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Julian Stirling 2025-07-10 17:57:43 +01:00
parent e33fecaef0
commit 7e6017f648
25 changed files with 113 additions and 85 deletions
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2
tests/mock_things/__init__.py
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@ -1,5 +1,5 @@
"""A package of test module providing mock Things for testing.
The mock things do not subclass the origninal things to minimise the inflation of
The mock things do not subclass the original things to minimise the inflation of
test coverage.
"""

4
tests/test_camera_buffer.py
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@ -113,7 +113,7 @@ def test_buffer_size_changing():
misc_image3 = random_image()
buffer_id1 = mem_buf.add_image(misc_image1, buffer_max=3)
buffer_id2 = mem_buf.add_image(misc_image2, buffer_max=3)
# Third capture doen't set buffer size, so it will be reset
# Third capture doesn't set buffer size, so it will be reset
buffer_id3 = mem_buf.add_image(misc_image3)
# As buffer size was reset, images 1 and 2 are deleted
with pytest.raises(NoImageInMemoryError):
@ -201,7 +201,7 @@ def test_get_metadata_too():
# Preallocate zipped data, to avoid long confusing lines
zipped = zip(images, metadatas, buffer_ids)
# Check both image and metdata
# Check both image and metadata
for i, (image, metadata, buffer_id) in enumerate(zipped):
returned_image, returned_metadata = mem_buf.get_image(buffer_id)
assert image is returned_image

42
tests/test_scan_planners.py
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@ -37,24 +37,24 @@ def test_enforce_xyz_tuple():
def test_base_class_not_implemented():
"""Check NotImplementedError is raised when initialising ScanPlanner directly."""
intial_position = (100, 50)
initial_position = (100, 50)
with pytest.raises(NotImplementedError):
scan_planners.ScanPlanner(intial_position=intial_position)
scan_planners.ScanPlanner(initial_position=initial_position)
def test_v_basic_smart_spiral():
"""Check that a SmartSpiral where the first image is not sample completes."""
intial_position = (100, 50)
initial_position = (100, 50)
planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
# Create a planner. It shouldn't be complete.
assert not planner.scan_complete
# When we start it should want to stay in the inital pos and have
# When we start it should want to stay in the initial pos and have
# no z_estimate
xy_pos, z_pos = planner.get_next_location_and_z_estimate()
assert xy_pos == intial_position
assert xy_pos == initial_position
assert z_pos is None
# Try to mark location as imaged with only xy_position
@ -76,11 +76,11 @@ def test_v_basic_smart_spiral():
def test_bad_smart_spiral_settings():
"""Check that KeyError is raised when SmartSpiral is given bad settings."""
intial_position = (100, 50)
initial_position = (100, 50)
# Class init should raise error if no planner_settings dictionary set
with pytest.raises(ValueError):
scan_planners.SmartSpiral(intial_position=intial_position)
scan_planners.SmartSpiral(initial_position=initial_position)
planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
keys = ["dx", "dy", "max_dist"]
@ -91,7 +91,7 @@ def test_bad_smart_spiral_settings():
del bad_planner_settings[delkey]
with pytest.raises(KeyError):
scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=bad_planner_settings
initial_position=initial_position, planner_settings=bad_planner_settings
)
# Class init should raise error if planner_settings if any value can't be cast
@ -102,7 +102,7 @@ def test_bad_smart_spiral_settings():
bad_planner_settings[badkey] = "I can't be converted to an int"
with pytest.raises(ValueError):
scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=bad_planner_settings
initial_position=initial_position, planner_settings=bad_planner_settings
)
@ -113,18 +113,18 @@ def test_smart_spiral_first_few_pos():
that data is added correctly for the first few positions in a scan. It is
intended to catch basic issues if the algorithm is updated.
"""
intial_position = (100, 50)
initial_position = (100, 50)
planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
# Create a planner
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
# it shouldn't start complete
assert not planner.scan_complete
# When we start it should want to stay in the inital pos and have
# When we start it should want to stay in the initial pos and have
# no z_estimate
xy_pos1, z_pos1 = planner.get_next_location_and_z_estimate()
assert xy_pos1 == intial_position
assert xy_pos1 == initial_position
assert z_pos1 is None
# Set a focus value
z_focus = 10
@ -201,11 +201,11 @@ def test_smart_spiral_first_few_pos():
def test_smart_spiral_stops_on_max_dist():
"""Test that if max distance is reached smart spiral really does stop."""
intial_position = (0, 0)
initial_position = (0, 0)
planner_settings = {"dx": 100, "dy": 100, "max_dist": 1000}
# Create a planner
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
while not planner.scan_complete:
xy_pos, _ = planner.get_next_location_and_z_estimate()
@ -219,11 +219,11 @@ def test_smart_spiral_stops_on_max_dist():
def test_mark_wrong_location():
"""Check that an error is raised if a scan marks the wrong location as visited."""
intial_position = (100, 50)
initial_position = (100, 50)
planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
# Create a planner
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
xy_pos, _ = planner.get_next_location_and_z_estimate()
@ -233,18 +233,18 @@ def test_mark_wrong_location():
planner.mark_location_visited(wrong_xyz_pos, imaged=True, focused=True)
def test_closest_focus_wth_large_numbers():
def test_closest_focus_with_large_numbers():
"""Tests to check that everything works well with huge numbers of steps.
The number of steps gets very large on the micorscope. But most of the tests
above use smaller numbers for clarity.
"""
intial_position = (0, 0)
initial_position = (0, 0)
# Set this up, but we won't use the settings
planner_settings = {"dx": 10000, "dy": 10000, "max_dist": 100000}
# Create a planner
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
# Directly overwrite the private focussed locations list for test

10
tests/test_smart_scan.py
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@ -65,7 +65,7 @@ def test_initial_properties(smart_scan_thing):
def test_inaccessible_scan_methods(smart_scan_thing):
"""Test that method with @_scan_running decorator is inaccessible.
The @_scan_running decorator makes these functions inacessible unless
The @_scan_running decorator makes these functions inaccessible unless
a scan is running.
"""
with pytest.raises(ScanNotRunningError):
@ -151,7 +151,7 @@ def test_delete_all_scans(smart_scan_thing, caplog):
assert len(caplog.records) == 0
def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None):
def _run_only_outer_scan(adjust_initial_state: Optional[Callable] = None):
"""Create a subclass of SmartScanThing to mock _run_scan and run sample_scan.
This should do all the set up for a scan, move into the mocked
@ -199,8 +199,8 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None):
# mock smart scan thing
mock_ss_thing = MockedSmartScanThing(SCAN_DIR)
if adjust_inital_state is not None:
adjust_inital_state(mock_ss_thing)
if adjust_initial_state is not None:
adjust_initial_state(mock_ss_thing)
exec_info = None
try:
@ -232,7 +232,7 @@ def _run_only_outer_scan(adjust_inital_state: Optional[Callable] = None):
assert mock_ss_thing._scan_images_taken is None
# Return the mock thing for further state testing, and the
# exec_info of any uncaught exeptions that were raised
# exec_info of any uncaught exceptions that were raised
return mock_ss_thing, exec_info

6
tests/utilities/scan_test_helpers.py
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@ -90,7 +90,7 @@ def interp_closed_path(xy_points: list[tuple[int, int]], n_points: int) -> MatPa
Modified from:
https://stackoverflow.com/questions/33962717/interpolating-a-closed-curve-using-scipy
"""
# Use zip to seperate x and y points into tuples
# Use zip to separate x and y points into tuples
x, y = zip(*xy_points)
# Append first point and convert to array
@ -119,10 +119,10 @@ def example_smart_spiral(
xy_sample_points = load_sample_points(sample_name)
sample = FakeSample(xy_sample_points)
img_size = (1000, 1000)
intial_position = (0, 0)
initial_position = (0, 0)
planner_settings = {"dx": 1200, "dy": 800, "max_dist": 100000}
planner = scan_planners.SmartSpiral(
intial_position=intial_position, planner_settings=planner_settings
initial_position=initial_position, planner_settings=planner_settings
)
while not planner.scan_complete: