Merge pull request #193 from mesoscope/feature/results-in-memory

Feature/results in memory

cellpack/autopack/Analysis.py

@@ -170,7 +170,7 @@ def getDistanceFrom(self, target, parents=None, **options):
         objects : list of object or list of points
         """
         # get distance from object to the target.
-        # all object are in h.molecules and orga.molecules
+        # all object are in env.packed_objects
         # get options
 
         if type(target) == list or type(target) == tuple:
@@ -447,23 +447,6 @@ def rectangle_circle_area(self, bbox, center, radius):
                 area = bbox[0][1] ** 2
         return area
 
-    def getAxeValue(self, ingrname, axe=0):
-        ingredient_positions = [
-            self.env.molecules[i][0][axe]
-            for i in range(len(self.env.molecules))
-            if self.env.molecules[i][2].name == ingrname
-        ]
-        return ingredient_positions
-
-    def getAxesValues(self, positions):
-        pp = numpy.array(positions).transpose()
-        if len(positions) == 0:
-            return 1, 1, 1
-        px = pp[0]
-        py = pp[1]
-        pz = pp[2]
-        return px, py, pz
-
     def getVolumeShell(self, bbox, radii, center):
         # rectangle_circle_area
         volumes = []
@@ -473,9 +456,6 @@ def getVolumeShell(self, bbox, radii, center):
             r2 = radii[i + 1]
             v1 = self.g.calc_volume(r1, box_size0 / 2.0)
             v2 = self.g.calc_volume(r2, box_size0 / 2.0)
-            #            if v1 == 0 or v2 == 0 :
-            #                volumes.append((4./3.)*numpy.pi*(numpy.power(r2,3)-numpy.power(r1, 3)))
-            #            else :
             volumes.append(v2 - v1)
         return volumes
 
@@ -1774,7 +1754,7 @@ def pack(
         t2 = time()
         run_time = t2 - t1
         print(f"time to run pack_grid for {self.env.place_method}: {run_time:0.2f}")
-        print(f"num placed: {len(self.env.molecules)}")
+        print(f"num placed: {len(self.env.packed_objects.get_ingredients())}")
         if show_plotly_plot:
             min_bound, max_bound = self.env.get_bounding_box_limits()
             width = max_bound - min_bound
@@ -1787,7 +1767,7 @@ def pack(
                 range=[min_bound[1] - 0.2 * width[1], max_bound[1] + 0.2 * width[1]]
             )
             self.plotly.update_title(
-                f"{self.env.place_method} took {str(round(t2 - t1, 2))}s, packed {len(self.env.molecules)}"
+                f"{self.env.place_method} took {str(round(t2 - t1, 2))}s, packed {len(self.env.packed_objects.get_ingredients())}"
             )
             self.plotly.make_grid_heatmap(self.env)
             self.plotly.add_ingredient_positions(self.env)
@@ -1875,29 +1855,6 @@ def plot_one_result_2d(
             plt.close()  # closes the current figure
         return ingrpos
 
-    #        res=plotOneResult(None,filename="results_seed_8.json")
-
-    def plot_one_result_3D(self, filename, width=1000.0):
-        plt.close("all")  # closes the current figure
-        pos = []
-        s = []
-        c = []
-        for i in range(len(self.env.molecules)):
-            m = self.env.molecules[i]
-            pos.append(numpy.array(m[0]).tolist())
-            s.append(m[2].encapsulating_radius ** 2)
-            c.append(m[2].color)
-        fig = plt.figure()
-        ax = fig.gca(projection="3d")
-        x, y, z = numpy.array(pos).transpose()
-        ax.scatter(x, y, z, s=s, c=c)
-        ax.legend()
-        ax.set_xlim3d(0, width)
-        ax.set_ylim3d(0, width)
-        ax.set_zlim3d(0, width)
-        plt.savefig(filename)
-        return x, y, z, s, c
-
     def set_ingredient_color(self, ingr):
         """
         Sets the color of an ingredient

cellpack/autopack/Compartment.py

@@ -68,6 +68,10 @@
 import cellpack.autopack as autopack
 from cellpack.autopack import transformation as tr, binvox_rw
 from cellpack.autopack.BaseGrid import gridPoint
+from cellpack.autopack.interface_objects.packed_objects import (
+    PackedObject,
+    PackedObjects,
+)
 from .Recipe import Recipe
 from .ray import (
     makeMarchingCube,
@@ -138,6 +142,7 @@ def __init__(self, name, object_info):
         self.ref_obj = None
         self.meshType = None
         self.representations = object_info["representations"]
+        self.packed_objects = PackedObjects()
         if self.representations.has_mesh():
             self.gname = self.representations.get_mesh_name()
             self.meshType = self.representations.get_mesh_format()
@@ -172,7 +177,6 @@ def __init__(self, name, object_info):
         # is added to a Environment. Positivefor surface pts
         # negative for interior points
         # self.parent = None
-        self.molecules = []
         # list of ( (x,y,z), rotation, ingredient) triplet generated by fill
         self.overwriteSurfacePts = True
         # do we discretize surface point per edges
@@ -207,7 +211,6 @@ def reset(self):
         # list of grid point indices on compartment surface
         self.surfacePoints = None
         self.surfacePointsNormals = {}  # will be point index:normal
-        # self.molecules = []
 
     def transformMesh(self, pos, rotation):
         rot = tr.matrix_from_quaternion(rotation).transpose()
@@ -266,6 +269,17 @@ def initialize_shape(self, mesh_store):
                 self.encapsulating_radius = radius
                 self.radius = mesh_store.get_smallest_radius(self.gname, center)
 
+    def store_packed_object(self, env):
+        packed_object = PackedObject(
+            position=[0, 0, 0],
+            rotation=numpy.identity(4),
+            radius=self.radius,
+            pt_index=-1,
+            ingredient=self,
+            is_compartment=True,
+        )
+        env.packed_objects.add(packed_object)
+
     def addShapeRB(self, env):
         # in case our shape is a regular primitive
         if self.stype == "capsule":
@@ -503,10 +517,10 @@ def setInnerRecipe(self, recipe):
         self.innerRecipe.number = self.number
         recipe.compartment = self  # weakref.ref(self)
         for ingr in recipe.ingredients:
-            ingr.compNum = -self.number
+            ingr.compartment_id = -self.number
             if hasattr(ingr, "compMask"):
                 if not ingr.compMask:
-                    ingr.compMask = [ingr.compNum]
+                    ingr.compMask = [ingr.compartment_id]
 
     def setSurfaceRecipe(self, recipe):
         """set the inner recipe that define the ingredient to pack at the surface"""
@@ -516,7 +530,7 @@ def setSurfaceRecipe(self, recipe):
         self.surfaceRecipe.number = self.number
         recipe.compartment = self  # weakref.ref(self)
         for ingr in recipe.ingredients:
-            ingr.compNum = self.number
+            ingr.compartment_id = self.number
 
     def getCenter(self):
         """get the center of the mesh (vertices barycenter)"""
@@ -3200,12 +3214,19 @@ def create_voxelization(
         voxel_size,
         image_size,
         position,
-        mesh_store,
-        hollow=False,
+        **kwargs,
     ):
         """
         Creates a voxelization mask at the position of the compartment
         """
+        if "mesh_store" not in kwargs:
+            raise RuntimeError(
+                "mesh_store must be provided for compartment voxelization"
+            )
+
+        mesh_store = kwargs["mesh_store"]
+        hollow = kwargs.get("hollow", False)
+
         relative_position = position - bounding_box[0]
         mask = self.create_voxelized_mask(
             *image_size,