fixed index issue - using the powers of reading comprehension and hel…

…pful convo with @wang-boyu (projectmesa/mesa-geo#267)

vegetation/app.py

@@ -52,11 +52,8 @@ def cell_portrayal(agent):
         # life stage of any Joshua Tree agent in the cell. If there are no agents,
         # we color based on elevation.
 
-        # patch_life_stages = [agent.life_stage for agent in agent.jotr_agents]
-
         if agent.jotr_max_life_stage and agent.jotr_max_life_stage > 0:
 
-            # max_stage = max(patch_life_stages)
             rgba = LIFE_STAGE_RGB_VIZ_MAP[agent.jotr_max_life_stage]
 
         else:

vegetation/patch/model.py

@@ -62,10 +62,13 @@ def __init__(self, model, geometry, crs, age=None, parent_id=None):
         # pos = (np.float64(geometry.x), np.float64(geometry.y))
         # self._pos = pos
 
-        self.indices = (int(self.float_indices[0]), int(self.float_indices[1]))
+        self.indices = (
+            int(self.float_indices[0]),
+            self.model.space.raster_layer.height - int(self.float_indices[1]),
+        )
         self._pos = (
-            self.indices[0],
-            self.model.space.raster_layer.height - self.indices[1],
+            int(self.float_indices[0]),
+            int(self.float_indices[1]),
         )
 
         # TODO: Figure out how to set the life stage on init