Adjust CSM Thing to allow calculation of stage coords from img coords and use this in stage measure

Using this stops the z-axis being flipped when the off diagonal elements of the CSM are different
signs.

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -268,10 +268,18 @@ class CameraStageMapper(lt.Thing):
         an image usually helps resolve any ambiguity.
         """
         self.assert_calibrated()
+        stage.move_relative(**self.convert_image_to_stage_coordinates(x=x, y=y))
+
+    @lt.thing_action
+    def convert_image_to_stage_coordinates(
+        self, x: float, y: float
+    ) -> Mapping[str, int]:
+        """Convert image coordinates to stage coordinates."""
+        self.assert_calibrated()
         relative_move: np.ndarray = np.dot(
             np.array([y, x]), np.array(self.image_to_stage_displacement_matrix)
         )
-        stage.move_relative(x=relative_move[0], y=relative_move[1])
+        return {"x": int(relative_move[0]), "y": int(relative_move[1])}
 
     @lt.thing_property
     def thing_state(self) -> Mapping[str, Any]:

src/openflexure_microscope_server/things/stage_measure.py

@@ -74,30 +74,23 @@ class RomDataTracker:
 
     def predict_z_displacement(
         self,
-        movement: dict[str, int],
+        axis: Literal["x", "y"],
+        stage_movement: dict[str, int],
         stage_position: dict[str, int],
-        csm_matrix: list[list[int]],
     ) -> int:
         """Predict the z-displacement needed for a given movement.
 
-        :param movement: The movement to be performed in image coordinates.
+        :param axis: The axis which is being measured. This must be 'x' or 'y'.
+        :param stage_movement: The movement to be performed in stage coordinates.
         :param stage_position: The current stage position in stage coordinates.
-        :param csm_matrix: The camera stage mapping matrix.
         :returns: The predicted relative z displacement needed to stay in focus.
         """
-        pixel_step = {
+        # x or y positions
-            "x": 1 / csm_matrix[0][1],
+        lateral_positions = [i[axis] for i in self.stage_coords]
-            "y": 1 / csm_matrix[1][0],
-        }
-
-        axis = _axis_from_movement_dict(movement)
-
-        lateral_positions = [i[axis] for i in self.stage_coords]  # x or y positions
         z_positions = [i["z"] for i in self.stage_coords]
         fit_params, *_others = curve_fit(quadratic, lateral_positions, z_positions)
-        z_dest = quadratic(
+        z_dest = quadratic(stage_position[axis] + stage_movement[axis], *fit_params)
-            stage_position[axis] + (movement[axis] / pixel_step[axis]), *fit_params
+
-        )
         return int(z_dest - stage_position["z"])
 
 
@@ -248,7 +241,6 @@ class RangeofMotionThing(lt.Thing):
                 self._big_z_corrected_movement(
                     axis=axis, direction=direction, rom_deps=rom_deps
                 )
-
                 # Autofocus and record position
                 rom_deps.autofocus.looping_autofocus(dz=800)
                 self._rom_data.stage_coords.append(rom_deps.stage.position)
@@ -334,7 +326,6 @@ class RangeofMotionThing(lt.Thing):
         )
         for _loop in range(5):
             offset = self._move_and_measure(movement=movement, rom_deps=rom_deps)
-
             rom_deps.logger.info(f"Offset measured as {offset[axis]}")
 
             self._rom_data.record_movement(rom_deps.stage.position, offset)
@@ -351,16 +342,19 @@ class RangeofMotionThing(lt.Thing):
         :param direction: The direction to move in.
         :param rom_deps: All dependencies that were passed to the calling Action
         """
-        big_movement = self._movement_in_img_coords(
+        movement = self._movement_in_img_coords(
             fov_perc=BIG_STEP, axis=axis, direction=direction
         )
+        # Convert to stage coordinates
+        stage_movemenet = rom_deps.csm.convert_image_to_stage_coordinates(**movement)
+
         z_disp = self._rom_data.predict_z_displacement(
-            movement=big_movement,
+            axis=axis,
+            stage_movement=stage_movemenet,
             stage_position=rom_deps.stage.position,
-            csm_matrix=rom_deps.csm.image_to_stage_displacement_matrix,
         )
         rom_deps.stage.move_relative(z=z_disp)
-        rom_deps.csm.move_in_image_coordinates(**big_movement)
+        rom_deps.csm.move_in_image_coordinates(**movement)
 
     def _stage_still_moves(
         self,

tests/test_stage_measure.py

@@ -45,7 +45,7 @@ def increasing_xyz_dict_generator(*_args, **_kwargs):
 def csm_matrix():
     """Return an example CSM matrix."""
     return [
-        [0.03061156624485296, 1.8031242270940833],
+        [0.03061156624485296, -1.8031242270940833],
         [1.773236372778601, 0.006660431608601435],
     ]
 
@@ -70,12 +70,12 @@ def example_rom_data():
     return rom_data
 
 
-def test_predict_z(csm_matrix, example_rom_data):
+def test_predict_z(example_rom_data):
     """Check that the prediction for the next z position is correct."""
     mock_z_diff = example_rom_data.predict_z_displacement(
-        movement={"x": 2908, "y": 0},
+        axis="x",
+        stage_movement={"x": 5243, "y": 0},
         stage_position={"x": 3635, "y": 10, "z": 617},
-        csm_matrix=csm_matrix,
     )
     expected_z_diff = 1343
     assert mock_z_diff == expected_z_diff
@@ -157,9 +157,16 @@ def rom_thing(example_rom_data) -> stage_measure.RangeofMotionThing:
 @pytest.fixture
 def mock_rom_deps(csm_matrix, mocker) -> stage_measure.RomDeps:
     """Return a RomDeps object full of mocks, except the logger which is LOGGER."""
+
+    def apply_csm(x: float, y: float) -> dict[str, int]:
+        """Convert image coordinates to stage coordinates."""
+        vec = np.dot(np.array([y, x]), np.array(csm_matrix))
+        return {"x": int(vec[0]), "y": int(vec[1])}
+
     mock_csm = mocker.Mock()
     # Set up mock csm to return a CSM matrix
     mock_csm.image_to_stage_displacement_matrix = csm_matrix
+    mock_csm.convert_image_to_stage_coordinates.side_effect = apply_csm
 
     return stage_measure.RomDeps(
         autofocus=mocker.Mock(),
@@ -367,7 +374,7 @@ def test_big_z_corrected_movement(rom_thing, mock_rom_deps):
     assert "x" not in move_kwargs
     assert "y" not in move_kwargs
     assert "z" in move_kwargs
-    move_kwargs["z"] = 1162
+    assert move_kwargs["z"] == 1148
 
     # And one move in image coordinates
     assert mock_rom_deps.csm.move_in_image_coordinates.call_count == 1