Small fixes before autumn 2025 semester

src/Carnutes/create_mesh.py

@@ -1,6 +1,11 @@
+"""
+This function creates a mesh from a Rhino point cloud.
+"""
+
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 

src/Carnutes/database_recap.py

@@ -3,8 +3,9 @@
 """
 
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 

src/Carnutes/draw_connectivity_grah.py

@@ -4,8 +4,8 @@
 
 #! python3
 
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 

src/Carnutes/find_multiple_trees_with_optimisation.py

@@ -1,6 +1,11 @@
+"""
+This function finds multiple trees in the database that best fit the given element, starting by the element that has the most connections to make. It also optimizes for the tree usage.
+"""
+
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 
@@ -59,20 +64,32 @@ def main():
     )
 
     # Create the model
-    current_model = interact_with_rhino.create_model_from_rhino_selection()
+    current_model, layer_ids = interact_with_rhino.create_model_from_rhino_selection()
 
     # For each element in the model, replace it with a point cloud. Starting from the elements with the highest degree.
     db_path = os.path.dirname(os.path.realpath(__file__)) + "/database/tree_database.fs"
 
     all_rmse = []
 
-    for element in current_model.elements:
+    for i, element in enumerate(current_model.elements):
         if element.type == elem.ElementType.Point:
             continue
-        reference_pc_as_list = []
+        reference_pc_as_list = [
+            [
+                element.geometry.PointAtStart.X,
+                element.geometry.PointAtStart.Y,
+                element.geometry.PointAtStart.Z,
+            ],
+            [
+                element.geometry.PointAtEnd.X,
+                element.geometry.PointAtEnd.Y,
+                element.geometry.PointAtEnd.Z,
+            ],
+        ]
         element_guid = element.GUID
         target_diameter = element.diameter
-        reference_pc_as_list = element.locations
+        for location in element.locations:
+            reference_pc_as_list.append(location)
 
         # at this point the reference_pc_as_list should contain the points, but they are not ordered. We need to order them.
         reference_pc_as_list = geometry.sort_points(reference_pc_as_list)
@@ -101,7 +118,9 @@ def main():
         best_tree.create_mesh()
 
         tree_mesh = conversions.convert_carnutes_mesh_to_rhino_mesh(best_tree.mesh)
-        scriptcontext.doc.Objects.AddMesh(tree_mesh)
+        attributes = Rhino.DocObjects.ObjectAttributes()
+        attributes.LayerIndex = layer_ids[i]
+        scriptcontext.doc.Objects.AddMesh(tree_mesh, attributes)
 
     return all_rmse
 

src/Carnutes/find_multiple_trees_without_optimisation.py

@@ -1,6 +1,11 @@
+"""
+This function finds multiple trees in the database that best fit the given element, starting by the element that has the most connections to make. It does not optimize for the tree usage.
+"""
+
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 
@@ -48,19 +53,34 @@ def crop(tree: tree, bounding_volume: Rhino.Geometry.Brep):
 
 def main():
     # Create the model
-    current_model = interact_with_rhino.create_model_from_rhino_selection()
+    current_model, layer_ids = interact_with_rhino.create_model_from_rhino_selection()
 
     # For each element in the model, replace it with a point cloud. Starting from the elements with the highest degree.
     db_path = os.path.dirname(os.path.realpath(__file__)) + "/database/tree_database.fs"
 
     all_rmse = []
 
-    for element in current_model.elements:
+    for i, element in enumerate(current_model.elements):
         if element.type == elem.ElementType.Point:
             continue
 
         # at this point the reference_pc_as_list should contain the points, but they are not ordered. We need to order them.
-        reference_pc_as_list = geometry.sort_points(element.locations)
+        reference_pc_as_list = [
+            [
+                element.geometry.PointAtStart.X,
+                element.geometry.PointAtStart.Y,
+                element.geometry.PointAtStart.Z,
+            ],
+            [
+                element.geometry.PointAtEnd.X,
+                element.geometry.PointAtEnd.Y,
+                element.geometry.PointAtEnd.Z,
+            ],
+        ]
+        for location in element.locations:
+            reference_pc_as_list.append(location)
+        reference_pc_as_list = geometry.sort_points(reference_pc_as_list)
+        print(reference_pc_as_list)
         reference_skeleton = geometry.Pointcloud(reference_pc_as_list)
         best_tree, best_rmse, init_rotation = element.allocate_trees(
             db_path=db_path, optimized=False
@@ -80,7 +100,9 @@ def main():
         best_tree.create_mesh()
 
         tree_mesh = conversions.convert_carnutes_mesh_to_rhino_mesh(best_tree.mesh)
-        scriptcontext.doc.Objects.AddMesh(tree_mesh)
+        attributes = Rhino.DocObjects.ObjectAttributes()
+        attributes.LayerIndex = layer_ids[i]
+        scriptcontext.doc.Objects.AddMesh(tree_mesh, attributes)
 
     return all_rmse
 

src/Carnutes/find_single_tree.py

@@ -1,10 +1,11 @@
 """
-This is a dummy function, to test out the bones of the project.
+This function finds a single tree in the database that best fits the given element.
 """
 
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 
@@ -59,14 +60,15 @@ def main():
     """
 
     # Create the model
-    current_model = interact_with_rhino.create_model_from_rhino_selection()
+    current_model, layer_ids = interact_with_rhino.create_model_from_rhino_selection()
     if current_model is None:
         return
 
     # Ask user which element (s)he wants to replace with a point cloud
     (
         element_geometry,
         element_guid,
+        layer_index,
     ) = interact_with_rhino.select_single_element_to_replace()
 
     for element in current_model.elements:
@@ -75,7 +77,18 @@ def main():
             reference_diameter = element.diameter
             break
 
-    reference_pc_as_list = []
+    reference_pc_as_list = [
+        [
+            target.geometry.PointAtStart.X,
+            target.geometry.PointAtStart.Y,
+            target.geometry.PointAtStart.Z,
+        ],
+        [
+            target.geometry.PointAtEnd.X,
+            target.geometry.PointAtEnd.Y,
+            target.geometry.PointAtEnd.Z,
+        ],
+    ]
     # if isinstance(target.geometry, Rhino.Geometry.NurbsCurve):
     for vertex in current_model.connectivity_graph.graph.vs:
         if vertex["guid"] == target.GUID:
@@ -117,7 +130,9 @@ def main():
     my_tree.create_mesh()
 
     tree_mesh = conversions.convert_carnutes_mesh_to_rhino_mesh(my_tree.mesh)
-    scriptcontext.doc.Objects.AddMesh(tree_mesh)
+    attributes = Rhino.DocObjects.ObjectAttributes()
+    attributes.LayerIndex = layer_index
+    scriptcontext.doc.Objects.AddMesh(tree_mesh, attributes)
 
 
 if __name__ == "__main__":

src/Carnutes/output_database.py

@@ -4,8 +4,8 @@
 
 #! python3
 
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 

src/Carnutes/reset_database.py

@@ -3,20 +3,18 @@
 """
 
 #! python3
-# r: numpy==1.26.4
-# r: open3d==0.18.0
+
+# r: numpy==2.0.2
+# r: open3d==0.19.0
 # r: ZODB==6.0
 # r: igraph==0.11.6
 
-import ZODB
-import ZODB.FileStorage
 import open3d as o3d
 
 # import Rhino
 
 import os
 import transaction
-import BTrees.OOBTree
 import time
 
 import utils.tree as tree

src/Carnutes/utils/element.py

@@ -113,7 +113,21 @@ def allocate_trees(self, db_path: str, optimized: bool = False):
                 "The diameter of the element is not set. Check the layer name of the element in Rhino."
             )
         target_diameter = self.diameter
-        reference_pc_as_list = geometry.sort_points(self.locations)
+        reference_pc_as_list = [
+            [
+                self.geometry.PointAtStart.X,
+                self.geometry.PointAtStart.Y,
+                self.geometry.PointAtStart.Z,
+            ],
+            [
+                self.geometry.PointAtEnd.X,
+                self.geometry.PointAtEnd.Y,
+                self.geometry.PointAtEnd.Z,
+            ],
+        ]
+        for location in self.locations:
+            reference_pc_as_list.append(location)
+        reference_pc_as_list = geometry.sort_points(reference_pc_as_list)
         reference_skeleton = geometry.Pointcloud(reference_pc_as_list)
         if optimized:
             (

src/Carnutes/utils/interact_with_rhino.py

@@ -1,5 +1,4 @@
 from utils import model, warnings, geometry, element
-from utils.element import Element
 import Rhino
 
 
@@ -35,6 +34,8 @@ def create_model_from_rhino_selection(max_elements: int = 100000):
         The maximum number of elements that can be selected. Default is 100000.
     :return: model.Model
         The model created from the selected geometries.
+    :return: Rhino.DocObjects.Layer.LayerIndex
+        The layer index of the selected geometries.
     """
 
     go = Rhino.Input.Custom.GetObject()
@@ -73,10 +74,12 @@ def create_model_from_rhino_selection(max_elements: int = 100000):
         Rhino.RhinoDoc.ActiveDoc.Layers[layer_id].Name for layer_id in layer_ids
     ]
     elements = [
-        Element(converted_geometries[i], go.Object(i).ObjectId, float(layer_names[i]))
+        element.Element(
+            converted_geometries[i], go.Object(i).ObjectId, float(layer_names[i])
+        )
         for i in range(go.ObjectCount)
     ]
-    return model.Model(elements)
+    return model.Model(elements), layer_ids
 
 
 def select_single_element_to_replace():
@@ -87,6 +90,8 @@ def select_single_element_to_replace():
         The geometry of the selected element.
     :return: str
         The GUID of the selected element.
+    :return: int
+        The layer index of the selected element.
     """
     go = Rhino.Input.Custom.GetObject()
     go.SetCommandPrompt("Select the element to replace with a point cloud")
@@ -96,10 +101,11 @@ def select_single_element_to_replace():
     go.GetMultiple(1, 1)
     element_geometry = go.Object(0).Geometry()
     element_guid = go.Object(0).ObjectId
+    layer_index = go.Object(0).Object().Attributes.LayerIndex
     if go.CommandResult() != Rhino.Commands.Result.Success:
         print("No object selected.")
         return
-    return element_geometry, element_guid
+    return element_geometry, element_guid, layer_index
 
 
 def generic_object_getter(