Rename output folders

PyNutil/main.py

@@ -320,8 +320,8 @@ class PyNutil:
         if not os.path.exists(output_folder):
             os.makedirs(output_folder)
             
-        if not os.path.exists(f"{output_folder}/sections_combined_report"):
-            os.makedirs(f"{output_folder}/sections_combined_report")
+        if not os.path.exists(f"{output_folder}/whole_series_report"):
+            os.makedirs(f"{output_folder}/whole_series_report")
 
         if not hasattr(self, "label_df"):
             print("no quantification found so we will only save the coordinates")
@@ -331,14 +331,14 @@ class PyNutil:
         else:
             
             self.label_df.to_csv(
-                f"{output_folder}/sections_combined_report/counts.csv", sep=";", na_rep="", index=False
+                f"{output_folder}/whole_series_report/counts.csv", sep=";", na_rep="", index=False
             )
         if not os.path.exists(f"{output_folder}/per_section_meshview"):
             os.makedirs(f"{output_folder}/per_section_meshview")
         if not os.path.exists(f"{output_folder}/per_section_reports"):
             os.makedirs(f"{output_folder}/per_section_reports")
-        if not os.path.exists(f"{output_folder}/sections_combined_meshview"):
-            os.makedirs(f"{output_folder}/sections_combined_meshview")
+        if not os.path.exists(f"{output_folder}/whole_series_meshview"):
+            os.makedirs(f"{output_folder}/whole_series_meshview")
 
         prev_pl = 0
         prev_cl = 0
@@ -377,14 +377,14 @@ class PyNutil:
             write_points_to_meshview(
                 self.pixel_points,
                 self.labeled_points,
-                f"{output_folder}/sections_combined_meshview/pixels_meshview.json",
+                f"{output_folder}/whole_series_meshview/pixels_meshview.json",
                 self.atlas_labels,
             )
         if hasattr(self, "centroids"):
             write_points_to_meshview(
                 self.centroids,
                 self.labeled_points_centroids,
-                f"{output_folder}/sections_combined_meshview/objects_meshview.json",
+                f"{output_folder}/whole_series_meshview/objects_meshview.json",
                 self.atlas_labels,
             )
         print("analysis saved ✅")