From a97be569af57b493280e226aaf2ed6fdad3d2de0 Mon Sep 17 00:00:00 2001
From: Saurabh Mogre <saurabh.mogre@alleninstitute.org>
Date: Tue, 25 Apr 2023 12:54:24 -0700
Subject: [PATCH] resolve compartment object for surface gradient (#168)

---
 cellpack/autopack/Environment.py | 20 +++++++++++++++-----
 cellpack/autopack/Gradient.py    | 13 +++++++++----
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/cellpack/autopack/Environment.py b/cellpack/autopack/Environment.py
index 419f5afc9..9cdfaedbc 100644
--- a/cellpack/autopack/Environment.py
+++ b/cellpack/autopack/Environment.py
@@ -793,6 +793,19 @@ def sortIngredient(self, reset=False):
             if o.surfaceRecipe:
                 o.surfaceRecipe.sort()
 
+    def resolve_gradient_data_objects(self, gradient_data):
+        """
+        Resolves gradient data objects for some modes
+        """
+        # TODO: check if other modes need to be resolved
+        if gradient_data["mode"] == "surface":
+            gradient_data["mode_settings"][
+                "object"
+            ] = self.get_compartment_object_by_name(
+                gradient_data["mode_settings"]["object"]
+            )
+        return gradient_data
+
     def set_gradient(self, gradient_data):
         """
         create a grdaient
@@ -800,10 +813,7 @@ def set_gradient(self, gradient_data):
         listorganelle influenced
         listingredient influenced
         """
-        if "surface_name" in gradient_data:
-            gradient_data["object"] = self.get_compartment_object_by_name(
-                gradient_data["surface_name"]
-            )
+        gradient_data = self.resolve_gradient_data_objects(gradient_data)
         gradient = Gradient(gradient_data)
         # default gradient 1-linear Decoy X
         self.gradients[gradient_data["name"]] = gradient
@@ -1369,7 +1379,7 @@ def buildGrid(self, rebuild=True):
             for g in self.gradients:
                 gradient = self.gradients[g]
                 if gradient.mode == "surface":
-                    gradient.object.get_surface_distances(
+                    gradient.mode_settings["object"].get_surface_distances(
                         self, self.grid.masterGridPositions
                     )
                 self.gradients[g].build_weight_map(
diff --git a/cellpack/autopack/Gradient.py b/cellpack/autopack/Gradient.py
index 518c69b34..62571e20b 100644
--- a/cellpack/autopack/Gradient.py
+++ b/cellpack/autopack/Gradient.py
@@ -157,12 +157,17 @@ def build_surface_distance_weight_map(self):
         build a map of weights based on the distance from a surface
         assumes self.distances include surface distances
         """
-        if getattr(self.object, "surface_distances", None) is None:
+        if getattr(self.mode_settings["object"], "surface_distances", None) is None:
             raise ValueError("Surface distances are not set")
-        elif self.scale_to_next_surface:
-            self.distances = self.object.scaled_distance_to_next_surface
+        elif self.mode_settings["scale_to_next_surface"]:
+            self.distances = self.mode_settings[
+                "object"
+            ].scaled_distance_to_next_surface
         else:
-            self.distances = self.object.surface_distances / self.object.max_distance
+            self.distances = (
+                self.mode_settings["object"].surface_distances
+                / self.mode_settings["object"].max_distance
+            )
         self.set_weights_by_mode()
 
     def build_directional_weight_map(self, bb, master_grid_positions):