Testing with Harry, clean up

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,
@@ -84,7 +83,7 @@ class PyNutil:
             )
         print("quantifying coordinates")
         labeled_points = labelPoints(
-            self.pixel_points, self.atlas_volume, scale_factor=2.5
+            self.pixel_points, self.atlas_volume, scale_factor=1
         )
         self.label_df = PixelCountPerRegion(labeled_points, self.atlas_labels)
         self.labeled_points = labeled_points

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")