ibois-epfl · DamienGilliard · Sep 5, 2024 · Jul 30, 2024 · Aug 4, 2024 · Aug 5, 2024
diff --git a/.github/workflows/test_geo_basics.yml b/.github/workflows/test_geo_basics.yml
@@ -21,10 +21,9 @@ jobs:
         with:
           activate-environment: Carnutes
           environment-file: environment.yml
-        
+
       - name: activate conda environment
         run: conda activate Carnutes
 
       - name: run tests
         run: pytest tests/test_geometry_basics.py
-
diff --git a/.gitignore b/.gitignore
@@ -162,4 +162,4 @@ cython_debug/
 #.idea/
 
 # MacOS specific
-.DS_Store
+.DS_Store
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,7 +1,7 @@
 As this project is seen as an experiment in parallel to an architecture studio, this repo is not going to be maintained on the long term. Another repository will be opened when the long-term code is developped, as part of Damien Gilliard's PhD thesis. Therefore, any contribution made by outside people is welcome but keep in mind the "one shot" nature of this repository.
 
 # Contributing
-To contribute to this repo, open a new branch, create a pull request, push your modifications, and explain in the thread what you want to change / add. 
+To contribute to this repo, open a new branch, create a pull request, push your modifications, and explain in the thread what you want to change / add.
 
 The commit message guidelines are:
 ```bash
@@ -17,6 +17,13 @@ git commit -m "REFACTOR:<description>"    <--- for refactored code
 git commit -m "MERGE:<description>"       <--- for merging operations
 ```
 
+The description of the pull request should ideally contain:
+- An explicit name. e.g. "improvement of registration of tree skeleton using pcl ICP registration" , and not "registration icp pcl"
+- A description in a few lines of the changes made.
+- A check if a test was adapted or created
+- If it is linked to an issue, mark it as such in the Developmement section of the PR.
+- As long as it is under development, mark it as Draft
+
 # Naming convention
 All code is in python
 [usual python naming convention](https://peps.python.org/pep-0008/#naming-conventions)
@@ -58,4 +65,4 @@ class MyClass(object):
         """
         a_lot = 1
         return a_lot
-```
+```
diff --git a/Carnutes.rhc b/Carnutes.rhc
@@ -1,29 +1,17 @@
 <?xml version="1.0" encoding="utf-8"?>
 <!--This file was generated by Rhinoceros, DO NOT modify this file-->
-<RhinoUI major_ver="1" minor_ver="0" created_on_platform="Mac" created_on_rhino_version="8.9.24194.18122" name="Standard Toolbars">
+<RhinoUI major_ver="1" minor_ver="0" created_on_platform="Mac" created_on_rhino_version="8.10.24228.13001" name="Standard Toolbars">
   <!--Window Layout display name for this file-->
   <name>
     <locale_1033>Standard Toolbars</locale_1033>
   </name>
   <!--Tab panel collection definitions and dock bar placement information-->
   <dock_bars major_ver="1" minor_ver="0">
     <dock_bar guid="171011a9-a956-41ee-853e-3ccc0c0db1d8" source_group_file="c7da84fc-2991-4824-832a-4f2509bd0ede" source_group="ac3566f9-fe75-4258-9210-b1e9c05a5881">
-      <placement dock_location="Top" recent_dock_location="Top" dock_band_size="36,48" dock_band_item_size="1,-1" docked_placement="0,0" float_point="215,77" float_size="1000,75" visible="True" />
+      <placement dock_location="Top" recent_dock_location="Top" dock_band_size="1977,48" dock_band_item_size="1,-1" docked_placement="1,0" float_point="215,77" float_size="1468,675" visible="True" />
       <tabs name="Standard Toolbars" selected_item="13738460-8ea9-470b-803c-527e8a1828ce" display_style="Text">
         <name>
           <locale_1033>Standard Toolbars</locale_1033>
-          <locale_1036>Barres d'outils Standard</locale_1036>
-          <locale_1029>Standardní palety nástrojů</locale_1029>
-          <locale_1031>Standard-Werkzeugleisten</locale_1031>
-          <locale_1034>Barras de herramientas estándar</locale_1034>
-          <locale_1040>Barre degli strumenti standard</locale_1040>
-          <locale_1041>標準ツールバー</locale_1041>
-          <locale_1042>표준 도구모음</locale_1042>
-          <locale_1045>Standardowe paski narzędzi</locale_1045>
-          <locale_2070>Barras de Ferramentas Standard</locale_2070>
-          <locale_2052>标准工具列</locale_2052>
-          <locale_1028>標準工具列</locale_1028>
-          <locale_1049>Стандартные панели инструментов</locale_1049>
         </name>
         <tool_bar guid="4bb9c817-d19f-45fd-8af2-39e9805f3e9f" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="42b36785-e767-4c66-8704-4d828bcb0225" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <tool_bar guid="32318c40-46e9-4aa3-8f73-09371ec27a4d" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="42b36785-e767-4c66-8704-4d828bcb0225" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
@@ -38,11 +26,10 @@
         <tool_bar guid="4cd9a071-9337-4389-aa40-2a20f570da3b" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="625e34b2-3b19-4aba-91c2-94f79e2e1d91" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <tool_bar guid="44619cf6-b73a-46ea-93f8-46f1fa333115" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="12428ca8-b9f4-4954-8f6e-8a139226b383" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <tool_bar guid="a5379863-ee51-4b77-ab0c-44ee93c92ca3" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="fa6d5bcc-8cd8-416b-8701-f89bd697e94d" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
-        <panel guid="1d3d1785-2332-428b-a838-b2fe39ec50f4" plug_in="a6f26df9-1ffd-4cf3-b1ec-a11a28a40892" name="Command History" />
         <tool_bar guid="d0a817a1-dea9-4e03-89e3-0d63d99b5e51" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="54dcdb3a-f098-49a4-9947-d5605d675be3" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <tool_bar guid="90fd89fc-e41f-49cc-bcf0-29e0d58017a1" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar_colletion="4b37b788-3a60-4c54-a4be-67e756115945" />
+        <tool_bar guid="16770b13-f7fb-4060-a6e6-607f90dd8bb3" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <tool_bar guid="13738460-8ea9-470b-803c-527e8a1828ce" file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
-        <tool_bar guid="16770b13-f7fb-4060-a6e6-607f90dd8bb3" file="c7da84fc-2991-4824-832a-4f2509bd0ede" side_bar="42b36785-e767-4c66-8704-4d828bcb0225" side_bar_file="c7da84fc-2991-4824-832a-4f2509bd0ede" />
         <panel guid="52606b82-9bc4-493a-b2b4-d2073d995529" plug_in="02bf604d-799c-4cc2-830e-8d72f21b14b7" name="Macro Editor" />
       </tabs>
     </dock_bar>
@@ -57,40 +44,115 @@
           <extend_rhino_menus />
           <menus />
           <tool_bars>
+            <tool_bar source_guid="6df8b63c-d9b5-4631-b2c8-24019573876b" modified="True" LastTornOffSize="103,116">
+              <tool_bar_items>
+                <tool_bar_item source_guid="182a725e-e9b5-4f9f-aeb1-ba1101da7b30" />
+                <tool_bar_item source_guid="59e8de3c-7ec7-4d8d-ba2f-98ac825ea233" />
+                <tool_bar_item source_guid="6312d993-175d-45b0-8299-7e717fe7dc80" />
+                <tool_bar_item source_guid="0859ece0-37e7-49f3-ad39-c766f7d2e1fd" />
+                <tool_bar_item source_guid="d084d8c4-cf8e-4017-aef6-47878af8c215" />
+                <tool_bar_item source_guid="e7fb3125-0bd9-45fe-b26d-14c27178cdaa" />
+                <tool_bar_item source_guid="bd5c12da-4d05-4cc7-86ff-aca1a3485740" />
+                <tool_bar_item source_guid="a09d076a-4830-46de-a7d8-17c978487ea2" />
+                <tool_bar_item source_guid="6b60c495-428a-4d19-9186-ce2fb38d56b9" />
+              </tool_bar_items>
+            </tool_bar>
+            <tool_bar source_guid="00211289-60a5-460b-88dc-cc667b234dbd" modified="True">
+              <tool_bar_items>
+                <tool_bar_item source_guid="08f422b0-883d-407e-9b32-0c7c2abdc566" />
+                <tool_bar_item source_guid="b7d32fef-c2b5-4e3c-be1a-1ba978a71713" />
+                <tool_bar_item />
+                <tool_bar_item />
+                <tool_bar_item />
+                <tool_bar_item source_guid="182a725e-e9b5-4f9f-aeb1-ba1101da7b30" />
+                <tool_bar_item source_guid="e1769652-07b4-40f9-9b08-6b9679c6e479" />
+                <tool_bar_item source_guid="9058ba63-aa75-4979-898a-37958da889ab" />
+                <tool_bar_item source_guid="d3c081db-0bf3-4af3-9c43-cff6680c7625" />
+                <tool_bar_item source_guid="cdef77dc-3471-4144-ad41-e2a46f4cd4b1" />
+              </tool_bar_items>
+            </tool_bar>
             <tool_bar guid="13738460-8ea9-470b-803c-527e8a1828ce" modified="True" bitmap_guid="3af63880-438e-4c87-89c6-d3ab68bafad9" item_display_style="BitmapAndText">
               <text>
                 <locale_1033>Carnutes</locale_1033>
               </text>
               <tool_bar_items>
+                <tool_bar_item guid="16f2ac30-ab7b-4a67-8c82-8f727cd5e6e1" modified="True" display_style_from_parent="False">
+                  <left_macro guid="de61ca19-e804-4e61-8e94-3e505e8b3aff" modified="True" />
+                </tool_bar_item>
                 <tool_bar_item guid="f45f9d11-d64f-4779-9727-63b07ec8f82f" modified="True" display_style_from_parent="False">
                   <left_macro guid="bfac1506-2819-4cd8-87d1-5524068b3945" modified="True" />
                 </tool_bar_item>
                 <tool_bar_item guid="a7e2c1ad-9c9c-4270-b029-814203692037" modified="True" button_type="Separator" />
-                <tool_bar_item guid="16f2ac30-ab7b-4a67-8c82-8f727cd5e6e1" modified="True" display_style_from_parent="False">
-                  <left_macro guid="de61ca19-e804-4e61-8e94-3e505e8b3aff" modified="True" />
-                </tool_bar_item>
                 <tool_bar_item guid="8608f3aa-8f9a-4606-a28b-538a0dcee1cc" modified="True" display_style_from_parent="False">
                   <left_macro guid="56c650a8-7ad6-4ddd-8b3c-a1749276257f" modified="True" />
                   <right_macro guid="add7d4fc-9918-408c-8447-10f0b9150a9b" modified="True" />
                 </tool_bar_item>
-              </tool_bar_items>
-            </tool_bar>
-            <tool_bar source_guid="00211289-60a5-460b-88dc-cc667b234dbd" modified="True">
-              <tool_bar_items>
-                <tool_bar_item />
-                <tool_bar_item source_guid="08f422b0-883d-407e-9b32-0c7c2abdc566" />
-                <tool_bar_item source_guid="e1769652-07b4-40f9-9b08-6b9679c6e479" />
-                <tool_bar_item source_guid="f6d7af12-0c34-4d5b-b325-7132167a85c8" />
-                <tool_bar_item source_guid="4ca65141-12cd-46e4-90b7-86f4e106688c" />
-                <tool_bar_item source_guid="292e811f-0fba-47bf-af32-776b7cf125b5" />
-                <tool_bar_item source_guid="4d9035f6-9a34-47bd-95e5-42bd38f2ced7" />
-                <tool_bar_item source_guid="71eac7d7-2ec3-4d82-9ae3-72ec4687a661" />
-                <tool_bar_item source_guid="593ef621-4288-4c5b-af19-f6cd726b446e" />
-                <tool_bar_item source_guid="338f5655-a0a2-4839-9114-ce51dc176fa4" />
+                <tool_bar_item guid="e2b24524-a1a3-4003-ae92-a1bc382536cd" modified="True">
+                  <left_macro guid="80421b7e-2cdf-4b51-aee1-c68c81f4c43c" modified="True" />
+                </tool_bar_item>
               </tool_bar_items>
             </tool_bar>
           </tool_bars>
           <icons>
+            <icon guid="53b742dd-0cbc-471f-9f0f-d2e0b965e02e" modified="True">
+              <svg_name>e47f272f-49b5-4aab-a482-0f28ab7347b5.svg</svg_name>
+              <light_svg>&lt;svg
+   width="24.564278mm"
+   height="25.531645mm"
+   viewBox="0 0 24.564278 25.531645"
+   version="1.1"
+   id="svg1"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"&gt;
+  &lt;defs
+     id="defs1" /&gt;
+  &lt;g
+     id="layer1"
+     transform="translate(-3.0578512,-2.8705765)"&gt;
+    &lt;rect
+       style="fill:#de8787;stroke-width:0.265001"
+       id="rect7"
+       width="22.480658"
+       height="14.077005"
+       x="5.1060171"
+       y="8.7936964" /&gt;
+    &lt;ellipse
+       style="fill:#445500;stroke-width:0.31973"
+       id="path1"
+       cx="16.323689"
+       cy="22.238592"
+       rx="11.298441"
+       ry="6.1636291" /&gt;
+    &lt;ellipse
+       style="fill:#668000;stroke-width:0.31973"
+       id="path1-4-5"
+       cx="16.294699"
+       cy="15.792293"
+       rx="11.298441"
+       ry="6.1636291" /&gt;
+    &lt;ellipse
+       style="fill:#aad400;stroke-width:0.31973"
+       id="path1-4"
+       cx="16.301134"
+       cy="9.0342054"
+       rx="11.298441"
+       ry="6.1636291" /&gt;
+    &lt;path
+       style="fill:#677821;stroke-width:0.264583"
+       d="M 5.0705587,22.799786 4.9641832,8.6164038 Z"
+       id="path3" /&gt;
+    &lt;path
+       style="fill:#677821;stroke-width:0.264583"
+       d="M 3.1581432,22.958923 3.0578513,18.646382"
+       id="path4" /&gt;
+    &lt;path
+       style="fill:#677821;stroke-width:0.264583"
+       d="M 4.9383199,8.6924347 5.0636846,22.883704"
+       id="path5" /&gt;
+  &lt;/g&gt;
+&lt;/svg&gt;
+</light_svg>
+            </icon>
             <icon guid="e43aced9-83c9-4467-b579-91c30cee4e95" modified="True">
               <svg_name>4ac7ba83-2b4f-4948-9ebb-c0423cb2baa1.svg</svg_name>
               <light_svg>&lt;svg version="1.1" width="48" height="48" viewBox="0 0 48 48" xmlns="http://www.w3.org/2000/svg"&gt;&lt;!--Rhino generated SVG--&gt;&lt;polyline  stroke-width="2" stroke="#00A2E8" stroke-opacity="1" fill="none" stroke-linecap="butt" points="5.5,3 6.5,3"/&gt;
@@ -424,21 +486,30 @@
             </icon>
           </icons>
           <macros>
-            <macro guid="bfac1506-2819-4cd8-87d1-5524068b3945" modified="True" bitmap_guid="310cad8e-9716-4cbd-abe0-51e3abe38200">
-              <button_text>function2</button_text>
-              <tooltip>blabla</tooltip>
-              <script>!_-RunPythonScript "src/function_2.py"</script>
+            <macro guid="80421b7e-2cdf-4b51-aee1-c68c81f4c43c" modified="True" bitmap_guid="53b742dd-0cbc-471f-9f0f-d2e0b965e02e">
+              <text>
+                <locale_1033>reset_database</locale_1033>
+              </text>
+              <script>!_-RunPythonScript "src/reset_database.py"</script>
             </macro>
             <macro guid="de61ca19-e804-4e61-8e94-3e505e8b3aff" modified="True" bitmap_guid="7170b8f2-7acb-4045-898f-02fb1c4365d6">
-              <button_text>Finds trunks basrd on cylinder model</button_text>
-              <tooltip>none</tooltip>
-              <script>!_-RunPythonScript "src/function_1.py"</script>
+              <text>
+                <locale_1033>test</locale_1033>
+              </text>
+              <script>!_-RunPythonScript "src/function_2.py"</script>
             </macro>
             <macro guid="56c650a8-7ad6-4ddd-8b3c-a1749276257f" modified="True" bitmap_guid="e43aced9-83c9-4467-b579-91c30cee4e95">
+              <button_text>test_3</button_text>
+              <menu_text>test_3</menu_text>
+              <help_text>test_3</help_text>
+              <tooltip>test_3</tooltip>
+              <script>!_-RunPythonScript "src/function_3.py"</script>
+            </macro>
+            <macro guid="bfac1506-2819-4cd8-87d1-5524068b3945" modified="True" bitmap_guid="310cad8e-9716-4cbd-abe0-51e3abe38200">
               <text>
-                <locale_1033>test_3</locale_1033>
+                <locale_1033>test_2</locale_1033>
               </text>
-              <script>!_-RunPythonScript "src/function_3.py"</script>
+              <script>!_-RunPythonScript "src/function_2.py"</script>
             </macro>
           </macros>
         </RhinoUI>

diff --git a/INSTALL.md b/INSTALL.md
@@ -1,7 +1,7 @@
-To use this tool (we avoid the term plugin, as it isn't a proper plugin), you need to follow those two steps. This solution is not very elegant but is adapted to the time available for this project 🏃‍♀️‍➡️. 
+To use this tool (we avoid the term plugin, as it isn't a proper plugin), you need to follow those two steps. This solution is not very elegant but is adapted to the time available for this project 🏃‍♀️‍➡️.
 
 # 2-step install:
-1) Add the src folder with the codes to the "scripts" folder of Rhino. (At every new release, the old files must be deleted). Please note that the Library (MacOS) and AppData (Windows) folders are "hidden folders". On MacOS press command+shift+. to reveal the hidden folders. On Windows 10 or 11, [see this link](https://support.microsoft.com/en-us/windows/view-hidden-files-and-folders-in-windows-97fbc472-c603-9d90-91d0-1166d1d9f4b5#WindowsVersion=Windows_11) 
+1) Add the src folder with the codes to the "scripts" folder of Rhino. (At every new release, the old files must be deleted). Please note that the Library (MacOS) and AppData (Windows) folders are "hidden folders". On MacOS press command+shift+. to reveal the hidden folders. On Windows 10 or 11, [see this link](https://support.microsoft.com/en-us/windows/view-hidden-files-and-folders-in-windows-97fbc472-c603-9d90-91d0-1166d1d9f4b5#WindowsVersion=Windows_11)
 
 Note that the "script" folder in the "8.0" folder might be missing, in which case you have to create it, respecting the exact spelling.
 
@@ -18,7 +18,7 @@ Windows path:
 C:\Users\<your_username>\AppData\Roaming\McNeel\Rhinoceros\8.0\scripts
 ```
 
-For each `function_<>.py`, change the `admin` by your user name. This step is particularly not elegant, but until pip packages via Rhino are not resolved, this is the way to go if you want to avoid creating a fully fledged plugin. 
+For each `function_<>.py`, change the `admin` by your user name. This step is particularly not elegant, but until pip packages via Rhino are not resolved, this is the way to go if you want to avoid creating a fully fledged plugin.
 
 2) Drag-and-drop the .rhc container file ( [Download link](https://github.com/ibois-epfl/Carnutes/raw/main/Carnutes.rhc) ). This file contains the metadata that creates the "Carnutes" toolbar tab with all the buttons calling the different scripts.
 
@@ -27,7 +27,7 @@ This solution is inelegant but corresponds to the developement time allocated to
 # Dependencies
 There is no need to install dependencies as they are all installed automatically using the `# r: <package>`
 
-The dependencies are nevertheless listed here: 
+The dependencies are nevertheless listed here:
 
 - [numpy (1.26.4)](https://numpy.org/) for basic mathematics. Note that [numpy 2.0.0 is not compatible with open3d 0.18.0](https://github.com/isl-org/Open3D/issues/6840)
 - [i-graph (0.11.6)](https://igraph.org/) for connectivity of elements
@@ -43,22 +43,22 @@ conda env create -f environment.yml
 conda activate Carnutes
 ```
 
-Navigate to the src directory: 
+Navigate to the src directory:
 
 ```bash
 cd src
 ```
 
-And run the python script with: 
+And run the python script with:
 
 MacOS:
 
 ```bash
 /Users/<your_username>/anaconda3/envs/database_creation/bin/python database_creator.py
 ```
 
-Windows: 
+Windows:
 
 ```bash
 C:\Users\<your_username>\anaconda3\envs\database_creation\python.exe .\database_creator.py
-```
+```