scipy.optimize.curve_fit Error

[Abeed.R]

Hi, I am pretty new to python (and programming in general), I am trying to create a curve fit to my data,

 

I am loading two arrays 'Tnn_month' and 'amon_month' from .mat files, I want to create a scatter plot of these two parameters and then assign a curve fit to show the correlation between both,

 

I tried to apply the curve_fit examples done on simple plots, but I still get this error: error: Result from function call is not a proper array of floats.

 

Tnn_month (x) and amon_month (y) are both  arrays of length 5433656

find attached the scatter plot

 

-----------------------------------------------------

input:

 

import numpy as np
import matplotlib.pyplot as plt
import scipy.io as io
import pandas as pd
import seaborn as sns
from matplotlib.pyplot import figure

 

MainFolder= r"/home/abeed/Documents/thesis/python/scatter/"
yyyymm_str= '201005'
d_or_n = 'day'

colors = (0,0,0)
area = np.pi*3

 

#load data
mat = io.loadmat('Tnn_amon0.01_201005.mat')

Tnn_month = mat['Tnn_index']
amon_month = mat['amon_index']

colors=np.array([0.1, 0.5, 0.5])

 

# scatter plot

figure(num=None, figsize=(8, 6), dpi=80, facecolor='w', edgecolor='k')

plt.scatter(Tnn_month, amon_month, s=area, c=colors, alpha=0.5)
plt.title('May 2010', fontsize=14)
plt.ylabel('Ammonia Total Concentration (molec/cm$^{2}$)',fontsize=14)
plt.xlabel('Skin Temperature (Kelvin)', fontsize=14)

plt.savefig(MainFolder + yyyymm_str + '_test_' + d_or_n +'.png', format='png', dpi=700)
#plt.show()

 

# curve_fit
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import numpy as np

Tnn_month[np.isnan(Tnn_month)]=0 #something for nans
amon_month[np.isnan(amon_month)]=0

def func(X, a, b, c):
    return a * np.exp(-b * X) + c

 

Y = func(Tnn_month, 2.5, 1.3, 0.5)

np.random.seed(len(Tnn_month))

 

print(Tnn_month)

 

popt, pcov = curve_fit(func, Tnn_month, amon_month)

 

plt.plot(Tnn_month, func(Tnn_month, *popt), 'g--',label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))

plt.show()

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

output:

[[272.64697509]
 [273.43998094]
 [272.89872854]
 ...
 [265.03563904]
 [264.87200613]
 [273.74241245]]

 

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
ValueError: object too deep for desired array

 

---------------------------------------------------------------------------
error                                     Traceback (most recent call last)
<ipython-input-2-2ed29e6832ed> in <module>
     71 print(Tnn_month)
     72 
---> 73 popt, pcov = curve_fit(func, Tnn_month, amon_month)
     74 
     75 plt.plot(Tnn_month, func(Tnn_month, *popt), 'g--',label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))

~/anaconda3/lib/python3.7/site-packages/scipy/optimize/minpack.py in curve_fit(f, xdata, ydata, p0, sigma, absolute_sigma, check_finite, bounds, method, jac, **kwargs)
    750         # Remove full_output from kwargs, otherwise we're passing it in twice.
    751         return_full = kwargs.pop('full_output', False)
--> 752         res = leastsq(func, p0, Dfun=jac, full_output=1, **kwargs)
    753         popt, pcov, infodict, errmsg, ier = res
    754         cost = np.sum(infodict['fvec'] ** 2)

~/anaconda3/lib/python3.7/site-packages/scipy/optimize/minpack.py in leastsq(func, x0, args, Dfun, full_output, col_deriv, ftol, xtol, gtol, maxfev, epsfcn, factor, diag)
    394             maxfev = 200*(n + 1)
    395         retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol,
--> 396                                  gtol, maxfev, epsfcn, factor, diag)
    397     else:
    398         if col_deriv:

error: Result from function call is not a proper array of floats.

[SansVarnic]

Hi @Abeed.R please include code tags in your post. 

Thank-you.

 

 

Quote

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