Merge branch 'tuning-tests-and-fixes' into 'v3'

Fix picamera default tuning being updated by calibrations, add tests

See merge request openflexure/openflexure-microscope-server!373

hardware-specific-tests/picamera2/test_acquisition.py

@@ -5,14 +5,13 @@ from PIL import Image
 import numpy as np
 from pytest import fixture
 
-from labthings_fastapi.server import ThingServer
-from labthings_fastapi.client import ThingClient
+import labthings_fastapi as lt
 
 from openflexure_microscope_server.things.camera.picamera import StreamingPiCamera2
 
 
 @fixture(scope="module")
-def client():
+def client() -> lt.ThingClient:
     """Initialise a test client for the StreamingPiCamera2 Thing.
 
     This fixture:
@@ -21,18 +20,13 @@ def client():
     * Registers a StreamingPiCamera2 instance at the "/camera/" endpoint
     * Provides a ThingClient for interacting with it during tests.
     """
-    server = ThingServer()
+    server = lt.ThingServer()
     server.add_thing(StreamingPiCamera2(), "/camera/")
     with TestClient(server.app) as test_client:
-        client = ThingClient.from_url("/camera/", client=test_client)
+        client = lt.ThingClient.from_url("/camera/", client=test_client)
         yield client
 
 
-def test_calibration(client):
-    """Check that full auto calibrate completes without an exception."""
-    client.full_auto_calibrate()
-
-
 def test_jpeg_and_array(client):
     """Check that a jpeg grabbed from the stream is the same size as other captures.
 
@@ -41,12 +35,15 @@ def test_jpeg_and_array(client):
     # Grab a jpeg from the stream
     blob = client.grab_jpeg()
     mjpeg_frame = Image.open(blob.open())
-    assert mjpeg_frame
+    # Verify throws an error if there are issues with the image
+    mjpeg_frame.verify()
+    assert mjpeg_frame.format == "JPEG"
 
     # Capture a jpeg
     blob = client.capture_jpeg(resolution="main")
     jpeg_capture = Image.open(blob.open())
-    assert jpeg_capture
+    jpeg_capture.verify()
+    assert jpeg_capture.format == "JPEG"
 
     # Capture an array
     arrlist = client.capture_array(stream_name="main")

hardware-specific-tests/picamera2/test_calibration.py

@@ -0,0 +1,102 @@
+"""Test data collection from the Raspberry Picamera."""
+
+import tempfile
+from copy import deepcopy
+
+from fastapi.testclient import TestClient
+import pytest
+
+import labthings_fastapi as lt
+
+from openflexure_microscope_server.things.camera.picamera import (
+    StreamingPiCamera2,
+    MissingCalibrationError,
+)
+
+
+@pytest.fixture()
+def picamera_thing() -> StreamingPiCamera2:
+    """Return a StreamingPiCamera2 Thing.
+
+    This is the Thing that the fixture client uses. It can be used to probe the
+    Thing directly to check actions had the expected response.
+    """
+    return StreamingPiCamera2()
+
+
+@pytest.fixture()
+def client(picamera_thing) -> lt.ThingClient:
+    """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.
+    """
+    temp_folder = tempfile.TemporaryDirectory()
+    server = lt.ThingServer(settings_folder=temp_folder.name)
+    server.add_thing(picamera_thing, "/camera/")
+    with TestClient(server.app) as test_client:
+        client = lt.ThingClient.from_url("/camera/", client=test_client)
+        yield client
+
+
+def test_get_tuning_algo(picamera_thing):
+    """Test that get_tuning algorithm retrieves tuning algorithms."""
+    # Missing algorithm raises an error.
+    with pytest.raises(MissingCalibrationError):
+        picamera_thing.get_tuning_algo("foo")
+    # Or returns None if explicitly told not to error.
+    assert picamera_thing.get_tuning_algo("foo", raise_if_missing=False) is None
+
+    # Real algorithm is a dict and contains expected keys
+    assert isinstance(picamera_thing.get_tuning_algo("rpi.geq"), dict)
+    assert "offset" in picamera_thing.get_tuning_algo("rpi.geq")
+
+    # Set the tuning to None as it is technically optional. And check this
+    # is handled gracefully. This needs to be done in a try block as LabThings
+    # tries and fails to emit an event.
+    try:
+        picamera_thing.tuning = None
+    except lt.exceptions.NotConnectedToServerError:
+        # Labthings will complain that it is not connected to a server
+        pass
+
+    # Check it is set to None despite the above LabThings issue.
+    assert picamera_thing.tuning is None
+
+    # Raises an error as there is no tuning file set.
+    with pytest.raises(MissingCalibrationError):
+        picamera_thing.get_tuning_algo("rpi.geq")
+    # Or returns None if explicitly told not to error.
+    assert picamera_thing.get_tuning_algo("rpi.geq", raise_if_missing=False) is None
+
+
+def test_calibration(picamera_thing, client):
+    """Check that full auto calibrate completes and set the expected values."""
+    # Save copy of default tuning file for end of test
+    original_default = deepcopy(picamera_thing.default_tuning)
+    # Tuning should start the same as the server is loading with no settings.
+    assert picamera_thing.default_tuning == picamera_thing.tuning
+    # lens_shading tables should be None when loaded on default tuning as it is
+    # adaptive
+    assert picamera_thing.lens_shading_tables is None
+    # The background detector isn't ready as there is no background image.
+    assert not picamera_thing.background_detector_status.ready
+
+    # Run full auto calibrate
+    client.full_auto_calibrate()
+
+    # After calibration the tuning files should be different
+    assert picamera_thing.default_tuning != picamera_thing.tuning
+    # The default should be unchanged
+    assert picamera_thing.default_tuning == original_default
+    # Lens shading tables should no longer be None
+    assert picamera_thing.lens_shading_tables is not None
+    # There should be exactly one colour correction matrix
+    # (no variations by colour temp)
+    assert len(picamera_thing.get_tuning_algo("rpi.ccm")["ccms"]) == 1
+    # Green equalisation offset should be set to maximum.
+    assert picamera_thing.get_tuning_algo("rpi.geq")["offset"] == 65535
+    assert picamera_thing.background_detector_status.ready

src/openflexure_microscope_server/things/camera/picamera.py

@@ -15,11 +15,12 @@ https://datasheets.raspberrypi.com/camera/raspberry-pi-camera-guide.pdf
 """
 
 from __future__ import annotations
-from typing import Annotated, Iterator, Literal, Mapping, Optional
+from typing import Annotated, Iterator, Literal, Mapping, Optional, overload
 from datetime import datetime
 import json
 import logging
 import os
+import copy
 import tempfile
 import time
 from contextlib import contextmanager
@@ -46,6 +47,10 @@ from . import picamera_recalibrate_utils as recalibrate_utils
 from . import BaseCamera, JPEGBlob, ArrayModel
 
 
+class MissingCalibrationError(RuntimeError):
+    """Picamera tuning file is missing or doesn't contain the requested algorithm."""
+
+
 class PicameraStreamOutput(Output):
     """An Output class that sends frames to a stream."""
 
@@ -138,7 +143,7 @@ class StreamingPiCamera2(BaseCamera):
         # Set tuning to default tuning. This will be overwritten when the Thing is
         # connects to the server if tuning is saved to disk.
         try:
-            self.tuning = self.default_tuning
+            self.tuning = copy.deepcopy(self.default_tuning)
         except NotConnectedToServerError:
             # This will throw an error after setting as we are not connected to
             # a server. But we know this, so we ignore the error.
@@ -307,6 +312,42 @@ class StreamingPiCamera2(BaseCamera):
     tuning = lt.ThingSetting(Optional[dict], None, readonly=True)
     """The Raspberry PiCamera Tuning File JSON."""
 
+    # Use overload to clarify that only a dictionary is returned if `raise_if_missing`
+    # is True
+    @overload
+    def get_tuning_algo(
+        self, algorithm_name: str, raise_if_missing: Literal[True]
+    ) -> dict: ...
+    # Otherwise may also be None
+    @overload
+    def get_tuning_algo(
+        self, algorithm_name: str, raise_if_missing: bool
+    ) -> Optional[dict]: ...
+
+    def get_tuning_algo(
+        self, algorithm_name: str, raise_if_missing: bool = True
+    ) -> Optional[dict]:
+        """Return the active tuning algorithm settings for the given algorithm.
+
+        :returns: The algorithm dictionary if found, returns None if no tuning data
+            is loaded or if the tuning algorithm is not found.
+
+        :raises MissingCalibrationError: If raise_if_missing is true and there is no
+            tuning file is available, or the requested algorithm is not present.
+        """
+        if self.tuning is None:
+            if raise_if_missing:
+                raise MissingCalibrationError("No tuning data is set.")
+            return None
+        try:
+            return Picamera2.find_tuning_algo(self.tuning, algorithm_name)
+        except StopIteration as e:
+            if raise_if_missing:
+                raise MissingCalibrationError(
+                    f"No tuning algorithm with name {algorithm_name}."
+                ) from e
+            return None
+
     def _initialise_picamera(self):
         """Acquire the picamera device and store it as ``self._picamera``.
 
@@ -753,6 +794,7 @@ class StreamingPiCamera2(BaseCamera):
         * ``auto_expose_from_minimum``
         * ``set_static_green_equalisation`` to set geq offset to max
         * ``calibrate_lens_shading``
+        * ``reset_ccm``
         * ``calibrate_white_balance``
         * ``set_background``
         """
@@ -760,8 +802,8 @@ class StreamingPiCamera2(BaseCamera):
         self.auto_expose_from_minimum()
         self.set_static_green_equalisation()
         self.calibrate_lens_shading()
-        self.calibrate_white_balance()
         self.reset_ccm()
+        self.calibrate_white_balance()
         self.set_background(portal)
 
     @lt.thing_action
@@ -880,7 +922,7 @@ class StreamingPiCamera2(BaseCamera):
             return None
 
         # Note "alsc" is the Picamera2 term for "Automatic Lens Shading Correction"
-        alsc = Picamera2.find_tuning_algo(self.tuning, "rpi.alsc")
+        alsc = self.get_tuning_algo("rpi.alsc")
 
         # Check there is exactly 1 correction table for red-difference chroma (Cr)
         # and blue-difference chroma (Cb)
@@ -951,7 +993,7 @@ class StreamingPiCamera2(BaseCamera):
         colour across the image.
         """
         with self._streaming_picamera(pause_stream=True):
-            alsc = Picamera2.find_tuning_algo(self.tuning, "rpi.alsc")
+            alsc = self.get_tuning_algo("rpi.alsc")
             luminance = alsc["luminance_lut"]
             flat = np.ones((12, 16))
             recalibrate_utils.set_static_lst(self.tuning, luminance, flat, flat)