Merge branch 'stack-trends' into 'v3'
Stack trends Closes #752 See merge request openflexure/openflexure-microscope-server!564
This commit is contained in:
Joe Knapper
commit
924676ff5d
3 changed files with 158 additions and 5 deletions
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@ -676,10 +676,11 @@ class AutofocusThing(lt.Thing):
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sharpness=self._cam.grab_jpeg_size(stream_name="lores"),
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)
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# Silence too many returns in this situation as refactoring to reduce returns is
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# unlikely to improve readability. This function is basically a complex switch
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# statement, having an explicit return after each option is clear.
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def check_stack_result( # noqa: PLR0911
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# Silence too many returns and complexity in this situation as refactoring to
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# reduce returns is unlikely to improve readability.
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# This function is basically a complex switch statement, having an explicit
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# return after each option is clear.
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def check_stack_result( # noqa: PLR0911 C901
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self, captures: list[CaptureInfo], check_turning_points: bool
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) -> tuple[Literal["success", "continue", "restart"], int]:
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"""Check if the sharpest image in a list of captures is central enough.
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@ -688,7 +689,7 @@ class AutofocusThing(lt.Thing):
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sharpness has converged in the centre
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:param check_turning_points: Whether to check the number of turning points in
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the sharpnesses of the images in the stack is exactly 1. (May fail with
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thick samples)
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thick samples and stacks with many images)
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:returns: A tuple with two values:
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@ -719,6 +720,13 @@ class AutofocusThing(lt.Thing):
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return "restart", capture_id
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return "continue", capture_id
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# Manually test for monotomically increasing or decreasing sharpnesses, as
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# fitting can struggle with these and their behaviour is simpler to hardcode
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if np.all(sharpnesses[:-1] <= sharpnesses[1:]):
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return "continue", capture_id
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if np.all(sharpnesses[:-1] >= sharpnesses[1:]):
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return "restart", capture_id
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try:
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turning = _get_peak_turning_point(sharpnesses)
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except NotAPeakError:
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43
tests/unit_tests/data/sharpness_test_cases.json
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43
tests/unit_tests/data/sharpness_test_cases.json
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@ -0,0 +1,43 @@
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[
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{"sharpnesses":[100000,300000,500000,300000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,400000,600000,400000,200000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,300000,400000,500000],"label":"continue"},
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{"sharpnesses":[500000,400000,300000,200000,100000],"label":"restart"},
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{"sharpnesses":[100000,200000,300000,200000,100000,50000],"label":["success"]},
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{"sharpnesses":[0,100000,200000,300000,400000,500000],"label":"continue"},
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{"sharpnesses":[500000,500000,500000,500000,500000],"label":"continue"},
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{"sharpnesses":[100000,200000,300000,300000,200000,100000],"label":["success"]},
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{"sharpnesses":[100000,200000,300000,400000,400000,300000,200000],"label":["success","continue"]},
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{"sharpnesses":[100000,300000,500000,500000,500000,300000,100000],"label":["success","continue"]},
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{"sharpnesses":[100000,300000,500000,400000,500000,300000,100000],"label":["continue","success"]},
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{"sharpnesses":[100000,400000,600000,500000,300000,200000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,500000,700000,600000,300000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,300000,500000,700000,600000,400000],"label":["success","continue"]},
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{"sharpnesses":[700000,600000,500000,400000,300000,200000,100000,0],"label":"restart"},
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{"sharpnesses":[100000,300000,600000,900000,600000,300000,200000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,400000,800000,900000,800000,400000,200000],"label":"success"},
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{"sharpnesses":[100000,200000,300000,400000,500000,600000,700000,800000],"label":"continue"},
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{"sharpnesses":[800000,700000,600000,500000,400000,300000,200000,100000],"label":"restart"},
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{"sharpnesses":[100000,200000,300000,400000,400000,400000,300000,200000],"label":["success","continue"]},
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{"sharpnesses":[100000,200000,300000,500000,500000,500000,500000,500000],"label":"continue"},
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{"sharpnesses":[500000,500000,500000,500000,500000,400000,300000,200000],"label":"restart"},
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{"sharpnesses":[100000,200000,300000,600000,900000,600000,300000,200000,100000],"label":"success"},
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{"sharpnesses":[100000,200000,400000,700000,1000000,900000,700000,400000,200000],"label":"success"},
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{"sharpnesses":[100000,200000,300000,400000,500000,600000,700000,800000,900000],"label":"continue"},
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{"sharpnesses":[900000,800000,700000,600000,500000,400000,300000,200000,100000],"label":"restart"},
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{"sharpnesses":[100000,200000,1000000,200000,1000000,200000,100000],"label":"continue"},
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{"sharpnesses":[100000,500000,100000,500000,100000,500000,100000],"label":["restart","continue"]},
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{"sharpnesses":[300000,300000,300000,300000,300000,300000,300000],"label":"continue"},
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{"sharpnesses":[500000,600000,800000,1100000,1500000,1100000,800000,600000,500000],"label":"success"},
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{"sharpnesses":[1000000,1100000,1300000,1600000,2000000,1600000,1300000,1100000,1000000],"label":"success"},
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{"sharpnesses":[2000000,1800000,1500000,1200000,1000000,900000,800000,700000,600000],"label":"restart"},
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{"sharpnesses":[600000,700000,800000,900000,1100000,1300000,1500000,1700000,1800000],"label":"continue"},
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{"sharpnesses":[500000,700000,1000000,1400000,1800000,1700000,1400000,1000000,700000],"label":"success"},
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{"sharpnesses":[500000,600000,900000,1300000,1800000,1900000,1700000,1300000,900000],"label":"success"},
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{"sharpnesses":[500000,500000,500000,500000,600000,900000,600000,500000,500000],"label":["success"],"allow_failure":true},
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{"sharpnesses":[500000,500000,500000,500000,500000,600000,900000,600000,500000],"label":["success","continue"]},
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{"sharpnesses":[500000,500000,500000,500000,500000,500000,600000,900000,600000],"label":"continue"},
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{"sharpnesses":[100000,100000,100000,100000,200000,500000,200000,100000,100000],"label":["success"],"allow_failure":true},
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{"sharpnesses":[100000,100000,100000,100000,100000,200000,500000,200000,100000],"label":["success","continue"]},
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{"sharpnesses":[100000,100000,100000,100000,100000,100000,200000,500000,200000],"label":"continue"}
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]
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102
tests/unit_tests/test_stack_examples.py
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102
tests/unit_tests/test_stack_examples.py
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@ -0,0 +1,102 @@
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"""Unit tests for validating stack classification logic in AutofocusThing.
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This module tests whether the `check_stack_result` method correctly classifies
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z-stack sharpness profiles into "success", "continue", or "restart" categories
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based on predefined test cases.
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Sharpness profiles are loaded from a JSON file and converted into mock capture
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objects to simulate real camera captures.
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"""
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import json
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import os
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import pytest
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from labthings_fastapi.testing import create_thing_without_server
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from openflexure_microscope_server.things.autofocus import AutofocusThing
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THIS_DIR = os.path.dirname(__file__)
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DATA_PATH = os.path.join(THIS_DIR, "data", "sharpness_test_cases.json")
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class MockCapture:
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"""Simple mock object representing a captured image.
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This class mimics the minimal interface required by
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`check_stack_result` by adding the `sharpness` and `buffer_id`
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attributes.
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:param sharpness: The sharpness value associated with the image.
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:param buffer_id: A unique identifier for the image buffer.
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"""
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def __init__(self, sharpness, buffer_id):
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"""Give each capture a sharpness and buffer_id."""
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self.sharpness = sharpness
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self.buffer_id = buffer_id
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def make_captures(sharpness_list):
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"""Convert a list of sharpness values into mock capture objects.
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:param sharpness_list: A list of numeric sharpness values.
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:returns: A list of MockCapture instances with sequential buffer IDs.
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"""
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return [MockCapture(s, i) for i, s in enumerate(sharpness_list)]
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def load_cases():
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"""Load the sharpness data from the json.
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Includes the sharpnesses to test, manually written labels
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on the required result, and whether the test is allowed to
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fail. This ensures future tests will flag any regression on
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tests while allowing improvements.
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"""
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with open(DATA_PATH) as f:
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data = json.load(f)
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params = []
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for i, case in enumerate(data):
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expected = case["label"]
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# Allow multiple acceptable labels
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if not isinstance(expected, list):
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expected = [expected]
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marks = []
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if case.get("allow_failure", False):
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marks.append(pytest.mark.xfail(reason="Known failing case"))
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params.append(
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pytest.param(
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case["sharpnesses"],
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expected,
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marks=marks,
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id=f"case_{i}",
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)
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)
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return params
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@pytest.mark.parametrize(("sharpnesses", "expected"), load_cases())
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def test_stack_labelling(sharpnesses, expected):
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"""Test stack classification accuracy against labelled sharpness cases.
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This test loads the test from load_cases and evaluates
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the classification returned by `check_stack_result`.
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The test ensures that only cases marked with "allow_failure: true" can fail.
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Expected labels may be a single value or a list of acceptable values.
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"""
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autofocus_thing = create_thing_without_server(AutofocusThing, mock_all_slots=True)
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captures = make_captures(sharpnesses)
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result, _ = autofocus_thing.check_stack_result(captures, check_turning_points=False)
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assert result in expected
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