* add datatypes to save memory

* remove extra version assignment in environment * add chunking for large meshes
mesoscope · Jul 31, 2023 · 8eeee86 · 8eeee86
1 parent 844e6d0
commit 8eeee86
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Showing 3 changed files with 24 additions and 13 deletions.
diff --git a/cellpack/autopack/Compartment.py b/cellpack/autopack/Compartment.py
@@ -1313,20 +1313,22 @@ def BuildGrid_trimesh(
                 self.center,
                 self.encapsulating_radius + env.grid.gridSpacing * 2,
                 return_sorted=True,
-            )
+            ),
+            dtype=numpy.int32,
         )
         self.log.info(f"GOT POINTS IN SPHERE {len(points_in_encap_sphere)}")
 
         point_compartment_ids = compartment_ids[points_in_encap_sphere]
         point_ids_to_assign = points_in_encap_sphere[point_compartment_ids == 0]
-        point_positions = master_grid_positions[point_ids_to_assign]
+        point_positions = numpy.float16(master_grid_positions[point_ids_to_assign])
 
         # check surface points
         points_on_surface = trimesh_grid_surface.is_filled(point_positions)
         compartment_ids[point_ids_to_assign[points_on_surface]] = number
 
         # check inside points
         points_in_mesh = mesh_store.contains_points_mesh(self.gname, point_positions)
+
         points_in_mesh = points_in_mesh & ~points_on_surface
         compartment_ids[point_ids_to_assign[points_in_mesh]] = -number
         insidePoints = point_ids_to_assign[points_in_mesh]
@@ -2466,7 +2468,7 @@ def find_nearest(self, array, value):
     # TOD add and store the grid_distances  (closest distance for each point). not only inside / outside
 
     def getSurfaceInnerPoints_sdf(
-        self, boundingBox, spacing, display=True, useFix=False
+        self, boundingBox, spacing, display=False, useFix=False
     ):
         """
         Only compute the inner point. No grid.
@@ -2538,7 +2540,7 @@ def getSurfaceInnerPoints_sdf(
         return pointinside[0], self.vertices
 
     def getSurfaceInnerPoints_kevin(
-        self, boundingBox, spacing, display=True, superFine=False
+        self, boundingBox, spacing, display=False, superFine=False
     ):
         """
         Takes a polyhedron, and builds a grid. In this grid:
@@ -2857,7 +2859,7 @@ def getSurfaceInnerPoints_kevin(
         return insidePoints, surfacePoints
 
     def getSurfaceInnerPoints_sdf_interpolate(
-        self, boundingBox, spacing, display=True, useFix=False
+        self, boundingBox, spacing, display=False, useFix=False
     ):
         """
         Only compute the inner point. No grid.
@@ -2923,7 +2925,7 @@ def getSurfaceInnerPoints_sdf_interpolate(
         # need to update the surface. need to create a aligned grid
         return pointinside[0], self.vertices
 
-    def getSurfaceInnerPoints(self, boundingBox, spacing, display=True, useFix=False):
+    def getSurfaceInnerPoints(self, boundingBox, spacing, display=False, useFix=False):
         """
         Only compute the inner point. No grid.
         This is independant from the packing. Help build ingredient sphere tree and representation
@@ -3208,7 +3210,7 @@ def create_voxelization(
         return image_data
 
     def getSurfaceInnerPointsPandaRay(
-        self, boundingBox, spacing, display=True, useFix=False
+        self, boundingBox, spacing, display=False, useFix=False
     ):
         """
         Only compute the inner point. No grid.
@@ -3363,7 +3365,7 @@ def getSurfaceInnerPointsPandaRay(
         return insidePoints, surfacePoints
 
     def getSurfaceInnerPointsPanda(
-        self, boundingBox, spacing, display=True, useFix=False
+        self, boundingBox, spacing, display=False, useFix=False
     ):
         """
         Only compute the inner point. No grid.

diff --git a/cellpack/autopack/Environment.py b/cellpack/autopack/Environment.py
@@ -213,9 +213,6 @@ def __init__(self, config=None, recipe=None):
         self.host = None
         self.afviewer = None
 
-        # version of setup used
-        self.version = "1.0"
-
         # option for packing using host dynamics capability
         self.windowsSize = 100
         self.windowsSize_overwrite = False
@@ -2200,7 +2197,7 @@ def pack_grid(
         stime = time()
         if self.show_progress_bar:
             pbar = tqdm(total=totalNumMols, mininterval=0, miniters=1)
-            pbar.set_description(f"Packing {self.name}")
+            pbar.set_description(f"Packing {self.name}_{self.version}")
         while nbFreePoints:
             self.log.info(
                 ".........At start of while loop, with vRangeStart = %d", vRangeStart

diff --git a/cellpack/autopack/MeshStore.py b/cellpack/autopack/MeshStore.py
@@ -4,6 +4,8 @@
 import trimesh
 from cellpack import autopack
 
+CHUNK_SIZE = 100000
+
 
 class MeshStore:
     def __init__(self):
@@ -267,7 +269,17 @@ def contains_points(self, geomname, points):
     def contains_points_mesh(self, geomname, points):
         mesh = self.get_object(geomname)
         if mesh is not None:
-            return mesh.contains(points)
+            if len(points) <= CHUNK_SIZE:
+                return mesh.contains(points)  #  TODO: check for memory leak
+            else:
+                # chunk the points
+                for i in range(0, len(points), CHUNK_SIZE):
+                    chunk = points[i : min(i + CHUNK_SIZE, len(points))]
+                    if i == 0:
+                        inside = mesh.contains(chunk)
+                    else:
+                        inside = numpy.append(inside, mesh.contains(chunk))
+                return inside
         return numpy.full(len(points), False)
 
     def get_smallest_radius(self, geomname, center):