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I tried using Numpy, Scipy and Scikitlearn, but couldn't find what I need in any of them, basically I need to fit a curve to a dataset, but restricting some of the coefficients to known values, I found how to do it in MATLAB, using fittype, but couldn't do it in python.
In my case I have a dataset of X and Y and I need to find the best fitting curve, I know it's a polynomial of second degree (ax^2 + bx + c) and I know it's values of b and c, so I just needed it to find the value of a.
The solution I found in MATLAB was https://www.mathworks.com/matlabcentral/answers/216688-constraining-polyfit-with-known-coefficients which is the same problem as mine, but with the difference that their polynomial was of degree 5th, how could I do something similar in python?
To add some info: I need to fit a curve to a dataset, so things like scipy.optimize.curve_fit that expects a function won't work (at least as far as I tried).
The tools you have available usually expect functions only inputting their parameters (a being the only unknown in your case), or inputting their parameters and some data (a, x, and y in your case).
Scipy's curve-fit handles that use-case just fine, so long as we hand it a function that it understands. It expects x first and all your parameters as the remaining arguments:
from scipy.optimize import curve_fit
import numpy as np
b = 0
c = 0
def f(x, a):
return c+x*(b+x*a)
x = np.linspace(-5, 5)
y = x**2
# params == [1.]
params, _ = curve_fit(f, x, y)
Alternatively you can reach for your favorite minimization routine. The difference here is that you manually construct the error function so that it only inputs the parameters you care about, and then you don't need to provide that data to scipy.
from scipy.optimize import minimize
import numpy as np
b = 0
c = 0
x = np.linspace(-5, 5)
y = x**2
def error(a):
prediction = c+x*(b+x*a)
return np.linalg.norm(prediction-y)/len(prediction)**.5
result = minimize(error, np.array([42.]))
assert result.success
# params == [1.]
params = result.x
I don't think scipy has a partially applied polynomial fit function built-in, but you could use either of the above ideas to easily build one yourself if you do that kind of thing a lot.
from scipy.optimize import curve_fit
import numpy as np
def polyfit(coefs, x, y):
# build a mapping from null coefficient locations to locations in the function
# coefficients we're passing to curve_fit
#
# idx[j]==i means that unknown_coefs[i] belongs in coefs[j]
_tmp = [i for i,c in enumerate(coefs) if c is None]
idx = {j:i for i,j in enumerate(_tmp)}
def f(x, *unknown_coefs):
# create the entire polynomial's coefficients by filling in the unknown
# values in the right places, using the aforementioned mapping
p = [(unknown_coefs[idx[i]] if c is None else c) for i,c in enumerate(coefs)]
return np.polyval(p, x)
# we're passing an initial value just so that scipy knows how many parameters
# to use
params, _ = curve_fit(f, x, y, np.zeros((sum(c is None for c in coefs),)))
# return all the polynomial's coefficients, not just the few we just discovered
return np.array([(params[idx[i]] if c is None else c) for i,c in enumerate(coefs)])
x = np.linspace(-5, 5)
y = x**2
# (unknown)x^2 + 1x + 0
# params == [1, 0, 0.]
params = fit([None, 0, 0], x, y)
Similar features exist in nearly every mainstream scientific library; you just might need to reshape your problem a bit to frame it in terms of the available primitives.
I need to find zero-crossings in a 1D array of a roughly periodic function. It will be the points where an orbiting satellite crosses the Earth's equator going north.
I've worked out a simple solution based on finding points where one value is zero or negative and the next is positive, then using a quadratic or cubic interpolator with scipy.optimize.brentq to find the nearby zeros.
The interpolator does not go beyond cubic, and before I learn to use a better interpolator I'd first like to check if there already exists a fast method in numpy or scipy to find all of the zero crossings in a large array (n = 1E+06 to 1E+09).
Question: So I'm asking does there already exist a faster method in numpy or scipy to find all of the zero crossings in a large array (n = 1E+06 to 1E+09) than the way I've done it here?
The plot shows the errors between the interpolated zeros and the actual value of the function, the smaller line is the cubic interpolation, the larger is quadratic.
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d
from scipy.optimize import brentq
def f(x):
return np.sin(x + np.sin(x*e)/e) # roughly periodic function
halfpi, pi, twopi = [f*np.pi for f in (0.5, 1, 2)]
e = np.exp(1)
x = np.arange(0, 10000, 0.1)
y = np.sin(x + np.sin(x*e)/e)
crossings = np.where((y[1:] > 0) * (y[:-1] <= 0))[0]
Qd = interp1d(x, y, kind='quadratic', assume_sorted=True)
Cu = interp1d(x, y, kind='cubic', assume_sorted=True)
x0sQd = [brentq(Qd, x[i-1], x[i+1]) for i in crossings[1:-1]]
x0sCu = [brentq(Cu, x[i-1], x[i+1]) for i in crossings[1:-1]]
y0sQd = [f(x0) for x0 in x0sQd]
y0sCu = [f(x0) for x0 in x0sCu]
if True:
plt.figure()
plt.plot(x0sQd, y0sQd)
plt.plot(x0sCu, y0sCu)
plt.show()
I'm trying to write a script that computes numerical derivatives using the forward, backward, and centered approximations, and plots the results. I've made a linspace from 0 to 2pi with 100 points. I've made many arrays and linspaces in the past, but I've never seen this error: "ValueError: sequence too large; cannot be greater than 32"
I don't understand what the problem is. Here is my script:
import numpy as np
import matplotlib.pyplot as plt
def f(x):
return np.cos(x) + np.sin(x)
def f_diff(x):
return np.cos(x) - np.sin(x)
def forward(x,h): #forward approximation
return (f(x+h)-f(x))/h
def backward(x,h): #backward approximation
return (f(x)-f(x-h))/h
def center(x,h): #center approximation
return (f(x+h)-f(x-h))/(2*h)
x0 = 0
x = np.linspace(0,2*np.pi,100)
forward_result = np.zeros(x)
backward_result = np.zeros(x)
center_result = np.zeros(x)
true_result = np.zeros(x)
for i in range(x):
forward_result[i] = forward[x0,i]
true_result[i] = f_diff[x0]
print('Forward (x0={}) = {}'.format(x0,forward(x0,x)))
#print('Backward (x0={}) = {}'.format(x0,backward(x0,dx)))
#print('Center (x0={}) = {}'.format(x0,center(x0,dx)))
plt.figure()
plt.plot(x, f)
plt.plot(x,f_diff)
plt.plot(x, abs(forward_result-true_result),label='Forward difference')
I did try setting the linspace points to 32, but that gave me another error: "TypeError: 'numpy.float64' object cannot be interpreted as an integer"
I don't understand that one either. What am I doing wrong?
The issue starts at forward_result = np.zeros(x) because x is a numpy array not a dimension. Since x has 100 entries, np.zeros wants to create object in R^x[0] times R^x[1] times R^x[3] etc. The maximum dimension is 32.
You need a flat np array.
UPDATE: On request, I add corrected lines from code above:
forward_result = np.zeros(x.size) creates the array of dimension 1.
Corrected evaluation of the function is done via circular brackets. Also fixed the loop:
for i, h in enumerate(x):
forward_result[i] = forward(x0,h)
true_result[i] = f_diff(x0)
Finally, in the figure, you want to plot numpy array vs function. Fixed version:
plt.plot(x, [f(val) for val in x])
plt.plot(x, [f_diff(val) for val in x])
I'm new to python (and programming in general) and want to make a polynomial fit using curve_fit, where the order of the polynomials (or the number of fit parameters) is variable.
I made this code which is working for a fixed number of 3 parameters a,b,c
# fit function
def fit_func(x, a,b,c):
p = np.polyval([a,b,c], x)
return p
# do the fitting
popt, pcov = curve_fit(fit_func, x_data, y_data)
But now I'd like to have my fit function to only depend on a number N of parameters instead of a,b,c,....
I'm guessing that's not a very hard thing to do, but because of my limited knowledge I can't get it work.
I've already looked at this question, but I wasn't able to apply it to my problem.
You can define the function to be fit to your data like this:
def fit_func(x, *coeffs):
y = np.polyval(coeffs, x)
return y
Then, when you call curve_fit, set the argument p0 to the initial guess of the polynomial coefficients. For example, this plot is generated by the script that follows.
import numpy as np
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
# Generate a sample input dataset for the demonstration.
x = np.arange(12)
y = np.cos(0.4*x)
def fit_func(x, *coeffs):
y = np.polyval(coeffs, x)
return y
fit_results = []
for n in range(2, 6):
# The initial guess of the parameters to be found by curve_fit.
# Warning: in general, an array of ones might not be a good enough
# guess for `curve_fit`, but in this example, it works.
p0 = np.ones(n)
popt, pcov = curve_fit(fit_func, x, y, p0=p0)
# XXX Should check pcov here, but in this example, curve_fit converges.
fit_results.append(popt)
plt.plot(x, y, 'k.', label='data')
xx = np.linspace(x.min(), x.max(), 100)
for p in fit_results:
yy = fit_func(xx, *p)
plt.plot(xx, yy, alpha=0.6, label='n = %d' % len(p))
plt.legend(framealpha=1, shadow=True)
plt.grid(True)
plt.xlabel('x')
plt.show()
The parameters of polyval specify p is an array of coefficients from the highest to lowest. With x being a number or array of numbers to evaluate the polynomial at. It says, the following.
If p is of length N, this function returns the value:
p[0]*x**(N-1) + p[1]*x**(N-2) + ... + p[N-2]*x + p[N-1]
def fit_func(p,x):
z = np.polyval(p,x)
return z
e.g.
t= np.array([3,4,5,3])
y = fit_func(t,5)
503
which is if you do the math here is right.
Recently I was working on some data for which I was able to obtain a curve using curve_fit after saving the plot and the values obtained I returned to the same code later only to find it does not work.
#! python 3.5.2
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats
from scipy.optimize import curve_fit
data= np.array([
[24, 0.176644513],
[27, 0.146382841],
[30, 0.129891534],
[33, 0.105370908],
[38, 0.077820511],
[50, 0.047407538]])
x, y = np.array([]), np.array([])
for val in data:
x = np.append(x, val[0])
y = np.append(y, (val[1]/(1-val[1])))
def f(x, a, b):
return (np.exp(-a*x)**b)
# The original a and b values obtained
a = -0.2 # after rounding
b = -0.32 # after rounding
plt.scatter(x, y)
Xcurve = np.linspace(x[0], x[-1], 500)
plt.plot(Xcurve, f(Xcurve,a,b), ls='--', color='k', lw=1)
plt.show()
# the original code to get the values
a = b = 1
popt, pcov = curve_fit(f, x, y, (a, b))
Whereas, previously curve_fit returned the values a, b = -0.2, -0.32 now returns:
Warning (from warnings module):
File "C:/Users ... line 22
return (np.exp(-a*x)**b)
RuntimeWarning: overflow encountered in exp
The code as far as I am aware did not change. Thanks
Without knowing what changed in the code, it is hard to say what changed between your state of "working" and "not working". It may be that changes in the version of scipy you used give different results: there have changes to the underlying implementation in curve_fit() over the past few years.
But also: curve_fit() (and the underlying python and Fortran code it uses) requires reasonably good initial guesses for the parameters for many problems to work at all. With bad guesses for the parameters, many problems will fail.
Exponential decay problems seem to be especially challenging for the Levenberg-Marquardt algorithm (and the implementations used by curve_fit(), and do require reasonable starting points. It's also easy to get into a part of parameter space where the function evaluates to zero, and changes in the parameter values have no effect.
If possible, if your problem involves exponential decay, it is helpful to work in log space. That is, model log(f), not f itself. For your problem in particular, your model function is exp(-a*x)**b. Is that really what you mean? a and bwill be exactly correlated.
In addition, you may find lmfit helpful. It has a Model class for curve-fitting, using similar underlying code, but allows fixing or setting bounds on any of the parameters. An example for your problem would be (approximately):
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats
from scipy.optimize import curve_fit
import lmfit
data= np.array([
[24, 0.176644513],
[27, 0.146382841],
[30, 0.129891534],
[33, 0.105370908],
[38, 0.077820511],
[50, 0.047407538]])
x, y = np.array([]), np.array([])
for val in data:
x = np.append(x, val[0])
y = np.append(y, (val[1]/(1-val[1])))
def f(x, a, b):
print("In f: a, b = " , a, b)
return (np.exp(-a*x)**b)
fmod = lmfit.Model(f)
params = fmod.make_params(a=-0.2, b=-0.4)
# set bounds on parameters
params['a'].min = -2
params['a'].max = 0
params['b'].vary = False
out = fmod.fit(y, params, x=x)
print(out.fit_report())
plt.plot(x, y)
plt.plot(x, out.best_fit, '--')
plt.show()