Merge branch 'region_mesh_redux' of github.com:Hjorthmedh/Snudda into…

… region_mesh_redux
Hjorthmedh · Oct 10, 2023 · a3d8d01 · a3d8d01
2 parents 63e054f + bca990b
commit a3d8d01
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Showing 16 changed files with 75,605 additions and 1 deletion.
diff --git a/snudda/data/mesh/GPe-left.obj b/snudda/data/mesh/GPe-left.obj
diff --git a/snudda/data/mesh/GPe-right.obj b/snudda/data/mesh/GPe-right.obj
diff --git a/snudda/data/mesh/GPi-left.obj b/snudda/data/mesh/GPi-left.obj
diff --git a/snudda/data/mesh/GPi-right.obj b/snudda/data/mesh/GPi-right.obj
diff --git a/snudda/data/mesh/SNc-left.obj b/snudda/data/mesh/SNc-left.obj
diff --git a/snudda/data/mesh/SNc-right.obj b/snudda/data/mesh/SNc-right.obj
diff --git a/snudda/data/mesh/SNr-left.obj b/snudda/data/mesh/SNr-left.obj
diff --git a/snudda/data/mesh/SNr-right.obj b/snudda/data/mesh/SNr-right.obj
diff --git a/snudda/data/mesh/STN-left.obj b/snudda/data/mesh/STN-left.obj
diff --git a/snudda/data/mesh/STN-right.obj b/snudda/data/mesh/STN-right.obj
diff --git a/snudda/data/mesh/Striatum-d-left.obj b/snudda/data/mesh/Striatum-d-left.obj
diff --git a/snudda/data/mesh/Striatum-d-right.obj b/snudda/data/mesh/Striatum-d-right.obj
diff --git a/snudda/data/mesh/Striatum-v-left.obj b/snudda/data/mesh/Striatum-v-left.obj
diff --git a/snudda/data/mesh/Striatum-v-right.obj b/snudda/data/mesh/Striatum-v-right.obj
diff --git a/snudda/data/mesh/cut_mesh.py b/snudda/data/mesh/cut_mesh.py
@@ -0,0 +1,24 @@
+import open3d as o3d
+import numpy as np
+
+
+def cut_mesh(path, save=False):
+    mesh = o3d.io.read_triangle_mesh(path)
+    x, y, z = np.array(mesh.vertices).T
+    left = z > np.mean(z)  # apparent mediolateral axis
+    left_idxs = np.where(left)[0]
+    left_mesh = mesh.select_by_index(left_idxs)
+    right_idxs = np.where(~left)[0]
+    right_mesh = mesh.select_by_index(right_idxs)
+
+    if save:
+        base = path.strip('.obj')
+        o3d.io.write_triangle_mesh(filename=base+'-left.obj', mesh=left_mesh)
+        o3d.io.write_triangle_mesh(filename=base+'-right.obj', mesh=right_mesh)
+
+    return mesh, right_mesh, left_mesh
+
+if __name__ == '__main__':
+    meshes = ['Striatum-v.obj', 'Striatum-d.obj', 'GPe.obj', 'GPi.obj', 'STN.obj', 'SNr.obj', 'SNc.obj']
+    for mesh_name in meshes:
+        cut_mesh(mesh_name, save=True)
diff --git a/snudda/place/region_mesh_redux.py b/snudda/place/region_mesh_redux.py
@@ -259,7 +259,7 @@ def __init__(self):
 
 if __name__ == "__main__":
 
-    mesh_path="/home/hjorth/HBP/Snudda/snudda/data/mesh/Striatum-dorsal-right-hemisphere.obj"
+    mesh_path="../data/mesh/Striatum-d-right.obj"
 
     # nep = NeuronPlacer(mesh_path=mesh_path, d_min=10e-6, n_putative_points=10000000)
     nep = NeuronPlacer(mesh_path=mesh_path, d_min=10e-6, n_putative_points=None, putative_density=100e3)