Update testing for multiple sample shapes

src/openflexure_microscope_server/scan_planners.py

@@ -240,129 +240,6 @@ class ScanPlanner:
 
 
 class SmartSpiral(ScanPlanner):
-    """
-    This is a smart spiral scan that spirals out from the centre.
-
-    Each time and image is taken the four neighbouring images are added
-    to the list of poisitions to image (unless they are already listed or
-    tried). However if a location is not imaged due no sample being detected
-    then neibouring positions are not imaged.
-
-    The next image taken is the closes to the centre (considering the largest
-    of vertical or horizontal distance), ties are broken by the distance from
-    the current position.
-    """
-
-    _max_dist: int = 0
-    _dx: int = 0
-    _dy: int = 0
-
-    def _parse(self, planner_settings: Optional[dict] = None) -> None:
-        """
-        Parse SmartSpiral Settings. This should be a dictionary
-
-        "dx" - the movement size in x
-        "dy" - the movement size in y
-        "max_dist" - The maximum distance to a location can be from the centre.
-        """
-
-        expected_keys = ["max_dist", "dx", "dy"]
-        invalid_msg = "SmartSpiral requires a planner_settings dictionary with keys: "
-        if not planner_settings:
-            raise ValueError(invalid_msg + ",".join(expected_keys))
-        if not all(keys in planner_settings for keys in expected_keys):
-            raise KeyError(invalid_msg + ",".join(expected_keys))
-
-        self._dx = int(planner_settings["dx"])
-        self._dy = int(planner_settings["dy"])
-        self._max_dist = int(planner_settings["max_dist"])
-
-    def _intial_location_list(self) -> XYPosList:
-        """
-        Called on initalisation. Sets the initial list of locations for this scan planner
-
-        For smart spiral this is just the first point
-        """
-        return [self._initial_position]
-
-    def mark_location_visited(
-        self, xyz_pos: XYZPos, imaged: bool = True, focused: bool = True
-    ) -> None:
-        """
-        Mark the location as visited. Adjust extra positions accordingly
-
-        Args:
-            xyz_pos: the x_y_z position
-            imaged: true if an image was taken, false if not (due to background detect)
-            focused: true if autofocus completed successfully
-        """
-        # First call the base class to update the positions
-        super().mark_location_visited(xyz_pos, imaged, focused)
-
-        xy_pos = enforce_xy_tuple(xyz_pos[:2])
-        if imaged:
-            self._add_surrounding_positions(xy_pos)
-        self._re_sort_remaining_locations(xy_pos)
-
-    def _add_surrounding_positions(self, xy_pos: XYPos) -> None:
-        """
-        This adds the surrounding (4 point connectivity) positions
-        to the remaining locations if they are not too far away or
-        already planned or already visited
-        """
-        new_positions = [
-            (xy_pos[0] - self._dx, xy_pos[1]),
-            (xy_pos[0] + self._dx, xy_pos[1]),
-            (xy_pos[0], xy_pos[1] - self._dy),
-            (xy_pos[0], xy_pos[1] + self._dy),
-        ]
-
-        for new_pos in new_positions:
-            # Skip position if already planned or visited
-            if self.position_planned(new_pos) or self.position_visited(new_pos):
-                continue
-
-            dist = distance_between(new_pos, self._initial_position)
-            if dist > self._max_dist:
-                LOGGER.debug("Rejected moving to %s as it is out of range", new_pos)
-                continue
-            self._remaining_locations.append(new_pos)
-
-    def _re_sort_remaining_locations(self, current_pos: XYPos) -> None:
-        """
-        Sort the remaining positions besed on the current location
-        """
-
-        # Defined rather than use a lambda for readability
-        def sort_key(pos):
-            return self.moves_from_centre(pos), distance_between(current_pos, pos)
-
-        self._remaining_locations.sort(key=sort_key)
-
-    def moves_from_centre(
-        self,
-        xy_pos: XYPos,
-    ) -> float:
-        """
-        Return the number of moves from the centre in the x or y direction
-        whichever is largest
-
-        Args:
-        xy_pos: the position
-
-        Note this has been renamed from `steps_from_centre` as that implied
-        stepper motor steps not number of moves in a scan
-        """
-        move_size = np.array([self._dx, self._dy])
-        starting_pos = np.array(self._initial_position, dtype="float64")
-        current_pos = np.array(xy_pos, dtype="float64")
-
-        displacement_in_moves = (current_pos - starting_pos) / move_size
-
-        return np.max(np.abs(displacement_in_moves))
-
-
-class ShortSmartSpiral(ScanPlanner):
     """
     This is a smart spiral scan that spirals out from the centre, but prioritises
     short moves over rigidly sticking to minimising radius from the centre of the

tests/test_scan_planners.py

@@ -253,7 +253,22 @@ def test_closest_focus_wth_large_numbers():
 
 
 def test_example_smart_spiral():
-    _, planner = scan_test_helpers.example_smart_spiral()
-    expected_planner = scan_test_helpers.get_expected_result_for_example_smart_spiral()
-    assert planner.path_history == expected_planner.path_history
-    assert planner.imaged_locations == expected_planner.imaged_locations
+    """Test the smart spiral scan algorithm on the sample types listed
+    below and defined in scan_test_helpers.load_sample_points
+
+    Will fail if the locations or path between locations visited has changed
+    for any of the samples listed"""
+    example_samples = [
+        "regular",
+        "lobed",
+        "core",
+    ]
+    for sample_type in example_samples:
+        _, planner = scan_test_helpers.example_smart_spiral(sample=sample_type)
+        expected_planner = (
+            scan_test_helpers.get_expected_result_for_example_smart_spiral(
+                sample=sample_type
+            )
+        )
+        assert planner.path_history == expected_planner.path_history
+        assert planner.imaged_locations == expected_planner.imaged_locations

tests/utilities/scan_test_helpers.py

@@ -111,23 +111,19 @@ def interp_closed_path(xy_points: list[tuple[int, int]], n_points: int) -> MatPa
     return MatPath(path_points, closed=True)
 
 
-def example_smart_spiral() -> tuple[FakeSample, scan_planners.ScanPlanner]:
+def example_smart_spiral(
+    sample: str = "lobed",
+) -> tuple[FakeSample, scan_planners.ScanPlanner]:
     """
     Run an example scan and return the sample scanned and the planner object
     after scan is complete
     """
-    xy_sample_points = [
-        (-5000, -5000),
-        (-2000, 10000),
-        (1000, 2000),
-        (6000, 7000),
-        (9000, 2000),
-    ]
+    xy_sample_points = load_sample_points(sample=sample)
     sample = FakeSample(xy_sample_points)
     img_size = (1000, 1000)
     intial_position = (0, 0)
-    planner_settings = {"dx": 700, "dy": 700, "max_dist": 100000}
-    planner = scan_planners.ShortSmartSpiral(
+    planner_settings = {"dx": 1200, "dy": 800, "max_dist": 100000}
+    planner = scan_planners.SmartSpiral(
         intial_position=intial_position, planner_settings=planner_settings
     )
 
@@ -166,7 +162,7 @@ def profile_and_save_plot_for_example_smart_spiral():
     run_stats.print_stats("scan_planners.py")
 
 
-def update_example_smart_spiral_pickle():
+def update_example_smart_spiral_pickle(sample: str):
     """
     Pickle the ScanPlanner for the example_smart_spiral(),
     this is done so the history can be compared by testing to check
@@ -174,23 +170,54 @@ def update_example_smart_spiral_pickle():
 
     If the algorithm is purposefully changed then this will need to be
     run to update the pickle for the test to pass.
+
+    Takes sample, the sample type we have generated, so we can make a
+    pickle for each sample type
     """
-    pkl_fname = os.path.join(THIS_DIR, "example_smart_spiral.pkl")
+    pkl_fname = os.path.join(THIS_DIR, f"example_smart_spiral_{sample}.pkl")
     with open(pkl_fname, "wb") as pkl_file_obj:
-        _, planner = example_smart_spiral()
+        _, planner = example_smart_spiral(sample=sample)
         pickle.dump(planner, pkl_file_obj, pickle.HIGHEST_PROTOCOL)
 
 
-def get_expected_result_for_example_smart_spiral():
+def get_expected_result_for_example_smart_spiral(sample: str):
     """
     Return the expected ScanPlanner object for the example_smart_spiral(),
     this is pickled, so that it can be committed.
     """
-    pkl_fname = os.path.join(THIS_DIR, "example_smart_spiral.pkl")
+    pkl_fname = os.path.join(THIS_DIR, f"example_smart_spiral_{sample}.pkl")
     with open(pkl_fname, "rb") as pkl_file_obj:
         planner = pickle.load(pkl_file_obj)
     return planner
 
 
+def load_sample_points(sample: str):
+    """Returns the points to generate a FakeSample of sample type "sample" """
+    sample_options = {
+        "lobed": [
+            (-5000, -5000),
+            (-2000, 16000),
+            (1000, 2000),
+            (6000, 7000),
+            (9000, 2000),
+        ],
+        "regular": [
+            (-5000, -5000),
+            (-5000, 5000),
+            (5000, 5000),
+            (5000, -5000),
+        ],
+        "core": [
+            (-12000, 2000),
+            (-12000, 1000),
+            (0, -2000),
+            (10000, -2000),
+            (10000, -1000),
+            (1000, 0),
+        ],
+    }
+    return sample_options[sample]
+
+
 if __name__ == "__main__":
     profile_and_save_plot_for_example_smart_spiral()