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From: Amritava D. <das...@um...> - 2015-10-23 22:50:22
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run run_JAK_mod.py
Initial cost: 298.94896354
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/home/amritava/programming/JAK-STAT/run_JAK_mod.py in <module>()
17
18 print 'Initial cost:', m.cost(params)
---> 19 params = Optimization.fmin_lm_log_params(m, params, maxiter=20, disp=False)
20 print 'Optimized cost:', m.cost(params)
21 print 'Optimized parameters:', params
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/Optimization.pyc in fmin_lm_log_params(m, params, *args, **kwargs)
135 jac = lambda lp: scipy.asarray(m.jacobian_log_params_sens(lp))
136 sln = lmopt.fmin_lm(f=func, x0=scipy.log(params), fprime=jac,
--> 137 *args, **kwargs)
138 if isinstance(params, KeyedList):
139 pout = params.copy()
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/lmopt.pyc in fmin_lm(f, x0, fprime, args, avegtol, epsilon, maxiter, full_output, disp, retall, lambdainit, jinit, trustradius)
173 func_calls = 0
174 grad_calls = 0
--> 175 res,currentcost = safe_res(f,x0,args)
176 func_calls+=1
177 m = res.shape[0]
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/lmopt.pyc in safe_res(f, x, args)
92 """
93 try:
---> 94 res = asarray(apply(f,(x,)+args))
95 cost = sum(res**2)
96 except (SloppyCell.Utility.SloppyCellException,OverflowError):
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/Optimization.pyc in func(log_params)
128 def func(log_params):
129 try:
--> 130 return m.res_log_params(log_params)
131 except Utility.SloppyCellException:
132 logger.warn('Exception in cost evaluation. Cost set to inf.')
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/Model_mod.pyc in res_log_params(self, log_params)
158 Return the residual values given the logarithm of the parameters
159 """
--> 160 return self.res(scipy.exp(log_params))
161
162 def res_dict(self, params):
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/Model_mod.pyc in res(self, params)
152 """
153
--> 154 return self._evaluate(params)[0]
155
156 def res_log_params(self, log_params):
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/Model_mod.pyc in _evaluate(self, params, T)
114 arrangment makes notification of observers much simpler.)
115 """
--> 116 self.params.update(params)
117 self.check_parameter_bounds(params)
118 self.CalculateForAllDataPoints(params)
/usr/local/lib/python2.7/dist-packages/SloppyCell-CVS-py2.7-linux-x86_64.egg/SloppyCell/KeyedList_mod.pyc in update(self, other)
113 else:
114 if(len(self) != len(other)):
--> 115 raise ValueError, 'Other list not of same length!'
116 for ii in range(len(self)):
117 self[ii] = other[ii]
ValueError: Other list not of same length!
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