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Initial commit, splitting params into focus, capture, stack

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Joe Knapper 2026-02-18 17:55:23 +00:00 • committed by Julian Stirling
parent de08bb1740
commit e750129de2
4 changed files with 150 additions and 76 deletions
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4
tests/unit_tests/test_scan_workflows.py
View file

@ -130,7 +130,7 @@ def test_histo_workflow_settings_generation(histo_workflow, mocker):
assert workflow_settings.dx == 123
assert workflow_settings.dy == 456
# And that the input image dir is passed to stack the stack parameter for saving
assert workflow_settings.smart_stack_params.images_dir == "/this/img_dir"
assert workflow_settings.capture_params.images_dir == "/this/img_dir"
# A CSM that is "normal" changing from camera maxtrix coordinates (y,x) to normal
@ -196,7 +196,7 @@ def test_histo_pre_scan_routine(histo_workflow, mocker):
# Rather than create a whole Setting class, just create a mock with the value
# we need set
mock_settings = mocker.Mock()
mock_settings.smart_stack_params.autofocus_dz = 1234
mock_settings.autofocus_params.dz = 1234
# Run the function
histo_workflow.pre_scan_routine(mock_settings)
# Check the autofocus was run using the mocked slot.

46
tests/unit_tests/test_stack.py
View file

@ -66,12 +66,7 @@ def test_stack_params_validation(save_ims, extra_ims):
# to do automatically in hypothesis. This clamps the number between 3 and 9.
min_images_to_test = max(min(save_ims + extra_ims, 9), 3)
SmartStackParams(
stack_dz=50,
images_to_save=save_ims,
min_images_to_test=min_images_to_test,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
stack_dz=50, images_to_save=save_ims, min_images_to_test=min_images_to_test
)
@ -96,9 +91,6 @@ def test_stack_params_not_enough_test_images(save_ims, extra_ims):
stack_dz=50,
images_to_save=save_ims,
min_images_to_test=save_ims + extra_ims,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
)
@ -121,9 +113,6 @@ def test_stack_params_negative_images_to_save(save_ims, extra_ims):
stack_dz=50,
images_to_save=save_ims,
min_images_to_test=save_ims + extra_ims,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
)
@ -147,9 +136,6 @@ def test_even_min_images_to_test(save_ims, extra_ims):
stack_dz=50,
images_to_save=save_ims,
min_images_to_test=save_ims + extra_ims,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
)
@ -171,9 +157,6 @@ def test_even_images_to_save(save_ims, extra_ims):
stack_dz=50,
images_to_save=save_ims,
min_images_to_test=save_ims + extra_ims,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
)
@ -183,12 +166,7 @@ def test_computed_stack_params():
Not using hypothesis or we will just copy in the same formulas.
"""
stack_parameters = SmartStackParams(
stack_dz=50,
images_to_save=5,
min_images_to_test=9,
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
stack_dz=50, images_to_save=5, min_images_to_test=9
)
assert stack_parameters.stack_z_range == 8 * 50
@ -279,9 +257,7 @@ def test_create_stack(histo_scan_workflow, caplog):
initial_min_images_to_test = histo_scan_workflow.stack_min_images_to_test
initial_images_to_save = histo_scan_workflow.stack_images_to_save
with caplog.at_level(logging.INFO):
stack_params = histo_scan_workflow.create_smart_stack_params(
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params = histo_scan_workflow.create_smart_stack_params()
assert len(caplog.records) == 0
assert histo_scan_workflow.stack_min_images_to_test == initial_min_images_to_test
@ -308,9 +284,7 @@ def test_coercing_stack_test_ims(
histo_scan_workflow.stack_min_images_to_test = initial_test_ims
with caplog.at_level(logging.WARNING):
stack_params = histo_scan_workflow.create_smart_stack_params(
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params = histo_scan_workflow.create_smart_stack_params()
assert len(caplog.records) == 1
assert str(caplog.records[0].msg).startswith(expected_log_start)
@ -338,9 +312,7 @@ def test_coercing_stack_save_ims(
histo_scan_workflow.stack_images_to_save = initial_save_ims
with caplog.at_level(logging.WARNING):
stack_params = histo_scan_workflow.create_smart_stack_params(
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params = histo_scan_workflow.create_smart_stack_params()
assert len(caplog.records) == 1
assert str(caplog.records[0].msg).startswith(expected_log_start)
@ -353,9 +325,7 @@ def test_coercing_stack_save_ims(
@pytest.mark.parametrize("pass_on", [1, 2, 3, 4])
def test_run_smart_stack(pass_on, histo_scan_workflow, autofocus_thing, mocker):
"""Test Running smart stack with the stack passing on different attempts."""
stack_params = histo_scan_workflow.create_smart_stack_params(
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params = histo_scan_workflow.create_smart_stack_params()
assert stack_params.max_attempts == 3
# Set up returns from z-stack
@ -417,9 +387,7 @@ def setup_and_run_smart_z_stack(
is a list, it will be set as a side effect (and should be a list of tuples of
results). If it a tuple (or anything else), it is set as a return value.
"""
stack_params = histo_scan_workflow.create_smart_stack_params(
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params = histo_scan_workflow.create_smart_stack_params()
stack_params.settling_time = 0 # Don't settle or tests take forever.
autofocus_thing.capture_stack_image = mocker.Mock()