From 10f2cae46f68d80d76e01848a44ef00b83deb59c Mon Sep 17 00:00:00 2001
From: Saurabh Mogre <saurabh.mogre@alleninstitute.org>
Date: Tue, 20 Feb 2024 16:39:45 -0800
Subject: [PATCH] Process arguments inside `doloop` function

---
 cellpack/autopack/Analysis.py | 52 ++++++++++++++++-------------------
 1 file changed, 23 insertions(+), 29 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index f1d281e5..03bfec63 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -33,7 +33,7 @@
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.upy import colors as col
 from cellpack.autopack.upy.colors import map_colors
-from cellpack.autopack.utils import check_paired_key, get_paired_key
+from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
 from cellpack.autopack.writers import Writer
 from cellpack.autopack.writers.ImageWriter import ImageWriter
 import concurrent.futures
@@ -2342,17 +2342,10 @@ def pack_one_seed(
 
     def doloop(
         self,
-        number_of_packings,
+        recipe_data,
+        packing_config_data,
         bounding_box,
         get_distance_distribution=True,
-        plot_figures=True,
-        show_grid=True,
-        seed_list=None,
-        config_name="default",
-        recipe_version="1.0.0",
-        image_export_options=None,
-        parallel=False,
-        save_gradient_data_as_image=False,
     ):
         """
         Runs multiple packings of the same recipe in a loop. This workflow
@@ -2363,26 +2356,17 @@ def doloop(
 
         Parameters
         ----------
-        number_of_packing : int
-            Number of repeats of a packing. Default: 1
-        bounding_box : np.ndarray
-            bounding box from the environment
+        recipe_data: dict
+            Dictionary containing recipe data
+        packing_config_data: dict
+            Dictionary containing packing configuration data
+        bounding_box: list
+            List of two lists containing the minimum and maximum coordinates
+            of the bounding box
         get_distance_distribution: bool
-            specify whether to calculate distance distributions
-        render: bool
-            ???
-        plot_figures: bool
-            specify whether to save figures generated by the analyses
-        show_grid: bool
-            specify whether to display packing grid in browser
-        fbox_bb: ???
-            ???
-        seed_list: List
-            list of seeds to use for the packing (for reproducibility)
-        config_name: string
-            name of the configuration used for the packing
-        recipe_version: string
-            version of the recipe used for the packing
+            Whether to calculate and store distance and angle distributions
+        seed_list: list
+            List of seeds to use for packings
 
         Outputs
         -------
@@ -2393,6 +2377,16 @@ def doloop(
             distributions as applicable for each seed, and a combined image
             across seeds
         """
+        number_of_packings = packing_config_data["number_of_packings"]
+        plot_figures = packing_config_data.get("save_plot_figures", True)
+        show_grid = packing_config_data["show_grid_plot"]
+        image_export_options = packing_config_data.get("image_export_options")
+        parallel = packing_config_data.get("parallel", False)
+        save_gradient_data_as_image = packing_config_data.get(
+            "save_gradient_data_as_image", False
+        )
+
+        seed_list = get_seed_list(packing_config_data, recipe_data)
         if seed_list is None:
             seed_list = self.getHaltonUnique(number_of_packings)
         packing_basename = self.env.base_name