Added ice model to simulate potential

src/parakeet/simulate/_potential.py

@@ -158,7 +158,27 @@ def __call__(self, index):
         potential.voxel_size = tuple((pixel_size, pixel_size, slice_thickness))
 
         # Simulate the potential
-        simulate.potential(potential, volume_z0)
+        if self.simulation["ice"] == True:
+            # Get the masker
+            masker = simulate.masker(
+                index,
+                pixel_size,
+                origin,
+                offset,
+                orientation,
+                position,
+                self.sample,
+                self.scan,
+                self.simulation,
+            )
+
+            # Run the simulation
+            image = simulate.potential(potential, volume_z0, masker)
+
+        else:
+            # Run the simulation
+            logger.info("Simulating")
+            simulate.potential(potential, volume_z0)
 
         # Compute the image scaled with Poisson noise
         return (index, None, None)

src/parakeet/simulate/engine.py

@@ -386,7 +386,7 @@ def ctf(self):
         """
         return np.array(multem.compute_ctf(self.system_conf, self.input)).T
 
-    def potential(self, out, volume_z0):
+    def potential(self, out, volume_z0, masker=None):
         """
         Simulate the potential
 
@@ -407,7 +407,12 @@ def callback(z0, z1, V):
                 out.data[index, :, :] = V[margin:-margin, margin:-margin].T
 
         # Run the simulation
-        multem.compute_projected_potential(self.system_conf, self.input, callback)
+        if masker is not None:
+            multem.compute_projected_potential(
+                self.system_conf, self.input, masker, callback
+            )
+        else:
+            multem.compute_projected_potential(self.system_conf, self.input, callback)
 
     def image(self, masker=None):
         """