removed redundant functions introduced by copilot

PyNutil/counting_and_load.py

@@ -92,4 +92,4 @@ def flat_to_array(flat_file):
    with open(base+".flat","rb") as f:
        b,w,h=struct.unpack(">BII",f.read(9))
        data=struct.unpack(">"+("xBH"[b]*(w*h)),f.read(b*w*h))
-"""
\ No newline at end of file
+"""

PyNutil/main.py

@@ -8,6 +8,68 @@ from datetime import datetime
 
 
 class PyNutil:
+    """A utility class for working with brain atlases and segmentation data.
+
+    Parameters
+    ----------
+    segmentation_folder : str
+        The path to the folder containing the segmentation data.
+    alignment_json : str
+        The path to the alignment JSON file.
+    colour : int
+        The colour of the segmentation data to extract.
+    volume_path : str
+        The name of the atlas volume to use.
+    settings_file : str, optional
+        The path to a JSON file containing the above parameters.
+
+    Raises
+    ------
+    ValueError
+        If any of the required parameters are None.
+
+    Attributes
+    ----------
+    segmentation_folder : str
+        The path to the folder containing the segmentation data.
+    alignment_json : str
+        The path to the alignment JSON file.
+    colour : int
+        The colour of the segmentation data to extract.
+    atlas : str
+        The name of the atlas volume being used.
+    atlas_volume : numpy.ndarray
+        The 3D array representing the atlas volume.
+    atlas_labels : pandas.DataFrame
+        A DataFrame containing the labels for the atlas volume.
+    pixel_points : numpy.ndarray
+        An array of pixel coordinates extracted from the segmentation data.
+    labeled_points : numpy.ndarray
+        An array of labeled pixel coordinates.
+    label_df : pandas.DataFrame
+        A DataFrame containing the pixel counts per region.
+
+    Methods
+    -------
+    load_atlas_data()
+        Loads the atlas volume and labels from disk.
+    get_coordinates(non_linear=True, method='all')
+        Extracts pixel coordinates from the segmentation data.
+    extract_coordinates(non_linear, method)
+        Extracts pixel coordinates from the segmentation data but is only used internally.
+    quantify_coordinates()
+        Quantifies the pixel coordinates by region.
+    label_points()
+        Labels the pixel coordinates by region but is only used internally.
+    count_pixels_per_region(labeled_points)
+        Counts the number of pixels per region but is only used internally.
+    save_analysis(output_folder)
+        Saves the pixel coordinates and pixel counts to disk.
+    write_points_to_meshview(output_folder)
+        Writes the pixel coordinates and labels to a JSON file for visualization but is only used internally.
+
+    """
+
     def __init__(
         self,
         segmentation_folder=None,
@@ -46,6 +108,14 @@ class PyNutil:
         self.atlas_volume, self.atlas_labels = self.load_atlas_data()
 
     def load_atlas_data(self):
+        """Loads the atlas volume and labels from disk.
+
+        Returns
+        -------
+        tuple
+            A tuple containing the atlas volume as a numpy.ndarray and the atlas labels as a pandas.DataFrame.
+
+        """
         # 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"]
@@ -62,6 +132,22 @@ class PyNutil:
         return atlas_volume, atlas_labels
 
     def get_coordinates(self, non_linear=True, method="all"):
+        """Extracts pixel coordinates from the segmentation data.
+
+        Parameters
+        ----------
+        non_linear : bool, optional
+            Whether to use non-linear registration. Default is True.
+        method : str, optional
+            The method to use for extracting coordinates. Valid options are 'per_pixel', 'per_object', or 'all'.
+            Default is 'all'.
+
+        Raises
+        ------
+        ValueError
+            If the specified method is not recognized.
+
+        """
         if not hasattr(self, "atlas_volume"):
             raise ValueError(
                 "Please run build_quantifier before running get_coordinates"
@@ -71,37 +157,55 @@ class PyNutil:
                 f"method {method} not recognised, valid methods are: per_pixel, per_object, or all"
             )
         print("extracting coordinates")
-        pixel_points = self.extract_coordinates(non_linear, method)
-        self.pixel_points = pixel_points
-
-    def extract_coordinates(self, non_linear, method):
-        return folder_to_atlas_space(
+        pixel_points = folder_to_atlas_space(
             self.segmentation_folder,
             self.alignment_json,
             pixel_id=self.colour,
             non_linear=non_linear,
             method=method,
         )
+        self.pixel_points = pixel_points
+
+
 
     def quantify_coordinates(self):
+        """Quantifies the pixel coordinates by region.
+
+        Raises
+        ------
+        ValueError
+            If the pixel coordinates have not been extracted.
+
+        """
         if not hasattr(self, "pixel_points"):
             raise ValueError(
                 "Please run get_coordinates before running quantify_coordinates"
             )
         print("quantifying coordinates")
-        labeled_points = self.label_points()
-        self.label_df = self.count_pixels_per_region(labeled_points)
+        labeled_points = label_points(self.pixel_points, self.atlas_volume, scale_factor=1)
+
+        self.label_df = pixel_count_per_region(labeled_points, self.atlas_labels)
         self.labeled_points = labeled_points
 
         print("quantification complete ✅")
 
-    def label_points(self):
-        return label_points(self.pixel_points, self.atlas_volume, scale_factor=1)
 
-    def count_pixels_per_region(self, labeled_points):
-        return pixel_count_per_region(labeled_points, self.atlas_labels)
 
     def save_analysis(self, output_folder):
+        """Saves the pixel coordinates and pixel counts to different files in the specified
+        output folder.
+
+        Parameters
+        ----------
+        output_folder : str
+            The path to the output folder.
+
+        Raises
+        ------
+        ValueError
+            If the pixel coordinates have not been extracted.
+
+        """
         if not hasattr(self, "pixel_points"):
             raise ValueError("Please run get_coordinates before running save_analysis")
 
@@ -116,13 +220,10 @@ class PyNutil:
             )
 
         else:
-            self.write_points_to_meshview(output_folder)
-        print("analysis saved ✅")
-
-    def write_points_to_meshview(self, output_folder):
-        write_points_to_meshview(
-            self.pixel_points,
-            self.labeled_points,
-            output_folder + "/pixels_meshview.json",
-            self.atlas_labels,
-        )
\ No newline at end of file
+            write_points_to_meshview(
+                self.pixel_points,
+                self.labeled_points,
+                output_folder + "/pixels_meshview.json",
+                self.atlas_labels,
+            )
+        print("analysis saved ✅")
\ No newline at end of file

PyNutil/read_and_write.py

@@ -112,4 +112,4 @@ def files_in_directory(directory):
 
 def read_atlas_volume(atlas_volume_path):
     data, header = nrrd.read(atlas_volume_path)
-    return data
\ No newline at end of file
+    return data