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Stop using print statments or root level loggers

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This commit is contained in:
Julian Stirling 2025-09-18 14:30:44 +01:00
parent 338d49f9e6
commit 65f172d650
9 changed files with 69 additions and 52 deletions
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11
pyproject.toml
View file

@ -114,8 +114,8 @@ select = [
"C", # Flake8 comprehensions
"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 statements, production code should log
"LOG", # Flake8 logging issues (pedantic logger formatting issues can be added with "G")
"T20", # Warns for print statements, production code should log
# "PT", # pytest linting
"RET", # Consistent clear return statements
"RSE", # Raise parentheses
@ -140,10 +140,17 @@ ignore = [
]
[tool.ruff.lint.per-file-ignores]
# All testing dirs
"{tests,integration-tests,hardware-specific-tests}/**" = [
"B018", # Complaining about useless attribute access in tests, but we need them to check errors are raised
"ANN", # Tests are not typehinted for fixtures etc
"S101", # Allow asserts in tests
"T20", # Allow prints in tests
"LOG015",# Allow tests to use the root logger.
]
# Developer CLI scripts
"{pull_webapp,picamera_tests,change_log_helper}.py" = [
"T20", # Printing is normal in small CLI scripts
]
[tool.ruff.lint.pydocstyle]

8
src/openflexure_microscope_server/logging.py
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@ -18,6 +18,7 @@ import os
from fastapi.responses import PlainTextResponse
from fastapi import HTTPException
LOGGER = logging.getLogger(__name__)
OFM_LOG_FILE = None
@ -58,12 +59,9 @@ def configure_logging(log_folder: str) -> None:
root_logger.addHandler(handler)
except PermissionError as e:
logging.error(f"Cannot create log file at {OFM_LOG_FILE}: {e}")
LOGGER.error(f"Cannot create log file at {OFM_LOG_FILE}: {e}")
logging.info("")
logging.info("****************************************************")
logging.info("OFM server root logger has been set up at INFO level")
logging.info("****************************************************")
LOGGER.info("OFM server root logger has been set up at INFO level")
def retrieve_log() -> PlainTextResponse:

10
src/openflexure_microscope_server/server/__init__.py
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@ -14,6 +14,8 @@ from .serve_static_files import add_static_files
from .legacy_api import add_v2_endpoints
from ..logging import configure_logging, retrieve_log, retrieve_log_from_file
LOGGER = logging.getLogger(__name__)
def set_shutdown_function(shutdown_function: Callable[[], None]) -> None:
"""Ensure a function is called before the shutdown.
@ -93,7 +95,7 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
# Catch anything and log as it is essential that this
# function cannot raise an unhandled exception or Uvicorn
# will never get a shutdown signal.
logging.error(e, exc_info=True)
LOGGER.error(e, exc_info=True)
# Monkey patch uvicorn's exit handling to stop the MJPEG Streams
# before waiting for background tasks to complete.
@ -109,9 +111,11 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
except BaseException as e:
if args.fallback:
print(f"Error: {e}")
# Allow printing to the terminal for fallback errors so they are not
# presented in the fallback logs.
print(f"Error: {e}") # noqa: T201
fallback_server = "labthings_fastapi.server.fallback:app"
print(f"Starting fallback server {fallback_server}.")
print(f"Starting fallback server {fallback_server}.") # noqa: T201
app = lt.cli.object_reference_to_object(fallback_server)
app.labthings_config = config
app.labthings_server = server

6
src/openflexure_microscope_server/things/autofocus.py
View file

@ -25,6 +25,8 @@ from .camera import RawCameraDependency as RawCamera
from .camera import CameraDependency as CameraClient
from .stage import StageDependency as Stage
LOGGER = logging.getLogger(__name__)
class NotStreamingError(RuntimeError):
"""No images captured from stream. The camera is almost certainly not streaming."""
@ -228,7 +230,7 @@ class JPEGSharpnessMonitor:
self.camera = camera
self.stage = stage
self.portal = portal
print(f"Created sharpness monitor with {stage}, {camera}, {portal}")
LOGGER.debug(f"Created sharpness monitor with {stage}, {camera}, {portal}")
self.stage_positions: list[Mapping[str, int]] = []
self.stage_times: list[float] = []
self.jpeg_times: list[float] = []
@ -307,7 +309,7 @@ class JPEGSharpnessMonitor:
raise e
if stop < 1:
stop = len(jpeg_times)
logging.debug("changing stop to %s", (stop))
LOGGER.debug("changing stop to %s", (stop))
jpeg_times = jpeg_times[start:stop]
jpeg_heights: np.ndarray = np.interp(jpeg_times, stage_times, stage_heights)
return jpeg_times, jpeg_heights, jpeg_sizes[start:stop]

14
src/openflexure_microscope_server/things/camera/opencv.py
View file

@ -21,6 +21,8 @@ from labthings_fastapi.types.numpy import NDArray
from . import BaseCamera
LOGGER = logging.getLogger(__name__)
class OpenCVCamera(BaseCamera):
"""A Thing that provides and interface to an OpenCV Camera."""
@ -70,9 +72,7 @@ class OpenCVCamera(BaseCamera):
while self._capture_enabled:
ret, frame = self.cap.read()
if not ret:
logging.error(
f"Failed to capture frame from camera {self.camera_index}"
)
LOGGER.error(f"Failed to capture frame from camera {self.camera_index}")
break
jpeg = cv2.imencode(".jpg", frame)[1].tobytes()
self.mjpeg_stream.add_frame(jpeg, portal)
@ -99,8 +99,8 @@ class OpenCVCamera(BaseCamera):
binary image formats will be added in due course.
"""
if wait is not None:
logging.warning("OpenCV camera has no wait option. Use None.")
logging.warning(f"OpenCV camera doesn't respect {stream_name=}")
LOGGER.warning("OpenCV camera has no wait option. Use None.")
LOGGER.warning(f"OpenCV camera doesn't respect {stream_name=}")
ret, frame = self.cap.read()
if not ret:
raise RuntimeError(
@ -118,6 +118,6 @@ class OpenCVCamera(BaseCamera):
This function will produce a JPEG image.
"""
if wait is not None:
logging.warning("OpenCV camera has no wait option. Use None.")
logging.warning(f"OpenCV camera doesn't respect {stream_name=}")
LOGGER.warning("OpenCV camera has no wait option. Use None.")
LOGGER.warning(f"OpenCV camera doesn't respect {stream_name=}")
return Image.fromarray(self.capture_array())

26
src/openflexure_microscope_server/things/camera/picamera.py
View file

@ -47,6 +47,8 @@ from . import picamera_tuning_file_utils as tf_utils
from . import BaseCamera, ArrayModel
LOGGER = logging.getLogger(__name__)
SUPPORTED_CAMS_SENSOR_INFO = {
"picamera_v2": recalibrate_utils.IMX219_SENSOR_INFO,
"picamera_hq": recalibrate_utils.IMX477_SENSOR_INFO,
@ -397,16 +399,16 @@ class StreamingPiCamera2(BaseCamera):
os.environ["LIBCAMERA_RPI_TUNING_FILE"] = tuning_file.name
if self._picamera is not None:
logging.info("Closing picamera object for reinitialisation")
logging.info(
LOGGER.info("Closing picamera object for reinitialisation")
LOGGER.info(
"Camera object already exists, closing for reinitialisation"
)
self._picamera.close()
logging.info("Picamera closed, deleting picamera")
LOGGER.info("Picamera closed, deleting picamera")
del self._picamera
recalibrate_utils.recreate_camera_manager()
logging.info("Creating new Picamera2 object")
LOGGER.info("Creating new Picamera2 object")
# Specify tuning file otherwise it will be overwritten with None.
self._picamera = Picamera2(
camera_num=self._camera_num,
@ -519,7 +521,7 @@ class StreamingPiCamera2(BaseCamera):
)
stream_config["buffer_count"] = buffer_count
picam.configure(stream_config)
logging.info("Starting picamera MJPEG stream...")
LOGGER.info("Starting picamera MJPEG stream...")
stream_name = "lores" if main_resolution[0] > 1280 else "main"
picam.start_recording(
MJPEGEncoder(self.mjpeg_bitrate),
@ -538,11 +540,11 @@ class StreamingPiCamera2(BaseCamera):
name="lores",
)
except Exception as e:
logging.exception("Error while starting preview: {e}")
logging.exception(e)
LOGGER.exception("Error while starting preview: {e}")
LOGGER.exception(e)
else:
self.stream_active = True
logging.debug(
LOGGER.debug(
"Started MJPEG stream at %s on port %s", self.stream_resolution, 1
)
@ -553,15 +555,15 @@ class StreamingPiCamera2(BaseCamera):
try:
picam.stop_recording() # This should also stop the extra lores encoder
except Exception as e:
logging.info("Stopping recording failed")
logging.exception(e)
LOGGER.info("Stopping recording failed")
LOGGER.exception(e)
else:
self.stream_active = False
if stop_web_stream:
portal = lt.get_blocking_portal(self)
self.mjpeg_stream.stop(portal)
self.lores_mjpeg_stream.stop(portal)
logging.info("Stopped MJPEG stream.")
LOGGER.info("Stopped MJPEG stream.")
# Adding a sleep to prevent camera getting confused by rapid commands
time.sleep(self._sensor_info.short_pause)
@ -579,7 +581,7 @@ class StreamingPiCamera2(BaseCamera):
Restarts stream when complete.
"""
with self._streaming_picamera(pause_stream=True) as cam:
logging.debug("Reconfiguring camera for full resolution capture")
LOGGER.debug("Reconfiguring camera for full resolution capture")
cam.configure(cam.create_still_configuration(sensor=self._sensor_mode))
cam.start()
time.sleep(self._sensor_info.short_pause)

26
src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py
View file

@ -52,6 +52,8 @@ from scipy.ndimage import zoom
from picamera2 import Picamera2
import picamera2
LOGGER = logging.getLogger(__name__)
class SensorInfo(BaseModel):
"""Information about the sensor used for calibration and property setting."""
@ -167,7 +169,7 @@ def adjust_shutter_and_gain_from_raw(
# Check whether the shutter speed is still going up - if not, we've hit a maximum
if camera.capture_metadata()["ExposureTime"] == test.exposure_time:
logging.info(f"Shutter speed has maxed out at {test.exposure_time}")
LOGGER.info(f"Shutter speed has maxed out at {test.exposure_time}")
break
# Now, if we've not converged, increase gain until we converge or run out of options.
@ -185,13 +187,13 @@ def adjust_shutter_and_gain_from_raw(
# Check the gain is still changing - if not, we have probably hit the maximum
if camera.capture_metadata()["AnalogueGain"] == test.analog_gain:
logging.info(f"Gain has maxed out at {test.analog_gain}")
LOGGER.info(f"Gain has maxed out at {test.analog_gain}")
break
if _check_convergence(test, target_white_level, tolerance):
logging.info(f"Brightness has converged to within {tolerance * 100:.0f}%.")
LOGGER.info(f"Brightness has converged to within {tolerance * 100:.0f}%.")
else:
logging.warning(
LOGGER.warning(
f"Failed to reach target brightness of {target_white_level}."
f"Brightness reached {test.level} after {iterations} iterations."
)
@ -230,11 +232,9 @@ def adjust_white_balance_from_raw(
channel_gains = 1 / grids
if channel_gains.shape[1:] != channels.shape[1:]:
channel_gains = _upsample_channels(channel_gains, channels.shape[1:])
logging.info(
f"Before gains, channel maxima are {np.max(channels, axis=(1, 2))}"
)
LOGGER.info(f"Before gains, channel maxima are {np.max(channels, axis=(1, 2))}")
channels = channels * channel_gains
logging.info(f"After gains, channel maxima are {np.max(channels, axis=(1, 2))}")
LOGGER.info(f"After gains, channel maxima are {np.max(channels, axis=(1, 2))}")
if method == "centre":
_, height, width = channels.shape
# Cut out the central 10% from 9/20 to 11/20...
@ -261,7 +261,7 @@ def adjust_white_balance_from_raw(
# Here, we decrease the gains by the minimum value of Cr and Cb.
new_awb_gains = (green / red * np.min(Cr), green / blue * np.min(Cb))
logging.info(
LOGGER.info(
f"Raw white point is R: {red} G: {green} B: {blue}, "
f"setting AWB gains to ({new_awb_gains[0]:.2f}, "
f"{new_awb_gains[1]:.2f})."
@ -270,7 +270,7 @@ def adjust_white_balance_from_raw(
camera.controls.ColourGains = new_awb_gains
time.sleep(sensor_info.long_pause)
m = camera.capture_metadata()
print(f"Camera confirms gains are now {m['ColourGains']}")
LOGGER.debug(f"Camera confirms gains are now {m['ColourGains']}")
return new_awb_gains
@ -334,7 +334,7 @@ def _test_exposure_settings(camera: Picamera2, percentile: float) -> _ExposureTe
# because of black level compensation. The line below forces a
# minimum value of 1 which will keep things well-behaved!
if max_brightness < 1:
logging.warning(
LOGGER.warning(
f"Measured brightness of {max_brightness}. "
"This should normally be >= 1, and may indicate the "
"camera's black level compensation has gone wrong."
@ -346,7 +346,7 @@ def _test_exposure_settings(camera: Picamera2, percentile: float) -> _ExposureTe
exposure_time=int(metadata["ExposureTime"]),
analog_gain=float(metadata["AnalogueGain"]),
)
logging.info(f"{result.model_dump()}")
LOGGER.info(f"{result.model_dump()}")
return result
@ -490,5 +490,5 @@ def _raw_channels_from_camera(
# de-mosaicing has been done, so 2/3 of the values are zero (3/4 for R and B
# channels, 1/2 for green because there's twice as many green pixels).
raw_format = camera.camera_configuration()["raw"]["format"]
print(f"Acquired a raw image in format {raw_format}")
LOGGER.debug(f"Acquired a raw image in format {raw_format}")
return _channels_from_bayer_array(raw_image)

16
src/openflexure_microscope_server/things/camera/simulation.py
View file

@ -30,6 +30,8 @@ from openflexure_microscope_server.ui import (
from . import BaseCamera, ArrayModel
from ..stage import BaseStage
LOGGER = logging.getLogger(__name__)
# The ratio between "motor" steps and pixels
# higher related to a faster movement
RATIO = 0.2
@ -204,7 +206,7 @@ class SimulatedCamera(BaseCamera):
try:
pos = self.get_stage_position()
except Exception as e:
print(f"Failed to get stage position: {e}")
LOGGER.debug(f"Failed to get stage position: {e}")
pos = {"x": 0, "y": 0, "z": 0}
return self.generate_image((pos["y"], pos["x"], pos["z"]))
@ -238,7 +240,7 @@ class SimulatedCamera(BaseCamera):
If called while already streaming, the warning will be emitted and no other
action will be taken.
"""
logging.warning(
LOGGER.warning(
f"Simulation camera doesn't respect {main_resolution=} or {buffer_count=} "
"arguments."
)
@ -271,7 +273,7 @@ class SimulatedCamera(BaseCamera):
jpeg_lores = cv2.imencode(".jpg", ds_frame)[1].tobytes()
self.lores_mjpeg_stream.add_frame(jpeg_lores, portal)
except Exception as e:
logging.exception(f"Failed to capture frame: {e}, retrying...")
LOGGER.exception(f"Failed to capture frame: {e}, retrying...")
@lt.thing_action
def discard_frames(self) -> None:
@ -293,8 +295,8 @@ class SimulatedCamera(BaseCamera):
binary image formats will be added in due course.
"""
if wait is not None:
logging.warning("Simulation camera has no wait option. Use None.")
logging.warning(f"Simulation camera camera doesn't respect {stream_name=}")
LOGGER.warning("Simulation camera has no wait option. Use None.")
LOGGER.warning(f"Simulation camera camera doesn't respect {stream_name=}")
return self.generate_frame()
def capture_image(
@ -307,8 +309,8 @@ class SimulatedCamera(BaseCamera):
It is used for capture to memory.
"""
if wait is not None:
logging.warning("Simulation camera has no wait option. Use None.")
logging.warning(f"Simulation camera camera doesn't respect {stream_name=}")
LOGGER.warning("Simulation camera has no wait option. Use None.")
LOGGER.warning(f"Simulation camera camera doesn't respect {stream_name=}")
return Image.fromarray(self.generate_frame())
@lt.thing_action

4
src/openflexure_microscope_server/things/stage/sangaboard.py
View file

@ -15,6 +15,8 @@ import labthings_fastapi as lt
from . import BaseStage
LOGGER = logging.getLogger(__name__)
class SangaboardThing(BaseStage):
"""A Thing to manage a Sangaboard motor controller.
@ -168,7 +170,7 @@ class SangaboardThing(BaseStage):
# cannot be used.
intended_brightness = float(return_value[7:])
on_brightness = 0.32
logging.warning(
LOGGER.warning(
"Brightness control is not yet implemented. Desired brightness: "
f"{intended_brightness}. Set brightness: {on_brightness}"
)