From 4464958b35c41d4b033df5a7fa993ab4d6a019f4 Mon Sep 17 00:00:00 2001
From: Harry Carey <harry.carey95@gmail.com>
Date: Thu, 25 May 2023 16:40:58 +0200
Subject: [PATCH] removed redundant functions introduced by copilot
---
PyNutil/counting_and_load.py | 2 +-
PyNutil/main.py | 143 ++++++++++++++++++++++++++++++-----
PyNutil/read_and_write.py | 2 +-
3 files changed, 124 insertions(+), 23 deletions(-)
diff --git a/PyNutil/counting_and_load.py b/PyNutil/counting_and_load.py
index b31daa8..efb8017 100644
--- a/PyNutil/counting_and_load.py
+++ b/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
+"""
diff --git a/PyNutil/main.py b/PyNutil/main.py
index b5a8a82..af5a7e8 100644
--- a/PyNutil/main.py
+++ b/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
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index 8de8ce0..a662371 100644
--- a/PyNutil/read_and_write.py
+++ b/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
--
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