Updates for variable count and size experiments (#215)

* set `grid_file_out` even if file does not exist

* * calculate seed before updating base name
* return count as integer
* allow specifying seed list in the recipe

* set default value for randomness seed in recipe

* * automatically specify seeds for multiple packings
* add sphere mesh objects for tests
* add recipe for nested mesh testing

* refactor seed list processing

---------

Co-authored-by: meganrm <[email protected]>

cellpack/autopack/Analysis.py

@@ -2173,8 +2173,8 @@ def pack_one_seed(
         """
         Packs one seed of a recipe and returns the recipe object
         """
-        seed_basename = self.env.add_seed_number_to_base_name(seed_index)
-        seed = seed_list[seed_index]
+        seed = int(seed_list[seed_index])
+        seed_basename = self.env.add_seed_number_to_base_name(seed)
         # Clear
         if self.afviewer:
             self.afviewer.clearFill("Test_Spheres2D")

cellpack/autopack/Environment.py

@@ -157,8 +157,7 @@ def __init__(self, config=None, recipe=None):
             f"{self.out_folder}/{self.name}_{config['name']}_{self.version}_grid.dat"
         )
         if recipe.get("grid_file_path") is not None:
-            if os.path.isfile(recipe["grid_file_path"]):
-                self.grid_file_out = recipe["grid_file_path"]
+            self.grid_file_out = recipe["grid_file_path"]
 
         should_load_grid_file = (
             os.path.isfile(self.grid_file_out) and self.load_from_grid_file
@@ -1832,7 +1831,8 @@ def update_variable_ingredient_attributes(self, allIngredients):
             if hasattr(ingr, "count_options") and ingr.count_options is not None:
 
                 count = get_value_from_distribution(
-                    distribution_options=ingr.count_options
+                    distribution_options=ingr.count_options,
+                    return_int=True,
                 )
                 if count is not None:
                     ingr.count = count

cellpack/autopack/utils.py

@@ -257,3 +257,26 @@ def get_value_from_distribution(distribution_options, return_int=False):
         value = int(numpy.rint(value))
 
     return value
+
+
+def get_seed_list(packing_config_data, recipe_data):
+    # Returns a list of seeds to use for packing
+    if packing_config_data["randomness_seed"] is not None:
+        seed_list = packing_config_data["randomness_seed"]
+    elif recipe_data.get("randomness_seed") is not None:
+        seed_list = recipe_data["randomness_seed"]
+    else:
+        seed_list = None
+
+    if isinstance(seed_list, int):
+        seed_list = [seed_list]
+
+    if (seed_list is not None) and (
+        len(seed_list) != packing_config_data["number_of_packings"]
+    ):
+        base_seed = int(seed_list[0])
+        seed_list = [
+            base_seed + i for i in range(packing_config_data["number_of_packings"])
+        ]
+
+    return seed_list

cellpack/bin/pack.py

@@ -12,6 +12,7 @@
 from cellpack.autopack.loaders.config_loader import ConfigLoader
 from cellpack.autopack.loaders.recipe_loader import RecipeLoader
 from cellpack.autopack.loaders.analysis_config_loader import AnalysisConfigLoader
+from cellpack.autopack.utils import get_seed_list
 
 ###############################################################################
 log_file_path = path.abspath(path.join(__file__, "../../logging.conf"))
@@ -56,12 +57,15 @@ def pack(recipe, config_path=None, analysis_config_path=None):
             result_file=None,
         )
         log.info(f"saving to {env.out_folder}")
+
+        seed_list = get_seed_list(packing_config_data, recipe_data)
+
         analyze.doloop(
             packing_config_data["number_of_packings"],
             env.boundingBox,
             plot_figures=packing_config_data.get("save_plot_figures", True),
             show_grid=packing_config_data["show_grid_plot"],
-            seed_list=packing_config_data["randomness_seed"],
+            seed_list=seed_list,
             config_name=packing_config_data["name"],
             recipe_version=recipe_data["version"],
             image_export_options=packing_config_data.get("image_export_options"),