This commit refactors the PyNutil class to make it more modular and easier to...

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/folder_of_segmentations_to_meshview.py

@@ -36,7 +36,7 @@ label_path = "../annotation_volumes//allen2022_colours.csv"
 label_df = pd.read_csv(label_path)
 # read the annotation volume, it also has a header but we don't need it
 # now we can get the labels for each point
-labels = labelPoints(points, data, scale_factor=2.5)
+labels = labelPoints(points, data, scale_factor=1)
 # save points to a meshview json
 WritePointsToMeshview(points, labels, "../outputs/points.json", label_df)
 

PyNutil/main.py

@@ -6,7 +6,6 @@ import json
 import pandas as pd
 from datetime import datetime
 
-
 class PyNutil:
     def __init__(
         self,

PyNutil/metadata/config.json

@@ -5,7 +5,7 @@
     },
     "allen2017":{
         "labels":"allen2017_colours.csv",
-        "volume":"annotation_10_reoriented_2017.nrrd"
+        "volume":"annotation_25_reoriented_2017.nrrd"
     },
     "allen2022":{
         "labels":"allen2022_colours.csv",

PyNutil/oop_example.py

+class Demo:
+        def __init__(self, test):
+            self.test = test
+    
+        def print_test(self):
+            print(self.test)
+            self.output = 'success'
+    
+    
+    
+    
+    
+    
+   
\ No newline at end of file

PyNutil/testing_openflatfile.py

@@ -3,9 +3,10 @@ import numpy as np
 import struct
 import pandas as pd
 import matplotlib.pyplot as plt
+import cv2
 
 """read flat file and write into an np array"""
-
+np.set_printoptions(suppress=True)
 with open(base, "rb") as f:
     # i dont know what b is, w and h are the width and height that we get from the
     # flat file header
@@ -27,12 +28,17 @@ with open(base, "rb") as f:
             image[y, x] = imagedata[x + y * w]
 
     image_arr = np.array(image)
+    print(image_arr.shape)
+    image_arr = cv2.resize(image_arr,(9848,12784),interpolation=cv2.INTER_NEAREST)
+    print(image_arr.shape)
+    val,count = np.unique(image_arr, return_counts=True)
+    print(list(zip(val,count)))
 
 # show image with plt.imshow(image_arr)
 
 """assign label file values into image array"""
 
-labelfile = pd.read_csv(r"../annotation_volumes\allen2017_colours.csv")
+labelfile = pd.read_csv(r"../metadata/annotation_volumes\allen2017_colours.csv")
 allen_id_image = np.zeros((h, w))  # create an empty image array
 
 """for ph in range(h):

test/test5_NOP_s037.json

-{   "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
-    "label_path": "../annotation_volumes/allen2017_colours.csv",
-    "segmentation_folder": "../test_data/ttA_2877_NOP_s037_seg",
-    "alignment_json": "../test_data/ttA_2877_NOP_horizontal_final_2017.json",
+{   "volume_path": "allen2017",
+    "label_path": "annotation_volumes/allen2017_colours.csv",
+    "segmentation_folder": "test_data/ttA_2877_NOP_s037_seg",
+    "alignment_json": "test_data/ttA_2877_NOP_horizontal_final_2017.json",
     "nonlinear": false,
     "colour": [0, 0, 255],
-    "points_json_path": "../outputs/test5_points.json",
-    "counts_per_label_name": "../outputs/test5_counts_per_allenID_2017_false.csv"
+    "points_json_path": "outputs/test5_points.json",
+    "counts_per_label_name": "outputs/test5_counts_per_allenID_2017_false.csv"
 }
 

testOOP.py

 from PyNutil import PyNutil
 
-pnt = PyNutil(settings_file=r"test/test4_2017.json")
+pnt = PyNutil(settings_file=r"test/test5_NOP_s037.json")
 # pnt.build_quantifier()
 
 pnt.get_coordinates()
 
 pnt.quantify_coordinates()
 
-pnt.save_analysis("outputs/test4_2017")
+pnt.save_analysis("outputs/test5_NOP_25")