The following code comes from an example on http://cars9.uchicago.edu/software/python/lmfit/parameters.html.
from lmfit import minimize, Minimizer, Parameters, Parameter, report_fit
import numpy as np
# create data to be fitted
x = np.linspace(0, 15, 301)
data = (5. * np.sin(2 * x - 0.1) * np.exp(-x*x*0.025) +
np.random.normal(size=len(x), scale=0.2) )
# define objective function: returns the array to be minimized
def fcn2min(params, x, data):
""" model decaying sine wave, subtract data"""
amp = params['amp']
shift = params['shift']
omega = params['omega']
decay = params['decay']
model = amp * np.sin(x * omega + shift) * np.exp(-x*x*decay)
return model - data
# create a set of Parameters
params = Parameters()
params.add('amp', value= 10, min=0)
params.add('decay', value= 0.1)
params.add('shift', value= 0.0, min=-np.pi/2., max=np.pi/2)
params.add('omega', value= 3.0)
# do fit, here with leastsq model
minner = Minimizer(fcn2min, params, fcn_args=(x, data))
result = minner.minimize()
# calculate final result
final = data + result.residual
# write error report
report_fit(result)
# try to plot results
try:
import pylab
pylab.plot(x, data, 'k+')
pylab.plot(x, final, 'r')
pylab.show()
except:
pass
I tried to run this code in Canopy. When using Canopy 64 bit for Python 3.5 it ran fine. I need to use it in Canopy 32 using Python 2.7. When I changed to use the other editor, it no longer worked. Here is the issue it gives me:
13 omega = params['omega']
14 decay = params['decay']
---> 15 model = amp * np.sin(x * omega + shift) * np.exp(-x*x*decay)
16 return model - data
17 # create a set of Parameters
AttributeError: 'numpy.float64' object has no attribute 'sin'
I am confused because the only thing I changed is the version of Python and the version of Canopy. Could this be caused by difference between Python 2.7 and Python 3.5?
Please verify the version of lmfit being used for each version of Python. Prior to lmfit version 0.9.4, you would need to use amp = params['amp'].value (and so on: param.value for all parameters).
That is, params['amp'] is an instance of an lmfit.Parameter -- it has several attributes, including .value holding it's floating point valuepy. It was only with version 0.9.4 that automatic coercion to numpy arrays became possible.