Merge pull request #77 from EveCharbie/biobuddy

[RTR] BioBuddy interface

Author: Ipuch

.gitignore

@@ -168,3 +168,4 @@ cython_debug/
 sandbox/
 
 .DS_Store
+.aider*

README.md

@@ -6,6 +6,7 @@ And also animate biorbd models from the pyomeca organization.
 
 ``` conda install -c conda-forge pyorerun rerun-sdk=0.24.1```
 ``` conda install opensim-org::opensim   # not a mandatory dependency```
+``` conda install -c conda-forge biobuddy=0.2.0   # not a mandatory dependency```
 
 # Rerun .c3d - As simple as that
 
@@ -62,6 +63,10 @@ animation.rerun()
 if you want to use the OpenSim, you also need to install separately:
 ```conda install -c opensim-org::opensim```
 
+if you want to use the BioBuddy, you also need to install separately:
+```conda install -c conda-forge biobuddy=0.2.0``` or
+```pip install biobuddy==0.2.0```
+
 Then, ensure it is accessible in your Python environment by installing the package:
 
 ``` pip install . ``` or ``` python setup.py install ```

examples/biobuddy/from_biobuddy_model.py

@@ -0,0 +1,45 @@
+"""
+To run this example, you need to install biobuddy:
+    `pip install biobuddy == 0.2.0`
+    or
+    `conda-forge install -c conda-forge biobuddy=0.2.0`
+"""
+
+import numpy as np
+import biobuddy
+
+from pyorerun import PhaseRerun, BiobuddyModel, DisplayModelOptions
+
+
+def main():
+
+    # building some time components
+    nb_frames = 50
+    nb_seconds = 1
+    t_span = np.linspace(0, nb_seconds, nb_frames)
+
+    # Creating the model
+    model_path = "../biorbd/models/Wu_Shoulder_Model_kinova_scaled_adjusted_2.bioMod"
+    biobuddy_model = biobuddy.BiomechanicalModelReal().from_biomod(model_path)
+    biobuddy_model.change_mesh_directories("../biorbd/models/Geometry_cleaned")
+    display_options = DisplayModelOptions()
+    prr_model = BiobuddyModel.from_biobuddy_object(biobuddy_model, options=display_options)
+
+    # building some generalized coordinates
+    q = np.zeros((biobuddy_model.nb_q, nb_frames))
+    q[10, :] = np.linspace(0, np.pi / 8, nb_frames)
+    q[12, :] = np.linspace(0, np.pi / 3, nb_frames)
+    q[11, :] = np.linspace(0, np.pi / 4, nb_frames)
+    q[13, :] = np.linspace(0, np.pi / 8, nb_frames)
+    q[14, :] = np.linspace(0, np.pi / 8, nb_frames)
+    q[15, :] = np.linspace(0, np.pi / 8, nb_frames)
+
+    # Animate the model
+    viz = PhaseRerun(t_span)
+    viz.add_animated_model(prr_model, q)
+    # viz.rerun("msk_model")
+    viz.rerun_by_frame("msk_model")
+
+
+if __name__ == "__main__":
+    main()

pyorerun/__init__.py

@@ -3,13 +3,24 @@
 from .model_components.model_display_options import DisplayModelOptions
 from .model_components.model_updapter import ModelUpdater
 
+# Opensim
 try:
     from .model_interfaces import (
         OsimModel,
         OsimModelNoMesh,
     )
 except ImportError:
-    # OpenSim n'est pas installé, ces classes ne seront pas disponibles
+    # OpenSim is not installed, these classes will not be available
+    pass
+
+# biobuddy
+try:
+    from .model_interfaces import (
+        BiobuddyModel,
+        BiobuddyModelNoMesh,
+    )
+except ImportError:
+    # BioBuddy is not installed, these classes will not be available
     pass
 
 from .model_interfaces import (

pyorerun/model_interfaces/__init__.py

@@ -1,10 +1,18 @@
 from .abstract_model_interface import AbstractSegment, AbstractModel, AbstractModelNoMesh
 from .biorbd_model_interface import BiorbdModelNoMesh, BiorbdModel
 
+# Opensim
 try:
     from .osim_model_interface import OsimModelNoMesh, OsimModel
 except ImportError:
-    # OpenSim n'est pas installé, ces classes ne seront pas disponibles
+    # OpenSim is not installed, these classes will not be available
+    pass
+
+# Biobuddy
+try:
+    from .biobuddy_model_interface import BiobuddyModelNoMesh, BiobuddyModel
+except ImportError:
+    # BioBuddy is not installed, these classes will not be available
     pass
 
 from .available_interfaces import model_from_file