diff --git a/bioptim/examples/getting_started/pendulum.py b/bioptim/examples/getting_started/pendulum.py
index fb1e7c790..3c6aa34a9 100644
--- a/bioptim/examples/getting_started/pendulum.py
+++ b/bioptim/examples/getting_started/pendulum.py
@@ -152,10 +152,14 @@ def main():
# --- Solve the ocp. Please note that online graphics only works with the Linux operating system --- #
sol = ocp.solve(Solver.IPOPT(show_online_optim=platform.system() == "Linux"))
- # --- Show the results (graph or animation) --- #
+ # --- Show the results graph --- #
sol.print_cost()
# sol.graphs(show_bounds=True, save_name="results.png")
- sol.animate(n_frames=100)
+
+ # --- Animate the solution --- #
+ viewer = "bioviz"
+ # viewer = "pyorerun"
+ sol.animate(n_frames=0, viewer=viewer, show_now=True)
# # --- Saving the solver's output after the optimization --- #
# Here is an example of how we recommend to save the solution. Please note that sol.ocp is not picklable and that sol will be loaded using the current bioptim version, not the version at the time of the generation of the results.
diff --git a/bioptim/examples/holonomic_constraints/two_pendulums.py b/bioptim/examples/holonomic_constraints/two_pendulums.py
index 911009945..a25cfc0ae 100644
--- a/bioptim/examples/holonomic_constraints/two_pendulums.py
+++ b/bioptim/examples/holonomic_constraints/two_pendulums.py
@@ -6,7 +6,6 @@
import matplotlib.pyplot as plt
import numpy as np
-
from casadi import MX, Function
from bioptim import (
@@ -213,11 +212,21 @@ def main():
# --- Show results --- #
q, qdot, qddot, lambdas = compute_all_states(sol, bio_model)
- import bioviz
+ viewer = "pyorerun"
+ if viewer == "bioviz":
+ import bioviz
+
+ viz = bioviz.Viz(model_path)
+ viz.load_movement(q)
+ viz.exec()
+
+ if viewer == "pyorerun":
+ import pyorerun
+
+ viz = pyorerun.PhaseRerun(t_span=np.concatenate(sol.decision_time()).squeeze())
+ viz.add_animated_model(pyorerun.BiorbdModel(model_path), q=q)
- viz = bioviz.Viz(model_path)
- viz.load_movement(q)
- viz.exec()
+ viz.rerun("double_pendulum")
time = sol.decision_time(to_merge=SolutionMerge.NODES)
plt.title("Lagrange multipliers of the holonomic constraint")
diff --git a/bioptim/examples/moving_horizon_estimation/mhe.py b/bioptim/examples/moving_horizon_estimation/mhe.py
index ea16f0e99..36955f42d 100644
--- a/bioptim/examples/moving_horizon_estimation/mhe.py
+++ b/bioptim/examples/moving_horizon_estimation/mhe.py
@@ -15,11 +15,12 @@
from copy import copy
-import matplotlib.pyplot as plt
-from scipy.integrate import solve_ivp
+import biorbd_casadi as biorbd
import casadi as cas
+import matplotlib.pyplot as plt
import numpy as np
-import biorbd_casadi as biorbd
+from scipy.integrate import solve_ivp
+
from bioptim import (
BioModel,
BiorbdModel,
@@ -232,12 +233,12 @@ def target(i: int):
sol = mhe.solve(update_functions, **get_solver_options(solver))
sol_states = sol.decision_states(to_merge=SolutionMerge.NODES)
- print("ACADOS with Bioptim")
+ print(f"{solver} with Bioptim")
print(f"Window size of MHE : {window_duration} s.")
print(f"New measurement every : {1 / n_shoot_per_second} s.")
print(f"Average time per iteration of MHE : {sol.solver_time_to_optimize / (n_frames_total - 1)} s.")
print(f"Average real time per iteration of MHE : {sol.real_time_to_optimize / (n_frames_total - 1)} s.")
- print(f"Norm of the error on q = {np.linalg.norm(states[:bio_model.nb_q, :n_frames_total] - sol_states['q'])}")
+ print(f"Norm of the error on q = {np.linalg.norm(states[:bio_model.nb_q, :n_frames_total + 1] - sol_states['q'])}")
markers_estimated = states_to_markers(bio_model, sol_states["q"])
@@ -256,7 +257,7 @@ def target(i: int):
plt.figure()
plt.plot(sol_states["q"].T, "--", label="States estimate (q)")
plt.plot(sol_states["qdot"].T, "--", label="States estimate (qdot)")
- plt.plot(sol_states[:, :n_frames_total].T, label="State truth")
+ plt.plot(states[:, :n_frames_total].T, label="State truth")
plt.legend()
plt.show()
diff --git a/bioptim/examples/moving_horizon_estimation/models/cart_pendulum.bioMod b/bioptim/examples/moving_horizon_estimation/models/cart_pendulum.bioMod
index 26cfed4b2..1035aafbe 100644
--- a/bioptim/examples/moving_horizon_estimation/models/cart_pendulum.bioMod
+++ b/bioptim/examples/moving_horizon_estimation/models/cart_pendulum.bioMod
@@ -41,7 +41,7 @@ segment Arm
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Markers
diff --git a/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.STL b/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.STL
new file mode 100755
index 000000000..fb6f4bc66
Binary files /dev/null and b/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.STL differ
diff --git a/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.vtp b/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.vtp
deleted file mode 100644
index 36b98aa9b..000000000
--- a/bioptim/examples/moving_horizon_estimation/models/mesh/pendulum.vtp
+++ /dev/null
@@ -1,1973 +0,0 @@
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- 4737 4740 4743 4746 4749 4752
- 4755 4758 4761 4764 4767 4770
- 4773 4776 4779 4782 4785 4788
- 4791 4794 4797 4800 4803 4806
- 4809 4812 4815 4818 4821 4824
- 4827 4830 4833 4836 4839 4842
- 4845 4848 4851 4854 4857 4860
- 4863 4866 4869 4872 4875 4878
- 4881 4884 4887 4890 4893 4896
- 4899 4902 4905 4908 4911 4914
- 4917 4920 4923 4926 4929 4932
- 4935 4938 4941 4944 4947 4950
- 4953 4956 4959 4962 4965 4968
- 4971 4974 4977 4980 4983 4986
- 4989 4992 4995 4998 5001 5004
- 5007 5010 5013 5016 5019 5022
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- 5043 5046 5049 5052 5055 5058
- 5061 5064 5067 5070 5073 5076
- 5079 5082 5085 5088 5091 5094
- 5097 5100 5103 5106 5109 5112
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- 5133 5136 5139 5142 5145 5148
- 5151 5154 5157 5160 5163 5166
- 5169 5172 5175 5178 5181 5184
- 5187 5190 5193 5196 5199 5202
- 5205 5208 5211 5214 5217 5220
- 5223 5226 5229 5232 5235 5238
- 5241 5244 5247 5250 5253 5256
- 5259 5262 5265 5268 5271 5274
- 5277 5280 5283 5286 5289 5292
- 5295 5298 5301 5304 5307 5310
- 5313 5316 5319 5322 5325 5328
- 5331 5334 5337 5340 5343 5346
- 5349 5352 5355 5358 5361 5364
- 5367 5370 5373 5376 5379 5382
- 5385 5388 5391 5394 5397 5400
- 5403 5406 5409 5412 5415 5418
- 5421 5424 5427 5430 5433 5436
- 5439 5442 5445 5448 5451 5454
- 5457 5460 5463 5466 5469 5472
- 5475 5478 5481 5484 5487 5490
- 5493 5496 5499 5502 5505 5508
- 5511 5514 5517 5520 5523 5526
- 5529 5532 5535 5538 5541 5544
- 5547 5550 5553 5556 5559 5562
- 5565 5568 5571 5574 5577 5580
- 5583 5586 5589 5592 5595 5598
- 5601 5604 5607 5610 5613 5616
- 5619 5622 5625 5628 5631 5634
- 5637 5640 5643 5646 5649 5652
- 5655 5658 5661 5664 5667 5670
- 5673 5676 5679 5682 5685 5688
- 5691 5694 5697 5700 5703 5706
- 5709 5712 5715 5718 5721 5724
- 5727 5730 5733 5736 5739 5742
- 5745 5748 5751 5754 5757 5760
- 5763 5766 5769 5772 5775 5778
- 5781 5784 5787 5790 5793 5796
- 5799 5802 5805 5808 5811 5814
- 5817 5820 5823 5826 5829 5832
- 5835 5838 5841 5844 5847 5850
- 5853 5856 5859 5862 5865 5868
- 5871 5874 5877 5880 5883 5886
- 5889 5892 5895 5898 5901 5904
- 5907 5910 5913 5916 5919 5922
- 5925 5928 5931 5934 5937 5940
- 5943 5946 5949 5952 5955 5958
- 5961 5964 5967 5970 5973 5976
- 5979 5982 5985 5988 5991 5994
- 5997 6000 6003 6006 6009 6012
- 6015 6018 6021 6024 6027 6030
- 6033 6036 6039 6042 6045 6048
- 6051 6054 6057 6060 6063 6066
- 6069 6072 6075 6078 6081 6084
- 6087 6090 6093 6096 6099 6102
- 6105 6108 6111 6114 6117 6120
- 6123 6126 6129 6132 6135 6138
- 6141 6144 6147 6150 6153 6156
- 6159 6162 6165 6168 6171 6174
- 6177 6180 6183 6186 6189 6192
- 6195 6198 6201 6204 6207 6210
- 6213 6216 6219 6222 6225 6228
- 6231 6234 6237 6240 6243 6246
- 6249 6252 6255 6258 6261 6264
- 6267 6270 6273 6276 6279 6282
- 6285 6288
-
-
-
-
-
diff --git a/bioptim/examples/muscle_driven_with_contact/muscle_activations_contacts_tracker.py b/bioptim/examples/muscle_driven_with_contact/muscle_activations_contacts_tracker.py
index 53cb7300f..223a91c3f 100644
--- a/bioptim/examples/muscle_driven_with_contact/muscle_activations_contacts_tracker.py
+++ b/bioptim/examples/muscle_driven_with_contact/muscle_activations_contacts_tracker.py
@@ -1,14 +1,14 @@
"""
-# TODO: Remove all the examples/muscle_driven_with_contact and make sure everything is properly tested
All the examples in muscle_driven_with_contact are merely to show some dynamics and prepare some OCP for the tests.
It is not really relevant and will be removed when unitary tests for the dynamics will be implemented
"""
import importlib.util
-from pathlib import Path
import platform
+from pathlib import Path
import numpy as np
+
from bioptim import (
BiorbdModel,
OptimalControlProgram,
@@ -21,6 +21,7 @@
OdeSolver,
Solver,
SolutionMerge,
+ Node,
)
# Load track_segment_on_rt
@@ -41,8 +42,12 @@ def prepare_ocp(
# Add objective functions
objective_functions = ObjectiveList()
- objective_functions.add(ObjectiveFcn.Lagrange.TRACK_CONTROL, key="muscles", target=muscle_activations_ref)
- objective_functions.add(ObjectiveFcn.Lagrange.TRACK_CONTACT_FORCES, target=contact_forces_ref)
+ objective_functions.add(
+ ObjectiveFcn.Lagrange.TRACK_CONTROL, key="muscles", target=muscle_activations_ref, node=Node.ALL_SHOOTING
+ )
+ objective_functions.add(
+ ObjectiveFcn.Lagrange.TRACK_CONTACT_FORCES, target=contact_forces_ref, node=Node.ALL_SHOOTING
+ )
objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_STATE, key="qdot", weight=0.001)
objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_STATE, key="q", weight=0.001)
objective_functions.add(ObjectiveFcn.Lagrange.MINIMIZE_CONTROL, key="muscles", weight=0.001)
@@ -53,40 +58,38 @@ def prepare_ocp(
dynamics.add(DynamicsFcn.MUSCLE_DRIVEN, with_residual_torque=True, with_contact=True)
# Path constraint
- n_q = bio_model.nb_q
- n_qdot = n_q
- pose_at_first_node = [0, 0, -0.75, 0.75]
+ q_at_first_node = [0, 0, -0.75, 0.75]
# Initialize x_bounds
x_bounds = BoundsList()
- x_bounds.add(bounds=bio_model.bounds_from_ranges(["q", "qdot"]))
- x_bounds[0][:, 0] = pose_at_first_node + [0] * n_qdot
+ x_bounds["q"] = bio_model.bounds_from_ranges("q")
+ x_bounds["qdot"] = bio_model.bounds_from_ranges("qdot")
+ x_bounds["q"][:, 0] = q_at_first_node
# Initial guess
x_init = InitialGuessList()
- x_init.add(pose_at_first_node + [0] * n_qdot)
+ x_init["q"] = q_at_first_node
# Define control path constraint
u_bounds = BoundsList()
- u_bounds.add(
- [tau_min] * bio_model.nb_tau + [activation_min] * bio_model.nb_muscles,
- [tau_max] * bio_model.nb_tau + [activation_max] * bio_model.nb_muscles,
- )
+ u_bounds["tau"] = ([tau_min] * bio_model.nb_tau, [tau_max] * bio_model.nb_tau)
+ u_bounds["muscles"] = ([activation_min] * bio_model.nb_muscles, [activation_max] * bio_model.nb_muscles)
u_init = InitialGuessList()
- u_init.add([tau_init] * bio_model.nb_tau + [activation_init] * bio_model.nb_muscles)
+ u_init["tau"] = [tau_init] * bio_model.nb_tau
+ u_init["muscles"] = [activation_init] * bio_model.nb_muscles
# ------------- #
return OptimalControlProgram(
- bio_model,
- dynamics,
- n_shooting,
- phase_time,
- x_init,
- u_init,
- x_bounds,
- u_bounds,
+ bio_model=bio_model,
+ dynamics=dynamics,
+ n_shooting=n_shooting,
+ phase_time=phase_time,
+ x_init=x_init,
+ u_init=u_init,
+ x_bounds=x_bounds,
+ u_bounds=u_bounds,
objective_functions=objective_functions,
ode_solver=ode_solver,
)
@@ -112,9 +115,13 @@ def main():
controls = sol.decision_controls(to_merge=SolutionMerge.NODES)
q, qdot, tau, mus = states["q"], states["qdot"], controls["tau"], controls["muscles"]
- x = np.concatenate((q, qdot))
- u = np.concatenate((tau, mus))
- contact_forces_ref = np.array(ocp_to_track.nlp[0].contact_forces_func(x[:, :-1], u[:, :-1], []))
+ x = np.concatenate((q, qdot), axis=0)
+ u = np.concatenate((tau, mus), axis=0)
+ contact_forces_ref = (
+ np.array([ocp_to_track.nlp[0].contact_forces_func([], x[:, i], u[:, i], [], [], []) for i in range(ns)])
+ .squeeze()
+ .T
+ )
muscle_activations_ref = mus
# Track these data
@@ -122,7 +129,7 @@ def main():
biorbd_model_path=model_path,
phase_time=final_time,
n_shooting=ns,
- muscle_activations_ref=muscle_activations_ref[:, :-1],
+ muscle_activations_ref=muscle_activations_ref,
contact_forces_ref=contact_forces_ref,
)
diff --git a/bioptim/examples/torque_driven_ocp/example_minimize_segment_velocity.py b/bioptim/examples/torque_driven_ocp/example_minimize_segment_velocity.py
index fa775feab..477234106 100644
--- a/bioptim/examples/torque_driven_ocp/example_minimize_segment_velocity.py
+++ b/bioptim/examples/torque_driven_ocp/example_minimize_segment_velocity.py
@@ -5,6 +5,7 @@
"""
import numpy as np
+
from bioptim import (
BiorbdModel,
OptimalControlProgram,
diff --git a/bioptim/examples/torque_driven_ocp/example_multi_biorbd_model.py b/bioptim/examples/torque_driven_ocp/example_multi_biorbd_model.py
index d35fbc2c5..7d9b58b46 100644
--- a/bioptim/examples/torque_driven_ocp/example_multi_biorbd_model.py
+++ b/bioptim/examples/torque_driven_ocp/example_multi_biorbd_model.py
@@ -85,16 +85,19 @@ def main():
sol.graphs(show_bounds=True)
- # --- Show results --- #
- show_solution_animation = False
- if show_solution_animation:
- states = sol.decision_states(to_merge=SolutionMerge.NODES)
- q = states["q"]
- import bioviz
-
- b = bioviz.Viz("models/triple_pendulum_both_inertia.bioMod")
- b.load_movement(q)
- b.exec()
+ # --- Animate results with bioviz --- #
+ # show_solution_animation = False
+ # if show_solution_animation:
+ # states = sol.decision_states(to_merge=SolutionMerge.NODES)
+ # q = states["q"]
+ # import bioviz
+ #
+ # b = bioviz.Viz("models/triple_pendulum_both_inertia.bioMod")
+ # b.load_movement(q)
+ # b.exec()
+
+ # --- Animate results with pyorerun --- #
+ sol.animate(viewer="pyorerun")
if __name__ == "__main__":
diff --git a/bioptim/examples/torque_driven_ocp/example_quaternions.py b/bioptim/examples/torque_driven_ocp/example_quaternions.py
index bff8d44b6..2978704da 100644
--- a/bioptim/examples/torque_driven_ocp/example_quaternions.py
+++ b/bioptim/examples/torque_driven_ocp/example_quaternions.py
@@ -7,9 +7,10 @@
import platform
-import numpy as np
import biorbd_casadi as biorbd
+import numpy as np
from casadi import MX, Function
+
from bioptim import (
BiorbdModel,
OptimalControlProgram,
diff --git a/bioptim/examples/torque_driven_ocp/models/double_pendulum.bioMod b/bioptim/examples/torque_driven_ocp/models/double_pendulum.bioMod
index 0b14a07d6..db3e969a8 100644
--- a/bioptim/examples/torque_driven_ocp/models/double_pendulum.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/double_pendulum.bioMod
@@ -10,7 +10,7 @@ segment Seg1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
@@ -38,7 +38,7 @@ segment Seg2
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 3
diff --git a/bioptim/examples/torque_driven_ocp/models/double_pendulum_both_inertia.bioMod b/bioptim/examples/torque_driven_ocp/models/double_pendulum_both_inertia.bioMod
index 5771c40de..48961b19b 100644
--- a/bioptim/examples/torque_driven_ocp/models/double_pendulum_both_inertia.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/double_pendulum_both_inertia.bioMod
@@ -11,7 +11,7 @@ segment Seg1_1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 1 0 0
endsegment
@@ -40,7 +40,7 @@ segment Seg2_1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 1 0 0
endsegment
@@ -66,7 +66,7 @@ segment Seg1_2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 0 0 1
endsegment
@@ -95,7 +95,7 @@ segment Seg2_2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 0 0 1
endsegment
diff --git a/bioptim/examples/torque_driven_ocp/models/double_pendulum_modified_inertia.bioMod b/bioptim/examples/torque_driven_ocp/models/double_pendulum_modified_inertia.bioMod
index 4e938b933..27f5e3951 100644
--- a/bioptim/examples/torque_driven_ocp/models/double_pendulum_modified_inertia.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/double_pendulum_modified_inertia.bioMod
@@ -10,7 +10,7 @@ segment Seg1
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
@@ -38,7 +38,7 @@ segment Seg2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 3
diff --git a/bioptim/examples/torque_driven_ocp/models/double_pendulum_with_translations.bioMod b/bioptim/examples/torque_driven_ocp/models/double_pendulum_with_translations.bioMod
index 2d6a6eedb..fc452fcda 100644
--- a/bioptim/examples/torque_driven_ocp/models/double_pendulum_with_translations.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/double_pendulum_with_translations.bioMod
@@ -12,7 +12,7 @@ segment Seg1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
@@ -40,7 +40,7 @@ segment Seg2
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 3
diff --git a/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.STL b/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.STL
new file mode 100755
index 000000000..fb6f4bc66
Binary files /dev/null and b/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.STL differ
diff --git a/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.vtp b/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.vtp
deleted file mode 100644
index 36b98aa9b..000000000
--- a/bioptim/examples/torque_driven_ocp/models/mesh/pendulum.vtp
+++ /dev/null
@@ -1,1973 +0,0 @@
-
-
-
-
-
-
-
-
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- 6267 6270 6273 6276 6279 6282
- 6285 6288
-
-
-
-
-
diff --git a/bioptim/examples/torque_driven_ocp/models/pendulum.bioMod b/bioptim/examples/torque_driven_ocp/models/pendulum.bioMod
index 35ae9c3da..ee849a3c4 100644
--- a/bioptim/examples/torque_driven_ocp/models/pendulum.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/pendulum.bioMod
@@ -12,7 +12,7 @@ segment Seg1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
diff --git a/bioptim/examples/torque_driven_ocp/models/pendulum_with_passive_torque.bioMod b/bioptim/examples/torque_driven_ocp/models/pendulum_with_passive_torque.bioMod
index 8c22b6750..5e096a929 100644
--- a/bioptim/examples/torque_driven_ocp/models/pendulum_with_passive_torque.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/pendulum_with_passive_torque.bioMod
@@ -12,7 +12,7 @@ segment Seg1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
diff --git a/bioptim/examples/torque_driven_ocp/models/triple_pendulum.bioMod b/bioptim/examples/torque_driven_ocp/models/triple_pendulum.bioMod
index e2f097ff5..444626f70 100644
--- a/bioptim/examples/torque_driven_ocp/models/triple_pendulum.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/triple_pendulum.bioMod
@@ -10,7 +10,7 @@ segment Seg1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
@@ -38,7 +38,7 @@ segment Seg2
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 3
@@ -66,7 +66,7 @@ segment Seg3
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 5
diff --git a/bioptim/examples/torque_driven_ocp/models/triple_pendulum_both_inertia.bioMod b/bioptim/examples/torque_driven_ocp/models/triple_pendulum_both_inertia.bioMod
index b095d3282..2f05417d6 100644
--- a/bioptim/examples/torque_driven_ocp/models/triple_pendulum_both_inertia.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/triple_pendulum_both_inertia.bioMod
@@ -11,7 +11,7 @@ segment Seg1_1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 1 0 0
endsegment
@@ -40,7 +40,7 @@ segment Seg2_1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 1 0 0
endsegment
@@ -69,7 +69,7 @@ segment Seg3_1
0.0000 0.0335 -0.0032
0.0000 -0.0032 0.0090
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 1 0 0
endsegment
@@ -95,7 +95,7 @@ segment Seg1_2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 0 0 1
endsegment
@@ -124,7 +124,7 @@ segment Seg2_2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 0 0 1
endsegment
@@ -153,7 +153,7 @@ segment Seg3_2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
meshcolor 0 0 1
endsegment
diff --git a/bioptim/examples/torque_driven_ocp/models/triple_pendulum_modified_inertia.bioMod b/bioptim/examples/torque_driven_ocp/models/triple_pendulum_modified_inertia.bioMod
index a35fc517a..b6d15be8d 100644
--- a/bioptim/examples/torque_driven_ocp/models/triple_pendulum_modified_inertia.bioMod
+++ b/bioptim/examples/torque_driven_ocp/models/triple_pendulum_modified_inertia.bioMod
@@ -10,7 +10,7 @@ segment Seg1
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 1
@@ -38,7 +38,7 @@ segment Seg2
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 3
@@ -66,7 +66,7 @@ segment Seg3
0.0000 0.03 -0.0032
0.0000 -0.0032 0.02
com -0.0005 0.0688 -0.9542
- meshfile mesh/pendulum.vtp
+ meshfile mesh/pendulum.STL
endsegment
// Marker 5
diff --git a/bioptim/examples/torque_driven_ocp/torque_driven_free_floating_base.py b/bioptim/examples/torque_driven_ocp/torque_driven_free_floating_base.py
index 4a6a53a65..73250949e 100644
--- a/bioptim/examples/torque_driven_ocp/torque_driven_free_floating_base.py
+++ b/bioptim/examples/torque_driven_ocp/torque_driven_free_floating_base.py
@@ -4,9 +4,10 @@
This specific problem generates one somersault in straight position with 1 twist.
"""
-import numpy as np
import platform
+import numpy as np
+
from bioptim import (
BiorbdModel,
OptimalControlProgram,
@@ -17,7 +18,6 @@
ObjectiveList,
ObjectiveFcn,
InterpolationType,
- BiMappingList,
Solver,
Node,
)
diff --git a/bioptim/models/biorbd/biorbd_model.py b/bioptim/models/biorbd/biorbd_model.py
index 3586d3c14..5ddb09224 100644
--- a/bioptim/models/biorbd/biorbd_model.py
+++ b/bioptim/models/biorbd/biorbd_model.py
@@ -7,7 +7,7 @@
GeneralizedAcceleration,
)
from casadi import SX, MX, vertcat, horzcat, norm_fro
-from typing import Callable, Any
+from typing import Callable
from ..utils import _var_mapping, bounds_from_ranges
from ...limits.path_conditions import Bounds
@@ -733,62 +733,17 @@ def partitioned_forward_dynamics(self, q_u, qdot_u, tau, external_forces=None, f
@staticmethod
def animate(
ocp,
- solution: "SolutionData",
+ solution,
show_now: bool = True,
- tracked_markers: list[np.ndarray] = None,
- **kwargs: Any,
- ) -> None | list:
- try:
- import bioviz
- except ModuleNotFoundError:
- raise RuntimeError("bioviz must be install to animate the model")
-
- check_version(bioviz, "2.0.0", "2.4.0")
-
- if "q_roots" in solution and "q_joints" in solution:
- states = np.vstack((solution["q_roots"], solution["q_joints"]))
- else:
- states = solution["q"]
-
- if not isinstance(states, (list, tuple)):
- states = [states]
-
- if tracked_markers is None:
- tracked_markers = [None] * len(states)
-
- all_bioviz = []
- for idx_phase, data in enumerate(states):
- if not isinstance(ocp.nlp[idx_phase].model, BiorbdModel):
- raise NotImplementedError("Animation is only implemented for biorbd models")
-
- # This calls each of the function that modify the internal dynamic model based on the parameters
- nlp = ocp.nlp[idx_phase]
-
- # noinspection PyTypeChecker
- biorbd_model: BiorbdModel = nlp.model
-
- all_bioviz.append(bioviz.Viz(biorbd_model.path, **kwargs))
- all_bioviz[-1].load_movement(ocp.nlp[idx_phase].variable_mappings["q"].to_second.map(solution["q"]))
+ show_tracked_markers: bool = False,
+ viewer: str = "pyorerun",
+ n_frames: int = 0,
+ **kwargs,
+ ):
+ from .viewer_bioviz import animate_with_bioviz_for_loop
+ from .viewer_pyorerun import animate_with_pyorerun
- if "q_roots" in solution and "q_joints" in solution:
- # TODO: Fix the mapping for this case
- raise NotImplementedError("Mapping is not implemented for this case")
- q = data
- else:
- q = ocp.nlp[idx_phase].variable_mappings["q"].to_second.map(data)
- all_bioviz[-1].load_movement(q)
-
- if tracked_markers[idx_phase] is not None:
- all_bioviz[-1].load_experimental_markers(tracked_markers[idx_phase])
-
- if show_now:
- b_is_visible = [True] * len(all_bioviz)
- while sum(b_is_visible):
- for i, b in enumerate(all_bioviz):
- if b.vtk_window.is_active:
- b.update()
- else:
- b_is_visible[i] = False
- return None
- else:
- return all_bioviz
+ if viewer == "bioviz":
+ return animate_with_bioviz_for_loop(ocp, solution, show_now, show_tracked_markers, n_frames, **kwargs)
+ if viewer == "pyorerun":
+ return animate_with_pyorerun(ocp, solution, show_now, show_tracked_markers, **kwargs)
diff --git a/bioptim/models/biorbd/multi_biorbd_model.py b/bioptim/models/biorbd/multi_biorbd_model.py
index e682dfa87..cfa44c39e 100644
--- a/bioptim/models/biorbd/multi_biorbd_model.py
+++ b/bioptim/models/biorbd/multi_biorbd_model.py
@@ -1,19 +1,12 @@
-from typing import Callable, Any
-
import biorbd_casadi as biorbd
-from biorbd_casadi import (
- GeneralizedCoordinates,
- GeneralizedVelocity,
-)
from casadi import SX, MX, vertcat
+from typing import Callable, Any
-from ...misc.utils import check_version
+from .biorbd_model import BiorbdModel
+from ..utils import _var_mapping
+from ..utils import bounds_from_ranges
from ...limits.path_conditions import Bounds
from ...misc.mapping import BiMapping, BiMappingList
-from ..utils import _var_mapping, bounds_from_ranges
-from ...optimization.solution.solution_data import SolutionMerge
-from ..utils import bounds_from_ranges
-from .biorbd_model import BiorbdModel
class MultiBiorbdModel:
@@ -738,51 +731,19 @@ def partitioned_forward_dynamics(self, q_u, qdot_u, tau, external_forces=None, f
raise NotImplementedError("partitioned_forward_dynamics is not implemented yet for MultiBiorbdModel")
@staticmethod
- def animate(solution: Any, show_now: bool = True, tracked_markers: list = None, **kwargs: Any) -> None | list:
- try:
- import bioviz
- except ModuleNotFoundError:
- raise RuntimeError("bioviz must be install to animate the model")
-
- check_version(bioviz, "2.3.0", "2.4.0")
-
- states = solution.stepwise_states(to_merge=SolutionMerge.NODES)
- if not isinstance(states, (list, tuple)):
- states = [states]
-
- if tracked_markers is None:
- tracked_markers = [None] * len(states)
-
- all_bioviz = []
- for idx_phase, data in enumerate(states):
- # This calls each of the function that modify the internal dynamic model based on the parameters
- nlp = solution.ocp.nlp[idx_phase]
-
- if isinstance(nlp.model, MultiBiorbdModel):
- if nlp.model.nb_models > 1:
- raise NotImplementedError(
- f"Animation is only implemented for MultiBiorbdModel with 1 model."
- f" There are {nlp.model.nb_models} models in the phase {idx_phase}."
- )
- else:
- model = nlp.model.models[0]
-
- biorbd_model: BiorbdModel = model
-
- all_bioviz.append(bioviz.Viz(biorbd_model.path, **kwargs))
- all_bioviz[-1].load_movement(solution.ocp.nlp[idx_phase].variable_mappings["q"].to_second.map(data["q"]))
-
- if tracked_markers[idx_phase] is not None:
- all_bioviz[-1].load_experimental_markers(tracked_markers[idx_phase])
-
- if show_now:
- b_is_visible = [True] * len(all_bioviz)
- while sum(b_is_visible):
- for i, b in enumerate(all_bioviz):
- if b.vtk_window.is_active:
- b.update()
- else:
- b_is_visible[i] = False
- return None
- else:
- return all_bioviz
+ def animate(
+ ocp,
+ solution,
+ show_now: bool = True,
+ show_tracked_markers: bool = False,
+ viewer: str = "pyorerun",
+ n_frames: int = 0,
+ **kwargs,
+ ):
+ from .viewer_bioviz import animate_with_bioviz_for_loop
+ from .viewer_pyorerun import animate_with_pyorerun
+
+ if viewer == "bioviz":
+ return animate_with_bioviz_for_loop(ocp, solution, show_now, show_tracked_markers, n_frames, **kwargs)
+ if viewer == "pyorerun":
+ return animate_with_pyorerun(ocp, solution, show_now, show_tracked_markers, **kwargs)
diff --git a/bioptim/models/biorbd/viewer_bioviz.py b/bioptim/models/biorbd/viewer_bioviz.py
new file mode 100644
index 000000000..8cbf1d91a
--- /dev/null
+++ b/bioptim/models/biorbd/viewer_bioviz.py
@@ -0,0 +1,161 @@
+import numpy as np
+from typing import Any
+
+from .biorbd_model import BiorbdModel
+from .viewer_utils import _prepare_tracked_markers_for_animation
+from ...limits.objective_functions import ObjectiveFcn
+from ...misc.enums import Node
+from ...misc.utils import check_version
+
+
+def animate_with_bioviz_for_loop(
+ ocp: "OptimalControlProgram",
+ solution: "Solution",
+ show_now: bool = True,
+ show_tracked_markers: bool = True,
+ n_frames: int = None,
+ **kwargs,
+):
+ """
+ Animate the solution(s) using bioviz
+
+ Parameters
+ ----------
+ ocp: OptimalControlProgram
+ The optimal control program
+ solution: Solution| List[Solution]
+ The solution(s) to animate
+ show_now: bool
+ If the animation should be shown immediately
+ show_tracked_markers: bool
+ If the tracked markers should be shown
+ n_frames: int
+ The number of frames to interpolate
+ kwargs
+ Any other parameters to pass to bioviz
+ """
+ n_frames = count_in_track_markers(ocp.nlp, n_frames)
+ data_to_animate = interpolate_data(solution, ocp, n_frames)
+ tracked_markers = get_tracked_markers(show_tracked_markers, ocp, n_frames)
+
+ all_bioviz = []
+ for i, data in enumerate(data_to_animate):
+ all_bioviz.append(
+ animate_with_bioviz(
+ ocp,
+ solution=data,
+ show_now=show_now,
+ tracked_markers=tracked_markers,
+ **kwargs,
+ )
+ )
+
+ return all_bioviz
+
+
+def animate_with_bioviz(
+ ocp,
+ solution: "SolutionData",
+ show_now: bool = True,
+ tracked_markers: list[np.ndarray] = None,
+ **kwargs: Any,
+) -> None | list:
+ try:
+ import bioviz
+ except ModuleNotFoundError:
+ raise RuntimeError("bioviz must be install to animate the model")
+
+ check_version(bioviz, "2.0.0", "2.4.0")
+
+ if "q_roots" in solution and "q_joints" in solution:
+ states = np.vstack((solution["q_roots"], solution["q_joints"]))
+ else:
+ states = solution["q"]
+
+ if not isinstance(states, (list, tuple)):
+ states = [states]
+
+ if tracked_markers is None:
+ tracked_markers = [None] * len(states)
+
+ all_bioviz = []
+ for idx_phase, data in enumerate(states):
+ if not isinstance(ocp.nlp[idx_phase].model, BiorbdModel):
+ raise NotImplementedError("Animation is only implemented for biorbd models")
+
+ # This calls each of the function that modify the internal dynamic model based on the parameters
+ nlp = ocp.nlp[idx_phase]
+
+ # noinspection PyTypeChecker
+ biorbd_model: BiorbdModel = nlp.model
+
+ all_bioviz.append(bioviz.Viz(biorbd_model.path, **kwargs))
+ all_bioviz[-1].load_movement(ocp.nlp[idx_phase].variable_mappings["q"].to_second.map(solution["q"]))
+
+ if "q_roots" in solution and "q_joints" in solution:
+ # TODO: Fix the mapping for this case
+ raise NotImplementedError("Mapping is not implemented for this case")
+ q = data
+ else:
+ q = ocp.nlp[idx_phase].variable_mappings["q"].to_second.map(data)
+ all_bioviz[-1].load_movement(q)
+
+ if tracked_markers[idx_phase] is not None:
+ all_bioviz[-1].load_experimental_markers(tracked_markers[idx_phase])
+
+ return play_bioviz_animation(all_bioviz) if show_now else all_bioviz
+
+
+def play_bioviz_animation(all_bioviz: list) -> None:
+ """Play the animation of the list of bioviz objects"""
+ b_is_visible = [True] * len(all_bioviz)
+ while sum(b_is_visible):
+ for i, b in enumerate(all_bioviz):
+ if b.vtk_window.is_active:
+ b.update()
+ else:
+ b_is_visible[i] = False
+ return None
+
+
+def count_in_track_markers(nlps, n_frames) -> int:
+ """Ipuch, Legacy Code: I'm very not sure what it does if anyone knows, fix the name of the function"""
+ for idx_phase in range(len(nlps)):
+ for objective in nlps[idx_phase].J:
+ if objective.target is not None:
+ if objective.type in (
+ ObjectiveFcn.Mayer.TRACK_MARKERS,
+ ObjectiveFcn.Lagrange.TRACK_MARKERS,
+ ) and objective.node[0] in (Node.ALL, Node.ALL_SHOOTING):
+ n_frames += objective.target.shape[2]
+ break
+ return n_frames
+
+
+def interpolate_data(solution, ocp, n_frames) -> list:
+ """Interpolate the data to be animated"""
+ data_to_animate = []
+ if n_frames == 0:
+ try:
+ data_to_animate = [solution.interpolate(sum([nlp.ns for nlp in ocp.nlp]) + 1)]
+ except ValueError:
+ data_to_animate = solution.interpolate([nlp.ns for nlp in ocp.nlp])
+ elif n_frames > 0:
+ data_to_animate = solution.interpolate(n_frames)
+ if not isinstance(data_to_animate, list):
+ data_to_animate = [data_to_animate]
+
+ return data_to_animate
+
+
+def get_tracked_markers(show_tracked_markers, ocp, n_frames):
+ """Get the tracked markers if needed"""
+ if show_tracked_markers and len(ocp.nlp) == 1:
+ return _prepare_tracked_markers_for_animation(ocp.nlp, n_shooting=n_frames)
+ elif show_tracked_markers and len(ocp.nlp) > 1:
+ raise NotImplementedError(
+ "Tracking markers is not implemented for multiple phases. "
+ "Set show_tracked_markers to False such that sol.animate(show_tracked_markers=False)."
+ )
+ else:
+ return [None for _ in range(len(ocp.nlp))]
diff --git a/bioptim/models/biorbd/viewer_pyorerun.py b/bioptim/models/biorbd/viewer_pyorerun.py
new file mode 100644
index 000000000..00d03bd0d
--- /dev/null
+++ b/bioptim/models/biorbd/viewer_pyorerun.py
@@ -0,0 +1,127 @@
+import biorbd_casadi as biorbd
+import numpy as np
+import pyorerun
+from typing import Any
+
+from .biorbd_model import BiorbdModel
+from .multi_biorbd_model import MultiBiorbdModel
+from ...optimization.solution.solution_data import SolutionMerge
+
+
+def animate_with_pyorerun(
+ ocp,
+ solution,
+ show_now: bool,
+ show_tracked_markers: bool,
+ **kwargs: Any,
+) -> None:
+ try:
+ import pyorerun
+ except ModuleNotFoundError:
+ raise RuntimeError("pyorerun must be install to animate the model")
+
+ data_to_animate, models, tracked_markers = prepare_pyorerun_animation(ocp, solution, show_now, show_tracked_markers)
+ launch_rerun(data_to_animate, show_now, tracked_markers, models, **kwargs)
+
+
+def prepare_pyorerun_animation(ocp, solution, show_now=True, show_tracked_markers=True) -> tuple[list, list, None]:
+ """Extract data from the solution to isolate the data for each phase and each model"""
+ n_phases = ocp.n_phases
+ data_to_animate = solution.decision_states(to_merge=SolutionMerge.NODES)
+ if n_phases == 1:
+ data_to_animate = [data_to_animate]
+
+ data_to_animate = set_time(solution, n_phases, data_to_animate)
+
+ models = []
+ for i, nlp in enumerate(ocp.nlp):
+ if isinstance(nlp.model, MultiBiorbdModel):
+ data_to_animate, models = set_data_for_multibiorbd_model(nlp, data_to_animate, models, i)
+ else:
+ models += [nlp.model.model]
+
+ if show_tracked_markers:
+ raise NotImplementedError(
+ "Tracking markers is not implemented for pyorerun. "
+ "Set show_tracked_markers to False such that sol.animate(show_tracked_markers=False)."
+ )
+ # TODO : Implement tracking markers for pyorerun
+ # with the _prepare_tracked_markers_for_animation in viewer_utils.py
+ else:
+ tracked_markers = None
+
+ return data_to_animate, models, tracked_markers
+
+
+def set_time(solution, n_phases, data_to_animate):
+ """Set the time in the data_to_animate, handles multiple phases"""
+ time = (
+ [np.concatenate(solution.decision_time()).squeeze()]
+ if n_phases == 1
+ else [np.concatenate(t).squeeze() for t in solution.decision_time()]
+ )
+
+ for i in range(n_phases):
+ data_to_animate[i]["time"] = time[i]
+
+ return data_to_animate
+
+
+def set_data_for_multibiorbd_model(nlp, data_to_animate: list, models: list, i: int):
+ """Duplicate the data for each model in the MultiBiorbdModel and models"""
+ models += [model for model in nlp.model.models]
+ temp_data_animate = [data_to_animate[i].copy() for _ in range(nlp.model.nb_models)]
+ for j, model in enumerate(nlp.model.models):
+ for key in data_to_animate[i].keys():
+ if key == "time":
+ continue
+ index = nlp.model.variable_index(key, j)
+ temp_data_animate[j][key] = temp_data_animate[j][key][index, :]
+
+ data_to_animate[i] = temp_data_animate[0]
+ data_to_animate += temp_data_animate[1:]
+
+ return data_to_animate, models
+
+
+def launch_rerun(
+ solution: "SolutionData",
+ show_now: bool = True,
+ tracked_markers: list[np.ndarray] = None,
+ models: BiorbdModel | list[BiorbdModel] = None,
+ **kwargs: Any,
+):
+ if not isinstance(solution, (list, tuple)):
+ solution = [solution]
+
+ if tracked_markers is None:
+ tracked_markers = [None] * len(solution)
+ prerun = pyorerun.MultiPhaseRerun()
+
+ for idx_phase, (data, model, tm) in enumerate(zip(solution, models, tracked_markers)):
+
+ if "q_roots" in data and "q_joints" in data:
+ try:
+ data["q"] = np.vstack((data["q_roots"], data["q_joints"]))
+ except:
+ raise NotImplementedError(
+ "Found q_roots and q_joints in the solution. This is not supported yet with animation in pyorerun"
+ )
+
+ prerun.add_phase(t_span=data["time"], phase=idx_phase)
+
+ if not isinstance(model, biorbd.Model):
+ raise NotImplementedError(
+ f"Animation is only implemented for biorbd models. Got {model.__class__.__name__}"
+ )
+
+ biorbd_model = pyorerun.BiorbdModel.from_biorbd_object(model)
+
+ prerun.add_animated_model(
+ biorbd_model,
+ data["q"],
+ tracked_markers=tm if tm is not None else None,
+ phase=idx_phase,
+ )
+
+ prerun.rerun(notebook=not show_now)
diff --git a/bioptim/models/biorbd/viewer_utils.py b/bioptim/models/biorbd/viewer_utils.py
new file mode 100644
index 000000000..067ae73e8
--- /dev/null
+++ b/bioptim/models/biorbd/viewer_utils.py
@@ -0,0 +1,61 @@
+import numpy as np
+from scipy.interpolate import interp1d
+
+from ...limits.objective_functions import ObjectiveFcn
+from ...misc.enums import Node
+
+
+def _prepare_tracked_markers_for_animation(
+ nlps: list["NonLinearProgram", ...], n_shooting: int = None
+) -> list[np.ndarray, ...]:
+ """Prepare the markers which are tracked to the animation"""
+
+ all_tracked_markers = []
+
+ for phase, nlp in enumerate(nlps):
+ n_frames = sum(nlp.ns) + 1 if n_shooting is None else n_shooting + 1
+
+ n_states_nodes = nlp.n_states_nodes
+
+ tracked_markers = None
+ for objective in nlp.J:
+ if objective.target is not None:
+ if objective.type in (
+ ObjectiveFcn.Mayer.TRACK_MARKERS,
+ ObjectiveFcn.Lagrange.TRACK_MARKERS,
+ ) and objective.node[0] in (Node.ALL, Node.ALL_SHOOTING):
+ tracked_markers = np.full((3, nlp.model.nb_markers, n_states_nodes), np.nan)
+
+ for i in range(len(objective.rows)):
+ tracked_markers[objective.rows[i], objective.cols, :] = objective.target[i, :, :]
+
+ missing_row = np.where(np.isnan(tracked_markers))[0]
+ if missing_row.size > 0:
+ tracked_markers[missing_row, :, :] = 0
+
+ # interpolation
+ if n_frames > 0 and tracked_markers is not None:
+ x = np.linspace(0, n_states_nodes - 1, n_states_nodes)
+ xnew = np.linspace(0, n_states_nodes - 1, n_frames)
+ f = interp1d(x, tracked_markers, kind="cubic")
+ tracked_markers = f(xnew)
+
+ all_tracked_markers.append(tracked_markers)
+
+ return all_tracked_markers
+
+
+def _check_models_comes_from_same_super_class(all_nlp: list["NonLinearProgram", ...]):
+ """Check that all the models comes from the same super class"""
+ for i, nlp in enumerate(all_nlp):
+ model_super_classes = nlp.model.__class__.mro()[:-1] # remove object class
+ nlps = all_nlp.copy()
+ del nlps[i]
+ for j, sub_nlp in enumerate(nlps):
+ if not any([isinstance(sub_nlp.model, super_class) for super_class in model_super_classes]):
+ raise RuntimeError(
+ f"The animation is only available for compatible models. "
+ f"Here, the model of phase {i} is of type {nlp.model.__class__.__name__} and the model of "
+ f"phase {j + 1 if i < j else j} is of type {sub_nlp.model.__class__.__name__} and "
+ f"they don't share the same super class."
+ )
diff --git a/bioptim/optimization/solution/solution.py b/bioptim/optimization/solution/solution.py
index ab1c90f69..9a65dbdd6 100644
--- a/bioptim/optimization/solution/solution.py
+++ b/bioptim/optimization/solution/solution.py
@@ -1,17 +1,14 @@
-from copy import deepcopy
-from typing import Any
-
import numpy as np
from casadi import vertcat, DM, Function
+from copy import deepcopy
from matplotlib import pyplot as plt
from scipy import interpolate as sci_interp
-from scipy.interpolate import interp1d
+from typing import Any
from .solution_data import SolutionData, SolutionMerge, TimeAlignment, TimeResolution
from ..optimization_vector import OptimizationVectorHelper
from ...dynamics.ode_solver import OdeSolver
from ...interfaces.solve_ivp_interface import solve_ivp_interface
-from ...limits.objective_functions import ObjectiveFcn
from ...limits.path_conditions import InitialGuess, InitialGuessList
from ...limits.penalty_helpers import PenaltyHelpers
from ...misc.enums import (
@@ -1225,6 +1222,7 @@ def animate(
shooting_type: Shooting = None,
show_now: bool = True,
show_tracked_markers: bool = False,
+ viewer: str = "bioviz",
**kwargs: Any,
) -> None | list:
"""
@@ -1241,6 +1239,8 @@ def animate(
If the bioviz exec() function should be called automatically. This is blocking method
show_tracked_markers: bool
If the tracked markers should be displayed
+ viewer: str
+ The viewer to use. Currently, bioviz or pyorerun
kwargs: Any
Any parameters to pass to bioviz
@@ -1249,108 +1249,22 @@ def animate(
A list of bioviz structures (one for each phase). So one can call exec() by hand
"""
+ from ...models.biorbd.viewer_utils import _check_models_comes_from_same_super_class
+
if shooting_type:
self.integrate(shooting_type=shooting_type)
- for idx_phase in range(len(self.ocp.nlp)):
- for objective in self.ocp.nlp[idx_phase].J:
- if objective.target is not None:
- if objective.type in (
- ObjectiveFcn.Mayer.TRACK_MARKERS,
- ObjectiveFcn.Lagrange.TRACK_MARKERS,
- ) and objective.node[0] in (Node.ALL, Node.ALL_SHOOTING):
- n_frames += objective.target.shape[2]
- break
-
- data_to_animate = []
- if n_frames == 0:
- try:
- data_to_animate = [self.interpolate(sum([nlp.ns for nlp in self.ocp.nlp]) + 1)]
- except ValueError:
- data_to_animate = self.interpolate([nlp.ns for nlp in self.ocp.nlp])
- elif n_frames > 0:
- data_to_animate = self.interpolate(n_frames)
- if not isinstance(data_to_animate, list):
- data_to_animate = [data_to_animate]
-
- if show_tracked_markers and len(self.ocp.nlp) == 1:
- tracked_markers = self._prepare_tracked_markers_for_animation(n_shooting=n_frames)
- elif show_tracked_markers and len(self.ocp.nlp) > 1:
- raise NotImplementedError(
- "Tracking markers is not implemented for multiple phases. "
- "Set show_tracked_markers to False such that sol.animate(show_tracked_markers=False)."
- )
- else:
- tracked_markers = [None for _ in range(len(self.ocp.nlp))]
-
- # assuming that all the models or the same type.
- self._check_models_comes_from_same_super_class()
-
- all_bioviz = []
- for i, data in enumerate(data_to_animate):
- all_bioviz.append(
- self.ocp.nlp[i].model.animate(
- self.ocp,
- solution=data,
- show_now=show_now,
- tracked_markers=tracked_markers,
- **kwargs,
- )
- )
-
- return all_bioviz
-
- def _check_models_comes_from_same_super_class(self):
- """Check that all the models comes from the same super class"""
- for i, nlp in enumerate(self.ocp.nlp):
- model_super_classes = nlp.model.__class__.mro()[:-1] # remove object class
- nlps = self.ocp.nlp.copy()
- del nlps[i]
- for j, sub_nlp in enumerate(nlps):
- if not any([isinstance(sub_nlp.model, super_class) for super_class in model_super_classes]):
- raise RuntimeError(
- f"The animation is only available for compatible models. "
- f"Here, the model of phase {i} is of type {nlp.model.__class__.__name__} and the model of "
- f"phase {j + 1 if i < j else j} is of type {sub_nlp.model.__class__.__name__} and "
- f"they don't share the same super class."
- )
-
- def _prepare_tracked_markers_for_animation(self, n_shooting: int = None) -> list:
- """Prepare the markers which are tracked to the animation"""
-
- all_tracked_markers = []
-
- for phase, nlp in enumerate(self.ocp.nlp):
- n_frames = sum(nlp.ns) + 1 if n_shooting is None else n_shooting + 1
-
- n_states_nodes = self.ocp.nlp[phase].n_states_nodes
-
- tracked_markers = None
- for objective in nlp.J:
- if objective.target is not None:
- if objective.type in (
- ObjectiveFcn.Mayer.TRACK_MARKERS,
- ObjectiveFcn.Lagrange.TRACK_MARKERS,
- ) and objective.node[0] in (Node.ALL, Node.ALL_SHOOTING):
- tracked_markers = np.full((3, nlp.model.nb_markers, n_states_nodes), np.nan)
+ _check_models_comes_from_same_super_class(self.ocp.nlp)
- for i in range(len(objective.rows)):
- tracked_markers[objective.rows[i], objective.cols, :] = objective.target[i, :, :]
-
- missing_row = np.where(np.isnan(tracked_markers))[0]
- if missing_row.size > 0:
- tracked_markers[missing_row, :, :] = 0
-
- # interpolation
- if n_frames > 0 and tracked_markers is not None:
- x = np.linspace(0, n_states_nodes - 1, n_states_nodes)
- xnew = np.linspace(0, n_states_nodes - 1, n_frames)
- f = interp1d(x, tracked_markers, kind="cubic")
- tracked_markers = f(xnew)
-
- all_tracked_markers.append(tracked_markers)
-
- return all_tracked_markers
+ type(self.ocp.nlp[0].model).animate(
+ ocp=self.ocp,
+ solution=self,
+ show_now=show_now,
+ show_tracked_markers=show_tracked_markers,
+ viewer=viewer,
+ n_frames=n_frames,
+ **kwargs,
+ )
@staticmethod
def _dispatch_params(params):
diff --git a/tests/shard3/test_global_torque_driven_ocp.py b/tests/shard3/test_global_torque_driven_ocp.py
index 52d23af0b..94b8e1f47 100644
--- a/tests/shard3/test_global_torque_driven_ocp.py
+++ b/tests/shard3/test_global_torque_driven_ocp.py
@@ -2,10 +2,11 @@
Test for file IO
"""
-import os
-import pytest
import numpy as np
import numpy.testing as npt
+import os
+import pytest
+
from bioptim import (
OdeSolver,
ConstraintList,
@@ -17,6 +18,7 @@
PhaseDynamics,
SolutionMerge,
)
+from bioptim.models.biorbd.viewer_utils import _prepare_tracked_markers_for_animation
from tests.utils import TestUtils
@@ -417,7 +419,7 @@ def test_track_marker_2D_pendulum(ode_solver, defects_type, phase_dynamics):
TestUtils.simulate(sol)
# testing that preparing tracked markers for animation properly works
- tracked_markers = sol._prepare_tracked_markers_for_animation(n_shooting)
+ tracked_markers = _prepare_tracked_markers_for_animation(sol.ocp.nlp, n_shooting)
npt.assert_equal(tracked_markers[0].shape, (3, 2, n_shooting + 1))
npt.assert_equal(tracked_markers[0][0, :, :], np.zeros((2, n_shooting + 1)))
npt.assert_almost_equal(tracked_markers[0][1:, :, 0], np.array([[0.82873751, 0.5612772], [0.22793516, 0.24205527]]))
diff --git a/tests/shard4/test_simulate.py b/tests/shard4/test_simulate.py
index fc3acfd6e..1f736d367 100644
--- a/tests/shard4/test_simulate.py
+++ b/tests/shard4/test_simulate.py
@@ -1,11 +1,13 @@
-import warnings
-import os
from sys import platform
-import pytest
import numpy as np
import numpy.testing as npt
+import os
+import pytest
+import warnings
+
from bioptim import Shooting, OdeSolver, SolutionIntegrator, Solver, PhaseDynamics, SolutionMerge, ControlType
+from bioptim.models.biorbd.viewer_utils import _check_models_comes_from_same_super_class
@pytest.mark.parametrize("scaled", [True, False])
@@ -648,7 +650,7 @@ def test_check_models_comes_from_same_super_class():
solver.set_print_level(0)
sol = ocp.solve(solver)
- sol._check_models_comes_from_same_super_class()
+ _check_models_comes_from_same_super_class(sol.ocp.nlp)
class FakeModel:
def __init__(self):
@@ -662,7 +664,7 @@ def __init__(self):
"Here, the model of phase 0 is of type FakeModel "
"and the model of phase 0 is of type BiorbdModel and they don't share the same super class.",
):
- sol._check_models_comes_from_same_super_class()
+ _check_models_comes_from_same_super_class(sol.ocp.nlp)
@pytest.mark.parametrize("phase_dynamics", [PhaseDynamics.SHARED_DURING_THE_PHASE, PhaseDynamics.ONE_PER_NODE])