From fd78ba58dc0856cbfe70cde83851dac0298a0728 Mon Sep 17 00:00:00 2001
From: Harry Carey <harry.carey95@gmail.com>
Date: Thu, 25 May 2023 11:56:13 +0200
Subject: [PATCH] This commit refactors the PyNutil class to make it more
 modular and easier to read and understand. The load_atlas_data method has
 been extracted to a separate function, and the coordinate extraction, pixel
 labeling and counting, and writing of points to Meshview have been extracted
 to separate methods. These changes make the code more modular and easier to
 maintain.

---
 PyNutil/dream_workflow.py |  1 +
 PyNutil/main.py           | 43 +++++++++++++++++++++++++--------------
 2 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/PyNutil/dream_workflow.py b/PyNutil/dream_workflow.py
index eedf748..1904c43 100644
--- a/PyNutil/dream_workflow.py
+++ b/PyNutil/dream_workflow.py
@@ -30,4 +30,5 @@ quantifier.get_objects()
 
 quantifier.get_loads()
 
+
 quantifier.save_segmentation_atlas_overlays()
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 33927b6..878cea3 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -43,20 +43,23 @@ class PyNutil:
         self.alignment_json = alignment_json
         self.colour = colour
         self.atlas = volume_path
+        self.atlas_volume, self.atlas_labels = self.load_atlas_data()
+
+    def load_atlas_data(self):
         # load the metadata json as well as the path to stored data files
         # this could potentially be moved into init
         atlas_root_path = self.config["annotation_volume_directory"]
         current_atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
         print("loading atlas volume")
         startTime = datetime.now()
-        self.atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
+        atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
         time_taken = datetime.now() - startTime
         print(f"atlas volume loaded in: {time_taken} ✅")
         atlas_label_path = self.config["annotation_volumes"][self.atlas]["labels"]
         print("loading atlas labels")
-        self.atlas_labels = pd.read_csv(atlas_root_path + atlas_label_path)
+        atlas_labels = pd.read_csv(atlas_root_path + atlas_label_path)
         print("atlas labels loaded ✅")
-
+        return atlas_volume, atlas_labels
 
     def get_coordinates(self, nonLinear=True, method="all"):
         if not hasattr(self, "atlas_volume"):
@@ -68,14 +71,17 @@ class PyNutil:
                 f"method {method} not recognised, valid methods are: per_pixel, per_object, or all"
             )
         print("extracting coordinates")
-        pixel_points = FolderToAtlasSpace(
+        pixel_points = self.extract_coordinates(nonLinear, method)
+        self.pixel_points = pixel_points
+
+    def extract_coordinates(self, nonLinear, method):
+        return FolderToAtlasSpace(
             self.segmentation_folder,
             self.alignment_json,
             pixelID=self.colour,
             nonLinear=nonLinear,
             method=method,
         )
-        self.pixel_points = pixel_points
 
     def quantify_coordinates(self):
         if not hasattr(self, "pixel_points"):
@@ -83,14 +89,18 @@ class PyNutil:
                 "Please run get_coordinates before running quantify_coordinates"
             )
         print("quantifying coordinates")
-        labeled_points = labelPoints(
-            self.pixel_points, self.atlas_volume, scale_factor=2.5
-        )
-        self.label_df = PixelCountPerRegion(labeled_points, self.atlas_labels)
+        labeled_points = self.label_points()
+        self.label_df = self.count_pixels_per_region(labeled_points)
         self.labeled_points = labeled_points
 
         print("quantification complete ✅")
 
+    def label_points(self):
+        return labelPoints(self.pixel_points, self.atlas_volume, scale_factor=2.5)
+
+    def count_pixels_per_region(self, labeled_points):
+        return PixelCountPerRegion(labeled_points, self.atlas_labels)
+
     def save_analysis(self, output_folder):
         if not hasattr(self, "pixel_points"):
             raise ValueError("Please run get_coordinates before running save_analysis")
@@ -106,10 +116,13 @@ class PyNutil:
             )
 
         else:
-            WritePointsToMeshview(
-                self.pixel_points,
-                self.labeled_points,
-                output_folder + "/pixels_meshview.json",
-                self.atlas_labels,
-            )
+            self.write_points_to_meshview(output_folder)
         print("analysis saved ✅")
+
+    def write_points_to_meshview(self, output_folder):
+        WritePointsToMeshview(
+            self.pixel_points,
+            self.labeled_points,
+            output_folder + "/pixels_meshview.json",
+            self.atlas_labels,
+        )
-- 
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