start_streaming() def __exit__(self, exc_type, exc_value, traceback): - # Shut down the camera + """Close the picamera connection when the Thing context manager is closed.""" self.stop_streaming() with self._streaming_picamera() as cam: cam.close() @@ -364,16 +386,16 @@ class StreamingPiCamera2(BaseCamera): def start_streaming( self, main_resolution: tuple[int, int] = (820, 616), buffer_count: int = 6 ) -> None: - """ - Start the MJPEG stream. This is where persistent controls are sent to camera. + """Start the MJPEG stream. This is where persistent controls are sent to camera. Sets the camera resolutions based on input parameters, and sets the low-res resolution to (320, 240). Note: (320, 240) is a standard from the Pi Camera manual. Create two streams: - - `lores_mjpeg_stream` for autofocus at low-res resolution - - `mjpeg_stream` for preview. This is the `main_resolution` if this is less + + * ``lores_mjpeg_stream`` for autofocus at low-res resolution + * ``mjpeg_stream`` for preview. This is the ``main_resolution`` if this is less than (1280, 960), or the low-res resolution if above. This allows for high resolution capture without streaming high resolution video. @@ -434,9 +456,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def stop_streaming(self, stop_web_stream: bool = True) -> None: - """ - Stop the MJPEG stream - """ + """Stop the MJPEG stream.""" with self._streaming_picamera() as picam: try: picam.stop_recording() # This should also stop the extra lores encoder @@ -478,7 +498,7 @@ class StreamingPiCamera2(BaseCamera): stream_name: Literal["main", "lores", "raw", "full"] = "main", wait: Optional[float] = 0.9, ) -> ArrayModel: - """Acquire one image from the camera and return as an array + """Acquire one image from the camera and return as an array. This function will produce a nested list containing an uncompressed RGB image. It's likely to be highly inefficient - raw and/or uncompressed captures using @@ -489,7 +509,6 @@ class StreamingPiCamera2(BaseCamera): A TimeoutError is raised if this time is exceeded during capture. Default = 0.9s, lower than the 1s timeout default in picamera yaml settings """ - # This was slower than capture_image for our use case, but directly returning # an image as an array is still a useful feature if stream_name == "full": @@ -501,7 +520,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def camera_configuration(self) -> Mapping: - """The "configuration" dictionary of the picamera2 object + """The "configuration" dictionary of the picamera2 object. The "configuration" sets the resolution and format of the camera's streams. Together with the "tuning" it determines how the sensor is configured and @@ -521,15 +540,15 @@ class StreamingPiCamera2(BaseCamera): resolution: Literal["lores", "main", "full"] = "main", wait: Optional[float] = 0.9, ) -> JPEGBlob: - """Acquire one image from the camera as a JPEG + """Acquire one image from the camera as a JPEG. - The JPEG will be acquired using `Picamera2.capture_file`. If the - `resolution` parameter is `main` or `lores`, it will be captured + The JPEG will be acquired using ``Picamera2.capture_file``. If the + ``resolution`` parameter is ``main`` or ``lores``, it will be captured from the main preview stream, or the low-res preview stream, respectively. This means the camera won't be reconfigured, and the stream will not pause (though it may miss one frame). - If `full` resolution is requested, we will briefly pause the + If ``full`` resolution is requested, we will briefly pause the MJPEG stream and reconfigure the camera to capture a full resolution image. @@ -572,7 +591,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def capture_metadata(self) -> dict: - """Return the metadata from the camera""" + """Return the metadata from the camera.""" with self._streaming_picamera() as cam: return cam.capture_metadata() @@ -582,17 +601,18 @@ class StreamingPiCamera2(BaseCamera): target_white_level: int = 700, percentile: float = 99.9, ): - """Adjust exposure until a the target white level is reached + """Adjust exposure until a the target white level is reached. Starting from the minimum exposure, gradually increase exposure until the image reaches the specified white level. :param target_white_level: The target 10bit white level. 10-bit data has a - theoretical maximum of 1023, but with black level correction the true maxiumum - is about 950. Default is 700 as this is approximately 70% saturated. + theoretical maximum of 1023, but with black level correction the true + maximum is about 950. Default is 700 as this is approximately 70% + saturated. :param percentile: The percentile to use instead of maximum. Default 99.9. When - calculating the brightest pixel, a percentile is used rather than the - maximum in order to be robust to a small number of noisy/bright pixels. + calculating the brightest pixel, a percentile is used rather than the + maximum in order to be robust to a small number of noisy/bright pixels. """ with self._streaming_picamera(pause_stream=True) as cam: recalibrate_utils.adjust_shutter_and_gain_from_raw( @@ -607,7 +627,7 @@ class StreamingPiCamera2(BaseCamera): method: Literal["percentile", "centre"] = "centre", luminance_power: float = 1.0, ): - """Correct the white balance of the image + """Correct the white balance of the image. This calibration requires a neutral image, such that the 99th centile of each colour channel should correspond to white. We calculate the @@ -615,7 +635,7 @@ class StreamingPiCamera2(BaseCamera): image with the lens shading correction applied, which should mean that the image is uniform, rather than weighted towards the centre. - If `method` is `"centre"`, we will correct the mean of the central 10% + If ``method`` is ``"centre"``, we will correct the mean of the central 10% of the image. """ with self._streaming_picamera(pause_stream=True) as cam: @@ -657,7 +677,7 @@ class StreamingPiCamera2(BaseCamera): def colour_correction_matrix( self, ) -> tuple[float, float, float, float, float, float, float, float, float]: - """The `colour_correction_matrix` from the tuning file. + """The ``colour_correction_matrix`` from the tuning file. This is broken out into its own property for convenience and compatibility with the micromanager API @@ -679,8 +699,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def reset_ccm(self): - """ - Overwrite the colour correction matrix in camera tuning with default values. + """Overwrite the colour correction matrix in camera tuning with default values. These values are from the Raspberry Pi Camera Algorithm and Tuning Guide, page 45. @@ -716,15 +735,15 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def full_auto_calibrate(self) -> None: - """Perform a full auto-calibration + """Perform a full auto-calibration. This function will call the other calibration actions in sequence: - * `flat_lens_shading` to disable flat-field - * `auto_expose_from_minimum` - * `set_static_green_equalisation` to set geq offset to max - * `calibrate_lens_shading` - * `calibrate_white_balance` + * ``flat_lens_shading`` to disable flat-field + * ``auto_expose_from_minimum`` + * ``set_static_green_equalisation`` to set geq offset to max + * ``calibrate_lens_shading`` + * ``calibrate_white_balance`` """ self.flat_lens_shading() self.auto_expose_from_minimum() @@ -734,13 +753,13 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def flat_lens_shading(self) -> None: - """Disable flat-field correction + """Disable flat-field correction. This method will set a completely flat lens shading table. It is not the same as the default behaviour, which is to use an adaptive lens shading table. - This flat table is used to take an image wth no lens shading so that the + This flat table is used to take an image with no lens shading so that the correct lens shading table can be calibrated. """ with self._streaming_picamera(pause_stream=True): @@ -753,7 +772,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def lens_shading_tables(self) -> Optional[LensShading]: - """The current lens shading (i.e. flat-field correction) + """The current lens shading (i.e. flat-field correction). Return the current lens shading correction, as three 2D lists each with dimensions 16x12, if a static lens shading table is in use. @@ -775,7 +794,7 @@ class StreamingPiCamera2(BaseCamera): return None def reshape_lst(lin: list[float]) -> list[list[float]]: - """Reshape the 192 element list into a 2D 16x12 list""" + """Reshape the 192 element list into a 2D 16x12 list.""" w, h = 16, 12 return [lin[w * i : w * (i + 1)] for i in range(h)] @@ -787,7 +806,7 @@ class StreamingPiCamera2(BaseCamera): @lens_shading_tables.setter def lens_shading_tables(self, lst: LensShading) -> None: - """Set the lens shading tables""" + """Set the lens shading tables.""" with self._streaming_picamera(pause_stream=True): recalibrate_utils.set_static_lst( self.tuning, @@ -800,19 +819,19 @@ class StreamingPiCamera2(BaseCamera): def correct_colour_gains_for_lens_shading( self, colour_gains: tuple[float, float] ) -> tuple[float, float]: - """Correct white balance gains for the effect of lens shading + """Correct white balance gains for the effect of lens shading. The white balance algorithm we use assumes the brightest pixels should be white, and that the only thing affecting the colour of - said pixels is the `colour_gains`. + said pixels is the ``colour_gains``. The lens shading correction is normalised such that the *minimum* - gain in the `Cr` and `Cb` channels is 1. The white balance + gain in the ``Cr`` and ``Cb`` channels is 1. The white balance assumption above requires that the gain for the brightest pixels is 1. The solution might be that, when calibrating, we note which pixels are brightest (usually the centre) and explicitly use the LST values for there. However, for now I will assume that we - need to normalise by the **maximum** of the `Cr` and `Cb` + need to normalise by the **maximum** of the ``Cr`` and ``Cb`` channels, which is correct the majority of the time. """ if not self.lens_shading_is_static: @@ -830,7 +849,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def flat_lens_shading_chrominance(self) -> None: - """Disable flat-field correction + """Disable flat-field correction. This method will set the chrominance of the lens shading table to be flat, i.e. we'll correct vignetting of intensity, but not any change in @@ -845,7 +864,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_action def reset_lens_shading(self) -> None: - """Revert to default lens shading settings + """Revert to default lens shading settings. This method will restore the default "adaptive" lens shading method used by the Raspberry Pi camera. @@ -856,7 +875,7 @@ class StreamingPiCamera2(BaseCamera): @lt.thing_property def lens_shading_is_static(self) -> bool: - """Whether the lens shading is static + """Whether the lens shading is static. This property is true if the lens shading correction has been set to use a static table (i.e. the number of automatic correction iterations is zero). diff --git a/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py b/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py index cf51efe8..fbf827df 100644 --- a/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py +++ b/src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py @@ -1,9 +1,8 @@ -""" -Functions to set up a Raspberry Pi Camera v2 for scientific use +"""Functions to set up a Raspberry Pi Camera v2 for scientific use. This module provides slower, simpler functions to set the gain, exposure, and white balance of a Raspberry Pi camera, using -the `picamera2` Python library. It's mostly used by the OpenFlexure +the ``picamera2`` Python library. It's mostly used by the OpenFlexure Microscope, though it deliberately has no hard dependencies on said software, so that it's useful on its own. @@ -20,14 +19,15 @@ to "memory" or nonlinearities in the camera's image processing pipeline, is to use raw images. This is quite slow, but very reliable. The three steps above can be accomplished by: -``` -picamera = picamera2.Picamera2() +.. code-block:: python + + picamera = picamera2.Picamera2() + + adjust_shutter_and_gain_from_raw(picamera) + adjust_white_balance_from_raw(picamera) + lst = lst_from_camera(picamera) + picamera.lens_shading_table = lst -adjust_shutter_and_gain_from_raw(picamera) -adjust_white_balance_from_raw(picamera) -lst = lst_from_camera(picamera) -picamera.lens_shading_table = lst -``` """ # Disable N806 & 803, which checks that all variables and args are lowercase. @@ -52,10 +52,10 @@ LensShadingTables = tuple[np.ndarray, np.ndarray, np.ndarray] def load_default_tuning(cam: Picamera2) -> dict: - """Load the default tuning file for the camera + """Load the default tuning file for the camera. This will open and close the camera to determine its model. If you are - using a model that's supported by `picamera2` it should have a tuning + using a model that's supported by ``picamera2`` it should have a tuning file built in. If not, this will probably crash with an error. Error handling for unsupported cameras is not something we are likely @@ -76,7 +76,7 @@ def load_default_tuning(cam: Picamera2) -> dict: def set_minimum_exposure(camera: Picamera2) -> None: - """Enable manual exposure, with low gain and shutter speed + """Enable manual exposure, with low gain and shutter speed. We set exposure mode to manual, analog and digital gain to 1, and shutter speed to the minimum (8us for Pi Camera v2) @@ -84,7 +84,7 @@ def set_minimum_exposure(camera: Picamera2) -> None: Note ISO is left at auto, because this is needed for the gains to be set correctly. """ - # Disable Automatic exposure and gain algoritm (AeEnable), and set analogue + # Disable Automatic exposure and gain algorithm (AeEnable), and set analogue # gain and exposure time. # Setting the shutter speed to 1us will result in it being set # to the minimum possible, which is ~8us for PiCamera v2 @@ -93,7 +93,7 @@ def set_minimum_exposure(camera: Picamera2) -> None: class ExposureTest(BaseModel): - """Record the results of testing the camera's current exposure settings""" + """Record the results of testing the camera's current exposure settings.""" level: int exposure_time: int @@ -101,7 +101,7 @@ class ExposureTest(BaseModel): def test_exposure_settings(camera: Picamera2, percentile: float) -> ExposureTest: - """Evaluate current exposure settings using a raw image + """Evaluate current exposure settings using a raw image. CAMERA SHOULD BE STARTED! @@ -136,7 +136,7 @@ def test_exposure_settings(camera: Picamera2, percentile: float) -> ExposureTest def check_convergence(test: ExposureTest, target: int, tolerance: float) -> bool: - """Check whether the brightness is within the specified target range""" + """Check whether the brightness is within the specified target range.""" return abs(test.level - target) < target * tolerance @@ -152,25 +152,19 @@ def adjust_shutter_and_gain_from_raw( This routine is slow but effective. It uses raw images, so we are not affected by white balance or digital gain. + :param camera: A Picamera2 object. + :param target_white_level: The raw, 10-bit value we aim for. The brightest pixels + should be approximately this bright. Maximum possible is about 900, 700 is + reasonable. + :param max_iterations: We will terminate once we perform this many iterations, + whether or not we converge. More than 10 shouldn't happen. + :param tolerance: How close to the target value we consider "done". Expressed as a + fraction of the ``target_white_level`` so 0.05 means +/- 5% + :param percentile: Rather then use the maximum value for each channel, we calculate + a percentile. This makes us robust to single pixels that are bright/noisy. + 99.9% still picks the top of the brightness range, but seems much more reliable + than just ``np.max()``. - Arguments: - target_white_level: - The raw, 10-bit value we aim for. The brightest pixels - should be approximately this bright. Maximum possible - is about 900, 700 is reasonable. - max_iterations: - We will terminate once we perform this many iterations, - whether or not we converge. More than 10 shouldn't happen. - tolerance: - How close to the target value we consider "done". Expressed - as a fraction of the ``target_white_level`` so 0.05 means - +/- 5% - percentile: - Rather then use the maximum value for each channel, we - calculate a percentile. This makes us robust to single - pixels that are bright/noisy. 99.9% still picks the top - of the brightness range, but seems much more reliable - than just ``np.max()``. """ # TODO: read black level and bit depth from camera? if target_white_level * (tolerance + 1) >= 959: @@ -327,7 +321,7 @@ def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray: def get_16x12_grid(chan: np.ndarray, dx: int, dy: int) -> np.ndarray: - """Compresses channel down to a 16x12 grid - from libcamera + """Compresses channel down to a 16x12 grid - from libcamera. This is taken from https://git.linuxtv.org/libcamera.git/tree/utils/raspberrypi/ctt/ctt_alsc.py @@ -349,9 +343,9 @@ def get_16x12_grid(chan: np.ndarray, dx: int, dy: int) -> np.ndarray: def upsample_channels(grids: np.ndarray, shape: tuple[int]) -> np.ndarray: - """Zoom an image in the last two dimensions + """Zoom an image in the last two dimensions. - This is effectively the inverse operation of `get_16x12_grid` + This is effectively the inverse operation of ``get_16x12_grid`` """ zoom_factors = [ 1, @@ -360,7 +354,7 @@ def upsample_channels(grids: np.ndarray, shape: tuple[int]) -> np.ndarray: def downsampled_channels(channels: np.ndarray, blacklevel=64) -> list[np.ndarray]: - """Generate a downsampled, un-normalised image from which to calculate the LST + """Generate a downsampled, un-normalised image from which to calculate the LST. TODO: blacklevel probably ought to be determined from the camera... """ @@ -381,22 +375,21 @@ def downsampled_channels(channels: np.ndarray, blacklevel=64) -> list[np.ndarray def lst_from_channels(channels: np.ndarray) -> LensShadingTables: """Given the 4 Bayer colour channels from a white image, generate a LST. - Internally, is just calls `downsampled_channels` and `lst_from_grids`. + Internally, is just calls ``downsampled_channels`` and ``lst_from_grids``. """ grids = downsampled_channels(channels) return lst_from_grids(grids) def lst_from_grids(grids: np.ndarray) -> LensShadingTables: - """Given 4 downsampled grids, generate the luminance and chrominance tables + """Given 4 downsampled grids, generate the luminance and chrominance tables. The grids are the 4 BAYER channels RGGB - The LST format has changed with `picamera2` and now uses a fixed resolution, + The LST format has changed with ``picamera2`` and now uses a fixed resolution, and is in luminance, Cr, Cb format. This function returns three ndarrays of luminance, Cr, Cb, each with shape (12, 16). """ - # Calculated red, green, and blue channels from Bayer data r: np.ndarray = grids[3, ...] g: np.ndarray = np.mean(grids[1:3, ...], axis=0) @@ -415,11 +408,11 @@ def lst_from_grids(grids: np.ndarray) -> LensShadingTables: def grids_from_lst(lum: np.ndarray, Cr: np.ndarray, Cb: np.ndarray) -> np.ndarray: - """Convert form luminance/chrominance dict to four RGGB channels + """Convert form luminance/chrominance dict to four RGGB channels. Note that these will be normalised - the maximum green value is always 1. Also, note that the channels are BGGR, to be consistent with the - `channels_from_raw_image` function. This should probably change in the + ``channels_from_raw_image`` function. This should probably change in the future. """ G = 1 / np.array(lum) @@ -434,9 +427,9 @@ def set_static_lst( cr: np.ndarray, cb: np.ndarray, ) -> None: - """Update the `rpi.alsc` section of a camera tuning dict to use a static correcton. + """Update the ``rpi.alsc`` section of a camera tuning dict to use a static correction. - `tuning` will be updated in-place to set its shading to static, and disable any + ``tuning`` will be updated in-place to set its shading to static, and disable any adaptive tweaking by the algorithm. """ for table in luminance, cr, cb: @@ -459,9 +452,9 @@ def set_static_ccm( float, float, float, float, float, float, float, float, float ], ) -> None: - """Update the `rpi.alsc` section of a camera tuning dict to use a static correcton. + """Update the ``rpi.alsc`` section of a camera tuning dict to use a static correction. - `tuning` will be updated in-place to set its shading to static, and disable any + ``tuning`` will be updated in-place to set its shading to static, and disable any adaptive tweaking by the algorithm. """ ccm = Picamera2.find_tuning_algo(tuning, "rpi.ccm") @@ -469,13 +462,13 @@ def set_static_ccm( def get_static_ccm(tuning: dict) -> None: - """Get the `rpi.ccm` section of a camera tuning dict""" + """Get the ``rpi.ccm`` section of a camera tuning dict.""" ccm = Picamera2.find_tuning_algo(tuning, "rpi.ccm") return ccm["ccms"] def lst_is_static(tuning: dict) -> bool: - """Whether the lens shading table is set to static""" + """Whether the lens shading table is set to static.""" alsc = Picamera2.find_tuning_algo(tuning, "rpi.alsc") return alsc["n_iter"] == 0 @@ -484,26 +477,29 @@ def set_static_geq( tuning: dict, offset: int = 65535, ) -> None: - """Update the `rpi.geq` section of a camera tuning dict to always use green - equalisation that averages the green pixels in the red and blue rows. + """Update the ``rpi.geq`` section of a camera tuning dict. - `tuning` will be updated in-place to set the geq offest to the given value. - The default 65535 is the maximum allowed value. This means - the brightness will always be below the threshold where averaging is used. + :param tuning: the raspberry pi tuning file. This will be updated in-place to + set the geq offset to the given value. + :param offset: The desired green equalisation offset. Default 65535. The default is + the maximum allowed value. This means the brightness will always be below the + threshold where averaging is used. This is default as we always need the green + equalisation to averages the green pixels in the red and blue rows due to the + chief ray angle compensation issue when the the stock lens is replaced by an + objective. """ - geq = Picamera2.find_tuning_algo(tuning, "rpi.geq") geq["offset"] = offset # max out offset to disable the adaptive green equalisation def _geq_is_static(tuning: dict) -> bool: - """Whether the green equalisation is set to static""" + """Whether the green equalisation is set to static.""" geq = Picamera2.find_tuning_algo(tuning, "rpi.geq") return geq["offset"] == 65535 def index_of_algorithm(algorithms: list[dict], algorithm: str) -> int: - """Find the index of an algorithm's section in the tuning file""" + """Find the index of an algorithm's section in the tuning file.""" for i, a in enumerate(algorithms): if algorithm in a: return i @@ -511,7 +507,7 @@ def index_of_algorithm(algorithms: list[dict], algorithm: str) -> int: def copy_alsc_section(from_tuning: dict, to_tuning: dict) -> None: - """Copy the `rpi.alsc` algorithm from one tuning to another. + """Copy the ``rpi.alsc`` algorithm from one tuning to another. This is done in-place, i.e. modifying to_tuning. """ @@ -561,5 +557,5 @@ def recreate_camera_manager() -> None: def as_flat_rounded_list(array: np.ndarray, round_to: int = 3) -> list[float]: - """Flatten array, round, and then convert to list""" + """Flatten array, round, and then convert to list.""" return np.reshape(array, -1).round(round_to).tolist() diff --git a/src/openflexure_microscope_server/things/camera/simulation.py b/src/openflexure_microscope_server/things/camera/simulation.py index c39e912a..ed2d7e14 100644 --- a/src/openflexure_microscope_server/things/camera/simulation.py +++ b/src/openflexure_microscope_server/things/camera/simulation.py @@ -1,4 +1,4 @@ -"""OpenFlexure Microscope OpenCV Camera +"""OpenFlexure Microscope OpenCV Camera. This module defines a Thing that is responsible for using the stage and camera together to perform an autofocus routine. @@ -30,7 +30,7 @@ RATIO = 0.2 class SimulatedCamera(BaseCamera): - """A Thing representing an OpenCV camera""" + """A Thing that simulates a camera for testing.""" _stage: Optional[BaseStage] = None _server: Optional[lt.ThingServer] = None @@ -42,6 +42,16 @@ class SimulatedCamera(BaseCamera): canvas_shape: tuple[int, int, int] = (3000, 4000, 3), frame_interval: float = 0.1, ): + """Initialise the simulated with settings for how images are generated. + + :param shape: The shape (size) of the generated image. + :param glyph_shape: The size randomly positioned glyphs. + :param canvas_shape: The shape (size) of the canvas generated on initialisation + that images are cropped from. If this is too large the it uses resources, + but its size limits the range of motion of the simulation. + :param frame_interval: Nominally the time between frames on the MJPEG stream, + however the rate may be slower due to calculation time for focus. + """ self.shape = shape self.glyph_shape = glyph_shape self.canvas_shape = canvas_shape @@ -53,7 +63,7 @@ class SimulatedCamera(BaseCamera): self.generate_canvas() def generate_sprites(self): - """Generate sprites to populate the image""" + """Generate sprites to populate the image.""" self.sprites = [] black = np.zeros(self.glyph_shape, dtype=np.uint8) x = np.arange(black.shape[0]) @@ -65,7 +75,7 @@ class SimulatedCamera(BaseCamera): self.sprites.append(sprite) def generate_blobs(self, n_blobs: int = 1000): - """Generate coordinates of blobs + """Generate coordinates of blobs. Blobs are characterised by X, Y, sprite We also generate a KD tree to rapidly find blobs in an image @@ -78,7 +88,7 @@ class SimulatedCamera(BaseCamera): self.blobs[:, 2] = rng.choice(len(self.sprites), n_blobs) def generate_canvas(self): - """Generate a blank canvas""" + """Generate a blank canvas.""" self.canvas = np.zeros(self.canvas_shape, dtype=np.uint8) self.canvas[...] = 255 w, h, _ = self.glyph_shape @@ -89,7 +99,7 @@ class SimulatedCamera(BaseCamera): ] -= self.sprites[int(sprite)] def generate_image(self, pos: tuple[int, int, int]): - """Generate an image with blobs based on supplied coordinates""" + """Generate an image with blobs based on supplied coordinates.""" canvas_width, canvas_height, _ = self.canvas_shape image_width, image_height, _ = self.shape pos = tuple(x * RATIO for x in pos) @@ -115,16 +125,26 @@ class SimulatedCamera(BaseCamera): def attach_to_server( self, server: lt.ThingServer, path: str, setting_storage_path: str ): + """Wrap the attach_to_server method so the server instance can be stored. + + Direct access to the server instance is needed to get the stage position while + maintaining the same public API as a real camera that doesn't need this access. + """ self._server = server return super().attach_to_server(server, path, setting_storage_path) def get_stage_position(self): + """Return the stage position. + + The simulation camera has access to the stage position so it can generate a + different image as the stage moves. + """ if not self._stage and self._server: self._stage = self._server.things["/stage/"] return self._stage.instantaneous_position def generate_frame(self): - """Generate a frame with blobs based on the stage coordinates""" + """Generate a frame with blobs based on the stage coordinates.""" try: pos = self.get_stage_position() except Exception as e: @@ -133,19 +153,21 @@ class SimulatedCamera(BaseCamera): return self.generate_image((pos["y"], pos["x"], pos["z"])) def __enter__(self): + """Start the capture thread when the Thing context manager is opened.""" self._capture_enabled = True self._capture_thread = Thread(target=self._capture_frames) self._capture_thread.start() return self def __exit__(self, _exc_type, _exc_value, _traceback): + """Close the capture thread when the Thing context manager is closed.""" if self.stream_active: self._capture_enabled = False self._capture_thread.join() @lt.thing_property def stream_active(self) -> bool: - "Whether the MJPEG stream is active" + """Whether the MJPEG stream is active.""" if self._capture_enabled and self._capture_thread: return self._capture_thread.is_alive() return False @@ -170,13 +192,13 @@ class SimulatedCamera(BaseCamera): self, resolution: Literal["main", "full"] = "full", ) -> ArrayModel: - """Acquire one image from the camera and return as an array + """Acquire one image from the camera and return as an array. This function will produce a nested list containing an uncompressed RGB image. It's likely to be highly inefficient - raw and/or uncompressed captures using binary image formats will be added in due course. """ - logging.warning(f"Simulation camera doen't respect {resolution} setting") + logging.warning(f"Simulation camera doesn't respect {resolution} setting") return self.generate_frame() @lt.thing_action @@ -185,11 +207,11 @@ class SimulatedCamera(BaseCamera): metadata_getter: lt.deps.GetThingStates, resolution: Literal["main", "full"] = "main", ) -> JPEGBlob: - """Acquire one image from the camera and return as a JPEG blob + """Acquire one image from the camera and return as a JPEG blob. This function will produce a JPEG image. """ - logging.warning(f"Simulation camera doen't respect {resolution} setting") + logging.warning(f"Simulation camera doesn't respect {resolution} setting") frame = self.capture_array() jpeg = cv2.imencode(".jpg", frame)[1].tobytes() exif_dict = { diff --git a/src/openflexure_microscope_server/things/camera_stage_mapping.py b/src/openflexure_microscope_server/things/camera_stage_mapping.py index ae969b6c..97aa5e25 100644 --- a/src/openflexure_microscope_server/things/camera_stage_mapping.py +++ b/src/openflexure_microscope_server/things/camera_stage_mapping.py @@ -1,5 +1,4 @@ -""" -OpenFlexure Microscope API extension for stage calibration +"""OpenFlexure Microscope API extension for stage calibration. This file contains the HTTP API for camera/stage calibration. It includes calibration functions that measure the relationship between @@ -46,6 +45,11 @@ XYCoordinateType = Tuple[float, float] class HardwareInterfaceModel(BaseModel): + """A pydantic base model for a stage and camera interface. + + This code has been flagged as confusing and will be replaced soon, see #476. + """ + move: Callable[[NDArray], None] get_position: Callable[[], NDArray] grab_image: Callable[[], NDArray] @@ -54,10 +58,10 @@ class HardwareInterfaceModel(BaseModel): def downsample(factor: int, image: np.ndarray) -> np.ndarray: - """Downsample an image by taking the mean of each nxn region + """Downsample an image by taking the mean of each nxn region. This should be very efficient: we calculate the mean of each - `factor * factor` square, no interpolation. If the image is + ``factor * factor`` square, no interpolation. If the image is not an integer multiple of the resampling factor, we discard the left-over pixels. This avoids odd edge effects and keeps performance quick. @@ -80,7 +84,7 @@ DEFAULT_SETTLING_TIME = 0.2 def make_hardware_interface( stage: Stage, camera: Camera, downsample_factor: int = 2 ) -> HardwareInterfaceModel: - """Construct the functions we need to interface with the hardware""" + """Construct the functions we need to interface with the hardware.""" axes = stage.axis_names def pos2dict(pos: Sequence[float]) -> Mapping[str, float]: @@ -124,6 +128,14 @@ HardwareInterfaceDep = Annotated[ class MoveHistory(NamedTuple): + """A named tuple containing the position over time for a single move. + + This a named tuple with elements: + + * ``times`` + * ``stage_positions`` + """ + times: List[float] stage_positions: List[CoordinateType] @@ -140,12 +152,16 @@ class LoggingMoveWrapper: """ def __init__(self, move_function: Callable): + """Set the movement function to be wrapped. + + :param move_function: the movement function to be wrapped + """ self._move_function: Callable = move_function self._current_position: Optional[CoordinateType] = None self.clear_history() def __call__(self, new_position: CoordinateType, *args, **kwargs): - """Move to a new position, and record it""" + """Move to a new position, and record it.""" self._history.append((time.time(), self._current_position)) self._move_function(new_position, *args, **kwargs) self._current_position = new_position @@ -153,18 +169,26 @@ class LoggingMoveWrapper: @property def history(self) -> MoveHistory: - """The history, as a numpy array of times and another of positions""" + """The history, as a numpy array of times and another of positions.""" times: List[float] = [t for t, p in self._history if p is not None] positions: List[CoordinateType] = [p for t, p in self._history if p is not None] return MoveHistory(times, positions) def clear_history(self): - """Reset our history to be an empty list""" + """Reset our history to be an empty list.""" self._history: List[Tuple[float, Optional[CoordinateType]]] = [] class CSMUncalibratedError(HTTPException): + """An HTTP Exception raised if camera stage mapping data is needed but unavailable. + + Camera Stage Mapping data is needed to convert from distances specified in fractions + of the field of view to distances in motor steps. This is used when clicking on the + live preview to move, or when performing a scan. + """ + def __init__(self): + """Customise the default error code and message of HTTPException.""" HTTPException.__init__( self, 503, @@ -176,7 +200,7 @@ class CSMUncalibratedError(HTTPException): class CameraStageMapper(lt.Thing): - """A Thing to manage mapping between image and stage coordinates""" + """A Thing to manage mapping between image and stage coordinates.""" @lt.thing_action def calibrate_1d( @@ -186,10 +210,9 @@ class CameraStageMapper(lt.Thing): logger: lt.deps.InvocationLogger, direction: Tuple[float, float, float], ) -> DenumpifyingDict: - """Move a microscope's stage in 1D, and figure out the relationship with the camera""" - move = LoggingMoveWrapper( - hw.move - ) # log positions and times for stage calibration + """Move a microscope's stage in 1D, and figure out the relationship with the camera.""" + # log positions and times for stage calibration + move = LoggingMoveWrapper(hw.move) tracker = Tracker(hw.grab_image, hw.get_position, settle=hw.settle) direction_array: np.ndarray = np.array(direction) @@ -215,7 +238,7 @@ class CameraStageMapper(lt.Thing): def calibrate_xy( self, hw: HardwareInterfaceDep, stage: Stage, logger: lt.deps.InvocationLogger ) -> DenumpifyingDict: - """Move the microscope's stage in X and Y, to calibrate its relationship to the camera + """Move the microscope's stage in X and Y, to calibrate its relationship to the camera. This performs two 1d calibrations in x and y, then combines their results. """ @@ -265,14 +288,16 @@ class CameraStageMapper(lt.Thing): that conversion. It is often helpful to give a concrete example: to make a move in image coordinates - (`dy`, `dx`), where `dx` is horizontal, i.e. the longer dimension of the image, you + (``dy``, ``dx``), where ``dx`` is horizontal, i.e. the longer dimension of the image, you should move the stage by: - ``` - stage_disp = np.dot( - np.array(image_to_stage_displacement_matrix), - np.array([dy,dx]), - ) - ``` + + .. code-block:: python + + stage_disp = np.dot( + np.array(image_to_stage_displacement_matrix), + np.array([dy,dx]), + ) + """ if self.last_calibration is None: return None @@ -282,21 +307,19 @@ class CameraStageMapper(lt.Thing): return np.array(displacement_matrix).tolist() last_calibration = lt.ThingSetting( - initial_value=None, - model=Optional[dict], - readonly=True, - description="The most recent CSM calibration", + initial_value=None, model=Optional[dict], readonly=True ) + """The most recent CSM calibration.""" @lt.thing_property def image_resolution(self) -> Optional[Tuple[float, float]]: - """The image size used to calibrate the image_to_stage_displacement_matrix""" + """The image size used to calibrate the image_to_stage_displacement_matrix.""" if self.last_calibration is None: return None return self.last_calibration["image_resolution"] def assert_calibrated(self): - """Raise an exception if the image_to_stage_displacement matrix is not set""" + """Raise an exception if the image_to_stage_displacement matrix is not set.""" if self.image_to_stage_displacement_matrix is None: # Disable check of no message in raised exception as the message is explicitly # added by CSMUncalibratedError @@ -309,15 +332,15 @@ class CameraStageMapper(lt.Thing): x: float, y: float, ): - """Move by a given number of pixels on the camera + """Move by a given number of pixels on the camera. NB x and y here refer to what is usually understood to be the horizontal and vertical axes of the image. In many toolkits, "matrix indices" are used, which swap the order of these coordinates. This includes opencv and PIL. So, don't be surprised if you find it necessary to swap x and y around. - As a general rule, `x` usually corresponds to the longer dimension of the image, - and `y` to the shorter one. Checking what shape your chosen toolkit reports for + As a general rule, ``x`` usually corresponds to the longer dimension of the image, + and ``y`` to the shorter one. Checking what shape your chosen toolkit reports for an image usually helps resolve any ambiguity. """ self.assert_calibrated() @@ -328,7 +351,7 @@ class CameraStageMapper(lt.Thing): @lt.thing_property def thing_state(self) -> dict[str, Any]: - """Summary metadata describing the current state of the Thing""" + """Summary metadata describing the current state of the Thing.""" return { k: getattr(self, k) for k in ["image_to_stage_displacement_matrix", "image_resolution"] diff --git a/src/openflexure_microscope_server/things/settings_manager.py b/src/openflexure_microscope_server/things/settings_manager.py index 6dacd7dd..8ae47a8f 100644 --- a/src/openflexure_microscope_server/things/settings_manager.py +++ b/src/openflexure_microscope_server/things/settings_manager.py @@ -1,5 +1,4 @@ -""" -OpenFlexure Settings Management +"""OpenFlexure Settings Management. This module provides some settings management across the other Things, and for code that currently lives in clients but needs to persist settings on @@ -15,6 +14,7 @@ import labthings_fastapi as lt def thing_server_from_request(request: Request) -> lt.ThingServer: + """Wrap lt.find_thing_server.""" return lt.find_thing_server(request.app) @@ -22,7 +22,7 @@ ThingServerDep = Annotated[lt.ThingServer, Depends(thing_server_from_request)] def recursive_update(old_dict: MutableMapping, update: Mapping): - """Update a dictionary recursively""" + """Update a dictionary recursively.""" for k, v in update.items(): if isinstance(v, Mapping): if k in old_dict and isinstance(old_dict[k], MutableMapping): @@ -34,7 +34,7 @@ def recursive_update(old_dict: MutableMapping, update: Mapping): def nested_dict_get(data: dict, key: Sequence[str], create=False) -> Any: - """Index a dict-of-dicts with a sequence of strings""" + """Index a dict-of-dicts with a sequence of strings.""" subdict = data for k in key: if k not in subdict and create: @@ -44,17 +44,23 @@ def nested_dict_get(data: dict, key: Sequence[str], create=False) -> Any: class SettingsManager(lt.Thing): + """Provides functionality to other Things about the current server state. + + The SettingsManager is used to get information the microscope ID, the hostname + and the state of other Things. + """ + external_metadata = lt.ThingSetting( initial_value={}, model=Mapping, - description="External metadata stored in the server's settings", ) + """External metadata stored in the server's settings.""" external_metadata_in_state = lt.ThingSetting( initial_value=[], model=Sequence[str], - description='A list of strings that are included in the "state" metadata', ) + """Keys from ``external_metadata`` that are included in the "state" metadata.""" @lt.thing_action def update_external_metadata( @@ -66,9 +72,9 @@ class SettingsManager(lt.Thing): recursively, i.e. if a key exists, it will be added to rather than replaced. - If a key is supplied, we will treat `data` as being relative to that - key, i.e. calling this action with `data={"a":1 }, key="foo/bar"` is - equivalent to calling it with `data={"foo": {"bar": {"a": 1}}}`. + If a key is supplied, we will treat ``data`` as being relative to that + key, i.e. calling this action with ``data={"a":1 }, key="foo/bar"`` is + equivalent to calling it with ``data={"foo": {"bar": {"a": 1}}}``. """ metadata = self.external_metadata subdict = metadata @@ -84,8 +90,8 @@ class SettingsManager(lt.Thing): """Delete a key from the stored metadata. The key may contain forward slashes, which are understood to separate - levels of the dictionary - i.e. `'a/c'` will remove the `c` key from a - dictionary that looks like: `{'a': {'c': 1}, 'b': {'d': 2}}` + levels of the dictionary - i.e. ``'a/c'`` will remove the ``c`` key from a + dictionary that looks like: ``{'a': {'c': 1}, 'b': {'d': 2}}`` """ metadata = self.external_metadata try: @@ -101,7 +107,7 @@ class SettingsManager(lt.Thing): @lt.thing_setting def microscope_id(self) -> UUID: - """A unique identifier for this microscope""" + """A unique identifier for this microscope.""" if self._microscope_id is None: self._microscope_id = str(uuid4()) return UUID(self._microscope_id) @@ -118,11 +124,12 @@ class SettingsManager(lt.Thing): @lt.thing_action def get_things_state(self, metadata_getter: lt.deps.GetThingStates) -> Mapping: - """Metadata summarising the current state of all Things in the server""" + """Metadata summarising the current state of all Things in the server.""" return metadata_getter() @property def thing_state(self) -> Mapping: + """Summary metadata describing the current state of the Thing.""" state = { "hostname": self.hostname, "microscope-uuid": str(self.microscope_id), diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py index c9c19627..f7e5d675 100644 --- a/src/openflexure_microscope_server/things/smart_scan.py +++ b/src/openflexure_microscope_server/things/smart_scan.py @@ -1,3 +1,12 @@ +"""The core sample scanning functionality for the OpenFlexure Microscope. + +SmartScan provides sample scanning functionality including automatic background +detection (via the `BackgroundDetectThing`) and automatic path planning via +`scan_planners`. It manages the directories of past scans via `scan_directories`. +It also controls external processes for live stitching composite images, and +the creation of the final stitched images. +""" + from typing import Optional, Mapping import threading import os @@ -42,11 +51,12 @@ STITCHING_RESOLUTION = (820, 616) class ScanNotRunningError(RuntimeError): - """Exception called when scan not running that requires a scan to be running""" + """Exception called when scan not running that requires a scan to be running.""" def _scan_running(method): - """ + """Decorate a method so that it will error if a scan is not running. + This decorator is used by all methods in SmartScanThing that are using the variables set for the scan. It will throw a runtime error if self._scan_logger is not set, as all scan variables are set at @@ -65,7 +75,20 @@ def _scan_running(method): class SmartScanThing(lt.Thing): - def __init__(self, scans_folder): + """A Thing for scanning samples and interacting with past scans. + + SmartScanThing exposes all functionality for automatically scanning samples, + previewing live stitching, retrieving data from past scans, and for deleting + past scans. + """ + + def __init__(self, scans_folder: str): + """Initialise a SmartScanThing saving to and loading from the input directory. + + :param scans_folder: This is the path to the directory where all scans will be + saved. Any scans already in this directory will be accessible through the + HTTP interface. + """ self._scan_dir_manager = scan_directories.ScanDirectoryManager(scans_folder) self._preview_stitch_popen = None self._preview_stitch_popen_lock = threading.Lock() @@ -114,7 +137,6 @@ class SmartScanThing(lt.Thing): stopping once it is surrounded by "background" (as detected by the background_detect Thing) or reaches the "max_range" measured in steps. """ - got_lock = self._scan_lock.acquire(timeout=0.1) if not got_lock: raise RuntimeError("Trying to run scan while scan is already running!") @@ -170,7 +192,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _check_background_and_csm_set(self): - """Before starting a scan, check that background and camera-stage-mapping are set + """Before starting a scan, check that background and camera-stage-mapping are set. Raise error if: - background is to be skipped but is not set @@ -207,14 +229,14 @@ class SmartScanThing(lt.Thing): def _move_to_next_point( self, next_point: tuple[int, int], z_estimate: Optional[int] = None ) -> tuple[int, int, int]: - """Moves the stage to the next poistion. If no z_estimate is given then - the current stage position is used. Must move to the estimated focused position - (although moving below would be marginally faster) because background detect is - most reliable at the focused position. + """Move the stage to the next position. - Returns the (x,y,z) with the chosen z_estimate + If no z_estimate is given then the current stage position is used. Must move + to the estimated focused position (although moving below would be marginally + faster) because background detect is most reliable at the focused position. + + :returns: the (x,y,z) with the chosen z_estimate """ - if z_estimate is None: z_estimate = self._stage.position["z"] @@ -229,13 +251,12 @@ class SmartScanThing(lt.Thing): @_scan_running def _calc_displacement_from_test_image(self, overlap: int) -> tuple[int, int]: - """ - Take a test image and use camera stage mapping to calculate x and y displacement + """Take a test image and use camera stage mapping to calculate x and y displacement. :param overlap: The desired overlap as a fraction of the image. i.e. 0.5 means - that each image should overlap its nearest neighbour by 50%. + that each image should overlap its nearest neighbour by 50%. - Return (dx, dy) - the x and y displacments in steps + :returns: (dx, dy) - the x and y displacements in steps """ test_jpg = self._cam.grab_jpeg() test_image = np.array(Image.open(test_jpg.open())) @@ -268,9 +289,9 @@ class SmartScanThing(lt.Thing): @_scan_running def _set_scan_data(self): - """ - This sets the self._scan_data dictionary. This needs to become a - dataclass. + """Set date for this scan to the ``self._scan_data`` variable. + + This needs to become a dataclass at some point. """ overlap = self.overlap dx, dy = self._calc_displacement_from_test_image(overlap) @@ -312,9 +333,9 @@ class SmartScanThing(lt.Thing): @_scan_running def _save_scan_inputs_json(self): - """ - Save scan inputs as a JSON file in the scan folder, to allow - the user to review the settings used in the scan + """Save scan inputs as a JSON file in the scan folder. + + This file allows the user to review the settings used in the scan. """ # Should this be a method of the scan_data dataclass? @@ -337,12 +358,10 @@ class SmartScanThing(lt.Thing): @_scan_running def _update_scan_data_json(self, scan_result: str): - """ - Update scan data as a JSON file in the scan folder, with - data only known at the end of the scan. + """Update scan data JSON file with data only known at the end of the scan. - Takes scan_result, a string that is either "success", - "cancelled by user", or the error that ended the scan. + Takes scan_result, a string that is either "success", "cancelled by user", + or the error that ended the scan. """ # Should this be a method of the scan_data dataclass? current_time = datetime.now().replace(microsecond=0) @@ -372,10 +391,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _manage_stitching_threads(self): - """ - Manage the stitching threads, starting them if needed and not already running. - """ - + """Manage the stitching threads, starting them if needed and not already running.""" # Assume 4 images means at least one offset in x and y, making the stitching # well constrained. if self._scan_images_taken > 3: @@ -384,13 +400,12 @@ class SmartScanThing(lt.Thing): @_scan_running def _run_scan(self): - """ - Prepare and run the main scan, handling the threads performing - stitching. Uses the result (or exception) from the scanning to - determine whether the scan should be stitched and the microscope - should return to the starting x,y,z position - """ + """Prepare and run the main scan, and perform final actions on completion. + The result (or exception) from the main scan loop determines whether the + scan should be stitched and whether the microscope should return to the + starting x,y,z position. + """ # Used to check if finally was reached via exception (except # cancel by user) scan_successful = True @@ -458,11 +473,11 @@ class SmartScanThing(lt.Thing): @_scan_running def _main_scan_loop(self): - """ - The loop to run through during a scan, until no more scan x,y positions + """Run the main loop of the scan. + + This loop runs during a scan, until no more scan x,y positions are remaining. """ - # The initial plan for the scan should be a single x,y position. All future # moves will be planned around this point. In future, route planner could # have multiple starting positions, each of which will be visited before the @@ -473,7 +488,7 @@ class SmartScanThing(lt.Thing): "max_dist": self._scan_data["max_dist"], } route_planner = scan_planners.SmartSpiral( - intial_position=(self._stage.position["x"], self._stage.position["y"]), + initial_position=(self._stage.position["x"], self._stage.position["y"]), planner_settings=planner_settings, ) @@ -527,7 +542,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _return_to_starting_position(self): - """Return to the initial scan position, if set""" + """Return to the initial scan position, if set.""" self._scan_logger.info("Returning to starting position.") if self._starting_position is not None: self._stage.move_absolute( @@ -536,8 +551,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _perform_final_stitch(self): - """Update the scan zip and perform final stitch of the data""" - + """Update the scan zip and perform final stitch of the data.""" if self._scan_images_taken <= 3: self._scan_logger.info("Not performing a stitch as 3 or fewer images taken") return @@ -586,59 +600,54 @@ class SmartScanThing(lt.Thing): save_resolution = lt.ThingSetting( initial_value=(1640, 1232), model=tuple[int, int], - description=("A tuple of the image resolution to capture."), ) + """A tuple of the image resolution to capture.""" max_range = lt.ThingSetting( initial_value=45000, model=int, - description=( - "The maximum distance from the centre of the scan before we break in steps" - ), ) + """The maximum distance in steps from the centre of the scan.""" stitch_tiff = lt.ThingSetting( initial_value=False, model=bool, - description="Whether or not to also produce a pyramidal tiff", ) + """Whether or not to also produce a pyramidal tiff at the end of a scan.""" skip_background = lt.ThingSetting( initial_value=True, model=bool, - description="""Whether to detect and skip empty fields of view - - This uses the settings from the `background_detect` Thing.""", ) + """Whether to detect and skip empty fields of view. + + This uses the settings from the ``BackgroundDetectThing``.""" autofocus_dz = lt.ThingSetting( initial_value=1000, model=int, - description="The z distance to perform an autofocus in steps", ) + """The z distance to perform an autofocus in steps.""" overlap = lt.ThingSetting( initial_value=0.45, model=float, - description="The fraction (0-1) that adjacent images should overlap in x or y", ) + """The fraction (0-1) that adjacent images should overlap in x or y.""" stitch_automatically = lt.ThingSetting( initial_value=True, model=bool, - description=( - "Whether to run a final stitch at the end of the scan (assuming scan " - "success)" - ), ) + """Whether to run a final stitch at the end of a successful scan.""" @lt.thing_property def scans(self) -> list[scan_directories.ScanInfo]: - """All the available scans + """All the available scans. Each scan has a name (which can be used to access it), along with its modified and created times (according to the filesystem) and - the number of items in the `images` folder. Note that image count + the number of items in the ``images`` folder. Note that image count uses a regular expression, and changes to the naming scheme will break it. """ @@ -660,8 +669,8 @@ class SmartScanThing(lt.Thing): """Return the stitched image corresponding to a given scan name, if it exists. Will only return a file ending in suffix STITCH_SUFFIX - Note: when downloading this, the default filename will be `scan_name`.jpeg""" - + Note: when downloading this, the default filename will be ``scan_name``.jpeg + """ stitch_path = self._scan_dir_manager.get_final_stitch_path(scan_name) if stitch_path is None: @@ -695,7 +704,7 @@ class SmartScanThing(lt.Thing): "scans", ) def delete_all_scans(self, logger: lt.deps.InvocationLogger) -> None: - """Delete all the scans on the microscope + """Delete all the scans on the microscope. **This will irreversibly remove all scanned data from the microscope!** @@ -706,18 +715,17 @@ class SmartScanThing(lt.Thing): @lt.thing_action def purge_empty_scans(self, logger: lt.deps.InvocationLogger) -> None: - """ - Delete all scan folders containing no images at the top level - """ - + """Delete all scan folders containing no images at the top level.""" # JSON is ignored as it's created before any images are captured for scan_info in self._scan_dir_manager.all_scans_info(): if scan_info.number_of_images == 0: self._delete_scan(scan_info.name, logger) def _delete_scan(self, scan_name, logger: lt.deps.InvocationLogger) -> bool: - """ - A wrapper around scan manager's delete_scan that logs to the invocation logger + """Delete a scan. + + This is a wrapper around scan manager's delete_scan that logs to the + invocation logger id there is a problem. """ try: self._scan_dir_manager.delete_scan(scan_name) @@ -731,8 +739,7 @@ class SmartScanThing(lt.Thing): @property def latest_preview_stitch_path(self) -> Optional[str]: - """The path of the latest preview stitched image, or None if not available""" - + """The path of the latest preview stitched image, or None if not available.""" if not self.latest_scan_name: return None @@ -742,11 +749,12 @@ class SmartScanThing(lt.Thing): @lt.thing_property def latest_preview_stitch_time(self) -> Optional[float]: - """The modification time of the latest preview image, to allow live updating + """The modification time of the latest preview image, to allow live updating. - This will return None (`null` to JS) if there is no preview image to return. + This will return None (``null`` to JS) if there is no preview image to return. This is used for two reasons: + 1. If all caching was turned off this stitch would be sent over the network repeatedly 2. If caching was is on, then the stitch will not update when needed. @@ -775,13 +783,12 @@ class SmartScanThing(lt.Thing): @_scan_running def _preview_stitch_start(self, overlap: float) -> None: - """Start stitching a preview of the scan in a background subprocess - + """Start stitching a preview of the scan in a background subprocess. This uses popen and returns immediately - self._preview_stitch_popen holds the popen for polling - - self._preview_stitch_popen_lock is a lock aquired while interacting + - self._preview_stitch_popen_lock is a lock acquired while interacting with Popen """ # Set minimum overlap to 90% of the scan overlap to catch only images directly adjacent, @@ -805,7 +812,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _preview_stitch_running(self) -> bool: - """Whether there is a preview stitch running in a subprocess""" + """Whether there is a preview stitch running in a subprocess.""" with self._preview_stitch_popen_lock: if self._preview_stitch_popen is None: return False @@ -815,9 +822,7 @@ class SmartScanThing(lt.Thing): @_scan_running def _preview_stitch_wait(self): - """ - Wait for an ongoing preview stitch to return - """ + """Wait for an ongoing preview stitch to return.""" if self._preview_stitch_running(): with self._preview_stitch_popen_lock: self._preview_stitch_popen.wait() @@ -828,18 +833,17 @@ class SmartScanThing(lt.Thing): cancel: lt.deps.CancelHook, cmd: list[str], ) -> CompletedProcess: - """ - Run a subprocess and log any output + """Run a subprocess and log any output. Raises: ChildProcessError if exit code is not zero InvocationCancelledError if the action is cancelled. + """ logger.info(f"Running command in subprocess: `{' '.join(cmd)}`") def log_buffer(buffer): - """A short internal function to read everything in the buffer to - the log""" + """Log everything in the buffer at INFO level.""" while line := buffer.readline(): logger.info(line) @@ -852,7 +856,7 @@ class SmartScanThing(lt.Thing): os.set_blocking(process.stdout.fileno(), False) logger.info(time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(time.time()))) - # Poll returns None while running, will return the error code when finnished + # Poll returns None while running, will return the error code when finished while process.poll() is None: log_buffer(process.stdout) # Once buffer is clear sleep for 0.2s before trying again. @@ -883,7 +887,7 @@ class SmartScanThing(lt.Thing): stitch_resize: Optional[float] = None, overlap: float = 0.0, ) -> None: - """Generate a stitched image based on stage position metadata + """Generate a stitched image based on stage position metadata. Note that as this is a lt.thing_action it needs the logger passed as a variable if called from another thing action @@ -967,7 +971,9 @@ class SmartScanThing(lt.Thing): self, scan_name: str, ): - """Update the zip to include the files left until the end, then return the - zip file as a Blob""" + """Return zip after including any files left until the end. + + The zipfile is returned as a Blob. + """ zip_fname = self._scan_dir_manager.zip_scan(scan_name, final_version=True) return ZipBlob.from_file(zip_fname) diff --git a/src/openflexure_microscope_server/things/stage/__init__.py b/src/openflexure_microscope_server/things/stage/__init__.py index 3a40d44d..fb58cb65 100644 --- a/src/openflexure_microscope_server/things/stage/__init__.py +++ b/src/openflexure_microscope_server/things/stage/__init__.py @@ -1,17 +1,27 @@ +"""A package for stage control Things. + +`BaseStage` is the base class that provides core stage functionality, but +no hardware interface control. To create a stage Thing to control a specific +piece of hardware the BaseStage should be subclassed, and any method raising +a NotImplementedError should be created. + +As the object will be used as a context manager create the hardware connection in +``__enter__`` (not in ``__init__``), and close the connection with ``__exit__``. +""" + from __future__ import annotations -from typing import TypeAlias from collections.abc import Sequence, Mapping import labthings_fastapi as lt class BaseStage(lt.Thing): - """A base stage class for OpenFlexure translation stages + """A base stage class for OpenFlexure translation stages. This can't be used directly but should reduce boilerplate code when implementing new stages. A minimal working stage must implement - `move_relative` and `move_absolute` actions, which update the - `position` property on completion, and provide `set_zero_position`. + ``move_relative`` and ``move_absolute`` actions, which update the + ``position`` property on completion, and provide ``set_zero_position``. """ _axis_names = ("x", "y", "z") @@ -24,22 +34,22 @@ class BaseStage(lt.Thing): position = lt.ThingProperty( Mapping[str, int], dict.fromkeys(_axis_names, 0), - description="Current position of the stage", readonly=True, observable=True, ) + """Current position of the stage.""" moving = lt.ThingProperty( bool, False, - description="Whether the stage is in motion", readonly=True, observable=True, ) + """Whether the stage is in motion.""" @property def thing_state(self): - """Summary metadata describing the current state of the stage""" + """Summary metadata describing the current state of the stage.""" return {"position": self.position} @lt.thing_action @@ -68,7 +78,7 @@ class BaseStage(lt.Thing): @lt.thing_action def set_zero_position(self): - """Make the current position zero in all axes + """Make the current position zero in all axes. This action does not move the stage, but resets the position to zero. It is intended for use after manually or automatically recentring the @@ -79,6 +89,4 @@ class BaseStage(lt.Thing): ) -StageDependency: TypeAlias = lt.deps.direct_thing_client_dependency( - BaseStage, "/stage/" -) +StageDependency = lt.deps.direct_thing_client_dependency(BaseStage, "/stage/") diff --git a/src/openflexure_microscope_server/things/stage/dummy.py b/src/openflexure_microscope_server/things/stage/dummy.py index cd3c6387..87109e4f 100644 --- a/src/openflexure_microscope_server/things/stage/dummy.py +++ b/src/openflexure_microscope_server/things/stage/dummy.py @@ -1,3 +1,5 @@ +"""Functionality for mimicking a stage during simulation and testing.""" + from __future__ import annotations from collections.abc import Mapping @@ -9,21 +11,29 @@ from . import BaseStage class DummyStage(BaseStage): - """A dummy stage for testing purposes + """A dummy stage for testing purposes. This stage should work similarly to a Sangaboard stage, but without any hardware attached. """ def __init__(self, step_time: float = 0.001, **kwargs): + """Initialise the Dummy stage, setting the step_time to adjust the speed. + + :param step_time: The time in seconds per "motor" step. The default of 0.001 + works well for the live simulation. For unit testing it is very slow + so the speed can be increased. Increasing it too far is problematic if + also doing computationally heavy tasks like simulated image blurring. + """ super().__init__(**kwargs) self.step_time = step_time def __enter__(self): + """Register the stage position when the Thing context manager is opened.""" self.instantaneous_position = self.position def __exit__(self, _exc_type, _exc_value, _traceback): - pass + """Nothing to do when the Thing context manager is closed.""" @lt.thing_action def move_relative( @@ -83,7 +93,7 @@ class DummyStage(BaseStage): @lt.thing_action def set_zero_position(self): - """Make the current position zero in all axes + """Make the current position zero in all axes. This action does not move the stage, but resets the position to zero. It is intended for use after manually or automatically recentring the diff --git a/src/openflexure_microscope_server/things/stage/sangaboard.py b/src/openflexure_microscope_server/things/stage/sangaboard.py index 35b3b79e..e78fa75c 100644 --- a/src/openflexure_microscope_server/things/stage/sangaboard.py +++ b/src/openflexure_microscope_server/things/stage/sangaboard.py @@ -1,3 +1,5 @@ +"""Provide a LabThings-FastAPI interface to the Sangaboard motor controller.""" + from __future__ import annotations import logging import threading @@ -13,18 +15,32 @@ from . import BaseStage class SangaboardThing(BaseStage): - def __init__(self, port: str = None, **kwargs): - """A Thing to manage a Sangaboard motor controller + """A Thing to manage a Sangaboard motor controller. + + Internally, this uses the ``pysangaboard`` package from PyPi. This imports + as ``sangaboard``. As ``pysangaboard`` does not support some features added + to the Sangaboard firmware v1 (LED flashing, aborting moves, etc) this + functionality is accessed by directly querying the serial interface. + """ + + def __init__(self, port: str = None, **kwargs): + """Initialise SangaboardThing. + + Initialise the "Thing", but do not initialise an underlying + ``Sangaboard`` object from ``pysangaboard`` until the Thing context + manager is started. + + :param port: The serial port for the Sangaboard. Optional, this is used + to stop the Sangaboard object querying available devices. + :param ``**kwargs``: Any other keyword arguments to be passed to the + Sangaboard class - Internally, this uses the `pysangaboard` package from PyPi. This imports - as `sangaboard`. As `pysangaboard` does not support some features added - to the Sangaboard firmware v1 (LED flashing, aborting moves, etc) this - functionality is accessed by directly querying the serial interface. """ self.sangaboard_kwargs = kwargs self.sangaboard_kwargs["port"] = port def __enter__(self): + """Connect to the sangaboard when the Thing context manager is opened.""" self._sangaboard = sangaboard.Sangaboard(**self.sangaboard_kwargs) self._sangaboard_lock = threading.RLock() with self.sangaboard() as sb: @@ -36,14 +52,15 @@ class SangaboardThing(BaseStage): self.update_position() def __exit__(self, _exc_type, _exc_value, _traceback): + """Close the sangaboard connection when the Thing context manager is closed.""" with self.sangaboard() as sb: sb.close() @contextmanager def sangaboard(self) -> Iterator[sangaboard.Sangaboard]: - """Return the wrapped `sangaboard.Sangaboard` instance. + """Return the wrapped ``sangaboard.Sangaboard`` instance. - This is protected by a `threading.RLock`, which may change in future. + This is protected by a ``threading.RLock``, which may change in future. """ with self._sangaboard_lock: yield self._sangaboard @@ -102,7 +119,7 @@ class SangaboardThing(BaseStage): @lt.thing_action def set_zero_position(self) -> None: - """Make the current position zero in all axes + """Make the current position zero in all axes. This action does not move the stage, but resets the position to zero. It is intended for use after manually or automatically recentring the @@ -119,7 +136,7 @@ class SangaboardThing(BaseStage): dt: float = 0.5, led_channel: Literal["cc"] = "cc", ) -> None: - """Flash the LED to identify the board + """Flash the LED to identify the board. This is intended to be useful in situations where there are multiple Sangaboards in use, and it is necessary to identify which one is diff --git a/src/openflexure_microscope_server/things/system_control.py b/src/openflexure_microscope_server/things/system_control.py index cbca06ab..82dc276a 100644 --- a/src/openflexure_microscope_server/things/system_control.py +++ b/src/openflexure_microscope_server/things/system_control.py @@ -1,5 +1,4 @@ -""" -OpenFlexure Microscope system control Thing +"""OpenFlexure Microscope system control Thing. This module defines a Thing that can shut down or restart the host computer. """ @@ -11,20 +10,18 @@ from pydantic import BaseModel class CommandOutput(BaseModel): + """A pydantic model passing the STDOUT and STDERR from a subprocess over HTTP.""" + output: str error: str class SystemControlThing(lt.Thing): - """ - Attempt to shutdown the device - """ + """Attempt to shutdown the device.""" @lt.thing_action def shutdown(self) -> CommandOutput: - """ - Attempt to shutdown the device - """ + """Attempt to shutdown the device.""" p = subprocess.Popen( ["sudo", "shutdown", "-h", "now"], stderr=subprocess.PIPE, @@ -36,14 +33,12 @@ class SystemControlThing(lt.Thing): @lt.thing_property def is_raspberrypi() -> bool: - """ - Checks if we are running on a Raspberry Pi. - """ + """Return True if running on a Raspberry Pi.""" return os.path.exists("/usr/bin/raspi-config") @lt.thing_action def reboot(self) -> CommandOutput: - """Attempt to reboot the device""" + """Attempt to reboot the device.""" p = subprocess.Popen( ["sudo", "shutdown", "-r", "now"], stderr=subprocess.PIPE, diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py index e514fc97..aceb7eac 100644 --- a/src/openflexure_microscope_server/utilities.py +++ b/src/openflexure_microscope_server/utilities.py @@ -1,14 +1,12 @@ -""" -This module contains some utility functions and classes -""" +"""Utility functions and classes.""" from threading import Thread class ErrorCapturingThread(Thread): - """ - This is a a subclass or Thread. It wraps the target function in a - try-except block. + """Subclass of Thread that captures exceptions from the target function. + + It wraps the target function in a try-except block. Execution will stop with an unhandled exception, but the exception will not be raised until the join method is called. When the join method is called, the exception is @@ -19,9 +17,7 @@ class ErrorCapturingThread(Thread): """ def __init__(self, group=None, target=None, args=None, kwargs=None, daemon=None): - """ - Initialise with the same arguments as Thread - """ + """Initialise with the same arguments as Thread.""" # As all inputs are keywords we need to set the default values for args and kwargs: if args is None: args = () @@ -47,9 +43,10 @@ class ErrorCapturingThread(Thread): ) def join(self, timeout=None): - """ - Join when the thread is complete. If the thread ended due to an unhandled exception, - the exception will be raised when this method is called. + """Join when the thread is complete. + + If the thread ended due to an unhandled exception, the exception will be raised + when this method is called. """ super().join(timeout) # If there is an error in the error buffer clear the buffer and raise it @@ -60,20 +57,18 @@ class ErrorCapturingThread(Thread): def _wrap_and_catch_errors(target, error_buffer, *args, **kwargs): - """ - This function is designed only to be used by - ErrorCapturingThread + """Run target function in a try-except block. - It will run a target function in a try-except block - any errors caught are added to an empty list that - should be supplied as a keyword argument + This function is designed only to be used by ErrorCapturingThread. - Arguments: - * target - The target function to call - * error_buffer - An empty list that is used for returning - the exception from the thread - *args: The arguments for the target function - **kwargs: The Keyword arguments for the target function + It will run a target function in a try-except block catching any exception. + If an exception is caught it is added to ``error_buffer``. + + :param target: The target function to call + :param error_buffer: An empty list that is used for returning the exception from + the thread. It is a list to ensure it is passed by reference. + :param ``*args``: The arguments for the target function + :param ``**kwargs``: The Keyword arguments for the target function """ try: target(*args, **kwargs) diff --git a/tests/__init__.py b/tests/__init__.py index e69de29b..b58ffa86 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,6 @@ +"""The unit-test suite for the OpenFlexure Microscope Server. + +This package contains all of the unit tests that can be run without specific +hardware. See also the `hardware-specific-tests` directory and the +`integration-tests` directory for more testing!. +""" diff --git a/tests/mock_things/__init__.py b/tests/mock_things/__init__.py index e69de29b..c65a6219 100644 --- a/tests/mock_things/__init__.py +++ b/tests/mock_things/__init__.py @@ -0,0 +1,5 @@ +"""A package of test module providing mock Things for testing. + +The mock things do not subclass the original things to minimise the inflation of +test coverage. +""" diff --git a/tests/mock_things/mock_autofocus.py b/tests/mock_things/mock_autofocus.py index d32b5a50..cf7de4f3 100644 --- a/tests/mock_things/mock_autofocus.py +++ b/tests/mock_things/mock_autofocus.py @@ -1,17 +1,24 @@ -"""This testing submodule contains mock autofocus things. +"""Testing submodule with mock Autofocus Things. -These mocks are designed to be inserted as dependencies to give specific -functionality and returns. +These mocks are designed to be inserted as dependencies to provide specific +functionality and return values. -The mocks do not subclass, and instead return very specific defined answers -to functions +The mocks do not subclass Things. Instead, they return predefined +answers to functions. """ class MockAutoFocusThing: + """A mock autofocus Thing that imports no code from AutofocusThing. + + The class needs functionality added to it over time as more complex + mocking is needed. It imports no code from AutofocusThing so that coverage + is not artificially inflated. + """ + # Counter for checking functions were called mock_call_count = {"looping_autofocus": 0} def looping_autofocus(self, dz: int = 2000, start: str = "centre") -> None: # noqa: ARG002 - """This function mocks autofocus with no return""" + """Mock autofocus with no return.""" self.mock_call_count["looping_autofocus"] += 1 diff --git a/tests/mock_things/mock_background_detect.py b/tests/mock_things/mock_background_detect.py index f79a1059..80419030 100644 --- a/tests/mock_things/mock_background_detect.py +++ b/tests/mock_things/mock_background_detect.py @@ -1,16 +1,23 @@ -"""This testing submodule contains mock background detect things. +"""Testing submodule with mock Background Detect Things. -These mocks are designed to be inserted as dependencies to give specific -functionality and returns. +These mocks are designed to be inserted as dependencies to provide specific +functionality and return values. -The mocks do not subclass, and instead return very specific defined answers -to functions +The mocks do not subclass Things. Instead, they return predefined +answers to functions. """ from openflexure_microscope_server.things.background_detect import ChannelDistributions -class MockBackgoundDetectThing: +class MockBackgroundDetectThing: + """A mock background detect Thing that imports no code from BackgroundDetectThing. + + The class needs functionality added to it over time as more complex + mocking is needed. It imports no code from BackgroundDetectThing so that coverage + is not artificially inflated. + """ + background_distributions = ChannelDistributions( means=[128.0, 128.0, 128.0], standard_deviations=[3.0, 3.0, 3.0], diff --git a/tests/mock_things/mock_csm.py b/tests/mock_things/mock_csm.py index 78930dae..20178a8b 100644 --- a/tests/mock_things/mock_csm.py +++ b/tests/mock_things/mock_csm.py @@ -1,12 +1,19 @@ -"""This testing submodule contains mock camera stage mapping things. +"""Testing submodule with mock Camera Stage Mapping Things. -These mocks are designed to be inserted as dependencies to give specific -functionality and returns. +These mocks are designed to be inserted as dependencies to provide specific +functionality and return values. -The mocks do not subclass, and instead return very specific defined answers -to functions +The mocks do not subclass Things. Instead, they return predefined +answers to functions. """ class MockCSMThing: + """A mock CSM Thing that imports no code from CameraStageMapper. + + The class needs functionality added to it over time as more complex + mocking is needed. It imports no code from CameraStageMapper so that coverage + is not artificially inflated. + """ + image_resolution = (123, 456) diff --git a/tests/mock_things/mock_stage.py b/tests/mock_things/mock_stage.py index 9b7a466d..9a36d044 100644 --- a/tests/mock_things/mock_stage.py +++ b/tests/mock_things/mock_stage.py @@ -1,12 +1,19 @@ -"""This testing submodule contains stage things. +"""Testing submodule with mocks StageThings. -These mocks are designed to be inserted as dependencies to give specific -functionality and returns. +These mocks are designed to be inserted as dependencies to provide specific +functionality and return values. -The mocks do not subclass, and instead return very specific defined answers -to functions +The mocks do not subclass existing Things. Instead, they return predefined +answers to functions. """ class MockStageThing: + """A mock Thing for a stage that imports no code from BaseStage. + + The class needs functionality added to it over time as more complex + mocking is needed. It imports no code from BaseStage so that coverage + is not artificially inflated. + """ + position = (111, 222, 333) diff --git a/tests/test_camera_buffer.py b/tests/test_camera_buffer.py index f8e7f30a..f7dda0c8 100644 --- a/tests/test_camera_buffer.py +++ b/tests/test_camera_buffer.py @@ -1,6 +1,4 @@ -""" -Tests for the built in buffer for the camera. -""" +"""Tests for the built in buffer for the camera.""" from random import randint @@ -18,7 +16,7 @@ RANDOM_GENERATOR = np.random.default_rng() def random_image(): - """Create a random image""" + """Create a random image.""" imarray = RANDOM_GENERATOR.integers( low=0, high=255, size=(100, 100, 3), dtype="uint8" ) @@ -26,14 +24,14 @@ def random_image(): def random_metadata(): - """Create a misc dictionary to pretend to be metadata""" + """Create a misc dictionary to pretend to be metadata.""" # Not very metadata like, but we are just checking that the same dict it # is returned return {"a": randint(1, 100), "b": randint(1, 100)} def test_add_and_get_image(): - """Check images can be captured and retrieved""" + """Check images can be captured and retrieved.""" mem_buf = CameraMemoryBuffer() misc_image = random_image() buffer_id = mem_buf.add_image(misc_image) @@ -46,7 +44,7 @@ def test_add_and_get_image(): def test_add_and_get_image_twice(): - """Check images can be retrieved twice if remove flag set false""" + """Check images can be retrieved twice if remove flag set false.""" mem_buf = CameraMemoryBuffer() misc_image = random_image() buffer_id = mem_buf.add_image(misc_image) @@ -62,7 +60,7 @@ def test_add_and_get_image_twice(): def test_get_without_id(): - """Check images can be captured and retrieved without ID""" + """Check images can be captured and retrieved without ID.""" mem_buf = CameraMemoryBuffer() misc_image = random_image() mem_buf.add_image(misc_image) @@ -94,7 +92,7 @@ def test_get_two_images(): def test_get_two_images_without_setting_buffer_size(): - """Check two images can't be retrieved if the buffer size isn't set""" + """Check two images can't be retrieved if the buffer size isn't set.""" mem_buf = CameraMemoryBuffer() misc_image1 = random_image() misc_image2 = random_image() @@ -108,14 +106,14 @@ def test_get_two_images_without_setting_buffer_size(): def test_buffer_size_changing(): - """Check buffer size resets back to 1 when if not set""" + """Check buffer size resets back to 1 when if not set.""" mem_buf = CameraMemoryBuffer() misc_image1 = random_image() misc_image2 = random_image() misc_image3 = random_image() buffer_id1 = mem_buf.add_image(misc_image1, buffer_max=3) buffer_id2 = mem_buf.add_image(misc_image2, buffer_max=3) - # Third capture doen't set buffer size, so it will be reset + # Third capture doesn't set buffer size, so it will be reset buffer_id3 = mem_buf.add_image(misc_image3) # As buffer size was reset, images 1 and 2 are deleted with pytest.raises(NoImageInMemoryError): @@ -128,7 +126,7 @@ def test_buffer_size_changing(): def test_capture_two_images_get_without_id(): - """Check that all images are deleted when getting without id""" + """Check that all images are deleted when getting without id.""" mem_buf = CameraMemoryBuffer() misc_image1 = random_image() misc_image2 = random_image() @@ -144,7 +142,7 @@ def test_capture_two_images_get_without_id(): def test_buffer_size_respected(): - """Capture 10 images with a buffer size of 5. Check only last 5 exist""" + """Capture 10 images with a buffer size of 5. Check only last 5 exist.""" mem_buf = CameraMemoryBuffer() images = [] @@ -165,7 +163,7 @@ def test_buffer_size_respected(): def test_clear_buffer(): - """Capture 10 images clear the buffer and check they are gone""" + """Capture 10 images clear the buffer and check they are gone.""" mem_buf = CameraMemoryBuffer() images = [] @@ -186,7 +184,7 @@ def test_clear_buffer(): def test_get_metadata_too(): - """Capture 10 images with metadata and check metadata is returned as expected""" + """Capture 10 images with metadata and check metadata is returned as expected.""" mem_buf = CameraMemoryBuffer() images = [] @@ -203,7 +201,7 @@ def test_get_metadata_too(): # Preallocate zipped data, to avoid long confusing lines zipped = zip(images, metadatas, buffer_ids) - # Check both image and metdata + # Check both image and metadata for i, (image, metadata, buffer_id) in enumerate(zipped): returned_image, returned_metadata = mem_buf.get_image(buffer_id) assert image is returned_image diff --git a/tests/test_dummy_server.py b/tests/test_dummy_server.py index ca286ebd..1fa2e2dc 100644 --- a/tests/test_dummy_server.py +++ b/tests/test_dummy_server.py @@ -1,3 +1,13 @@ +"""Test the server without creating a full HTTP server and socket connection. + +Rather than spinning up a full uvicorn webserver for each test these tests use +the FastAPI ``TestClient`` or to directly communicate with the underlying +LabThings-FastAPI code. This increases speed of testing significantly. + +For tests that require a full running server see the ``integration-tests`` +directory in the root of the repository. +""" + import json import os import tempfile @@ -21,6 +31,7 @@ camera_stage_mapping.DEFAULT_SETTLING_TIME = 0 # skip the settling time for tes @pytest.fixture def thing_server(): + """Yield a server with a very basic configuration.""" temp_folder = tempfile.TemporaryDirectory() server = lt.ThingServer(settings_folder=temp_folder.name) server.add_thing( @@ -33,36 +44,46 @@ def thing_server(): server.add_thing(AutofocusThing(), "/autofocus/") server.add_thing(CameraStageMapper(), "/camera_stage_mapping/") assert os.path.exists(os.path.join(temp_folder.name, "camera/")) - # NB yield is important: otherwise, the temp folder gets deleted before the test runs + # Note: yield is important. If return is used the temp folder gets deleted + # before the test runs yield server @pytest.fixture def client(thing_server): + """Yield a FastAPI TestClient for the server.""" with TestClient(thing_server.app) as client: yield client @pytest.fixture def slower_client(thing_server): + """Yield a FastAPI TestClient for the server with a slower moving stage. + + The step time for the stage is 100 microseconds rather than + 1 microsecond. + """ thing_server.things["/stage/"].step_time = 0.0001 with TestClient(thing_server.app) as client: yield client def test_autofocus(slower_client): + """Test Fast Autofocus can run doesn't raise an exception.""" client = slower_client autofocus = lt.ThingClient.from_url("/autofocus/", client) _ = autofocus.fast_autofocus() def test_grab_jpeg(client): + """Check that grab_jpeg returns a blob that can be opened.""" camera = lt.ThingClient.from_url("/camera/", client) blob = camera.grab_jpeg() _image = Image.open(blob.open()) def test_capture_jpeg_metadata(client): + """Check that the position is encoded into the image metadata.""" camera = lt.ThingClient.from_url("/camera/", client) blob = camera.capture_jpeg() image = Image.open(blob.open()) @@ -73,6 +94,7 @@ def test_capture_jpeg_metadata(client): def test_stage(client): + """Test moving th stage forwards and backwards.""" stage = lt.ThingClient.from_url("/stage/", client) start = stage.position move = {"x": 1, "y": 2, "z": 3} @@ -87,12 +109,13 @@ def test_stage(client): def test_capture_array(client): + """Capture array from simulation and check the size is as expected.""" camera = lt.ThingClient.from_url("/camera/", client) array = np.asarray(camera.capture_array()) assert array.shape == (240, 320, 3) -# Currently this fails, not yet sure why. def test_camera_stage_mapping_calibration(client): + """Check that camera stage mapping can run without an exception.""" camera_stage_mapping = lt.ThingClient.from_url("/camera_stage_mapping/", client) camera_stage_mapping.calibrate_xy() diff --git a/tests/test_scan_directories.py b/tests/test_scan_directories.py index 9471703c..1f6c0609 100644 --- a/tests/test_scan_directories.py +++ b/tests/test_scan_directories.py @@ -1,3 +1,5 @@ +"""Test the functionality in the scan_directories module.""" + import tempfile import os import math @@ -28,13 +30,13 @@ BASE_SCAN_DIR = os.path.join(tempfile.gettempdir(), "scans") def _clear_scan_dir() -> None: - """Delete the scan dir""" + """Delete the scan dir.""" if os.path.exists(BASE_SCAN_DIR): shutil.rmtree(BASE_SCAN_DIR) def _add_fake_image(scan_dir: ScanDirectory) -> None: - """Make a fake image on disk in the scan directory""" + """Make a fake image on disk in the scan directory.""" unique = False while not unique: x_pos = random.randint(-10000, 10000) @@ -63,12 +65,11 @@ def _add_fake_file( def _make_fake_dzi(scan_dir: ScanDirectory, n_layers: int = 8) -> None: - """Create a fake DZI in a scan + """Create a fake DZI in a scan. :param n_layers: The number of layers of tiles. I.e. tile directories numbered 0...(n_layers-1) will be created. Default 8 """ - # Add an a dzi image dzi_fname = scan_dir.name + ".dzi" dzi_path = os.path.join(scan_dir.images_dir, dzi_fname) @@ -97,7 +98,7 @@ def _make_fake_dzi(scan_dir: ScanDirectory, n_layers: int = 8) -> None: def test_basic_directory_operations(): - """Test some basic operations + """Test some basic operations. Test some basic operations, including: - ScanDirectoryManager creates a scan directory @@ -157,9 +158,7 @@ def test_basic_directory_operations(): def test_scan_sequence_and_listing(): - """ - Check created scans are added in order and listed correctly - """ + """Check created scans are added in order and listed correctly.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) # Make 4 scans @@ -186,10 +185,7 @@ def test_scan_sequence_and_listing(): def test_scan_name_non_sequential(): - """ - Check created scans is the correct name if the directories - are not sequential - """ + """Check new scan has the correct name if the directories are not sequential.""" _clear_scan_dir() os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_0001")) os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_0002")) @@ -214,9 +210,7 @@ def test_scan_name_non_sequential(): def test_all_scan_names_taken(): - """ - If the next sequential scan name needs more than 4 digits check error is thrown. - """ + """If the next sequential scan name needs more than 4 digits check error is thrown.""" _clear_scan_dir() os.makedirs(os.path.join(BASE_SCAN_DIR, "fake_scan_9999")) scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) @@ -225,9 +219,7 @@ def test_all_scan_names_taken(): def test_no_scan_names_given(): - """ - Check correct default scan name is used if empty string is given - """ + """Check correct default scan name is used if empty string is given.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) scan_dir = scan_dir_manager.new_scan_dir("") @@ -235,7 +227,7 @@ def test_no_scan_names_given(): def test_scan_info(): - """Test the scan info is correct even using fake scan data""" + """Test the scan info is correct even using fake scan data.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) scan_dir = scan_dir_manager.new_scan_dir("fake_scan") @@ -262,7 +254,7 @@ def test_scan_info(): def test_get_final_stitch(): - """Check that the final stitch can be retrieved""" + """Check that the final stitch can be retrieved.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) scan_dir = scan_dir_manager.new_scan_dir("fake_scan") @@ -290,7 +282,7 @@ def test_get_final_stitch(): def test_empty_scan_info(): - """Test the scan info is correct even if the scan is empty""" + """Test the scan info is correct even if the scan is empty.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) scan_dir = scan_dir_manager.new_scan_dir("fake_scan") @@ -308,8 +300,7 @@ def test_empty_scan_info(): def test_zipping_scan_data(): - """Test zipping the scan images with fake image data""" - + """Test zipping the scan images with fake image data.""" # Run twice, once calling the ScanDirectory directly, # Once calling the ScanDirectoryManager for caller in ["scan_dir", "manager"]: @@ -349,7 +340,7 @@ def test_zipping_scan_data(): def test_all_files(): - """Test all_files returns the path, and respects skipped directories""" + """Test all_files returns the path, and respects skipped directories.""" _clear_scan_dir() scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR) scan_dir = scan_dir_manager.new_scan_dir("fake_scan") @@ -404,7 +395,7 @@ def test_none_returned_for_missing_images_dir(): def test_extracting_files(): - """Test the private _find_files method of ScanDirectories + """Test the private _find_files method of ScanDirectories. Add files to directory and check expected returns. """ @@ -456,7 +447,7 @@ DiskUsage = namedtuple("DiskUsage", ["total", "used", "free"]) @pytest.mark.parametrize("free_space", [500_000_001, 700_000_000, 5_000_000_000]) def test_disk_not_full(mocker, free_space): - """Check no error thrown if disk has over 500MB of space""" + """Check no error thrown if disk has over 500MB of space.""" total_space = 16_000_000_000 # Mock the disk_usage mocker.patch( @@ -472,7 +463,7 @@ def test_disk_not_full(mocker, free_space): @pytest.mark.parametrize("free_space", [100_000_000, 499_999_999]) def test_disk_full(mocker, free_space): - """Check error thrown if disk has under 500MB of space""" + """Check error thrown if disk has under 500MB of space.""" total_space = 16_000_000_000 # Mock the disk_usage mocker.patch( diff --git a/tests/test_scan_planners.py b/tests/test_scan_planners.py index 9fe192ba..7a9344f9 100644 --- a/tests/test_scan_planners.py +++ b/tests/test_scan_planners.py @@ -1,3 +1,9 @@ +"""Test the scan planning algorithms of the Microscope. + +As well as low level function by function tests, this test suite also provides tests +that simulate scanning a sample, checking that the expected path is followed. +""" + import pytest from copy import copy @@ -6,6 +12,7 @@ from .utilities import scan_test_helpers def test_enforce_xy_tuple(): + """Check that 2 value tuples (or ValueErrors) are always returned.""" bad_len_vals = [[1], [], (1,), (2, 4, 4), [1, 4, 5, 7]] bad_type_vals = ["hi", 1, {"this": "that"}, {1, 2}] for value in bad_len_vals + bad_type_vals: @@ -17,6 +24,7 @@ def test_enforce_xy_tuple(): def test_enforce_xyz_tuple(): + """Check that 3 value tuples (or ValueErrors) are always returned.""" bad_len_vals = [[1], [], (1,), (2, 4), [1, 4, 5, 7]] bad_type_vals = ["hi!", 1, {"this": "that"}, {1, 2, 3}] for value in bad_len_vals + bad_type_vals: @@ -28,23 +36,25 @@ def test_enforce_xyz_tuple(): def test_base_class_not_implemented(): - intial_position = (100, 50) + """Check NotImplementedError is raised when initialising ScanPlanner directly.""" + initial_position = (100, 50) with pytest.raises(NotImplementedError): - scan_planners.ScanPlanner(intial_position=intial_position) + scan_planners.ScanPlanner(initial_position=initial_position) def test_v_basic_smart_spiral(): - intial_position = (100, 50) + """Check that a SmartSpiral where the first image is not sample completes.""" + initial_position = (100, 50) planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000} planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) # Create a planner. It shouldn't be complete. assert not planner.scan_complete - # When we start it should want to stay in the inital pos and have + # When we start it should want to stay in the initial pos and have # no z_estimate xy_pos, z_pos = planner.get_next_location_and_z_estimate() - assert xy_pos == intial_position + assert xy_pos == initial_position assert z_pos is None # Try to mark location as imaged with only xy_position @@ -65,11 +75,12 @@ def test_v_basic_smart_spiral(): def test_bad_smart_spiral_settings(): - intial_position = (100, 50) + """Check that KeyError is raised when SmartSpiral is given bad settings.""" + initial_position = (100, 50) # Class init should raise error if no planner_settings dictionary set with pytest.raises(ValueError): - scan_planners.SmartSpiral(intial_position=intial_position) + scan_planners.SmartSpiral(initial_position=initial_position) planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000} keys = ["dx", "dy", "max_dist"] @@ -80,7 +91,7 @@ def test_bad_smart_spiral_settings(): del bad_planner_settings[delkey] with pytest.raises(KeyError): scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=bad_planner_settings + initial_position=initial_position, planner_settings=bad_planner_settings ) # Class init should raise error if planner_settings if any value can't be cast @@ -91,29 +102,29 @@ def test_bad_smart_spiral_settings(): bad_planner_settings[badkey] = "I can't be converted to an int" with pytest.raises(ValueError): scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=bad_planner_settings + initial_position=initial_position, planner_settings=bad_planner_settings ) def test_smart_spiral_first_few_pos(): - """ - This test is VERY long, not really a "unit". It checks step-by-step - that data is added correctly for the first few postions in a scan. + """Test for correct data addition during initial scan positions. - This should catch basic cases of if the algorithm is updated. + This is a very long test, not strictly a "unit" test. It checks step by step + that data is added correctly for the first few positions in a scan. It is + intended to catch basic issues if the algorithm is updated. """ - intial_position = (100, 50) + initial_position = (100, 50) planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000} # Create a planner planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) # it shouldn't start complete assert not planner.scan_complete - # When we start it should want to stay in the inital pos and have + # When we start it should want to stay in the initial pos and have # no z_estimate xy_pos1, z_pos1 = planner.get_next_location_and_z_estimate() - assert xy_pos1 == intial_position + assert xy_pos1 == initial_position assert z_pos1 is None # Set a focus value z_focus = 10 @@ -189,11 +200,12 @@ def test_smart_spiral_first_few_pos(): def test_smart_spiral_stops_on_max_dist(): - intial_position = (0, 0) + """Test that if max distance is reached smart spiral really does stop.""" + initial_position = (0, 0) planner_settings = {"dx": 100, "dy": 100, "max_dist": 1000} # Create a planner planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) while not planner.scan_complete: xy_pos, _ = planner.get_next_location_and_z_estimate() @@ -206,17 +218,12 @@ def test_smart_spiral_stops_on_max_dist(): def test_mark_wrong_location(): - """ - This test is VERY long, not really a "unit". It checks step-by-step - that data is added correctly for the first few postions in a scan. - - This should catch basic caseses of if the algorithm is updated. - """ - intial_position = (100, 50) + """Check that an error is raised if a scan marks the wrong location as visited.""" + initial_position = (100, 50) planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000} # Create a planner planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) xy_pos, _ = planner.get_next_location_and_z_estimate() @@ -226,17 +233,18 @@ def test_mark_wrong_location(): planner.mark_location_visited(wrong_xyz_pos, imaged=True, focused=True) -def test_closest_focus_wth_large_numbers(): +def test_closest_focus_with_large_numbers(): + """Tests to check that everything works well with huge numbers of steps. + + The number of steps gets very large on the micorscope. But most of the tests + above use smaller numbers for clarity. """ - The number of steps gets very large in reality runs some tests to check - that everything works well with huge numbers of steps - """ - intial_position = (0, 0) + initial_position = (0, 0) # Set this up, but we won't use the settings planner_settings = {"dx": 10000, "dy": 10000, "max_dist": 100000} # Create a planner planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) # Directly overwrite the private focussed locations list for test @@ -253,11 +261,19 @@ def test_closest_focus_wth_large_numbers(): def test_example_smart_spiral(): - """Test the smart spiral scan algorithm on the sample types listed - below and defined in scan_test_helpers.load_sample_points + """Test the smart spiral scan algorithm on the different sample types. - Will fail if the locations or path between locations visited has changed - for any of the samples listed""" + The sample types: + + * ``regular`` + * ``lobed`` + * ``core"`` + + These are defined in scan_test_helpers.load_sample_points + + This will fail if the locations or path between locations visited has changed + for any of the samples listed. + """ example_samples = [ "regular", "lobed", diff --git a/tests/test_smart_scan.py b/tests/test_smart_scan.py index 2cd6d267..0ec1ae3f 100644 --- a/tests/test_smart_scan.py +++ b/tests/test_smart_scan.py @@ -1,5 +1,4 @@ -""" -Test the SmartScanThing *without* connecting it to a LabThings Server. +"""Test the SmartScanThing *without* connecting it to a LabThings Server. By testing without connecting to the LabThings server it is possible to directly poll any properties and to start any methods. @@ -31,7 +30,7 @@ from openflexure_microscope_server.things.smart_scan import ( from .mock_things.mock_csm import MockCSMThing from .mock_things.mock_autofocus import MockAutoFocusThing from .mock_things.mock_stage import MockStageThing -from .mock_things.mock_background_detect import MockBackgoundDetectThing +from .mock_things.mock_background_detect import MockBackgroundDetectThing # A global logger to pass in as an Invocation Logger LOGGER = logging.getLogger("mock-invocation_logger") @@ -42,14 +41,14 @@ SCAN_DIR = os.path.join(tempfile.gettempdir(), "scans") def _clear_scan_dir() -> None: - """Delete the scan dir""" + """Delete the scan dir.""" if os.path.exists(SCAN_DIR): shutil.rmtree(SCAN_DIR) @pytest.fixture def smart_scan_thing(): - """Return a smart scan thing as a fixture""" + """Return a smart scan thing as a fixture.""" return SmartScanThing(SCAN_DIR) @@ -64,8 +63,11 @@ def test_initial_properties(smart_scan_thing): def test_inaccessible_scan_methods(smart_scan_thing): - """The @_scan_running decorator should make some methods - inaccessible unless a scan is running""" + """Test that method with @_scan_running decorator is inaccessible. + + The @_scan_running decorator makes these functions inaccessible unless + a scan is running. + """ with pytest.raises(ScanNotRunningError): smart_scan_thing._run_scan() with pytest.raises(ScanNotRunningError): @@ -73,8 +75,7 @@ def test_inaccessible_scan_methods(smart_scan_thing): def test_private_delete_scan(smart_scan_thing, caplog): - """Test the private _delete_scan method deletes directories or warns if it can't""" - + """Test the private _delete_scan method deletes directories or warns if it can't.""" _clear_scan_dir() with caplog.at_level(logging.INFO): fake_scan_name = "fake_scan_0001" @@ -100,8 +101,7 @@ def test_private_delete_scan(smart_scan_thing, caplog): def test_public_delete_scan(smart_scan_thing, caplog): - """Test the delete_scan API call deletes directories or warns if it can't""" - + """Test the delete_scan API call deletes directories or warns if it can't.""" _clear_scan_dir() with caplog.at_level(logging.INFO): fake_scan_name = "fake_scan_0001" @@ -151,9 +151,8 @@ def test_delete_all_scans(smart_scan_thing, caplog): assert len(caplog.records) == 0 -def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None): - """ - Create a subclass of SmartScanThing to mock _run_scan and run sample_scan +def _run_only_outer_scan(adjust_initial_state: Optional[Callable] = None): + """Create a subclass of SmartScanThing to mock _run_scan and run sample_scan. This should do all the set up for a scan, move into the mocked _run_scan method where this can be tested. Once this is done @@ -166,7 +165,6 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None): This seems hard to do with a fixture so it is being done with a private function """ - # cancel handle shouldn't be used. Set to arbitrary value for checking cancel_mock = 1 # not called af_mock = MockAutoFocusThing() @@ -174,20 +172,14 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None): cam_mock = 4 # not called meta_mock = 5 # not called csm_mock = MockCSMThing() - bkgrnd_det_mock = MockBackgoundDetectThing() + bkgrnd_det_mock = MockBackgroundDetectThing() class MockedSmartScanThing(SmartScanThing): - """ - This is a subclass of SmartScanThing with a mocked method and - mocked thing_settings. - """ + """Mocked version of SmartScanThing with a patched _run_scan method.""" # Counter for checking functions were called mock_call_count = {"_run_scan": 0} - # Mock thing settings as a dictionary - thing_settings = {"skip_background": True} - def _run_scan(self): self.mock_call_count["_run_scan"] += 1 @@ -207,8 +199,8 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None): # mock smart scan thing mock_ss_thing = MockedSmartScanThing(SCAN_DIR) - if adjust_inital_state is not None: - adjust_inital_state(mock_ss_thing) + if adjust_initial_state is not None: + adjust_initial_state(mock_ss_thing) exec_info = None try: @@ -240,7 +232,7 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None): assert mock_ss_thing._scan_images_taken is None # Return the mock thing for further state testing, and the - # exec_info of any uncaught exeptions that were raised + # exec_info of any uncaught exceptions that were raised return mock_ss_thing, exec_info diff --git a/tests/test_stack.py b/tests/test_stack.py index e9295601..06e18686 100644 --- a/tests/test_stack.py +++ b/tests/test_stack.py @@ -1,5 +1,4 @@ -""" -Tests for the smart/fast stacking. +"""Tests for the smart/fast stacking. Currently these tests don't test the Thing itself, just surrounding functionality """ @@ -23,7 +22,7 @@ RANDOM_GENERATOR = np.random.default_rng() def odd_integers(min_value=0, max_value=1000): - """A hypothesis strategy for odd integers""" + """Return a hypothesis strategy for odd integers.""" min_base = (min_value) // 2 max_base = (max_value - 1) // 2 # Ensure the range allows at least one odd number @@ -33,7 +32,7 @@ def odd_integers(min_value=0, max_value=1000): def even_integers(min_value=0, max_value=1000): - """A hypothesis strategy for even integers""" + """Return a hypothesis strategy for even integers.""" min_base = (min_value + 1) // 2 max_base = (max_value) // 2 # Ensure the range allows at least one even number @@ -47,14 +46,13 @@ def even_integers(min_value=0, max_value=1000): extra_ims=even_integers(min_value=0, max_value=10), ) def test_stack_params_validation(save_ims, extra_ims): - """Tests specifically the validation on the image numbers + """Test the validation of the image numbers for a stack. save_ims is the number to save (must be odd and positive) extra_ims is how many more images there are in min_images_to_test than images_to_save. (even so that, min_images_to_test is odd and larger than images_to_save """ - StackParams( stack_dz=50, images_to_save=save_ims, @@ -70,8 +68,9 @@ def test_stack_params_validation(save_ims, extra_ims): extra_ims=even_integers(min_value=-10, max_value=-1), ) def test_stack_params_not_enough_test_images(save_ims, extra_ims): - """Set the extra_ims negative so that min_images_to_test is smaller - than images_to_save. + """Test error is raised if min_images_to_test is smaller than images_to_save. + + ``extra_ims`` negative so that min_images_to_test is smaller than images_to_save. For arguments see test_stack_params_validation """ @@ -91,7 +90,7 @@ def test_stack_params_not_enough_test_images(save_ims, extra_ims): extra_ims=even_integers(min_value=0, max_value=10), ) def test_stack_params_negative_images_to_save(save_ims, extra_ims): - """save_ims is negative so images_to_save is negative, failing validation + """save_ims is negative so images_to_save is negative, failing validation. For arguments see test_stack_params_validation """ @@ -111,7 +110,7 @@ def test_stack_params_negative_images_to_save(save_ims, extra_ims): extra_ims=odd_integers(min_value=0, max_value=10), ) def test_even_min_images_to_test(save_ims, extra_ims): - """extra_ims is odd so min_images_to_test is even, failing validation + """extra_ims is odd so min_images_to_test is even, failing validation. For arguments see test_stack_params_validation """ @@ -131,7 +130,7 @@ def test_even_min_images_to_test(save_ims, extra_ims): extra_ims=odd_integers(min_value=0, max_value=10), ) def test_even_images_to_save(save_ims, extra_ims): - """save_ims is even so images_to_save is even, failing validation + """save_ims is even so images_to_save is even, failing validation. For arguments see test_stack_params_validation """ @@ -147,8 +146,7 @@ def test_even_images_to_save(save_ims, extra_ims): def test_computed_stack_params(): - """ - Test StackParams computed properties are as expected + """Test StackParams computed properties are as expected. Not using hypothesis or we will just copy in the same formulas. """ @@ -189,8 +187,7 @@ def test_computed_stack_params(): def random_capture(set_id: Optional[int] = None): - """ - Create a capture with random values + """Create a capture with random values. :param set_id: Optional, use to set a fixed id rather than a random one """ @@ -207,18 +204,14 @@ def random_capture(set_id: Optional[int] = None): def test_capture_filename_matches_regex(): - """ - For 100 random captures check the image always matches the regex - """ + """For 100 random captures check the image always matches the regex.""" for _ in range(100): assert IMAGE_REGEX.search(random_capture().filename) @given(st.integers(min_value=0, max_value=5000)) def test_retrieval_of_captures(start): - """ - For 20 random captures, check each can be retrieved correctly by id - """ + """For 20 random captures, check each can be retrieved correctly by id.""" captures = [random_capture(start + i) for i in range(20)] for i, capture in enumerate(captures): diff --git a/tests/utilities/__init__.py b/tests/utilities/__init__.py index 6045086e..a261de29 100644 --- a/tests/utilities/__init__.py +++ b/tests/utilities/__init__.py @@ -1,8 +1,7 @@ -""" -This sub-package contains utilities that help with testing and debugging. +"""Utilities for testing and debugging. -At the top level are some very basic testing functions, more specific testing -is provided by modules inside the package. +At the top level are some basic testing functions. More specific testing utilities are +provided by modules inside the package. """ from typing import Protocol, Iterable @@ -10,9 +9,10 @@ from collections.abc import Hashable class SizedIterableHashable(Iterable[Hashable], Protocol): - """A protocol for sized iterable of hashable objects""" + """A protocol for sized iterable of hashable objects.""" - def __len__(self) -> int: ... + def __len__(self) -> int: + """Add a len function to protocol so Python knows the object is sized.""" def assert_unique_of_length(data: SizedIterableHashable, length: int) -> None: diff --git a/tests/utilities/scan_test_helpers.py b/tests/utilities/scan_test_helpers.py index 62bb7f73..8783e9f0 100644 --- a/tests/utilities/scan_test_helpers.py +++ b/tests/utilities/scan_test_helpers.py @@ -1,3 +1,9 @@ +"""Utility functions for testing scan planners. + +These including fake sample creation, scan path visualisation, and +persistent storage of expected scan paths for samples. +""" + import os import pickle @@ -14,26 +20,23 @@ THIS_DIR = os.path.dirname(os.path.realpath(__file__)) class FakeSample: - """ - A fake sample to test scan algorithms. The sample is able to return - whether a given position is sample, no image associated with the sample + """A fake sample to test scan algorithms. + + The sample is able to return whether a given position is sample, there is no image + associated with the sample """ def __init__(self, xy_points: list[tuple[int, int]]): - """ - Create the sample from a spline interpolation around - the given points. - """ + """Create the sample from a spline interpolation around the given points.""" self._sample_perimeter = interp_closed_path(xy_points, 500) def is_sample(self, pos: tuple[int, int], im_size: tuple[int, int]) -> bool: - """ - Return whether an image at a given location with a given image size - is on the sample + """Return True if an image at a given location is on the sample. - This doesn't check the entire image field as this is designed to be used - where the fake sample is much larger than the image and has smooth edges - It just checks the 4 corners + The image size is specified to check if it overlaps the sample. It doesn't + check the entire image field as this is designed to be used where the fake + sample is much larger than the image and has smooth edges. It just checks the + 4 corners. """ img_corners = [ (pos[0] + im_size[0], pos[1] + im_size[1]), @@ -47,18 +50,14 @@ class FakeSample: @property def patch(self) -> PathPatch: - """ - The sample as a matplotlib patch for plotting - """ + """The sample as a matplotlib patch for plotting.""" patch = PathPatch(self._sample_perimeter) patch.set(color=(1.0, 0.8, 1.0, 1.0)) return patch def visualise_scan(sample: FakeSample, planner: scan_planners.ScanPlanner) -> Figure: - """ - For a given sample and scanner object return a matplotlib figure of the scan - """ + """For a given sample and scanner object return a matplotlib figure of the scan.""" fig, ax = plt.subplots(figsize=(8, 8)) ax.add_artist(sample.patch) xh, yh = zip(*planner._path_history) @@ -84,15 +83,14 @@ def visualise_scan(sample: FakeSample, planner: scan_planners.ScanPlanner) -> Fi def interp_closed_path(xy_points: list[tuple[int, int]], n_points: int) -> MatPath: - """ - Given a lists of xy_points interpolate an n_point closed curve. This can be used - to create an arbitrary sample shape plan a scan. + """Interpolate an n_point closed curve from a lists of xy_points. + + This can be used to create an arbitrary sample shape for testing a scan planner. Modified from: https://stackoverflow.com/questions/33962717/interpolating-a-closed-curve-using-scipy """ - - # Use zip to seperate x and y points into tuples + # Use zip to separate x and y points into tuples x, y = zip(*xy_points) # Append first point and convert to array @@ -114,17 +112,17 @@ def interp_closed_path(xy_points: list[tuple[int, int]], n_points: int) -> MatPa def example_smart_spiral( sample_name: str = "lobed", ) -> tuple[FakeSample, scan_planners.ScanPlanner]: - """ - Run an example scan and return the sample scanned and the planner object - after scan is complete + """Run an example scan. + + :returns: The sample scanned and the planner object after scan is complete. """ xy_sample_points = load_sample_points(sample_name) sample = FakeSample(xy_sample_points) img_size = (1000, 1000) - intial_position = (0, 0) + initial_position = (0, 0) planner_settings = {"dx": 1200, "dy": 800, "max_dist": 100000} planner = scan_planners.SmartSpiral( - intial_position=intial_position, planner_settings=planner_settings + initial_position=initial_position, planner_settings=planner_settings ) while not planner.scan_complete: @@ -136,12 +134,11 @@ def example_smart_spiral( def profile_and_save_plot_for_example_smart_spiral(): - """ - Run the example scan and save a plot and the profile data - Also print the cumulative stats + """Run the example scan and save a plot and the profile data. + Also print the cumulative stats. - This runs if you run this file directly + This runs if you run this file directly. """ import pstats import cProfile @@ -163,9 +160,9 @@ def profile_and_save_plot_for_example_smart_spiral(): def update_example_smart_spiral_pickle(sample_name: str): - """ - Pickle the ScanPlanner for the example_smart_spiral(), - this is done so the history can be compared by testing to check + """Pickle the ScanPlanner for the example_smart_spiral(). + + This is done so the history can be compared by testing to check the algorithm is unchanged. If the algorithm is purposefully changed then this will need to be @@ -183,9 +180,9 @@ def update_example_smart_spiral_pickle(sample_name: str): def get_expected_result_for_example_smart_spiral( sample_name: str, ) -> scan_planners.ScanPlanner: - """ - Return the expected ScanPlanner object for the example_smart_spiral(), - this is pickled, so that it can be committed. + """Return the expected ScanPlanner object for the example_smart_spiral(). + + This is loaded from a pickle so that the object can be committed to the repo. """ pkl_fname = os.path.join(THIS_DIR, f"example_smart_spiral_{sample_name}.pkl") with open(pkl_fname, "rb") as pkl_file_obj: @@ -193,7 +190,7 @@ def get_expected_result_for_example_smart_spiral( def load_sample_points(sample_name: str): - """Return the points to generate the FakeSample corresponding to the given input name + """Return the points to generate the FakeSample corresponding to the given input name. Options are "lobed", "regular", and "core". """ diff --git a/webapp/src/main.js b/webapp/src/main.js index 2b6053ac..d49fbd5d 100644 --- a/webapp/src/main.js +++ b/webapp/src/main.js @@ -97,7 +97,7 @@ Vue.mixin({ } ) .finally(function() { - // Reenable the GPU preview, if it was active before the modal + // Re-enable the GPU preview, if it was active before the modal if (context.$store.state.autoGpuPreview) { context.$root.$emit("globalTogglePreview", true); }