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Fix confusion between (x,y) image coordinates and (y,x) matrix indicies

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This commit is contained in:
Julian Stirling 2025-11-05 12:27:49 +00:00
parent dcf4b0b383
commit f7d03d8c00
4 changed files with 70 additions and 78 deletions
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33
tests/test_stage_measure.py
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@ -12,7 +12,10 @@ import pytest
import labthings_fastapi as lt
from openflexure_microscope_server.things import stage_measure
from openflexure_microscope_server.utilities import apply_2d_matrix_to_mapping
from openflexure_microscope_server.things.camera_stage_mapping import (
csm_img_to_stage,
csm_stage_to_img,
)
LOGGER = logging.getLogger("mock-invocation_logger")
@ -163,15 +166,14 @@ def rom_thing(example_rom_data) -> stage_measure.RangeofMotionThing:
@pytest.fixture
def mock_rom_deps(csm_matrix, mocker) -> stage_measure.RomDeps:
"""Return a RomDeps object full of mocks, except the logger which is LOGGER."""
inverse_matrix = np.linalg.inv(csm_matrix)
def apply_csm(x: float, y: float, **_kwargs: float) -> dict[str, int]:
"""Convert image coordinates to stage coordinates."""
return apply_2d_matrix_to_mapping(csm_matrix, x=x, y=y, to_int=True)
return csm_img_to_stage(csm_matrix, x=x, y=y)
def un_apply_csm(x: float, y: float, **_kwargs: float) -> dict[str, float]:
"""Convert stage coordinates to image coordinates."""
return apply_2d_matrix_to_mapping(inverse_matrix, x=x, y=y, to_int=True)
return csm_stage_to_img(csm_matrix, x=x, y=y)
mock_cam = mocker.Mock()
mock_cam.image_is_sample.return_value = (True, "Mocked not measured.")
@ -194,12 +196,11 @@ def mock_rom_deps(csm_matrix, mocker) -> stage_measure.RomDeps:
@pytest.mark.parametrize(
("pos", "target_pos", "axis", "expected_dir"),
[
# X is flipped due to CSM sign
({"x": 5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", 1),
({"x": -5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", -1),
({"x": 0, "y": 0, "z": 0}, {"x": 5000, "y": 0, "z": 0}, "x", -1),
# Y is not flipped due to CSM sign
({"x": 0, "y": 5000, "z": 0}, {"x": 0, "y": 0, "z": 0}, "y", -1),
({"x": 5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", -1),
({"x": -5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", 1),
({"x": 0, "y": 0, "z": 0}, {"x": 5000, "y": 0, "z": 0}, "x", 1),
# Y is flipped due to CSM sign
({"x": 0, "y": 5000, "z": 0}, {"x": 0, "y": 0, "z": 0}, "y", 1),
],
)
def test_img_dir_from_stage_coords(
@ -223,11 +224,11 @@ def test_distance_in_img_percentage_err(rom_thing, mock_rom_deps):
@pytest.mark.parametrize(
("pos", "target_pos", "axis", "expected_perc"),
[
({"x": 5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", 346.625),
({"x": -5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", -346.625),
({"x": 0, "y": 0, "z": 0}, {"x": 5000, "y": 0, "z": 0}, "x", -346.625),
({"x": 5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", -352.44),
({"x": -5000, "y": 0, "z": 0}, {"x": 0, "y": 0, "z": 0}, "x", 352.44),
({"x": 0, "y": 0, "z": 0}, {"x": 5000, "y": 0, "z": 0}, "x", 352.44),
# Y is flipped due to CSM sign
({"x": 0, "y": 5000, "z": 0}, {"x": 0, "y": 0, "z": 0}, "y", -470.0),
({"x": 0, "y": 5000, "z": 0}, {"x": 0, "y": 0, "z": 0}, "y", 462.131),
],
)
def test_distance_in_img_percentage(
@ -236,7 +237,7 @@ def test_distance_in_img_percentage(
"""Check _distance_in_img_percentage calculates expected values based on mock CSM."""
mock_rom_deps.stage.position = pos
img_perc = rom_thing._distance_in_img_percentage(target_pos, axis, mock_rom_deps)
assert expected_perc == img_perc
assert round(img_perc, 3) == expected_perc
def test_offset_from(rom_thing, mock_rom_deps, mocker):
@ -703,7 +704,7 @@ def test_recentre_axis(true_on, rom_thing, mock_rom_deps, mocker):
This doesn't include deciding if we are centred or choosing the direction to move.
"""
## Start such that movement starts negative
mock_rom_deps.stage.position = {"x": -10000, "y": 10000, "z": 0}
mock_rom_deps.stage.position = {"x": 10000, "y": 10000, "z": 0}
mock_moves = mocker.patch.object(rom_thing, "_moves_for_z_prediction")
# Mock _recentre_decision so it returns (False, 1) a number of times then finally