The observed values obtained by experiments are usually discrete values, but there are times when you want to find the values in between. At that time, various interpolation methods (not complementation) and other curve fittings (curve approximation) are used. These solutions are often used as the subject of programming exercises, but there are many powerful libraries in practice, so it is more convenient to use existing libraries than to create your own.

Computer experiment

Here, the following three mathematical functions f (x), g (x), and h (x) are prepared as computer experiments.

import numpy as np
f = lambda x: 1/(1 + np.exp(-x))
g = lambda x: 1.0/(1.0+x**2)
h = lambda x: np.sin(x)

It is assumed that the above three mathematical functions show the phenomenon that is actually occurring.

Experimental observations

However, in reality, the observation points obtained in the experiment are discrete values as follows.

x_observed = np.linspace(-10, 10, 11)
x_observed

array([-10.,  -8.,  -6.,  -4.,  -2.,   0.,   2.,   4.,   6.,   8.,  10.])

At this time, let's illustrate what kind of value is observed by the experiment.

%matplotlib inline
import matplotlib.pyplot as plt

for func in [f, g, h]:
    y_observed = func(x_observed)
    plt.scatter(x_observed, y_observed)
    plt.grid()
    plt.show()

What kind of curve can you imagine from the above observations?

Unobserved truth

Let's illustrate the truth that is not observed in the experiment.

x_latent = np.linspace(-10, 10, 101)
x_latent

array([-10. ,  -9.8,  -9.6,  -9.4,  -9.2,  -9. ,  -8.8,  -8.6,  -8.4,
        -8.2,  -8. ,  -7.8,  -7.6,  -7.4,  -7.2,  -7. ,  -6.8,  -6.6,
        -6.4,  -6.2,  -6. ,  -5.8,  -5.6,  -5.4,  -5.2,  -5. ,  -4.8,
        -4.6,  -4.4,  -4.2,  -4. ,  -3.8,  -3.6,  -3.4,  -3.2,  -3. ,
        -2.8,  -2.6,  -2.4,  -2.2,  -2. ,  -1.8,  -1.6,  -1.4,  -1.2,
        -1. ,  -0.8,  -0.6,  -0.4,  -0.2,   0. ,   0.2,   0.4,   0.6,
         0.8,   1. ,   1.2,   1.4,   1.6,   1.8,   2. ,   2.2,   2.4,
         2.6,   2.8,   3. ,   3.2,   3.4,   3.6,   3.8,   4. ,   4.2,
         4.4,   4.6,   4.8,   5. ,   5.2,   5.4,   5.6,   5.8,   6. ,
         6.2,   6.4,   6.6,   6.8,   7. ,   7.2,   7.4,   7.6,   7.8,
         8. ,   8.2,   8.4,   8.6,   8.8,   9. ,   9.2,   9.4,   9.6,
         9.8,  10. ])

fig_idx = 0
plt.figure(figsize=(12,4))
for func in [f, g, h]:
    fig_idx += 1
    y_observed = func(x_observed)
    y_latent = func(x_latent)
    plt.subplot(1, 3, fig_idx)
    plt.scatter(x_observed, y_observed)
    plt.plot(x_latent, y_latent)
    plt.grid()
plt.show()

Now, what I want to ask here is how close to this "true figure" can be derived from the limited observation values.

Interpolation with Scipy.interpolate

scipy provides a powerful library called interpolate that allows you to use a variety of interpolation methods.

from scipy import interpolate

ip1 = ["Nearest point interpolation", lambda x, y: interpolate.interp1d(x, y, kind="nearest")]
ip2 = ["Linear interpolation", interpolate.interp1d]
ip3 = ["Lagrange interpolation", interpolate.lagrange]
ip4 = ["Center of gravity interpolation", interpolate.BarycentricInterpolator]
ip5 = ["Krogh interpolation", interpolate.KroghInterpolator]
ip6 = ["Second-order spline interpolation", lambda x, y: interpolate.interp1d(x, y, kind="quadratic")]
ip7 = ["3rd order spline interpolation", lambda x, y: interpolate.interp1d(x, y, kind="cubic")]
ip8 = ["Autumn interpolation", interpolate.Akima1DInterpolator]
ip9 = ["Piecewise third-order Hermite interpolation", interpolate.PchipInterpolator]

x_observed = np.linspace(-10, 10, 11)
x_observed

array([-10.,  -8.,  -6.,  -4.,  -2.,   0.,   2.,   4.,   6.,   8.,  10.])

y_observed = f(x_observed)
y_latent = f(x_latent)
for method_name, method in [ip1, ip2, ip3, ip4, ip5, ip6, ip7, ip8, ip9]:
    print(method_name)
    fitted_curve = method(x_observed, y_observed)
    plt.scatter(x_observed, y_observed, label="observed")
    plt.plot(x_latent, fitted_curve(x_latent), c="red", label="fitted")
    plt.plot(x_latent, y_latent, label="latent")
    plt.grid()
    plt.legend()
    plt.show()

Nearest point interpolation

Linear interpolation

Lagrange interpolation

Center of gravity interpolation

Krogh interpolation

Second-order spline interpolation

3rd order spline interpolation

Autumn interpolation

Piecewise third-order Hermite interpolation

Exercise 1

Interpolate g (x) with various interpolation methods.
Interpolate h (x) with various interpolation methods.
Interpolate the following measurements with various interpolation methods.

x_observed = np.array([9, 28, 38, 58, 88, 98, 108, 118, 128, 138, 148, 158, 168, 178, 188, 198, 208, 218, 228, 238, 278, 288, 298])
y_observed = np.array([51, 80, 112, 294, 286, 110, 59, 70, 56, 70, 104, 59, 59, 72, 87, 99, 64, 60, 74, 151, 157, 57, 83])

x_latent = np.linspace(min(x_observed), max(x_observed), 100)

Curve fitting with Numpy.polyfit

Numpy's .polfyfit makes curve fitting easy with least squares. If you recalculate the jumping observations observed by the experiment

x_observed = np.linspace(-10, 10, 11)
x_observed

array([-10.,  -8.,  -6.,  -4.,  -2.,   0.,   2.,   4.,   6.,   8.,  10.])

y_observed = f(x_observed)
y_observed

array([4.53978687e-05, 3.35350130e-04, 2.47262316e-03, 1.79862100e-02,
       1.19202922e-01, 5.00000000e-01, 8.80797078e-01, 9.82013790e-01,
       9.97527377e-01, 9.99664650e-01, 9.99954602e-01])

When linear regression is performed on the above x and y by the least squares method,

coefficients = np.polyfit(x_observed, y_observed, 1)
coefficients

array([0.06668944, 0.5       ])

The above return value directly corresponds to the coefficients a and b of y = ax + b. Expressed using Sympy,

import sympy as sym
from sympy.plotting import plot
sym.init_printing(use_unicode=True)
%matplotlib inline

x, y = sym.symbols("x y")

#If you are using Google Colab, run it to support TeX display by Sympy
def custom_latex_printer(exp,**options):
    from google.colab.output._publish import javascript
    url = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.3/latest.js?config=default"
    javascript(url=url)
    return sym.printing.latex(exp,**options)

sym.init_printing(use_latex="mathjax",latex_printer=custom_latex_printer)

expr = 0
for index, coefficient in enumerate(coefficients):
    expr += coefficient * x ** (len(coefficients) - index - 1)
display(sym.Eq(y, expr))

y = 0.0666894399883493 x + 0.5

That is the regression equation obtained.

You can specify the order of regression with the last argument. For example, if you want to fit in a cubic formula

coefficients = np.polyfit(x_observed, y_observed, 3)

expr = 0
for index, coefficient in enumerate(coefficients):
    expr += coefficient * x ** (len(coefficients) - index - 1)
display(sym.Eq(y, expr))

y = - 0.000746038674650085 x^{3} + 0.119807393623435 x + 0.5

It shows that we were able to return to.

To draw the resulting curve, we need multiple x's and their corresponding y's, which we get:

fitted_curve = np.poly1d(np.polyfit(x_observed, y_observed, 3))(x_latent)
fitted_curve

array([ 0.04796474,  0.02805317,  0.00989629, -0.00654171, -0.02129666,
       -0.03440435, -0.0459006 , -0.05582121, -0.064202  , -0.07107878,
       -0.07648735, -0.08046353, -0.08304312, -0.08426194, -0.08415579,
       -0.08276049, -0.08011184, -0.07624566, -0.07119776, -0.06500394,
       -0.05770001, -0.04932179, -0.03990508, -0.02948569, -0.01809944,
       -0.00578213,  0.00743042,  0.02150241,  0.03639803,  0.05208146,
        0.0685169 ,  0.08566854,  0.10350056,  0.12197717,  0.14106254,
        0.16072086,  0.18091634,  0.20161315,  0.22277549,  0.24436755,
        0.26635352,  0.28869759,  0.31136394,  0.33431678,  0.35752028,
        0.38093865,  0.40453606,  0.42827671,  0.45212479,  0.47604449,
        0.5       ,  0.52395551,  0.54787521,  0.57172329,  0.59546394,
        0.61906135,  0.64247972,  0.66568322,  0.68863606,  0.71130241,
        0.73364648,  0.75563245,  0.77722451,  0.79838685,  0.81908366,
        0.83927914,  0.85893746,  0.87802283,  0.89649944,  0.91433146,
        0.9314831 ,  0.94791854,  0.96360197,  0.97849759,  0.99256958,
        1.00578213,  1.01809944,  1.02948569,  1.03990508,  1.04932179,
        1.05770001,  1.06500394,  1.07119776,  1.07624566,  1.08011184,
        1.08276049,  1.08415579,  1.08426194,  1.08304312,  1.08046353,
        1.07648735,  1.07107878,  1.064202  ,  1.05582121,  1.0459006 ,
        1.03440435,  1.02129666,  1.00654171,  0.99010371,  0.97194683,
        0.95203526])

plt.scatter(x_observed, f(x_observed), label="observed")
plt.plot(x_latent, fitted_curve, c="red", label="fitted")
plt.plot(x_latent, f(x_latent), label="latent")
plt.grid()
plt.legend()

<matplotlib.legend.Legend at 0x7fb673a3c630>

Exercise 2

Approximate g (x) with a quintic equation.
Approximate h (x) with a 9th-order equation.
Approximate the following measured values with a 9th-order equation.

x_observed = np.array([9, 28, 38, 58, 88, 98, 108, 118, 128, 138, 148, 158, 168, 178, 188, 198, 208, 218, 228, 238, 278, 288, 298])
y_observed = np.array([51, 80, 112, 294, 286, 110, 59, 70, 56, 70, 104, 59, 59, 72, 87, 99, 64, 60, 74, 151, 157, 57, 83])

Curve fitting with Scipy.optimize.curve_fit

One way to do curve fitting (curve approximation) using Python is to use scipy.optimize.curve_fit.

Experimental values used

x_observed = [9, 28, 38, 58, 88, 98, 108, 118, 128, 138, 148, 158, 168, 178, 188, 198, 208, 218, 228, 238, 278, 288, 298]
y_observed = [51, 80, 112, 294, 286, 110, 59, 70, 56, 70, 104, 59, 59, 72, 87, 99, 64, 60, 74, 151, 157, 57, 83]

Let's convert from Python's List type to Numpy's Array type.

import numpy as np
x_observed = np.array(x_observed)
y_observed = np.array(y_observed)

Linear approximation

First, let's approximate it to a linear equation. Define the function func1. a and b are the values you want to find.

def func1(X, a, b): #Linear approximation
    Y = a + b * X
    return Y

Here is an example of using the func1 function.

func1(x_observed, 2, 2)

array([ 20,  58,  78, 118, 178, 198, 218, 238, 258, 278, 298, 318, 338,
       358, 378, 398, 418, 438, 458, 478, 558, 578, 598])

Now, let's approximate it using scipy.optimize.curve_fit.

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func1,x_observed,y_observed) #popt is the optimal estimate, pcov is the covariance
popt

array([125.77023172,  -0.1605313 ])

The popt obtained here stores the optimal estimate. Let's compare it with the estimates obtained by curve fitting with Numpy.polyfit.

Quadratic approximation

Next, let's approximate it to a quadratic equation. Define the function func2. a, b, and c are the values you want.

def func2(X, a, b, c): #Quadratic approximation
    Y = a + b * X + c * X ** 2
    return Y

Here is an example of using the func2 function.

func2(x_observed, 2, 2, 2)

array([   182,   1626,   2966,   6846,  15666,  19406,  23546,  28086,
        33026,  38366,  44106,  50246,  56786,  63726,  71066,  78806,
        86946,  95486, 104426, 113766, 155126, 166466, 178206])

Now, let's approximate it using scipy.optimize.curve_fit.

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func2,x_observed,y_observed) #popt is the optimal estimate, pcov is the covariance
popt

array([ 1.39787684e+02, -4.07809516e-01,  7.97183226e-04])

The popt obtained here stores the optimal estimate. Let's compare it with the estimates obtained by curve fitting with Numpy.polyfit.

You can draw an approximate curve using the optimal estimate by doing the following.

func2(x_observed, 1.39787684e+02, -4.07809516e-01,  7.97183226e-04)

array([136.1819702 , 128.9940092 , 125.44205497, 118.81645644,
       110.07383349, 107.47849913, 105.04260142, 102.76614035,
       100.64911593,  98.69152815,  96.89337701,  95.25466253,
        93.77538468,  92.45554348,  91.29513893,  90.29417102,
        89.45263976,  88.77054514,  88.24788717,  87.88466585,
        88.02614699,  88.46010889,  89.05350743])

Quantitative approximation

Similarly, let's approximate it to a cubic equation. Define the function func3. a, b, c, and d are the values you want to find.

def func3(X, a, b, c, d): #Quantitative approximation
    Y = a + b * X + c * X ** 2 + d * X ** 3
    return Y

Now, let's approximate it using scipy.optimize.curve_fit.

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func3,x_observed,y_observed) #popt is the optimal estimate, pcov is the covariance
popt

array([ 7.84214107e+01,  1.88213104e+00, -1.74165777e-02,  3.89638087e-05])

The popt obtained here stores the optimal estimate. Let's compare it with the estimates obtained by curve fitting with Numpy.polyfit.

You can draw an approximate curve using the optimal estimate by doing the following.

func3(x_observed, 7.84214107e+01,  1.88213104e+00, -1.74165777e-02,  3.89638087e-05)

array([ 93.97825188, 118.32181643, 126.93087413, 136.59795028,
       135.72770915, 132.27386543, 127.62777811, 122.02323006,
       115.69400413, 108.87388316, 101.79665001,  94.69608754,
        87.80597859,  81.36010602,  75.59225267,  70.73620141,
        67.02573508,  64.69463654,  63.97668864,  65.10567422,
        92.76660851, 106.63700433, 123.75703075])

I want to create a general-purpose function that can be used regardless of the order

So far, I have created separate functions for linear expressions, quadratic expressions, and cubic expressions, but this is too troublesome, so let's create a general-purpose function that can be used regardless of the order expression. The order of approximation is automatically determined by the number of parameters.

import numpy as np
def func(X, *params):
    Y = np.zeros_like(X)
    for i, param in enumerate(params):
        Y = Y + np.array(param * X ** i)
    return Y

Execute the following two codes to confirm that the calculation result by func2 and the calculation result by func3 above are the same.

func(x_observed, 1.39787684e+02, -4.07809516e-01,  7.97183226e-04)

array([136.1819702 , 128.9940092 , 125.44205497, 118.81645644,
       110.07383349, 107.47849913, 105.04260142, 102.76614035,
       100.64911593,  98.69152815,  96.89337701,  95.25466253,
        93.77538468,  92.45554348,  91.29513893,  90.29417102,
        89.45263976,  88.77054514,  88.24788717,  87.88466585,
        88.02614699,  88.46010889,  89.05350743])

func(x_observed, 7.84214107e+01,  1.88213104e+00, -1.74165777e-02,  3.89638087e-05)

array([ 93.97825188, 118.32181643, 126.93087413, 136.59795028,
       135.72770915, 132.27386543, 127.62777811, 122.02323006,
       115.69400413, 108.87388316, 101.79665001,  94.69608754,
        87.80597859,  81.36010602,  75.59225267,  70.73620141,
        67.02573508,  64.69463654,  63.97668864,  65.10567422,
        92.76660851, 106.63700433, 123.75703075])

Polynomial approximation by a general-purpose function that can be used with any degree expression

At this point, polynomial approximation can be performed on any degree expression. However, you will need to enter the required number of initial values with p0 = to specify the number of parameters.

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func,x_observed,y_observed, p0=[1, 1]) 
popt

array([125.77023172,  -0.1605313 ])

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func,x_observed,y_observed, p0=[1, 1, 1]) 
popt

array([ 1.39787684e+02, -4.07809516e-01,  7.97183226e-04])

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func,x_observed,y_observed, p0=[1, 1, 1, 1]) 
popt

array([ 7.84214107e+01,  1.88213104e+00, -1.74165777e-02,  3.89638087e-05])

from scipy.optimize import curve_fit  
popt, pcov = curve_fit(func,x_observed,y_observed, p0=[1, 1, 1, 1, 1]) 
popt

array([-7.54495613e+01,  1.13179580e+01, -1.50591743e-01,  7.02970546e-04,
       -1.07313869e-06])

Comparison with curve fitting using Numpy.polyfit

Let's compare the above calculation result with the estimated value obtained by curve fitting using Numpy.polyfit.

Numpy.polyfit is convenient and easy to use if you just want to approximate polynomials, but you can only approximate polynomials. If you want to approximate with other functions, it's a good idea to understand how to use scipy.optimize.curve_fit.

I want to know what other optimization methods are available

If you say "optimize?", There are various other methods explained. Although it is in English.

from scipy import optimize
optimize?

Of course it's okay to google, but if you use "?", You can go directly to the explanation, and it's good that you can use it offline.

Newton's method and dichotomy

The dichotomy and Newton's method are typical methods for finding the solution of the equation f (x) = 0. As an example, we will use this function.

import math
def f(x):
    return math.exp(x) - 3 * x

import math
f = lambda x: math.exp(x) - 3 * x

A library for scientific and technological calculations called scipy is convenient.

from scipy import optimize

Dichotomy

The dichotomy can be used when the function y = f (x) is continuous in the interval [a, b] and there is one solution. For example, if you know that there is a solution in the interval [0,1]

optimize.bisect(f, 0, 1)

0.619061286737633

Oh easy.

Newton's method

Newton's method can be used when the function y = f (x) is monotonically continuous, has no inflection points, and the derivative of f (x) is found. When you want to find x when f (x) = 0

optimize.newton(f, 0)

0.6190612867359452

Oh easy.

I want to know more detailed usage

You can use "?" To check parameter explanations and usage examples. Although it is in English.

optimize.bisect?

optimize.newton?

[PYTHON] Optimization such as interpolation and curve fitting

Computer experiment

Experimental observations

Unobserved truth

Interpolation with Scipy.interpolate

Exercise 1

Curve fitting with Numpy.polyfit

Exercise 2

Curve fitting with Scipy.optimize.curve_fit

Experimental values used

Linear approximation

Quadratic approximation

Quantitative approximation

I want to create a general-purpose function that can be used regardless of the order

Polynomial approximation by a general-purpose function that can be used with any degree expression

Comparison with curve fitting using Numpy.polyfit

I want to know what other optimization methods are available

Newton's method and dichotomy

Dichotomy

Newton's method

I want to know more detailed usage