* remove nans and sort grid values

* user relative size for grid points in simularium
mesoscope · Sep 12, 2023 · 91f4f17 · 91f4f17
1 parent c292f6f
commit 91f4f17
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Showing 2 changed files with 29 additions and 4 deletions.
diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py
@@ -332,12 +332,32 @@ def concatObjectMatrix(self):
 
     def GetAbsPosUntilRoot(self, obj):
         return [0, 0.0, 0.0]
+
+    @staticmethod
+    def remove_nans(positions, values):
+        naninds = np.isnan(values)
+        values = values[~naninds]
+        positions = positions[~naninds]
+        return positions, values
 
-    def add_grid_data_to_scene(self, incoming_name, positions, values, radius=0.5):
-        colormap = matplotlib.cm.Reds(values)
+    @staticmethod
+    def sort_values(positions, values):
         inds = np.argsort(values)
         values = values[inds]
         positions = positions[inds]
+        return positions, values
+
+    def add_grid_data_to_scene(self, incoming_name, positions, values, radius=0.5):
+
+        positions, values = self.remove_nans(positions, values)
+        if len(values) == 0:
+            print("no values to display")
+            return
+
+        positions, values = self.sort_values(positions, values)
+
+        colormap = matplotlib.cm.Reds(values)
+
         for index, value in enumerate(values):
             name = f"{incoming_name}#{value:.3f}"
             self.display_data[name] = DisplayData(
@@ -455,6 +475,7 @@ def init_scene_with_objects(
         grid_point_positions=None,
         grid_point_compartment_ids=None,
         show_sphere_trees=False,
+        grid_pt_radius=0.5,
     ):
         self.time = 0
         instance_number = 0
@@ -531,7 +552,7 @@ def init_scene_with_objects(
                         name,
                         None,
                         f"{name}-{index}",
-                        0.5,
+                        grid_pt_radius,
                         point_pos,
                         np.identity(4),
                         None,

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
@@ -155,7 +155,11 @@ def save_as_simularium(self, env, all_ingr_as_array, compartments):
         grid_positions = env.grid.masterGridPositions if env.show_grid_spheres else None
         compartment_ids = env.grid.compartment_ids if env.show_grid_spheres else None
         env.helper.init_scene_with_objects(
-            all_ingr_as_array, grid_positions, compartment_ids, env.show_sphere_trees
+            objects=all_ingr_as_array,
+            grid_point_positions=grid_positions,
+            grid_point_compartment_ids=compartment_ids,
+            show_sphere_trees=env.show_sphere_trees,
+            grid_pt_radius=env.grid.gridSpacing / 4,
         )
 
         if compartments is not None: