Finish basic tests of background detect

src/openflexure_microscope_server/background_detect.py

@@ -14,7 +14,7 @@ from scipy.stats import norm
 from labthings_fastapi.thing_description import type_to_dataschema
 
 
-class MissingBackgroundData(RuntimeError):
+class MissingBackgroundDataError(RuntimeError):
     """An error raised if checking for sample without background data set."""
 
 
@@ -177,7 +177,7 @@ class ColourChannelDetectLUV(BackgroundDetectAlgorithm):
         """
         d = self.background_data
         if not d:
-            raise MissingBackgroundData(
+            raise MissingBackgroundDataError(
                 "Background is not set: you need to calibrate background detection."
             )
         # Only use the U and V channels of as brightness (L) often changes as the

tests/test_background_detectors.py

@@ -12,12 +12,11 @@ import numpy as np
 
 # Just for testing importing as
 from openflexure_microscope_server.background_detect import (
-    MissingBackgroundData,
-    BackgroundDetectorStatus,
+    MissingBackgroundDataError,
     BackgroundDetectAlgorithm,
     ChannelDistributions,
     ColourChannelDetectSettings,
-    ColourChannelDetectLUV
+    ColourChannelDetectLUV,
 )
 
 RNG = np.random.default_rng()
@@ -26,8 +25,10 @@ BG_COLOR = [220, 215, 217]
 
 PERC_REGEX = re.compile(r"(\d+\.+\d)+%")
 
+
 @pytest.fixture
 def background_image():
+    """Generate a numpy array that simulates a background image."""
     image = np.ones(IMG_SHAPE, dtype=np.int16)
     image[:, :, 0] *= BG_COLOR[0]
     image[:, :, 1] *= BG_COLOR[1]
@@ -37,11 +38,13 @@ def background_image():
     image[image > 255] = 255
     return image.astype("uint8")
 
+
 @pytest.fixture
 def sample_image(background_image):
+    """Generate a numpy array of a simulated image where 50% is a block of red."""
     image = background_image.copy()
-    x_cent = IMG_SHAPE[0]//2
-    image[:x_cent,:,0] -= 180
+    x_cent = IMG_SHAPE[0] // 2
+    image[:x_cent, :, 0] -= 180
     return image
 
 
@@ -53,12 +56,14 @@ def test_bg_detect_base_class():
     with pytest.raises(NotImplementedError):
         BackgroundDetectAlgorithm()
 
+
 def test_partial_base_class(background_image):
     """Create a partial class so to initialise the base class and test other methods.
 
     This test is to check that if the necessary methods are not set, that an
     appropriate error is raise.
     """
+
     class BadAlgo1(BackgroundDetectAlgorithm):
         """Only has a settings model so it can initialise."""
 
@@ -80,12 +85,14 @@ def test_partial_base_class(background_image):
     with pytest.raises(NotImplementedError):
         bad_algo1.image_is_sample(background_image)
 
+
 def test_colour_channel_luv(background_image, sample_image):
+    """Test measuring if a sample is background."""
     cc_luv = ColourChannelDetectLUV()
 
     # No background data so it is not ready and will error if image_is_sample is called.
     assert not cc_luv.status.ready
-    with pytest.raises(MissingBackgroundData):
+    with pytest.raises(MissingBackgroundDataError):
         cc_luv.image_is_sample(background_image)
 
     # Set the background
@@ -102,5 +109,73 @@ def test_colour_channel_luv(background_image, sample_image):
     # Should be 50% background. Allowing 49.8-50.2% due to noise.
     assert 49.8 < float(match.group(1)) < 50.2
 
+    # Require 70% coverage
+    cc_luv.settings = ColourChannelDetectSettings(min_sample_coverage=75.0)
 
-# TODO Save data and reload it.
+    sample, message = cc_luv.image_is_sample(sample_image)
+    # No longer detected as a sample.
+    assert not sample
+    match = PERC_REGEX.search(message)
+    assert match is not None
+    # Still 50% background.
+    assert 49.8 < float(match.group(1)) < 50.2
+
+
+def test_colour_channel_luv_save_load(background_image, sample_image):
+    """Get settings and data as dicts, and creating new instance using these dicts.
+
+    This is how the camera will load/save settings from/to disk.
+    """
+    cc_luv = ColourChannelDetectLUV()
+    cc_luv.set_background(background_image)
+
+    # Check types for background data
+    assert cc_luv.background_data_model is ChannelDistributions
+    assert isinstance(cc_luv.background_data, cc_luv.background_data_model)
+    # Change Settings
+    cc_luv.settings = ColourChannelDetectSettings(min_sample_coverage=10.0)
+
+    setting_dict = cc_luv.settings.model_dump()
+    data_dict = cc_luv.background_data.model_dump()
+
+    # Remove the old detector one so we don't accidentally use it!
+    del cc_luv
+
+    # Create a new instance
+    cc_luv2 = ColourChannelDetectLUV()
+    assert not cc_luv2.status.ready
+    # Load settings and channels from dictionary as the camera will do on init.
+    cc_luv2.settings = setting_dict
+    cc_luv2.background_data = data_dict
+
+    # Now should be ready to use
+    assert cc_luv2.status.ready
+    assert cc_luv2.settings.min_sample_coverage == 10.0
+    sample, _ = cc_luv2.image_is_sample(sample_image)
+    assert sample
+
+    # One final test that None can be set explicitly to background data as this will
+    # happen if loading with background detect not saved.
+    cc_luv3 = ColourChannelDetectLUV()
+    assert not cc_luv3.status.ready
+    # Load settings and channels from dictionary as the camera will do on init.
+    cc_luv3.settings = setting_dict
+    cc_luv3.background_data = None
+    # Still not ready
+    assert not cc_luv3.status.ready
+
+
+def test_colour_channel_luv_load_bad_data():
+    """Check a type error is thrown on bad data input."""
+
+    class WrongModel(BaseModel):
+        """Using a different BaseModel as this is most ilkley to cause confusion."""
+
+        prop1: int = 8
+        prop2: str = "foo"
+
+    cc_luv = ColourChannelDetectLUV()
+    with pytest.raises(TypeError):
+        cc_luv.settings = WrongModel()
+    with pytest.raises(TypeError):
+        cc_luv.background_data = WrongModel()