Move unit tests to their own sub-dir in tests
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Julian Stirling
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35 changed files with 6 additions and 7 deletions
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"""Test the scan planning algorithms of the Microscope.
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As well as low level function by function tests, this test suite also provides tests
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that simulate scanning a sample, checking that the expected path is followed.
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"""
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from copy import copy
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import pytest
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from openflexure_microscope_server import scan_planners
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from .utilities import scan_test_helpers
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def test_enforce_xy_tuple():
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"""Check that 2 value tuples (or ValueErrors) are always returned."""
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bad_len_vals = [[1], [], (1,), (2, 4, 4), [1, 4, 5, 7]]
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for value in bad_len_vals:
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with pytest.raises(ValueError, match="2 value tuple expected"):
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scan_planners.enforce_xy_tuple(value)
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bad_type_vals = ["hi", 1, {"this": "that"}, {1, 2}]
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for value in bad_type_vals:
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with pytest.raises(TypeError):
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scan_planners.enforce_xy_tuple(value)
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assert scan_planners.enforce_xy_tuple((1, 6)) == (1, 6)
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assert scan_planners.enforce_xy_tuple([1, 6]) == (1, 6)
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def test_enforce_xyz_tuple():
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"""Check that 3 value tuples (or ValueErrors) are always returned."""
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bad_len_vals = [[1], [], (1,), (2, 4), [1, 4, 5, 7]]
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for value in bad_len_vals:
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with pytest.raises(ValueError, match="3 value tuple expected"):
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scan_planners.enforce_xyz_tuple(value)
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bad_type_vals = ["hi!", 1, {"this": "that"}, {1, 2, 3}]
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for value in bad_type_vals:
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with pytest.raises(TypeError):
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scan_planners.enforce_xyz_tuple(value)
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assert scan_planners.enforce_xyz_tuple((1, 6, 2)) == (1, 6, 2)
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assert scan_planners.enforce_xyz_tuple([1, 6, 6]) == (1, 6, 6)
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def test_base_class_not_implemented():
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"""Check NotImplementedError is raised when initialising ScanPlanner directly."""
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initial_position = (100, 50)
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with pytest.raises(NotImplementedError):
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scan_planners.ScanPlanner(initial_position=initial_position)
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def test_v_basic_smart_spiral():
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"""Check that a SmartSpiral where the first image is not sample completes."""
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initial_position = (100, 50)
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planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
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planner = scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=planner_settings
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)
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# Create a planner. It shouldn't be complete.
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assert not planner.scan_complete
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# When we start it should want to stay in the initial pos and have
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# no z_estimate
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xy_pos, z_pos = planner.get_next_location_and_z_estimate()
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assert xy_pos == initial_position
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assert z_pos is None
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# Try to mark location as imaged with only xy_position
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with pytest.raises(ValueError, match="3 value tuple expected"):
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planner.mark_location_visited(xy_pos, imaged=False, focused=False)
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# scan still not complete
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assert not planner.scan_complete
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# if we mark this position as visited but not imaged
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planner.mark_location_visited(
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(xy_pos[0], xy_pos[1], 10), imaged=False, focused=False
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)
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# scan is now complete
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assert planner.scan_complete
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# if scan is complete, asking for the next location returns an error
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with pytest.raises(RuntimeError):
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planner.get_next_location_and_z_estimate()
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def test_bad_smart_spiral_settings():
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"""Check that KeyError is raised when SmartSpiral is given bad settings."""
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initial_position = (100, 50)
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# Class init should raise error if no planner_settings dictionary set
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msg = "SmartSpiral requires a planner_settings dictionary with keys"
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with pytest.raises(ValueError, match=msg):
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scan_planners.SmartSpiral(initial_position=initial_position)
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planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
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keys = ["dx", "dy", "max_dist"]
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# Class init should raise error if planner_settings is missing any key
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for delkey in keys:
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bad_planner_settings = copy(planner_settings)
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del bad_planner_settings[delkey]
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with pytest.raises(KeyError):
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scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=bad_planner_settings
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)
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# Class init should raise error if planner_settings if any value can't be cast
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# to int
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keys = ["dx", "dy", "max_dist"]
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for badkey in keys:
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bad_planner_settings = copy(planner_settings)
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bad_planner_settings[badkey] = "I can't be converted to an int"
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with pytest.raises(ValueError, match="invalid literal for int()"):
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scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=bad_planner_settings
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)
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def test_smart_spiral_first_few_pos():
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"""Test for correct data addition during initial scan positions.
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This is a very long test, not strictly a "unit" test. It checks step by step
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that data is added correctly for the first few positions in a scan. It is
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intended to catch basic issues if the algorithm is updated.
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"""
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initial_position = (100, 50)
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planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
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# Create a planner
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planner = scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=planner_settings
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)
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# it shouldn't start complete
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assert not planner.scan_complete
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# When we start it should want to stay in the initial pos and have
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# no z_estimate
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xy_pos1, z_pos1 = planner.get_next_location_and_z_estimate()
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assert xy_pos1 == initial_position
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assert z_pos1 is None
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# Set a focus value
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z_focus = 10
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xyz_pos1 = (xy_pos1[0], xy_pos1[1], z_focus)
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# if we mark this position as visited, imaged, and focused
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planner.mark_location_visited(xyz_pos1, imaged=True, focused=True)
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# scan is not complete
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assert not planner.scan_complete
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# Lists should have updated to add the position to histories
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assert xyz_pos1 in planner.imaged_locations
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assert xyz_pos1 in planner.focused_locations
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assert xy_pos1 in planner.path_history
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# remove from planned
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assert xy_pos1 not in planner.remaining_locations
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# Add 4 new points to planned
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assert (100, 0) in planner.remaining_locations
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assert (100, 100) in planner.remaining_locations
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assert (150, 50) in planner.remaining_locations
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assert (50, 50) in planner.remaining_locations
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assert len(planner.remaining_locations) == 4
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# Now the next location is updated
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xy_pos2, z_pos2 = planner.get_next_location_and_z_estimate()
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# move in negative x-dir first
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assert xy_pos2 == (50, 50)
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# Focus set from closest point
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assert z_pos2 is z_focus
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xyz_pos2 = (xy_pos2[0], xy_pos2[1], z_focus)
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# if we mark this position as visited, imaged, and NOT focused
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planner.mark_location_visited(xyz_pos2, imaged=True, focused=False)
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# Check this position remove from planned
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assert xy_pos2 not in planner.remaining_locations
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# Check original position not re-added
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assert xy_pos1 not in planner.remaining_locations
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# 3 old points still planned
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assert (100, 0) in planner.remaining_locations
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assert (100, 100) in planner.remaining_locations
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assert (150, 50) in planner.remaining_locations
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# Add 3 new points to planned
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assert (0, 50) in planner.remaining_locations
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assert (50, 100) in planner.remaining_locations
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assert (50, 0) in planner.remaining_locations
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assert len(planner.remaining_locations) == 6
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# Now the next location is updated
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xy_pos3, z_pos3 = planner.get_next_location_and_z_estimate()
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# move in negative y-dir first next
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assert xy_pos3 == (50, 0)
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# Focus still set as before
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assert z_pos3 is z_focus
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# Check that the closest focus site to pos3 is pos 1 as
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# pos 2 is not focussed
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assert planner.closest_focus_site(xy_pos3) == xyz_pos1
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new_z_focus = 20
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xyz_pos3 = (xy_pos3[0], xy_pos3[1], new_z_focus)
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# Finally check that if this is focused...
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planner.mark_location_visited(xyz_pos3, imaged=True, focused=True)
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# ... then the new 4th point ...
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xy_pos4, z_pos4 = planner.get_next_location_and_z_estimate()
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# ...(100, 0)...
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assert xy_pos4 == (100, 0)
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# ... and it should get its focus from the lowest neighbouring point
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assert z_pos4 is z_focus
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assert planner.closest_focus_site(xy_pos4) == xyz_pos3
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def test_smart_spiral_stops_on_max_dist():
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"""Test that if max distance is reached smart spiral really does stop."""
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initial_position = (0, 0)
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planner_settings = {"dx": 100, "dy": 100, "max_dist": 1000}
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# Create a planner
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planner = scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=planner_settings
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)
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while not planner.scan_complete:
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xy_pos, _ = planner.get_next_location_and_z_estimate()
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xyz_pos = (xy_pos[0], xy_pos[1], 0)
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planner.mark_location_visited(xyz_pos, imaged=True, focused=True)
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# Estimate of radius = 10 scans, pir^2 = 314 images. In reality it works out as
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# 317
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assert len(planner.path_history) == 317
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def test_mark_wrong_location():
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"""Check that an error is raised if a scan marks the wrong location as visited."""
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initial_position = (100, 50)
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planner_settings = {"dx": 50, "dy": 50, "max_dist": 10000}
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# Create a planner
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planner = scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=planner_settings
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)
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xy_pos, _ = planner.get_next_location_and_z_estimate()
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# Trying to mark the wrong location as visited raises error
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wrong_xyz_pos = (xy_pos[0] + 1, xy_pos[1], 0)
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with pytest.raises(RuntimeError):
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planner.mark_location_visited(wrong_xyz_pos, imaged=True, focused=True)
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def test_closest_focus_with_large_numbers():
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"""Tests to check that everything works well with huge numbers of steps.
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The number of steps gets very large on the micorscope. But most of the tests
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above use smaller numbers for clarity.
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"""
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initial_position = (0, 0)
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# Set this up, but we won't use the settings
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planner_settings = {"dx": 10000, "dy": 10000, "max_dist": 100000}
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# Create a planner
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planner = scan_planners.SmartSpiral(
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initial_position=initial_position, planner_settings=planner_settings
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)
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# Directly overwrite the private path history locations list for test
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# For two points 1m points away it should choose the last as they are equal
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planner._path_history = [
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scan_planners.VisitedScanLocation((1000000, 0, 0), imaged=True, focused=True),
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scan_planners.VisitedScanLocation((0, 1000000, 0), imaged=True, focused=True),
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]
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assert planner.closest_focus_site((0, 0)) == (0, 1000000, 0)
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# Try similar
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planner._path_history = [
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scan_planners.VisitedScanLocation((1234567, 0, 0), imaged=True, focused=True),
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scan_planners.VisitedScanLocation((-1234567, 0, 0), imaged=True, focused=True),
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]
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assert planner.closest_focus_site((0, 0)) == (-1234567, 0, 0)
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# Make the first point 1 step closer
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planner._path_history = [
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scan_planners.VisitedScanLocation((1234566, 0, 0), imaged=True, focused=True),
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scan_planners.VisitedScanLocation((-1234567, 0, 0), imaged=True, focused=True),
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]
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assert planner.closest_focus_site((0, 0)) == (1234566, 0, 0)
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def test_example_smart_spiral():
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"""Test the smart spiral scan algorithm on the different sample types.
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The sample types:
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* ``regular``
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* ``lobed``
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* ``core"``
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These are defined in scan_test_helpers.load_sample_points
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This will fail if the locations or path between locations visited has changed
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for any of the samples listed.
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"""
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example_samples = [
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"regular",
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"lobed",
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"core",
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]
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for sample_name in example_samples:
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_, planner = scan_test_helpers.example_smart_spiral(sample_name)
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expected_planner = (
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scan_test_helpers.get_expected_result_for_example_smart_spiral(sample_name)
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)
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assert planner.path_history == expected_planner.path_history
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assert planner.imaged_locations == expected_planner.imaged_locations
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