From 6ba5a468d2b40f2c8997f4396ab166d9193aec1d Mon Sep 17 00:00:00 2001
From: Saurabh Mogre <saurabh.mogre@alleninstitute.org>
Date: Wed, 10 Jan 2024 14:03:57 -0800
Subject: [PATCH] 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 <meganrm@gmail.com>
---
 cellpack/autopack/Analysis.py                 |   4 +-
 cellpack/autopack/Environment.py              |   6 +-
 cellpack/autopack/utils.py                    |  23 +
 cellpack/bin/pack.py                          |   6 +-
 cellpack/tests/geometry/sphere_2.obj          | 483 ++++++++++++++++++
 cellpack/tests/geometry/sphere_4.obj          | 483 ++++++++++++++++++
 .../recipes/v2/test_nested_mesh_gradient.json | 104 ++++
 .../tests/recipes/v2/test_variable_count.json |   3 +-
 8 files changed, 1105 insertions(+), 7 deletions(-)
 create mode 100644 cellpack/tests/geometry/sphere_2.obj
 create mode 100644 cellpack/tests/geometry/sphere_4.obj
 create mode 100644 cellpack/tests/recipes/v2/test_nested_mesh_gradient.json

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 66d66d34a..59db980df 100644
--- a/cellpack/autopack/Analysis.py
+++ b/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")
diff --git a/cellpack/autopack/Environment.py b/cellpack/autopack/Environment.py
index 0ca92c806..a61cb22bb 100644
--- a/cellpack/autopack/Environment.py
+++ b/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
diff --git a/cellpack/autopack/utils.py b/cellpack/autopack/utils.py
index 1f720d006..01d856ce0 100644
--- a/cellpack/autopack/utils.py
+++ b/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
diff --git a/cellpack/bin/pack.py b/cellpack/bin/pack.py
index 3c420e2e3..6e8b92c13 100644
--- a/cellpack/bin/pack.py
+++ b/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"),
diff --git a/cellpack/tests/geometry/sphere_2.obj b/cellpack/tests/geometry/sphere_2.obj
new file mode 100644
index 000000000..1862cf481
--- /dev/null
+++ b/cellpack/tests/geometry/sphere_2.obj
@@ -0,0 +1,483 @@
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diff --git a/cellpack/tests/recipes/v2/test_nested_mesh_gradient.json b/cellpack/tests/recipes/v2/test_nested_mesh_gradient.json
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--- /dev/null
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+{
+    "version": "1.0.0",
+    "format_version": "2.1",
+    "name": "test_nested_mesh_gradient",
+    "bounding_box": [
+        [
+            -5,
+            -5,
+            -5
+        ],
+        [
+            5,
+            5,
+            5
+        ]
+    ],
+    "gradients": {
+        "surface_gradient": {
+            "description": "gradient based on distance from the surface of a mesh",
+            "pick_mode": "rnd",
+            "mode": "surface",
+            "mode_settings": {
+                "object": "nucleus",
+                "scale_to_next_surface": false,
+                "weight_mode": "exponential"
+            },
+            "weight_mode_settings": {
+                "decay_length": 0.3
+            }
+        }
+    },    
+    "objects": {
+        "membrane_mesh": {
+            "type": "mesh",
+            "color": [
+                1,
+                0,
+                1
+            ],
+            "representations": {
+                "mesh": {
+                    "path": "cellpack/tests/geometry",
+                    "name": "sphere_4.obj",
+                    "format": "obj"
+                }
+            }
+        },
+        "nucleus_mesh": {
+            "type": "mesh",
+            "color": [
+                0,
+                1,
+                1
+            ],
+            "representations": {
+                "mesh": {
+                    "path": "cellpack/tests/geometry",
+                    "name": "sphere_2.obj",
+                    "format": "obj"
+                }
+            }
+        },
+        "primitive_sphere": {
+            "type": "single_sphere",
+            "color": [
+                0.2,
+                0.7,
+                0.1
+            ],
+            "radius": 0.5,
+            "packing_mode": "gradient",
+            "gradient": "surface_gradient"
+        }
+    },
+    "composition": {
+        "bounding_area": {
+            "regions": {
+                "interior": [
+                    "membrane"
+                ]
+            }
+        },
+        "membrane": {
+            "object": "membrane_mesh",
+            "count": 1,
+            "regions": {
+                "interior": [
+                    "nucleus",
+                    {
+                        "object": "primitive_sphere",
+                        "count": 100
+                    }
+                ]
+            }
+        },
+        "nucleus": {
+            "object": "nucleus_mesh",
+            "count": 1,
+            "regions": {
+                "interior": []
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/cellpack/tests/recipes/v2/test_variable_count.json b/cellpack/tests/recipes/v2/test_variable_count.json
index af06457dc..94bcf165c 100644
--- a/cellpack/tests/recipes/v2/test_variable_count.json
+++ b/cellpack/tests/recipes/v2/test_variable_count.json
@@ -83,5 +83,6 @@
                 "max": 15
             }
         }
-    }
+    },
+    "randomness_seed": 0
 }
\ No newline at end of file