Fitting custom models in SciPy

Introduction

We fit custom models to find the best parameters that explain our data. This helps us understand patterns and make predictions.

You have data points and want to find a curve that best matches them.

You want to estimate parameters of a model that describes your experiment.

You need to predict future values based on a custom formula.

You want to compare how well different models fit your data.

You want to automate finding the best fit without guessing parameters.

Syntax

SciPy

from scipy.optimize import curve_fit

def model(x, a, b):
    return a * x + b

params, covariance = curve_fit(model, xdata, ydata, p0=[1, 0])

curve_fit finds the best parameters for your model function.

p0 is the initial guess for parameters; it helps the fitting start.

Examples

Fit a straight line to data points without initial guess.

SciPy

from scipy.optimize import curve_fit
import numpy as np

def linear_model(x, m, c):
    return m * x + c

xdata = np.array([1, 2, 3, 4, 5])
ydata = np.array([2.1, 4.1, 6.0, 8.1, 10.2])

params, _ = curve_fit(linear_model, xdata, ydata)
print(params)

Fit a quadratic curve with an initial guess for parameters.

SciPy

from scipy.optimize import curve_fit
import numpy as np

def quadratic_model(x, a, b, c):
    return a * x**2 + b * x + c

xdata = np.linspace(-5, 5, 11)
ydata = 2 * xdata**2 + 3 * xdata + 1 + np.random.normal(0, 1, len(xdata))

params, _ = curve_fit(quadratic_model, xdata, ydata, p0=[1, 1, 1])
print(params)

Sample Program

This program fits an exponential curve to noisy data. It prints the best parameters and shows a plot with data points and the fitted curve.

SciPy

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

def exponential_model(x, a, b):
    return a * np.exp(b * x)

# Create sample data with noise
xdata = np.linspace(0, 4, 50)
ydata = 2.5 * np.exp(1.3 * xdata) + np.random.normal(0, 0.2, xdata.size)

# Fit the model to data
params, covariance = curve_fit(exponential_model, xdata, ydata, p0=[1, 1])

# Print fitted parameters
a_fit, b_fit = params
print(f"Fitted parameters: a = {a_fit:.3f}, b = {b_fit:.3f}")

# Plot data and fitted curve
plt.scatter(xdata, ydata, label='Data')
plt.plot(xdata, exponential_model(xdata, *params), color='red', label='Fitted model')
plt.legend()
plt.xlabel('x')
plt.ylabel('y')
plt.title('Fitting custom exponential model')
plt.show()

Important Notes

Always provide a reasonable initial guess p0 to help the fitting process.

Check the covariance matrix to understand parameter uncertainty.

Plot your data and fitted curve to visually check the fit quality.

Summary

Use curve_fit to find best parameters for your custom model function.

Provide data and a model function that returns predicted values.

Check results by printing parameters and plotting the fit.

Practice

1. What is the main purpose of using scipy.optimize.curve_fit in fitting custom models?

easy

A. To find the best parameters that make the model fit the data

B. To plot the data points automatically

C. To generate random data for testing

D. To calculate the mean of the dataset

Solution

1. Step 1: Understand the role of curve_fit

   curve_fit is used to adjust parameters of a model function so that it best fits the given data points.

2. Step 2: Identify the correct purpose

   It does not plot data, generate random data, or calculate means. Its main job is parameter estimation for fitting.

3. Final Answer:

   To find the best parameters that make the model fit the data -> Option A

4. Quick Check:

   curve_fit finds best parameters [OK]

Hint: Remember: curve_fit adjusts parameters to fit data [OK]

Common Mistakes:

• Thinking curve_fit plots data automatically
• Confusing curve_fit with data generation functions
• Assuming curve_fit calculates statistics like mean

2. Which of the following is the correct way to define a custom model function for curve_fit that fits a line y = m*x + c?

easy

A. def model(m, c, x): return m + c * x

B. def model(x, m, c): return m * x + c

C. def model(x): return m * x + c

D. def model(x, m, c): return m + c / x

Solution

1. Step 1: Check parameter order for curve_fit

   The model function must have the independent variable as the first argument, followed by parameters to fit.

2. Step 2: Verify function matches y = m*x + c

   def model(x, m, c): return m * x + c correctly defines model(x, m, c) returning m * x + c. Others have wrong order or formula.

3. Final Answer:

   def model(x, m, c): return m * x + c -> Option B

4. Quick Check:

   Model args: x first, then parameters [OK]

Hint: Model function: x first, then parameters [OK]

Common Mistakes:

• Swapping parameter and variable order
• Missing parameters in function definition
• Using wrong formula inside the function

3. Given the code below, what will be the output of print(popt)?

import numpy as np
from scipy.optimize import curve_fit

def model(x, a, b):
    return a * np.exp(b * x)

xdata = np.array([0, 1, 2, 3])
ydata = np.array([1, 2.7, 7.4, 20.1])

popt, _ = curve_fit(model, xdata, ydata)
print(np.round(popt, 2))

medium

A. [1.0 0.99]

B. [1.0 1.0]

C. [1.0 1.0] but with a runtime error

D. [1.01 1.0]

Solution

1. Step 1: Understand the model and data

   The model is a * exp(b * x). Given ydata roughly follows exponential growth, parameters a and b will be close to 1.

2. Step 2: Check output of curve_fit

   Running the code fits parameters close to a=1.0 and b=0.99 (data approximates e^x but slightly less). Rounded to two decimals, popt is approximately [1.0 0.99].

3. Final Answer:

   [1.0 0.99] -> Option A

4. Quick Check:

   Exponential fit params ~ [1.0, 0.99] [OK]

Hint: Run curve_fit and round parameters to check values [OK]

Common Mistakes:

• Misestimating parameters as [1.0 1.0] due to data approximation
• Confusing parameter order
• Expecting runtime errors without cause

4. What is wrong with the following code snippet for fitting a quadratic model using curve_fit?

import numpy as np
from scipy.optimize import curve_fit

def quad(x, a, b, c):
    return a * x**2 + b * x + c

xdata = np.array([1, 2, 3, 4])
ydata = np.array([3, 7, 13, 21])

popt, pcov = curve_fit(quad, ydata, xdata)
print(popt)

medium

A. Missing initial guess for parameters

B. The model function has wrong formula for quadratic

C. The independent and dependent variables are swapped in curve_fit call

D. The print statement is incorrect

Solution

1. Step 1: Check curve_fit arguments

   curve_fit expects the model, xdata (independent), then ydata (dependent). Here, ydata and xdata are swapped.

2. Step 2: Identify the error impact

   Swapping causes wrong fitting or runtime errors because the model expects x values first.

3. Final Answer:

   The independent and dependent variables are swapped in curve_fit call -> Option C

4. Quick Check:

   curve_fit(xdata, ydata) order matters [OK]

Hint: Remember: curve_fit(model, xdata, ydata) [OK]

Common Mistakes:

• Swapping xdata and ydata in curve_fit
• Assuming model formula is incorrect
• Thinking initial guess is always required

5. You want to fit a custom model y = a * sin(b * x) + c to noisy data. Which approach correctly fits the model and plots the result?

hard

A. Plot data first, then call curve_fit without storing parameters

B. Use curve_fit without defining a model function, just pass np.sin

C. Fit the model by manually guessing parameters without curve_fit

D. Define model with def model(x, a, b, c): return a * np.sin(b * x) + c, use curve_fit with data, then plot original and fitted curves

Solution

1. Step 1: Define the correct model function

   Model must be defined as model(x, a, b, c) returning a * np.sin(b * x) + c.

2. Step 2: Use curve_fit and plot results

   Call curve_fit(model, xdata, ydata) to get parameters, then plot original data and fitted curve for comparison.

3. Final Answer:

   Define model with def model(x, a, b, c): return a * np.sin(b * x) + c, use curve_fit with data, then plot original and fitted curves -> Option D

4. Quick Check:

   Model function + curve_fit + plot = correct approach [OK]

Hint: Always define model function before curve_fit and plot results [OK]

Common Mistakes:

• Passing np.sin directly without parameters
• Skipping model function definition
• Not storing or using fitted parameters for plotting