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Remove unneeded moves from basic stack

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Update tests with better comments

Test a stack with both backlash compensation and offset
This commit is contained in:
jaknapper 2026-02-24 12:35:41 +00:00 • committed by Julian Stirling
parent c28afe30ab
commit 565204da59
2 changed files with 129 additions and 35 deletions
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145
tests/unit_tests/test_stack.py
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@ -690,7 +690,8 @@ def fake_move_relative(autofocus_thing):
def test_run_basic_stack_simple(
autofocus_thing, mocker, fake_capture, fake_move_relative
):
"""Basic stack captures correct number of images and saves them."""
"""Basic stack captures the correct number of images at correct Z positions."""
# Stack parameters: small 3-image stack, 10-step spacing
stack_params = StackParams(
stack_dz=10,
images_to_save=3,
@ -699,16 +700,17 @@ def test_run_basic_stack_simple(
origin=StackOrigin.START,
)
# Capture parameters for the test
capture_params = mocker.Mock()
capture_params.images_dir = "dummy"
capture_params.save_resolution = (100, 100)
# Reset stage position
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 0}
# Patch capture and stage movement
autofocus_thing.capture_stack_image = mocker.Mock(side_effect=fake_capture)
autofocus_thing._stage.move_relative = mocker.Mock(side_effect=fake_move_relative)
autofocus_thing._cam.save_from_memory = mocker.Mock()
autofocus_thing._cam.clear_buffers = mocker.Mock()
@ -717,12 +719,36 @@ def test_run_basic_stack_simple(
capture_parameters=capture_params,
)
assert z_positions == [0, 10, 20]
assert final_z == 30
# Expect 3 captures from the stack at Z = 0, 10, 20
assert z_positions == [0, 10, 20], (
"Z positions captured do not match expected values"
)
assert final_z == 20, "Final Z position is incorrect"
# Check that capture_stack_image was called exactly 3 times
assert autofocus_thing.capture_stack_image.call_count == 3, (
"Incorrect number of captures"
)
# Check that stage moved correctly (should match z_positions relative increments)
moves = [
call.kwargs["z"] for call in autofocus_thing._stage.move_relative.call_args_list
]
# Two moves in the stack, no other movement as stack began from the starting position
expected_moves = [10, 10]
assert moves == expected_moves, (
"Stage move_relative calls do not match expected increments"
)
def test_run_basic_stack_center_origin(autofocus_thing, mocker):
"""Stack should shift start position when origin is CENTER."""
def test_run_basic_stack_center_origin(
autofocus_thing, mocker, fake_capture, fake_move_relative
):
"""Stack should shift start position when origin is CENTER.
CENTER should cause the stage to move down by half the z range before
the stack begins.
"""
stack_params = StackParams(
stack_dz=10,
images_to_save=5,
@ -735,28 +761,39 @@ def test_run_basic_stack_center_origin(autofocus_thing, mocker):
capture_params.images_dir = "dummy"
capture_params.save_resolution = (100, 100)
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 100}
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 0}
autofocus_thing.capture_stack_image = mocker.Mock(
return_value=CaptureInfo("id", {"x": 0, "y": 0, "z": 0}, 1)
)
# Patch capture and stage movement
autofocus_thing.capture_stack_image = mocker.Mock(side_effect=fake_capture)
autofocus_thing._stage.move_relative = mocker.Mock(side_effect=fake_move_relative)
autofocus_thing._cam.save_from_memory = mocker.Mock()
autofocus_thing._cam.clear_buffers = mocker.Mock()
autofocus_thing._stage.move_relative = mocker.Mock()
autofocus_thing.run_basic_stack(stack_params, capture_params)
# Run stack
final_z, z_positions = autofocus_thing.run_basic_stack(
stack_parameters=stack_params,
capture_parameters=capture_params,
)
total_range = 10 * (5 - 1) # 40
expected_offset = -total_range // 2 # -20
# Calculate expected starting offset - moving down by half the stack height
total_range = 10 * (5 - 1)
expected_offset = -total_range // 2
# First move should be to CENTER offset (with backlash logic)
# First move should apply center offset
first_call = autofocus_thing._stage.move_relative.call_args_list[0]
assert first_call.kwargs["z"] == expected_offset
assert first_call.kwargs["z"] == expected_offset, (
"Center origin offset not applied correctly"
)
# Check 5 images captured, at expected heights
assert z_positions == [-20, -10, 0, 10, 20], (
"Z positions captured do not match expected values"
)
assert final_z == 20, "Final Z position is incorrect"
def test_run_basic_stack_backlash_applied(autofocus_thing, mocker, fake_capture):
"""Backlash correction should overshoot and move back."""
"""Backlash correction should overshoot first, then move back before starting stack."""
stack_params = StackParams(
stack_dz=10,
images_to_save=3,
@ -765,12 +802,12 @@ def test_run_basic_stack_backlash_applied(autofocus_thing, mocker, fake_capture)
origin=StackOrigin.START,
)
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 0}
capture_params = mocker.Mock()
capture_params.images_dir = "dummy"
capture_params.save_resolution = (100, 100)
autofocus_thing.capture_stack_image = mocker.Mock(side_effect=fake_capture)
autofocus_thing._stage.move_relative = mocker.Mock()
autofocus_thing._cam.save_from_memory = mocker.Mock()
autofocus_thing._cam.clear_buffers = mocker.Mock()
@ -779,14 +816,54 @@ def test_run_basic_stack_backlash_applied(autofocus_thing, mocker, fake_capture)
calls = autofocus_thing._stage.move_relative.call_args_list
# First call = overshoot
assert calls[0].kwargs["z"] == -50
# Second call = move back
assert calls[1].kwargs["z"] == 50
# First move is overshoot for backlash
assert calls[0].kwargs["z"] == -50, "Backlash overshoot not applied correctly"
# Second move corrects back to start
assert calls[1].kwargs["z"] == 50, "Backlash correction move not applied correctly"
def test_run_basic_stack_backlash_and_offset(autofocus_thing, mocker, fake_capture):
"""Backlash correction and stack offset both applied.
Stack should begin by moving down by half the height of the stack,
plus backlash correction, then move up by backlash correction, then run the basic stack.
"""
stack_params = StackParams(
stack_dz=100,
images_to_save=3,
settling_time=0,
backlash_correction=50,
origin=StackOrigin.CENTER,
)
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 0}
capture_params = mocker.Mock()
capture_params.images_dir = "dummy"
capture_params.save_resolution = (100, 100)
autofocus_thing.capture_stack_image = mocker.Mock(side_effect=fake_capture)
autofocus_thing._stage.move_relative = mocker.Mock()
autofocus_thing._cam.save_from_memory = mocker.Mock()
autofocus_thing._cam.clear_buffers = mocker.Mock()
# Run stack
autofocus_thing.run_basic_stack(stack_params, capture_params)
calls = autofocus_thing._stage.move_relative.call_args_list
# First move is overshoot for backlash and stack offset
assert calls[0].kwargs["z"] == -150, "Combined overshoot not applied correctly"
# Second move corrects back to base of stack
assert calls[1].kwargs["z"] == 50, "Backlash correction move not applied correctly"
# Third move is the first move in the stack
assert calls[2].kwargs["z"] == 100, "Backlash correction move not applied correctly"
def test_run_basic_stack_end_origin(autofocus_thing, mocker, fake_capture):
"""END origin should shift stack fully negative before starting."""
"""END origin should shift stack down by full stack height before starting."""
stack_params = StackParams(
stack_dz=10,
images_to_save=4,
@ -795,19 +872,33 @@ def test_run_basic_stack_end_origin(autofocus_thing, mocker, fake_capture):
origin=StackOrigin.END,
)
autofocus_thing._stage.position = {"x": 0, "y": 0, "z": 0}
capture_params = mocker.Mock()
capture_params.images_dir = "dummy"
capture_params.save_resolution = (100, 100)
autofocus_thing.capture_stack_image = mocker.Mock(side_effect=fake_capture)
autofocus_thing._stage.move_relative = mocker.Mock()
autofocus_thing._cam.save_from_memory = mocker.Mock()
autofocus_thing._cam.clear_buffers = mocker.Mock()
autofocus_thing.run_basic_stack(stack_params, capture_params)
total_range = 10 * (4 - 1) # 30
# Calculate the stack offset based on StackOrigin.END - moving down by the full stack height
total_range = 10 * (4 - 1)
# First move should shift fully down
first_call = autofocus_thing._stage.move_relative.call_args_list[0]
assert first_call.kwargs["z"] == -total_range
assert first_call.kwargs["z"] == -total_range, (
"End origin offset not applied correctly"
)
# Check number of captures
assert autofocus_thing.capture_stack_image.call_count == 4, (
"Incorrect number of captures for END origin"
)
# Check final Z is equal to starting Z, as StackOrigin.END should finish at the starting height
final_z = autofocus_thing._stage.position["z"]
expected_final_z = 0
assert final_z == expected_final_z, "Final Z position for END origin incorrect"