* add progress bar

* disable save dumps
* update compartment grid saving and loading
* load specific compartment grid attributes
* add power-law and exponential weight mode fro gradients

cellpack/autopack/Analysis.py

@@ -2423,7 +2423,6 @@ def doloop(
         """
         if seed_list is None:
             seed_list = self.getHaltonUnique(number_of_packings)
-
         packing_basename = f"{self.env.name}_{config_name}_{recipe_version}"
         numpy.savetxt(
             self.env.out_folder / f"seeds_{packing_basename}.txt",

cellpack/autopack/Environment.py

@@ -91,6 +91,7 @@
 from .randomRot import RandomRot
 
 from cellpack.autopack.interface_objects.meta_enum import MetaEnum
+from tqdm import tqdm
 
 try:
     helper = autopack.helper
@@ -167,6 +168,7 @@ def __init__(self, config=None, recipe=None):
         self.boundingBox = numpy.array(recipe["bounding_box"])
         self.spacing = config["spacing"]
         self.load_from_grid_file = config["load_from_grid_file"]
+        self.show_progress_bar = config["show_progress_bar"]
         self.name = name
         self.version = recipe.get("version", "default")
         # saving/pickle option
@@ -292,7 +294,7 @@ def __init__(self, config=None, recipe=None):
         self.rb_func_dic = {}
         # need options for the save/server data etc....
         # should it be in __init__ like other general options ?
-        self.dump = True
+        self.dump = False
         self.dump_freq = 120.0
         self.jsondic = None
 
@@ -1016,7 +1018,6 @@ def saveGridToFile(self, gridFileOut):
         Save the current grid and the compartment grid information in a file. (pickle)
         """
         d = os.path.dirname(gridFileOut)
-        print("SAVED GRID TO ", gridFileOut)
         if not os.path.exists(d):
             print("gridfilename path problem", gridFileOut)
             return
@@ -1025,6 +1026,7 @@ def saveGridToFile(self, gridFileOut):
 
         for compartment in self.compartments:
             compartment.saveGridToFile(f)
+        print("SAVED GRID TO ", gridFileOut)
         f.close()
 
     def saveGridLogsAsJson(self, gridFileOut):
@@ -1053,26 +1055,60 @@ def saveGridLogsAsJson(self, gridFileOut):
             json.dump(data, fp=f)
         f.close()
 
+    @staticmethod
+    def get_attributes_to_update():
+        return [
+            "faces",
+            "vertices",
+            "vnormals",
+            "filename",
+            "ref_obj",
+            "bb",
+            "center",
+            "encapsulating_radius",
+            "radius",
+            "insidePoints",
+            "surfacePoints",
+            "surfacePointsCoords",
+            "surfacePointsNormals",
+            "ogsurfacePoints",
+            "ogsurfacePointsNormals",
+            "OGsrfPtsBht",
+            "closestId",
+        ]
+
     def restore_grids_from_pickle(self, grid_file_path):
         """
         Read and setup the grid from the given filename. (pickle)
         """
         print(f"Loading grid from {grid_file_path}")
+
         with open(grid_file_path, "rb") as file_obj:
             # load env grid
-            self.grid = load_object_from_pickle(self.grid, file_obj)
+            grid_obj = load_object_from_pickle(file_obj)
+            self.grid = grid_obj
 
             # load compartment grids
-            for ct, compartment in enumerate(self.compartments):
-                self.compartments[ct] = load_object_from_pickle(compartment, file_obj)
+            for ct, _ in enumerate(self.compartments):
+                comp_obj = load_object_from_pickle(file_obj)
+                for update_attr in self.get_attributes_to_update():
+                    setattr(
+                        self.compartments[ct],
+                        update_attr,
+                        getattr(comp_obj, update_attr),
+                    )
 
             # load mesh store
-            self.mesh_store = load_object_from_pickle(self.mesh_store, file_obj)
+            mesh_store_obj = load_object_from_pickle(file_obj)
+            self.mesh_store = mesh_store_obj
 
             # clear the triangles_tree cache
             for _, geom in self.mesh_store.scene.geometry.items():
                 geom._cache.delete("triangles_tree")
 
+            # reset grid
+            self.grid.reset()
+
     def save_grids_to_pickle(self, grid_file_path):
         """
         Save the current grid and compartment grids to file. (pickle)
@@ -1101,8 +1137,8 @@ def restoreGridFromFile(self, gridFileName):
         f = open(gridFileName, "rb")
         self.readArraysFromFile(f)
         for ct, compartment in enumerate(self.compartments):
-            # compartment.readGridFromFile(f)
-            compartment = compartment.load_compartment_object(f)
+            compartment.readGridFromFile(f)
+            # compartment = compartment.load_compartment_object(f)
             aInteriorGrids.append(compartment.insidePoints)
             aSurfaceGrids.append(compartment.surfacePoints)
             compartment.OGsrfPtsBht = spatial.cKDTree(
@@ -1417,45 +1453,42 @@ def buildGrid(self, rebuild=True):
         else:
             self.build_compartment_grids()
 
-            self.exteriorVolume = self.grid.computeExteriorVolume(
-                compartments=self.compartments,
-                space=self.smallestProteinSize,
-                fbox_bb=self.fbox_bb,
-            )
+            # save grids to pickle
+            # self.saveGridToFile(self.grid_file_out)
+            self.grid.filename = self.grid_file_out
+            self.previous_grid_file = self.grid_file_out
+            self.save_grids_to_pickle(self.grid_file_out)
 
-            r = self.exteriorRecipe
-            if r:
-                r.setCount(self.exteriorVolume)  # should actually use the fillBB
+        self.exteriorVolume = self.grid.computeExteriorVolume(
+            compartments=self.compartments,
+            space=self.smallestProteinSize,
+            fbox_bb=self.fbox_bb,
+        )
 
-            if not rebuild:
-                for c in self.compartments:
-                    c.setCount()
-            else:
-                self.grid.distToClosestSurf_store = self.grid.distToClosestSurf[:]
+        r = self.exteriorRecipe
+        if r:
+            r.setCount(self.exteriorVolume)  # should actually use the fillBB
 
-            distance = self.grid.distToClosestSurf  # [:]
-            nbFreePoints = nbPoints  # -1
+        if not rebuild:
+            for c in self.compartments:
+                c.setCount()
+        else:
+            self.grid.distToClosestSurf_store = self.grid.distToClosestSurf[:]
+
+        distance = self.grid.distToClosestSurf  # [:]
+        nbFreePoints = nbPoints  # -1
+        for i, mingrs in enumerate(self.molecules):  # ( jtrans, rotMatj, self, ptInd )
+            nbFreePoints = self.onePrevIngredient(
+                i, mingrs, distance, nbFreePoints, self.molecules
+            )
+        for organelle in self.compartments:
             for i, mingrs in enumerate(
-                self.molecules
+                organelle.molecules
             ):  # ( jtrans, rotMatj, self, ptInd )
                 nbFreePoints = self.onePrevIngredient(
-                    i, mingrs, distance, nbFreePoints, self.molecules
+                    i, mingrs, distance, nbFreePoints, organelle.molecules
                 )
-            for organelle in self.compartments:
-                for i, mingrs in enumerate(
-                    organelle.molecules
-                ):  # ( jtrans, rotMatj, self, ptInd )
-                    nbFreePoints = self.onePrevIngredient(
-                        i, mingrs, distance, nbFreePoints, organelle.molecules
-                    )
-            self.grid.nbFreePoints = nbFreePoints
-
-            # save grids to pickle
-            # self.saveGridToFile(self.grid_file_out)
-            self.grid.filename = self.grid_file_out
-            self.previous_grid_file = self.grid_file_out
-
-            self.save_grids_to_pickle(self.grid_file_out)
+        self.grid.nbFreePoints = nbFreePoints
 
         if self.use_gradient and len(self.gradients) and rebuild:
             for g in self.gradients:
@@ -1663,7 +1696,7 @@ def reset(self):
         self.resetIngrRecip(r)
         self.molecules = []
         for orga in self.compartments:
-            # orga.reset()
+            orga.reset()
             rs = orga.surfaceRecipe
             self.resetIngrRecip(rs)
             ri = orga.innerRecipe
@@ -2208,7 +2241,8 @@ def pack_grid(
         dump_freq = self.dump_freq  # 120.0#every minute
         dump = self.dump
         stime = time()
-
+        if self.show_progress_bar:
+            pbar = tqdm(total=totalNumMols, mininterval=0, miniters=1)
         while nbFreePoints:
             self.log.info(
                 ".........At start of while loop, with vRangeStart = %d", vRangeStart
@@ -2252,7 +2286,6 @@ def pack_grid(
                     )
                     if self.afviewer.renderDistance:
                         self.afviewer.vi.displayParticleVolumeDistance(distances, self)
-
             current_ingr_compartment = ingr.compNum
             # compute dpad which is the distance at which we need to update
             # distances after the drop is successfull
@@ -2342,6 +2375,8 @@ def pack_grid(
                 # if ingredient_too_close:
                 #     print("GOT A FAIL", self.grid.masterGridPositions[ptInd])
                 #     nbFreePoints = 0
+                if self.show_progress_bar:
+                    pbar.update(1)
             else:
                 self.log.info("rejected %r", ingr.rejectionCounter)
 
@@ -2399,6 +2434,7 @@ def pack_grid(
                     self.thresholdPriorities.append(np + previousThresh)
                     previousThresh = np + float(previousThresh)
                 self.activeIngr = self.activeIngr0 + self.activeIngr12
+
             if dump and ((time() - stime) > dump_freq):
                 print("SAVING", self.result_file)
                 all_ingr_as_array = self.prep_molecules_for_save(
@@ -2420,6 +2456,8 @@ def pack_grid(
                     )
 
         t2 = time()
+        if self.show_progress_bar:
+            pbar.close()
         self.log.info("time to fill %d", t2 - t1)
         all_ingr_as_array = self.prep_molecules_for_save(
             distances, free_points, nbFreePoints

cellpack/autopack/Gradient.py

@@ -216,8 +216,10 @@ def set_weights_by_mode(self):
         elif self.weight_mode == "power":
             self.weight = (1.0 - scaled_distances) ** self.weight_mode_settings["power"]
         elif self.weight_mode == "exponential":
-            self.weight = numpy.exp(-scaled_distances / self.weight_mode_settings["decay_length"])
-
+            self.weight = numpy.exp(
+                -scaled_distances / self.weight_mode_settings["decay_length"]
+            )
+
         self.weight[numpy.isnan(self.weight)] = 0
         # TODO: talk to Ludo about calculating gaussian weights
 

cellpack/autopack/interface_objects/gradient_data.py

@@ -25,6 +25,7 @@ class WeightModes(MetaEnum):
     """
     All available weight modes
     """
+
     LINEAR = "linear"
     SQUARE = "square"
     CUBE = "cube"
@@ -63,6 +64,7 @@ class WeightModeOptions(MetaEnum):
     """
     All available options for individual weight modes
     """
+
     power = "power"
     decay_length = "decay_length"
 
@@ -132,8 +134,10 @@ def validate_mode_settings(self, mode_name, mode_settings_dict):
                 raise ValueError(
                     f"Missing required mode setting {option} for {mode_name}"
                 )
-
-    def validate_weight_mode_settings(self, weight_mode_name, weight_mode_settings_dict):
+
+    def validate_weight_mode_settings(
+        self, weight_mode_name, weight_mode_settings_dict
+    ):
         required_options = REQUIRED_WEIGHT_MODE_OPTIONS.get(weight_mode_name)
 
         if required_options is None:

cellpack/autopack/loaders/config_loader.py

@@ -41,6 +41,7 @@ class ConfigLoader(object):
         "save_converted_recipe": False,
         "show_grid_plot": False,
         "show_sphere_trees": False,
+        "show_progress_bar": False,
         "spacing": None,
         "use_periodicity": False,
         "version": 1.0,

cellpack/autopack/utils.py

@@ -172,12 +172,12 @@ def get_paired_key(val_dict, key1=None, key2=None):
             return key
 
 
-def load_object_from_pickle(input_object, pickle_file_object):
+def load_object_from_pickle(pickle_file_object):
     """
     Update an object from a pickle file
     """
     try:
-        input_object = pickle.load(pickle_file_object)
+        output_object = pickle.load(pickle_file_object)
     except Exception as e:
         raise ValueError(f"Error loading saved object: {e}")
-    return input_object
+    return output_object

cellpack/tests/test_gradient_data.py

@@ -135,9 +135,7 @@ def test_gradient_data(input, expected_options):
                 {
                     "mode": "surface",
                     "weight_mode": "power",
-                    "mode_settings": {
-                        "object": "object_name"
-                    }
+                    "mode_settings": {"object": "object_name"},
                 },
                 "gradient_name",
             ),