add custom region param and reformat with black

Author: PolarBean

PyNutil/io/file_operations.py

@@ -21,7 +21,7 @@ def save_analysis_output(
     atlas_name=None,
     atlas_path=None,
     label_path=None,
-    settings_file=None
+    settings_file=None,
 ):
     """
     Save the analysis output to the specified folder.

PyNutil/main.py

@@ -32,6 +32,7 @@ def __init__(
         atlas_name=None,
         atlas_path=None,
         label_path=None,
+        custom_region_path=None,
         settings_file=None,
     ):
         """
@@ -51,6 +52,8 @@ def __init__(
             The path to the custom atlas volume file, only specify if you don't want to use brainglobe (default is None).
         label_path : str, optional
             The path to the custom atlas label file, only specify if you don't want to use brainglobe (default is None).
+        custom_region_path : str, optional
+            The path to a custom region id file. This can be found
         settings_file : str, optional
             The path to the settings JSON file. This file contains the above parameters and is used for automation (default is None).
 
@@ -69,6 +72,8 @@ def __init__(
                     segmentation_folder = settings["segmentation_folder"]
                     alignment_json = settings["alignment_json"]
                     colour = settings["colour"]
+                    if "custom_region_path" in settings:
+                        custom_region_path = settings["custom_region_path"]
                     if "atlas_path" in settings and "label_path" in settings:
                         atlas_path = settings["atlas_path"]
                         label_path = settings["label_path"]
@@ -83,7 +88,14 @@ def __init__(
             self.alignment_json = alignment_json
             self.colour = colour
             self.atlas_name = atlas_name
-
+            if custom_region_path:
+                custom_regions_rgb, custom_regions_ids = open_custom_region_file(
+                    custom_region_path
+                )
+            else:
+                custom_regions_rgb, custom_regions_ids = None, None
+            self.custom_regions_rgb = custom_regions_rgb
+            self.custom_regions_ids = custom_regions_ids
             if (atlas_path or label_path) and atlas_name:
                 raise ValueError(
                     "Please specify either atlas_path and label_path or atlas_name. Atlas and label paths are only used for loading custom atlases."
@@ -217,12 +229,11 @@ def save_analysis(self, output_folder):
                 segmentation_folder=self.segmentation_folder,
                 alignment_json=self.alignment_json,
                 colour=self.colour,
-                atlas_name=getattr(self, 'atlas_name', None),
-                atlas_path=getattr(self, 'atlas_path', None),
-                label_path=getattr(self, 'label_path', None),
-                settings_file=getattr(self, 'settings_file', None)
+                atlas_name=getattr(self, "atlas_name", None),
+                atlas_path=getattr(self, "atlas_path", None),
+                label_path=getattr(self, "label_path", None),
+                settings_file=getattr(self, "settings_file", None),
             )
             print(f"Saved output to {output_folder}")
         except Exception as e:
             raise ValueError(f"Error saving analysis: {e}")
-

PyNutil/processing/coordinate_extraction.py

@@ -45,7 +45,6 @@ def get_centroids_and_area(segmentation, pixel_cut_off=0):
     return centroids, area, coords
 
 
-
 def create_threads(
     segmentations,
     slices,
@@ -144,8 +143,8 @@ def folder_to_atlas_space(
     slices = load_visualign_json(quint_alignment)
     segmentations = get_segmentations(folder)
     flat_files, flat_file_nrs = get_flat_files(folder, use_flat)
-    points_list, centroids_list, region_areas_list, centroids_labels, points_labels = initialize_lists(
-        len(segmentations)
+    points_list, centroids_list, region_areas_list, centroids_labels, points_labels = (
+        initialize_lists(len(segmentations))
     )
     threads = create_threads(
         segmentations,
@@ -165,8 +164,8 @@ def folder_to_atlas_space(
         use_flat,
     )
     start_and_join_threads(threads)
-    points, centroids, points_labels, centroids_labels, points_len, centroids_len = process_results(
-        points_list, centroids_list, points_labels, centroids_labels
+    points, centroids, points_labels, centroids_labels, points_len, centroids_len = (
+        process_results(points_list, centroids_list, points_labels, centroids_labels)
     )
     return (
         points,
@@ -180,9 +179,6 @@ def folder_to_atlas_space(
     )
 
 
-
-
-
 def initialize_lists(length):
     """
     Initializes lists for storing points, centroids, and region areas.
@@ -195,8 +191,8 @@ def initialize_lists(length):
     """
     points_list = [np.array([])] * length
     centroids_list = [np.array([])] * length
-    centroids_labels  = [np.array([])] * length
-    points_labels  = [np.array([])] * length
+    centroids_labels = [np.array([])] * length
+    points_labels = [np.array([])] * length
 
     region_areas_list = [
         pd.DataFrame(
@@ -213,7 +209,13 @@ def initialize_lists(length):
             }
         )
     ] * length
-    return points_list, centroids_list, region_areas_list, centroids_labels, points_labels
+    return (
+        points_list,
+        centroids_list,
+        region_areas_list,
+        centroids_labels,
+        points_labels,
+    )
 
 
 def create_threads(
@@ -427,11 +429,16 @@ def segmentation_to_atlas_space(
     )
     scaled_y, scaled_x = get_scaled_pixels(segmentation, pixel_id, y_scale, x_scale)
     if scaled_x is not None:
-        per_point_labels = atlas_map[np.round(scaled_x).astype(int), np.round(scaled_y).astype(int)]
+        per_point_labels = atlas_map[
+            np.round(scaled_x).astype(int), np.round(scaled_y).astype(int)
+        ]
     else:
         per_point_labels = np.array([])
     if scaled_centroidsX is not None:
-        per_centroid_labels = atlas_map[np.round(scaled_centroidsX).astype(int), np.round(scaled_centroidsY).astype(int)]
+        per_centroid_labels = atlas_map[
+            np.round(scaled_centroidsX).astype(int),
+            np.round(scaled_centroidsY).astype(int),
+        ]
     else:
         per_centroid_labels = np.array([])
 
@@ -458,9 +465,12 @@ def segmentation_to_atlas_space(
     points_list[index] = np.array(points if points is not None else [])
     centroids_list[index] = np.array(centroids if centroids is not None else [])
     region_areas_list[index] = region_areas
-    centroids_labels[index] = np.array(per_centroid_labels if centroids is not None else [])
+    centroids_labels[index] = np.array(
+        per_centroid_labels if centroids is not None else []
+    )
     points_labels[index] = np.array(per_point_labels if points is not None else [])
 
+
 def get_triangulation(slice_dict, reg_width, reg_height, non_linear):
     """
     Gets the triangulation for the slice.

PyNutil/processing/counting_and_load.py

@@ -79,7 +79,7 @@ def pixel_count_per_region(
         counts_per_label, columns=["idx", "pixel_count", "object_count"]
     )
     for clc, lcc in zip(counted_labels_centroids, label_counts_centroids):
-        df_counts_per_label.loc[df_counts_per_label['idx'] == clc, 'object_count'] = lcc
+        df_counts_per_label.loc[df_counts_per_label["idx"] == clc, "object_count"] = lcc
     new_rows = []
     for index, row in df_counts_per_label.iterrows():
         mask = df_label_colours["idx"] == row["idx"].astype(int)

PyNutil/processing/utils.py

@@ -218,9 +218,7 @@ def process_results(points_list, centroids_list, points_labels, centroids_labels
         centroids for centroids in centroids_list if None not in centroids
     ]
     points_labels = [pl for pl in points_labels if None not in pl]
-    centroids_labels = [
-        cl for cl in centroids_labels if None not in cl
-    ]
+    centroids_labels = [cl for cl in centroids_labels if None not in cl]
     if len(points_list) == 0:
         points = np.array([])
         points_labels = np.array([])

demos/basic_example.py

@@ -6,8 +6,12 @@
 
 # Configuration
 script_dir = os.path.dirname(os.path.abspath(__file__))
-segmentation_folder = os.path.join(script_dir, "../tests/test_data/nonlinear_allen_mouse/")
-alignment_json = os.path.join(script_dir, "../tests/test_data/nonlinear_allen_mouse/alignment.json")
+segmentation_folder = os.path.join(
+    script_dir, "../tests/test_data/nonlinear_allen_mouse/"
+)
+alignment_json = os.path.join(
+    script_dir, "../tests/test_data/nonlinear_allen_mouse/alignment.json"
+)
 colour = [0, 0, 0]
 atlas_name = "allen_mouse_25um"
 output_folder = "../test_result/bg_test"

demos/basic_example_custom_atlas.py

@@ -33,7 +33,6 @@
     label_path=os.path.join(
         script_dir, "../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv"
     ),
-
 )
 pnt.get_coordinates(object_cutoff=0, use_flat=False)
 pnt.quantify_coordinates()