Fix tests and also the bugs which caused the tests to fail

micro_manager/adaptivity/adaptivity.py

@@ -35,9 +35,6 @@ def __init__(self, configurator, logger) -> None:
             configurator.get_adaptivity_similarity_measure()
         )
 
-        self._active_sim_ids = np.array([], dtype=int)
-        self._inactive_sim_ids = np.array([], dtype=int)
-
     def _get_similarity_dists(
         self, dt: float, similarity_dists: np.ndarray, data: dict
     ) -> np.ndarray:

micro_manager/adaptivity/global_adaptivity.py

@@ -127,13 +127,6 @@ def compute_adaptivity(
             similarity_dists, is_sim_active, sim_is_associated_to
         )
 
-        self._active_sim_ids = np.where(
-            is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1]
-        )[0]
-        self._inactive_sim_ids = np.where(
-            is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1] == False
-        )[0]
-
         self._logger.info(
             "{} active simulations, {} inactive simulations".format(
                 np.count_nonzero(
@@ -148,27 +141,41 @@ def compute_adaptivity(
 
         return [similarity_dists, is_sim_active, sim_is_associated_to]
 
-    def get_active_sim_ids(self) -> np.ndarray:
+    def get_active_sim_ids(self, is_sim_active: np.array) -> np.ndarray:
         """
         Get the ids of active simulations.
 
+        Parameters
+        ----------
+        is_sim_active : numpy array
+            1D array having state (active or inactive) of each micro simulation
+
         Returns
         -------
         numpy array
             1D array of active simulation ids
         """
-        return self._active_sim_ids
+        return np.where(is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1])[
+            0
+        ]
 
-    def get_inactive_sim_ids(self) -> np.ndarray:
+    def get_inactive_sim_ids(self, is_sim_active: np.array) -> np.ndarray:
         """
         Get the ids of inactive simulations.
 
+        Parameters
+        ----------
+        is_sim_active : numpy array
+            1D array having state (active or inactive) of each micro simulation
+
         Returns
         -------
         numpy array
             1D array of inactive simulation ids
         """
-        return self._inactive_sim_ids
+        return np.where(
+            is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1] == False
+        )[0]
 
     def get_full_field_micro_output(
         self, adaptivity_data: list, micro_output: list

micro_manager/adaptivity/local_adaptivity.py

@@ -82,32 +82,39 @@ def compute_adaptivity(
             )
         )
 
-        self._active_sim_ids = np.where(is_sim_active)[0]
-        self._inactive_sim_ids = np.where(is_sim_active == False)[0]
-
         return [similarity_dists, is_sim_active, sim_is_associated_to]
 
-    def get_active_sim_ids(self) -> np.ndarray:
+    def get_active_sim_ids(self, is_sim_active) -> np.ndarray:
         """
         Get the ids of active simulations.
 
+        Parameters
+        ----------
+        is_sim_active : numpy array
+            1D array having state (active or inactive) of each micro simulation
+
         Returns
         -------
         numpy array
             1D array of active simulation ids
         """
-        return self._active_sim_ids
+        return np.where(is_sim_active)[0]
 
-    def get_inactive_sim_ids(self) -> np.ndarray:
+    def get_inactive_sim_ids(self, is_sim_active: np.array) -> np.ndarray:
         """
         Get the ids of inactive simulations.
 
+        Parameters
+        ----------
+        is_sim_active : numpy array
+            1D array having state (active or inactive) of each micro simulation
+
         Returns
         -------
         numpy array
             1D array of inactive simulation ids
         """
-        return self._inactive_sim_ids
+        return np.where(is_sim_active == False)[0]
 
     def get_full_field_micro_output(
         self, adaptivity_data: list, micro_output: list
@@ -119,6 +126,7 @@ def get_full_field_micro_output(
         ----------
         adaptivity_data : list
             List of numpy arrays:
+                similarity_dists (2D array having similarity distances between each micro simulation pair)
                 is_sim_active (1D array having state (active or inactive) of each micro simulation)
                 sim_is_associated_to (1D array with values of associated simulations of inactive simulations. Active simulations have None)
         micro_output : list
@@ -133,7 +141,9 @@ def get_full_field_micro_output(
 
         sim_is_associated_to = adaptivity_data[2]
 
-        for inactive_id in self._inactive_sim_ids:
+        inactive_sim_ids = self.get_inactive_sim_ids(adaptivity_data[1])
+
+        for inactive_id in inactive_sim_ids:
             micro_sims_output[inactive_id] = deepcopy(
                 micro_sims_output[sim_is_associated_to[inactive_id]]
             )

micro_manager/micro_manager.py

@@ -707,13 +707,19 @@ def _solve_micro_simulations_with_adaptivity(
                 self._data_for_adaptivity,
             )
 
-            active_sim_ids = self._adaptivity_controller.get_active_sim_ids()
+            active_sim_ids = self._adaptivity_controller.get_active_sim_ids(
+                adaptivity_data[1]
+            )
 
             for active_id in active_sim_ids:
                 self._micro_sims_active_steps[active_id] += 1
 
-        active_sim_ids = self._adaptivity_controller.get_active_sim_ids()
-        inactive_sim_ids = self._adaptivity_controller.get_inactive_sim_ids()
+        active_sim_ids = self._adaptivity_controller.get_active_sim_ids(
+            adaptivity_data[1]
+        )
+        inactive_sim_ids = self._adaptivity_controller.get_inactive_sim_ids(
+            adaptivity_data[1]
+        )
 
         micro_sims_output = [None] * self._local_number_of_sims
 
@@ -779,7 +785,7 @@ def _solve_micro_simulations_with_adaptivity(
                     micro_sims_input, micro_sims_output, unset_sim, active_sim_ids
                 )
 
-        self._adaptivity_controller.get_full_field_micro_output(
+        micro_sims_output = self._adaptivity_controller.get_full_field_micro_output(
             adaptivity_data, micro_sims_output
         )
 

tests/unit/test_micro_simulation_crash_handling.py

@@ -98,10 +98,15 @@ def test_crash_handling_with_adaptivity(self):
         )
         manager._micro_sims = [MicroSimulation(i) for i in range(5)]
 
-        is_sim_active = np.array([True, True, True, True, False])
-        sim_is_associated_to = np.array([-2, -2, -2, -2, 2])
+        adaptivity_data = []
+        adaptivity_data.append(np.array([0, 0, 0, 0, 0]))  # similarity_dists
+        adaptivity_data.append(
+            np.array([True, True, True, True, False])
+        )  # is_sim_active
+        adaptivity_data.append(np.array([-2, -2, -2, -2, 2]))  # sim_is_associated_to
+
         micro_sims_output = manager._solve_micro_simulations_with_adaptivity(
-            macro_data, is_sim_active, sim_is_associated_to, 1.0
+            macro_data, 1.0, adaptivity_data
         )
 
         # Crashed simulation has interpolated value