Run formatting

examples/simulate_planar_hsa.py

@@ -70,7 +70,9 @@ def draw_robot(
         params, q, s_ps
     )  # poses of virtual backbone
     chiL_ps = batched_forward_kinematics_rod_fn(params, q, s_ps, 0)  # poses of left rod
-    chiR_ps = batched_forward_kinematics_rod_fn(params, q, s_ps, 1)  # poses of right rod
+    chiR_ps = batched_forward_kinematics_rod_fn(
+        params, q, s_ps, 1
+    )  # poses of right rod
     # poses of the platforms
     chip_ps = batched_forward_kinematics_platform_fn(
         params, q, jnp.arange(0, num_segments)

src/jsrm/parameters/hsa_params.py

@@ -1,7 +1,10 @@
 __all__ = [
-    "generate_base_params_for_fpu", "generate_base_params_for_epu",
-    "PARAMS_FPU_CONTROL", "PARAMS_FPU_SYSTEM_ID",
-    "PARAMS_EPU_CONTROL", "PARAMS_EPU_SYSTEM_ID",
+    "generate_base_params_for_fpu",
+    "generate_base_params_for_epu",
+    "PARAMS_FPU_CONTROL",
+    "PARAMS_FPU_SYSTEM_ID",
+    "PARAMS_EPU_CONTROL",
+    "PARAMS_EPU_SYSTEM_ID",
 ]
 
 from jax import Array
@@ -10,9 +13,9 @@
 
 
 def generate_common_base_params(
-        num_segments: int = 1,
-        num_rods_per_segment: int = 4,
-        end_effector_attached: int = False
+    num_segments: int = 1,
+    num_rods_per_segment: int = 4,
+    end_effector_attached: int = False,
 ) -> Dict[str, Array]:
     assert num_rods_per_segment % 2 == 0, "num_rods_per_segment must be even"
 
@@ -52,7 +55,9 @@ def generate_common_base_params(
     if end_effector_attached:
         # the end-effector is moved by 25mm in the y-dir relative to the top surface of the HSA platform
         params["chiee_off"] = jnp.array([0.0, 0.025, 0.0])
-        params["mpl"] = jnp.array(0.018)  # the end-effector attachment has a mass of 18g
+        params["mpl"] = jnp.array(
+            0.018
+        )  # the end-effector attachment has a mass of 18g
         # the end-effector attachment has a center of gravity of 3.63mm in y-dir from its base.
         # as it has a thickness of 25mm, this is -21.37mm from the top surface (i.e., end-effector position)
         params["CoGpl"] = jnp.array([0.0, -0.02137])
@@ -61,12 +66,14 @@ def generate_common_base_params(
 
 
 def generate_base_params_for_fpu(
-        num_segments: int = 1,
-        num_rods_per_segment: int = 4,
-        rod_multiplier: int = 1,
-        **kwargs
+    num_segments: int = 1,
+    num_rods_per_segment: int = 4,
+    rod_multiplier: int = 1,
+    **kwargs,
 ) -> Dict[str, Array]:
-    common_params = generate_common_base_params(num_segments, num_rods_per_segment, **kwargs)
+    common_params = generate_common_base_params(
+        num_segments, num_rods_per_segment, **kwargs
+    )
 
     ones_rod = jnp.ones((num_segments, num_rods_per_segment))
     # old params (1st ISER submission)
@@ -144,7 +151,9 @@ def generate_base_params_for_fpu(
         "rin": (25.4e-3 / 2 - 2.43e-3) * ones_rod,  # this is for FPU rods
         # mass of FPU rod: 14 g
         # For FPU, this corresponds to a measure volume of 0000175355 m^3 --> rho = 798.38 kg/m^3
-        "rhor": 798.38 * rod_multiplier * ones_rod,  # Volumetric density of rods [kg/m^3],
+        "rhor": 798.38
+        * rod_multiplier
+        * ones_rod,  # Volumetric density of rods [kg/m^3],
         # Volumetric density of platform [kg/m^3],
         # weight of platform + marker holder + cylinder top piece: 0.107 kg
         # subtracting 4 x 9g for distal cap: 0.071 kg
@@ -185,12 +194,14 @@ def generate_base_params_for_fpu(
 
 
 def generate_base_params_for_epu(
-        num_segments: int = 1,
-        num_rods_per_segment: int = 4,
-        rod_multiplier: int = 1,
-        **kwargs
+    num_segments: int = 1,
+    num_rods_per_segment: int = 4,
+    rod_multiplier: int = 1,
+    **kwargs,
 ) -> Dict[str, Array]:
-    common_params = generate_common_base_params(num_segments, num_rods_per_segment, **kwargs)
+    common_params = generate_common_base_params(
+        num_segments, num_rods_per_segment, **kwargs
+    )
 
     ones_rod = jnp.ones((num_segments, num_rods_per_segment))
     params = common_params | {
@@ -200,7 +211,9 @@ def generate_base_params_for_epu(
         "rin": (25.4e-3 / 2 - 4.76e-3) * ones_rod,  # this is for EPU rods
         # mass of EPU rod: 26 g
         # For EPU, this corresponds to a measure volume of 0000314034 m^3 --> rho = 827.94 kg/m^3
-        "rhor": 827.94 * rod_multiplier * ones_rod,  # Volumetric density of rods [kg/m^3],
+        "rhor": 827.94
+        * rod_multiplier
+        * ones_rod,  # Volumetric density of rods [kg/m^3],
         # Volumetric density of platform [kg/m^3],
         # weight of platform + marker holder + cylinder top piece: 0.107 kg
         # subtracting 4 x 9g for distal cap: 0.071 kg
@@ -218,7 +231,7 @@ def generate_base_params_for_epu(
         # Nominal shear stiffness of each rod [N]
         "S_sh_hat": 4.28135773e-02 * rod_multiplier * ones_rod,
         # Nominal axial stiffness of each rod [N]
-        "S_a_hat": 0. * rod_multiplier * ones_rod,
+        "S_a_hat": 0.0 * rod_multiplier * ones_rod,
         # Elastic coupling between bending and shear [Nm/rad]
         "S_b_sh": 5.04204068e-04 * rod_multiplier * ones_rod,
         # Scaling of bending stiffness with twist strain [Nm^3/rad]
@@ -240,21 +253,29 @@ def generate_base_params_for_epu(
     return params
 
 
-PARAMS_FPU_SYSTEM_ID = generate_base_params_for_fpu(num_segments=1, num_rods_per_segment=4)
+PARAMS_FPU_SYSTEM_ID = generate_base_params_for_fpu(
+    num_segments=1, num_rods_per_segment=4
+)
 PARAMS_FPU_SYSTEM_ID.update(
     {
         "h": jnp.array([[1.0, -1.0, 1.0, -1.0]]),
         "roff": 24e-3 * jnp.array([[1.0, 1.0, -1.0, -1.0]]),
     }
 )
-PARAMS_FPU_CONTROL = generate_base_params_for_fpu(num_segments=1, num_rods_per_segment=2, rod_multiplier=2)
+PARAMS_FPU_CONTROL = generate_base_params_for_fpu(
+    num_segments=1, num_rods_per_segment=2, rod_multiplier=2
+)
 
-PARAMS_EPU_SYSTEM_ID = generate_base_params_for_epu(num_segments=1, num_rods_per_segment=4)
+PARAMS_EPU_SYSTEM_ID = generate_base_params_for_epu(
+    num_segments=1, num_rods_per_segment=4
+)
 PARAMS_EPU_SYSTEM_ID.update(
     {
         "h": jnp.array([[1.0, -1.0, 1.0, -1.0]]),
         "roff": 24e-3 * jnp.array([[1.0, 1.0, -1.0, -1.0]]),
     }
 )
 
-PARAMS_EPU_CONTROL = generate_base_params_for_epu(num_segments=1, num_rods_per_segment=2, rod_multiplier=2)
+PARAMS_EPU_CONTROL = generate_base_params_for_epu(
+    num_segments=1, num_rods_per_segment=2, rod_multiplier=2
+)

src/jsrm/symbolic_derivation/planar_hsa.py

@@ -160,7 +160,9 @@ def symbolically_derive_planar_hsa_model(
     # bending rest strain of each rod
     kappa_b_eq = sp.Matrix(kappa_b_eq_syms).reshape(num_segments, num_rods_per_segment)
     # shear rest strain of each rod
-    sigma_sh_eq = sp.Matrix(sigma_sh_eq_syms).reshape(num_segments, num_rods_per_segment)
+    sigma_sh_eq = sp.Matrix(sigma_sh_eq_syms).reshape(
+        num_segments, num_rods_per_segment
+    )
     # axial rest strain of each rod
     sigma_a_eq = sp.Matrix(sigma_a_eq_syms).reshape(num_segments, num_rods_per_segment)
     C_varepsilon = sp.Matrix(C_varepsilon_syms).reshape(
@@ -303,7 +305,9 @@ def symbolically_derive_planar_hsa_model(
 
             # strains in physical HSA rod
             pxir = _sym_beta_fn(vxi, roff[i, j])
-            pxi_eqr = sp.Matrix([[kappa_b_eq[i, j]], [sigma_sh_eq[i, j]], [sigma_a_eq[i, j]]])
+            pxi_eqr = sp.Matrix(
+                [[kappa_b_eq[i, j]], [sigma_sh_eq[i, j]], [sigma_a_eq[i, j]]]
+            )
             # twist angle of the current rod
             phir = phi[i * num_rods_per_segment + j]
 
@@ -468,7 +472,9 @@ def symbolically_derive_planar_hsa_model(
     pee = p_prev  # end-effector position
     thee = th_prev  # end-effector orientation
     # rotation matrix of the last platform
-    R_last_last_platform = sp.Matrix([[sp.cos(thee), -sp.sin(thee)], [sp.sin(thee), sp.cos(thee)]])
+    R_last_last_platform = sp.Matrix(
+        [[sp.cos(thee), -sp.sin(thee)], [sp.sin(thee), sp.cos(thee)]]
+    )
     # add the rigid offset of the end-effector from the distal end of the last platform
     pee += R_last_last_platform @ sp.Matrix([chiee_off_syms[0], chiee_off_syms[1]])
     thee += chiee_off_syms[2]

src/jsrm/systems/planar_hsa.py

@@ -462,28 +462,34 @@ def inverse_kinematics_end_effector_fn(
         )
 
         # transformation from the base to the end-effector
-        T_b_to_ee = jnp.array([
-            [jnp.cos(chiee[2]), -jnp.sin(chiee[2]), chiee[0]],
-            [jnp.sin(chiee[2]), jnp.cos(chiee[2]), chiee[1]],
-            [0.0, 0.0, 1.0]
-        ])
+        T_b_to_ee = jnp.array(
+            [
+                [jnp.cos(chiee[2]), -jnp.sin(chiee[2]), chiee[0]],
+                [jnp.sin(chiee[2]), jnp.cos(chiee[2]), chiee[1]],
+                [0.0, 0.0, 1.0],
+            ]
+        )
 
         # transformation from the distal end of the virtual backbone to the end-effector
-        T_de_to_ee = jnp.array([
-            [jnp.cos(chiee_off[2]), -jnp.sin(chiee_off[2]), chiee_off[0]],
-            [jnp.sin(chiee_off[2]), jnp.cos(chiee_off[2]), ldc + hp + chiee_off[1]],
-            [0.0, 0.0, 1.0]
-        ])
+        T_de_to_ee = jnp.array(
+            [
+                [jnp.cos(chiee_off[2]), -jnp.sin(chiee_off[2]), chiee_off[0]],
+                [jnp.sin(chiee_off[2]), jnp.cos(chiee_off[2]), ldc + hp + chiee_off[1]],
+                [0.0, 0.0, 1.0],
+            ]
+        )
 
         # compute the transformation from the proximal to the distal end of the virtual backbone
-        T_pe_to_de = jnp.linalg.inv(T_b_to_pe) @  T_b_to_ee @ jnp.linalg.inv(T_de_to_ee)
+        T_pe_to_de = jnp.linalg.inv(T_b_to_pe) @ T_b_to_ee @ jnp.linalg.inv(T_de_to_ee)
 
         # compute the SE(2) pose from the transformation matrix
-        vchi_pe_to_de = jnp.array([
-            T_pe_to_de[0, 2],
-            T_pe_to_de[1, 2],
-            jnp.arctan2(T_pe_to_de[1, 0], T_pe_to_de[0, 0])
-        ])
+        vchi_pe_to_de = jnp.array(
+            [
+                T_pe_to_de[0, 2],
+                T_pe_to_de[1, 2],
+                jnp.arctan2(T_pe_to_de[1, 0], T_pe_to_de[0, 0]),
+            ]
+        )
 
         # extract the x and y position and the orientation
         px, py, th = vchi_pe_to_de[0], vchi_pe_to_de[1], vchi_pe_to_de[2]