Added curvature

Author: c-h-benedetti

exercise-02/i2k_mesh_vesicles/__init__.py

@@ -15,6 +15,7 @@
 from .cut_and_close import cut_and_close
 from .closest_nuclei import spot_to_closest_nucleus
 from .filter_by_volume import find_objects_by_volume
+from .process_curvature import process_curvature
 
 ### > Functions call have to be done wrapped in an operator.
 
@@ -92,6 +93,17 @@ def execute(self, context):
         return {'FINISHED'}
 
 
+class OBJECT_OT_nuclei_curvature(bpy.types.Operator):
+    bl_idname = "object.nuclei_curvature"
+    bl_label = "Nuclei curvature"
+    bl_description = "Process the local vertex curvature of the nuclei"
+
+    def execute(self, context):
+        process_curvature()
+        self.report({'INFO'}, "Produced vertex attribute")
+        return {'FINISHED'}
+
+
 # We make our panel (looking like a tab) in the viewer's side panel 
 # (the one that you can open with N)
 class VIEW3D_PT_vesicles_tools_panel(bpy.types.Panel):
@@ -116,6 +128,7 @@ def draw(self, context):
 
         layout.operator("object.spots_as_empties", text="Spots as empties")
         layout.operator("object.spots_ownership", text="Spots ownership")
+        layout.operator("object.nuclei_curvature", text="Nuclei curvature")
 
 
 # In Blender, you need to register your classes if you want them to be loaded in the pool of operators.
@@ -135,6 +148,7 @@ def unregister_props():
     OBJECT_OT_select_by_volume,
     OBJECT_OT_spots_as_empties,
     OBJECT_OT_spots_ownership,
+    OBJECT_OT_nuclei_curvature,
     VIEW3D_PT_vesicles_tools_panel
 )
 

exercise-02/i2k_mesh_vesicles/process_curvature.py

@@ -0,0 +1,44 @@
+import bpy
+import bmesh
+import mathutils
+
+def _process_curvature(obj, attribute_name):
+    mesh = obj.data
+    bm = bmesh.new()
+    bm.from_mesh(mesh)
+
+    if bm.verts.layers.float.get(attribute_name):
+        curvature_layer = bm.verts.layers.float[attribute_name]
+    else:
+        curvature_layer = bm.verts.layers.float.new(attribute_name)
+    
+    for vert in bm.verts:
+        if len(vert.link_edges) == 0:
+            continue
+        angle_sum = 0.0
+        for edge in vert.link_edges:
+            faces = edge.link_faces
+            if len(faces) == 2:
+                normal1 = faces[0].normal
+                normal2 = faces[1].normal
+                angle = normal1.angle(normal2)
+                angle_sum += angle
+
+        avg_curvature = angle_sum / len(vert.link_edges)
+        vert[curvature_layer] = avg_curvature
+    
+    bm.to_mesh(mesh)
+    bm.free()
+    mesh.update()
+
+def process_curvature():
+    attribute_name = "vertex_curvature"
+    bpy.ops.object.mode_set(mode='OBJECT')
+    for obj in bpy.data.collections['Nuclei'].objects:
+        if obj.type != 'MESH':
+            continue
+        _process_curvature(obj, attribute_name)
+
+
+if __name__ == "__main__":
+    process_curvature()

exercise-03/astrocytes.py

@@ -23,7 +23,7 @@ def makeSourceName(name):
     return os.path.basename(name).split('.')[0]
 
 
-class AstrocytesContactState(object):
+class AstrocytesContact(object):
 
     def __init__(self):
         self.meshes = None
@@ -416,7 +416,7 @@ def show_in_napari(acs):
 
 
 def run_workflow():
-    acs = AstrocytesContactState()
+    acs = AstrocytesContact()
     target_folder = "/home/benedetti/Downloads/I2K/data/astrocytes"
     target_path = os.path.join(target_folder, "contact-surface.ply")
     acs.open_mesh(target_path)
@@ -441,7 +441,7 @@ def run_workflow():
 
 
 def dump():
-    acs = AstrocytesContactState()
+    acs = AstrocytesContact()
     target_folder = "/home/benedetti/Downloads/I2K/data/"
     target_path = os.path.join(target_folder, "test-holes.ply")
     acs.open_mesh(target_path)
@@ -455,4 +455,4 @@ def dump():
 
 if __name__ == "__main__":
     run_workflow()
-    # show_in_napari(acs)
+    # show_in_napari(acs)