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musculoskeletal
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@demotu
demotu committed Mar 20, 2015
1 parent 40a8f33 commit 299287f
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -70,6 +70,7 @@ Modeling and simulation of human movement
-----------------------------------------
- [Muscle modeling](http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/MuscleModeling.ipynb)
- [Muscle simulation](http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/MuscleSimulation.ipynb)
- [Musculoskeletal modeling and simulation](http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/MusculoskeletaModelingSimulation.ipynb)

Stabilography
-------------
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107 changes: 107 additions & 0 deletions data/vas_int_r.mot
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@@ -0,0 +1,107 @@
UNKNOWN
version=1
nRows=100
nColumns=3
inDegrees=no
endheader
time knee_angle_r vas_int_r
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30 changes: 20 additions & 10 deletions functions/muscles.py
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Expand Up @@ -343,7 +343,7 @@ def calc_data(self, t, lm, lm0, lmt0, ltslack, lmopt, alpha0, fm0):
fce_t = fse/np.cos(alpha) - fpe
vm = self.velo_fm(fm=fce_t, a=a, fl=fl, lmopt=lmopt)
fm = self.force_vm(vm=vm, fl=fl, lmopt=lmopt, a=a) + fpe
data = [t, lmt, lm, lt, vm, fm*fm0, fse*fm0, a*fl*fm0, fpe*fm0]
data = [t, lmt, lm, lt, vm, fm*fm0, fse*fm0, a*fl*fm0, fpe*fm0, alpha]

return data

Expand All @@ -368,7 +368,8 @@ def muscle_plot(self, a=1, axs=None):
lm0 = self.S['lm0']
lmt0 = self.S['lmt0']
lt0 = self.S['lt0']
if np.isnan(lt0): lt0 = lmt0 - lm0*np.cos(alpha0)
if np.isnan(lt0):
lt0 = lmt0 - lm0*np.cos(alpha0)

lm = np.linspace(0, 2, 101)
lt = np.linspace(0, 1, 101)*0.05 + 1
Expand Down Expand Up @@ -449,10 +450,12 @@ def muscle_plot(self, a=1, axs=None):
plt.tight_layout(w_pad=.1)
plt.show()


def lm_plot(self, x, axs):
return axs


def lm_plot(self, x, axs=None):
"""Plot results of actdyn_ode45 function.
data = [t, lmt, lm, lt, vm, fm*fm0, fse*fm0, fl*fm0, fpe*fm0]
data = [t, lmt, lm, lt, vm, fm*fm0, fse*fm0, fl*fm0, fpe*fm0, alpha]
"""

try:
Expand All @@ -465,7 +468,11 @@ def lm_plot(self, x, axs):
_, axs = plt.subplots(nrows=3, ncols=2, sharex=True, figsize=(10, 6))

axs[0, 0].plot(x[:, 0], x[:, 1], 'b', label='LMT')
axs[0, 0].plot(x[:, 0], x[:, 2] + x[:, 3], 'g--', label='LM+LT')
lmt = x[:, 2]*np.cos(x[:, 9]) + x[:, 3]
if np.sum(x[:, 9]) > 0:
axs[0, 0].plot(x[:, 0], lmt, 'g--', label=r'$LM \cos \alpha + LT$')
else:
axs[0, 0].plot(x[:, 0], lmt, 'g--', label=r'LM+LT')
ylim = self.margins(x[:, 1], margin=.1)
axs[0, 0].set_ylim(ylim)
axs[0, 0].legend(framealpha=.5, loc='best')
Expand Down Expand Up @@ -497,10 +504,9 @@ def lm_plot(self, x, axs):
axs[2, 1].set_xlabel('Time (s)')
axs[2, 1].legend(framealpha=.5, loc='best')

axs = axs.flatten()
ylabel = ['$L_{MT}\,(m)$', '$L_{T}\,(m)$', '$L_{M}\,(m)$',
'$V_{CE}\,(m/s)$', '$Force\,(N)$', '$Force\,(N)$']
for i, axi in enumerate(axs):
for i, axi in enumerate(axs.flat):
axi.set_ylabel(ylabel[i], fontsize=14)
axi.yaxis.set_major_locator(plt.MaxNLocator(4))
axi.yaxis.set_label_coords(-.2, 0.5)
Expand All @@ -510,6 +516,8 @@ def lm_plot(self, x, axs):
plt.tight_layout()
plt.show()

return axs


def penn_ang(self, lmt, lm, lt=None, lm0=None, alpha0=None):
"""Pennation angle.
Expand Down Expand Up @@ -689,7 +697,7 @@ def activation(self, t=None):
return a


def actvation_plot(self, data, axs):
def actvation_plot(self, data, axs=None):
"""Plot results of actdyn_ode45 function."""

try:
Expand All @@ -708,7 +716,9 @@ def actvation_plot(self, data, axs):
axs.legend()
plt.title('Activation dynamics')
plt.tight_layout()
plt.show()
plt.show()

return axs


def margins(self, x, margin=0.01, minmargin=True):
Expand Down
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