Merge branch 'main' of https://github.com/Neural-Systems-at-UIO/PyNutil

PyNutil/read_and_write.py

@@ -32,8 +32,15 @@ def load_visualign_json(filename):
           # save with .json extension need to see if i can remove this
         with open(filename.replace(".waln", ".json").replace(".wwrp", ".json"), "w") as f:
             json.dump(lz_compat_file, f, indent=4)
+        for slice in slices:
+            if "markers" in slice:
+                slice["markers"] = [
+                    [marker["x"], marker["y"], marker["nx"], marker["ny"]
+                     ] for marker in slice["markers"]
+                ]
     else:
         slices = vafile["slices"]
+    
     slices = propagate(slices)
     return slices
 

PyNutil/visualign_deformations.py

 """This code was written by Gergely Csucs and Rembrandt Bakker"""
-
 import numpy as np
-
+from scipy.spatial import Delaunay
 
 def triangulate(w, h, markers):
     vertices = [
@@ -10,6 +9,7 @@ def triangulate(w, h, markers):
         [-0.1 * w,  1.1 * h, -0.1 * w,  1.1 * h],
         [ 1.1 * w,  1.1 * h,  1.1 * w,  1.1 * h],
     ]
+
     edges = [0] * ((len(markers) + 4) * (len(markers) + 4 - 1) // 2)
     triangles = [Triangle(0, 1, 2, vertices, edges), Triangle(1, 2, 3, vertices, edges)]
     edges[0] = edges[1] = edges[4] = edges[5] = 2
@@ -233,3 +233,22 @@ class Triangle:
             + (self.B[1] - self.A[1]) * uv1[ok, 0]
             + (self.C[1] - self.A[1]) * uv1[ok, 1]
         )
+
+
+##below this is a test 
+
+
+vertices = [[0, 0,43.54623148539514, 26.174656909777603],
+            [0, 0,90.8065913697207, 46.20231798893295],
+            [0, 0,56.29635559428633, 51.23696264352707],
+            [0, 0,90.87928419178107, 15.497996125973435],
+            [0, 0,33.966820908745454, 11.999395004637503],
+            [0, 0,37.29543353675751, 79.4420010252766]]
+triangulation = triangulate(100,100,vertices)
+new_coords = transform(triangulation, new_coords[0], new_coords[1])
+
+
+from scipy.spatial import Delaunay
+
+# assuming you have a list of points called "points"
+tri = Delaunay(points)