First commit + file in french

.gitignore

@@ -6,6 +6,7 @@ __pycache__/
 # C extensions
 *.so
 
+
 # Distribution / packaging
 .Python
 build/
@@ -21,6 +22,8 @@ sdist/
 var/
 wheels/
 share/python-wheels/
+.idea/
+
 *.egg-info/
 .installed.cfg
 *.egg

show_scap.py

@@ -0,0 +1,43 @@
+import biorbd
+import bioviz
+import numpy as np
+from biosiglive import load, MskFunctions, InverseKinematicsMethods, save
+
+data_mat = load("data_scap/P8/markers_file_recons.bio", merge=False)
+all_bioviz = []
+
+for i, data in enumerate(data_mat):
+    if "abduction_max_2" in data["file: "]:
+        print("curent_file is ", data["file: "])
+        mat_sl = data["data"]["mat_sl"]
+        mat_cluster = data["data"]["mat_cluster"]
+        mat_scap = data["data"]["mat_scap"]
+        idx_nan = np.argwhere(np.isnan(mat_sl[:, 0, :]))
+        mat_sl[idx_nan[:, 0], 0, idx_nan[:, 1]] = mat_cluster[idx_nan[:, 0], 0, idx_nan[:, 1]]
+        # mat_scap[idx_nan[:, 0], 0, idx_nan[:, 1]] = mat_cluster[idx_nan[:, 0], 0, idx_nan[:, 1]]
+
+        mat_sl[:, 0, :] = mat_cluster[:, 0, :]
+        model = biorbd.Model("wu_reduc_left.bioMod")
+        all_mark = np.concatenate((mat_sl, mat_cluster, mat_scap), axis=1)
+        ik_function = MskFunctions(model=model, data_buffer_size=mat_sl[:, :, :].shape[2])
+        q, _ =  ik_function.compute_inverse_kinematics(markers=all_mark[:3, :, :]*0.001,
+                                               method=InverseKinematicsMethods.BiorbdLeastSquare)
+        print("q sl:", np.mean(q[:3, :], axis=1) * 180 / np.pi)
+        print("q cluster:", np.mean(q[6:9, :], axis=1) * 180 / np.pi)
+        print("q scap:", np.mean(q[12:15, :], axis=1) * 180 / np.pi)
+        # q_cluster, _ =  ik_function.compute_inverse_kinematics(markers=mat_cluster[:3, :, :]*0.001,
+        #                                        method=InverseKinematicsMethods.BiorbdKalman)
+        b = bioviz.Viz(loaded_model=model, show_markers=True)
+        b.load_movement(q)
+        b.load_experimental_markers(all_mark[:3, :, :]*0.001)
+        b.exec()
+
+should_continue = True
+while should_continue:
+    for i, b in enumerate(all_bioviz):
+        if b.vtk_window.is_active:
+            b.update()
+        else:
+            should_continue = False
+# b.exec()
+# bioviz.Kinogram()