Tidy post refactor of cameras

pyproject.toml

@@ -83,8 +83,8 @@ addopts = [
 ]
 
 norecursedirs = [".git", "build", "node_modules"]
-
 pythonpath = ["."]
+testpaths = ["tests"]
 
 [tool.ruff.format]
 # Use native line endings for all files

src/openflexure_microscope_server/things/autofocus.py

@@ -24,7 +24,6 @@ from labthings_fastapi.dependencies.blocking_portal import BlockingPortal
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.dependencies.metadata import GetThingStates
 from labthings_fastapi.types.numpy import NDArray
-from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
 from labthings_fastapi.dependencies.invocation import InvocationLogger
 
 from .camera import RawCameraDependency as Camera

src/openflexure_microscope_server/things/camera/__init__.py

@@ -7,11 +7,12 @@ See repository root for licensing information.
 """
 
 from __future__ import annotations
-import logging
 from typing import Literal, Optional, Tuple
+import json
 
 from pydantic import RootModel
 from PIL import Image
+import piexif
 
 from labthings_fastapi.thing import Thing
 from labthings_fastapi.decorators import thing_action, thing_property

src/openflexure_microscope_server/things/camera/opencv.py

@@ -19,7 +19,6 @@ import piexif
 from labthings_fastapi.utilities import get_blocking_portal
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.dependencies.metadata import GetThingStates
-from labthings_fastapi.outputs.mjpeg_stream import MJPEGStreamDescriptor
 from labthings_fastapi.types.numpy import NDArray
 
 from . import BaseCamera, JPEGBlob

src/openflexure_microscope_server/things/camera/picamera.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
-from dataclasses import dataclass
 from datetime import datetime
-import io
 import json
 import logging
 import os
@@ -12,19 +10,14 @@ from tempfile import TemporaryDirectory
 from pydantic import BaseModel, BeforeValidator
 
 from labthings_fastapi.descriptors.property import PropertyDescriptor
-from labthings_fastapi.thing import Thing
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.outputs.mjpeg_stream import MJPEGStream
 from labthings_fastapi.utilities import get_blocking_portal
-from labthings_fastapi.types.numpy import NDArray
 from labthings_fastapi.dependencies.metadata import GetThingStates
 from labthings_fastapi.dependencies.blocking_portal import BlockingPortal
-from typing import Annotated, Any, Iterator, Literal, Mapping, Optional, Self
+from typing import Annotated, Any, Iterator, Literal, Mapping, Optional
 from contextlib import contextmanager
 import piexif
-from scipy.ndimage import zoom
-from scipy.interpolate import interp1d
-from PIL import Image
 from threading import RLock
 import picamera2
 from picamera2 import Picamera2
@@ -33,7 +26,7 @@ from picamera2.outputs import Output
 import numpy as np
 from . import picamera_recalibrate_utils as recalibrate_utils
 
-from . import BaseCamera, JPEGBlob, PNGBlob, ArrayModel
+from . import BaseCamera, JPEGBlob, ArrayModel
 
 
 class PicameraControl(PropertyDescriptor):
@@ -636,7 +629,9 @@ class StreamingPiCamera2(BaseCamera):
         the processed images. It should not affect raw images.
         """
         with self.picamera(pause_stream=True) as cam:
-            L, Cr, Cb = recalibrate_utils.lst_from_camera(cam)
+            # Suppress lint warning that L, Cr, and Cb are not lowercase, as this is the
+            # Standard format for these mathematical vars.
+            L, Cr, Cb = recalibrate_utils.lst_from_camera(cam)  # noqa: N806
             recalibrate_utils.set_static_lst(self.tuning, L, Cr, Cb)
             self.initialise_picamera()
 

src/openflexure_microscope_server/things/camera/picamera_recalibrate_utils.py

@@ -30,6 +30,11 @@ picamera.lens_shading_table = lst
 ```
 """
 
+# Disable N806 & 803, which checks that all variables and args are lowercase.
+# This is due to the number of matrix calculations and colour channel
+# calculations that are clearer using the standard R, G, B, or L, Cr, Cb terms.
+# ruff: noqa: N806 N803
+
 from __future__ import annotations
 import gc
 import logging
@@ -43,6 +48,9 @@ from picamera2 import Picamera2
 import picamera2
 
 
+LensShadingTables = tuple[np.ndarray, np.ndarray, np.ndarray]
+
+
 def load_default_tuning(cam: Picamera2) -> dict:
     """Load the default tuning file for the camera
 
@@ -58,12 +66,13 @@ def load_default_tuning(cam: Picamera2) -> dict:
     try:
         return cam.load_tuning_file(fname)
     except RuntimeError:
-        dir = "/usr/share/libcamera/ipa/raspberrypi"  # from picamera2 v0.3.9
-        # The directory above has been removed from the search path, which I
+        tuning_dir = "/usr/share/libcamera/ipa/raspberrypi"
+        # from picamera2 v0.3.9
+        # The directory above has been removed from the search path seems
         # find odd - as that's where the files currently are on a default
         # Raspbian image. This may need updating if the files have moved
         # in future updates to the system libcamera package
-        return cam.load_tuning_file(fname, dir=dir)
+        return cam.load_tuning_file(fname, dir=tuning_dir)
 
 
 def set_minimum_exposure(camera: Picamera2):
@@ -312,9 +321,6 @@ def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray:
     return channels
 
 
-LensShadingTables = tuple[np.ndarray, np.ndarray, np.ndarray]
-
-
 def get_16x12_grid(chan: np.ndarray, dx: int, dy: int):
     """Compresses channel down to a 16x12 grid - from libcamera
 
@@ -527,8 +533,8 @@ def raw_channels_from_camera(camera: Picamera2) -> LensShadingTables:
     # raw_image is a 3D array, with full resolution and 3 colour channels.  No
     # 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).
-    format = camera.camera_configuration()["raw"]["format"]
-    print(f"Acquired a raw image in format {format}")
+    raw_format = camera.camera_configuration()["raw"]["format"]
+    print(f"Acquired a raw image in format {raw_format}")
     return channels_from_bayer_array(raw_image)
 
 
@@ -540,24 +546,3 @@ def recreate_camera_manager():
     del Picamera2._cm
     gc.collect()
     Picamera2._cm = picamera2.picamera2.CameraManager()
-
-
-if __name__ == "__main__":
-    """This block is untested but has been updated."""
-    with Picamera2() as cam:
-        tuning = load_default_tuning(cam)
-    f = np.ones((12, 16))
-    set_static_lst(tuning, f, f, f)
-    set_static_geq(tuning)
-    with Picamera2(tuning=tuning) as cam:
-        cam.start_preview()
-        time.sleep(3)
-        logging.info("Recalibrating...")
-        adjust_shutter_and_gain_from_raw(cam)
-        adjust_white_balance_from_raw(cam)
-        lst = lst_from_camera(cam)
-        set_static_lst(tuning, *lst)
-        logging.info("Done.")
-    with Picamera2(tuning=tuning) as cam:
-        cam.start_preview()
-        time.sleep(2)

src/openflexure_microscope_server/things/camera/simulation.py

@@ -22,9 +22,7 @@ from scipy.ndimage import gaussian_filter
 from labthings_fastapi.utilities import get_blocking_portal
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.dependencies.metadata import GetThingStates
-from labthings_fastapi.types.numpy import NDArray
 from labthings_fastapi.server import ThingServer
-from pydantic import RootModel
 
 from . import BaseCamera, JPEGBlob, ArrayModel
 from ..stage import StageProtocol as Stage
@@ -33,7 +31,6 @@ from ..stage import StageProtocol as Stage
 # higher related to a faster movement
 RATIO = 0.2
 
-
 class SimulatedCamera(BaseCamera):
     """A Thing representing an OpenCV camera"""