matplotlib - 在python中拟合sigmoid曲线

Question

先谢谢了!我正在尝试在一些数据上拟合 sigmoid 曲线，下面是我的代码

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

====== some code in between =======

plt.scatter(drag[0].w,drag[0].s, s = 10, label = 'drag%d'%0)
def sigmoid(x,x0,k):
    y = 1.0/(1.0+np.exp(-x0*(x-k)))
    return y
popt,pcov = curve_fit(sigmoid, drag[0].w, drag[0].s)
xx = np.linspace(10,1000,10)
yy = sigmoid(xx, *popt)
plt.plot(xx,yy,'r-', label='fit')
plt.legend(loc='upper left')
plt.xlabel('weight(kg)', fontsize=12)
plt.ylabel('wing span(m)', fontsize=12)
plt.show()

现在显示的图表不太正确 fitting curve is the red one at bottom

可能的解决方案是什么？

我也对在这组数据上拟合逻辑曲线的其他方法持开放态度

再次感谢!

Answer 1

这是一个示例图形拟合器，使用您的方程和我的测试数据的幅度缩放因子。此代码使用 scipy 的差分进化遗传算法为 curve_fit() 提供初始参数估计，因为所有 1.0 的 scipy 默认初始参数估计并不总是最佳的。差分进化的 scipy 实现使用拉丁超立方体算法来确保对参数空间的彻底搜索，这需要搜索的边界。在本例中，这些界限取自我提供的示例数据，在使用您自己的数据时，请检查界限是否合理。请注意，参数范围比初始参数估计的特定值更容易提供。

import numpy, scipy, matplotlib
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from scipy.optimize import differential_evolution
import warnings

xData = numpy.array([19.1647, 18.0189, 16.9550, 15.7683, 14.7044, 13.6269, 12.6040, 11.4309, 10.2987, 9.23465, 8.18440, 7.89789, 7.62498, 7.36571, 7.01106, 6.71094, 6.46548, 6.27436, 6.16543, 6.05569, 5.91904, 5.78247, 5.53661, 4.85425, 4.29468, 3.74888, 3.16206, 2.58882, 1.93371, 1.52426, 1.14211, 0.719035, 0.377708, 0.0226971, -0.223181, -0.537231, -0.878491, -1.27484, -1.45266, -1.57583, -1.61717])
yData = numpy.array([0.644557, 0.641059, 0.637555, 0.634059, 0.634135, 0.631825, 0.631899, 0.627209, 0.622516, 0.617818, 0.616103, 0.613736, 0.610175, 0.606613, 0.605445, 0.603676, 0.604887, 0.600127, 0.604909, 0.588207, 0.581056, 0.576292, 0.566761, 0.555472, 0.545367, 0.538842, 0.529336, 0.518635, 0.506747, 0.499018, 0.491885, 0.484754, 0.475230, 0.464514, 0.454387, 0.444861, 0.437128, 0.415076, 0.401363, 0.390034, 0.378698])


def sigmoid(x, amplitude, x0, k):
    return amplitude * 1.0/(1.0+numpy.exp(-x0*(x-k)))


# function for genetic algorithm to minimize (sum of squared error)
def sumOfSquaredError(parameterTuple):
    warnings.filterwarnings("ignore") # do not print warnings by genetic algorithm
    val = sigmoid(xData, *parameterTuple)
    return numpy.sum((yData - val) ** 2.0)


def generate_Initial_Parameters():
    # min and max used for bounds
    maxX = max(xData)
    minX = min(xData)
    maxY = max(yData)
    minY = min(yData)

    parameterBounds = []
    parameterBounds.append([minY, maxY]) # search bounds for amplitude
    parameterBounds.append([minX, maxX]) # search bounds for x0
    parameterBounds.append([minX, maxX]) # search bounds for k

    # "seed" the numpy random number generator for repeatable results
    result = differential_evolution(sumOfSquaredError, parameterBounds, seed=3)
    return result.x

# by default, differential_evolution completes by calling curve_fit() using parameter bounds
geneticParameters = generate_Initial_Parameters()

# now call curve_fit without passing bounds from the genetic algorithm,
# just in case the best fit parameters are aoutside those bounds
fittedParameters, pcov = curve_fit(sigmoid, xData, yData, geneticParameters)
print('Fitted parameters:', fittedParameters)
print()

modelPredictions = sigmoid(xData, *fittedParameters) 

absError = modelPredictions - yData

SE = numpy.square(absError) # squared errors
MSE = numpy.mean(SE) # mean squared errors
RMSE = numpy.sqrt(MSE) # Root Mean Squared Error, RMSE
Rsquared = 1.0 - (numpy.var(absError) / numpy.var(yData))

print()
print('RMSE:', RMSE)
print('R-squared:', Rsquared)

print()


##########################################################
# graphics output section
def ModelAndScatterPlot(graphWidth, graphHeight):
    f = plt.figure(figsize=(graphWidth/100.0, graphHeight/100.0), dpi=100)
    axes = f.add_subplot(111)

    # first the raw data as a scatter plot
    axes.plot(xData, yData,  'D')

    # create data for the fitted equation plot
    xModel = numpy.linspace(min(xData), max(xData))
    yModel = sigmoid(xModel, *fittedParameters)

    # now the model as a line plot
    axes.plot(xModel, yModel)

    axes.set_xlabel('X Data') # X axis data label
    axes.set_ylabel('Y Data') # Y axis data label

    plt.show()
    plt.close('all') # clean up after using pyplot

graphWidth = 800
graphHeight = 600
ModelAndScatterPlot(graphWidth, graphHeight)