1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275
|
# -*- coding: utf-8 -*-
#
# Licensed under the terms of the BSD 3-Clause
# (see sigima/LICENSE for details)
"""
Curve fitting operations
========================
This module provides curve fitting operations for signal objects:
- Linear and polynomial fits
- Gaussian, Lorentzian, and Voigt fits
- Exponential and CDF fits
.. note::
Most operations use functions from :mod:`sigima.tools.signal.fitting` for
actual computations.
"""
from __future__ import annotations
from typing import Callable
import guidata.dataset as gds
import numpy as np
from sigima.config import _
from sigima.objects import SignalObj
from sigima.proc.base import dst_2_to_1
from sigima.proc.decorator import computation_function
from sigima.tools.signal import fitting
from .base import dst_1_to_1
def __generic_fit(
src: SignalObj,
fitfunc: Callable[[np.ndarray, np.ndarray], tuple[np.ndarray, dict[str, float]]],
) -> SignalObj:
"""Generic fitting function.
Args:
src: source signal
fitfunc: fitting function
Returns:
Fitting result signal object
"""
dst = dst_1_to_1(src, fitfunc.__name__)
# Fit only on ROI if available
x_roi = src.x[~src.get_masked_view().mask]
y_roi = src.get_masked_view().compressed()
_fitted_y_roi, fit_params = fitfunc(x_roi, y_roi)
# Evaluate fit on full x range
fitted_y = fitting.evaluate_fit(src.x, **fit_params)
dst.set_xydata(src.x, fitted_y)
# Store fit parameters in metadata
dst.metadata["fit_params"] = fit_params
return dst
@computation_function()
def linear_fit(src: SignalObj) -> SignalObj:
"""Compute linear fit with :py:func:`numpy.polyfit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.linear_fit)
class PolynomialFitParam(gds.DataSet, title=_("Polynomial fit")):
"""Polynomial fitting parameters"""
degree = gds.IntItem(_("Degree"), 3, min=1, max=10, slider=True)
@computation_function()
def polynomial_fit(src: SignalObj, p: PolynomialFitParam) -> SignalObj:
"""Compute polynomial fit with :py:func:`numpy.polyfit`
Args:
src: source signal
p: polynomial fitting parameters
Returns:
Result signal object
"""
# Note: no need to check degree here as gds.IntItem already enforces min=1
return __generic_fit(src, lambda x, y: fitting.polynomial_fit(x, y, p.degree))
@computation_function()
def gaussian_fit(src: SignalObj) -> SignalObj:
"""Compute Gaussian fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.gaussian_fit)
@computation_function()
def lorentzian_fit(src: SignalObj) -> SignalObj:
"""Compute Lorentzian fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.lorentzian_fit)
@computation_function()
def voigt_fit(src: SignalObj) -> SignalObj:
"""Compute Voigt fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.voigt_fit)
@computation_function()
def exponential_fit(src: SignalObj) -> SignalObj:
"""Compute exponential fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.exponential_fit)
@computation_function()
def cdf_fit(src: SignalObj) -> SignalObj:
"""Compute CDF fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.cdf_fit)
@computation_function()
def planckian_fit(src: SignalObj) -> SignalObj:
"""Compute Planckian fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.planckian_fit)
@computation_function()
def twohalfgaussian_fit(src: SignalObj) -> SignalObj:
"""Compute two-half-Gaussian fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.twohalfgaussian_fit)
@computation_function()
def sigmoid_fit(src: SignalObj) -> SignalObj:
"""Compute sigmoid fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.sigmoid_fit)
@computation_function()
def piecewiseexponential_fit(src: SignalObj) -> SignalObj:
"""Compute piecewise exponential fit (raise-decay) with
:py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.piecewiseexponential_fit)
@computation_function()
def sinusoidal_fit(src: SignalObj) -> SignalObj:
"""Compute sinusoidal fit with :py:func:`scipy.optimize.curve_fit`
Args:
src: source signal
Returns:
Result signal object
"""
return __generic_fit(src, fitting.sinusoidal_fit)
def extract_fit_params(signal: SignalObj) -> dict[str, float | str]:
"""Extract fit parameters from a fitted signal.
Args:
signal: Signal object containing fit metadata
Returns:
Fit parameters
"""
if "fit_params" not in signal.metadata:
raise ValueError("Signal does not contain fit parameters")
fit_params_dict: dict[str, float | str] = signal.metadata["fit_params"]
assert "fit_type" in fit_params_dict, "No valid fit parameters found"
return fit_params_dict
@computation_function()
def evaluate_fit(src1: SignalObj, src2: SignalObj) -> SignalObj:
"""Evaluate fit function from src1 on the x-axis of src2.
This function extracts fit parameters from `src1` (which must contain fit metadata
from a previous fitting operation) and evaluates the fit function on the x-axis
of `src2`.
Args:
src1: Signal object containing fit parameters in metadata (from a fit operation)
src2: Signal object whose x-axis will be used for evaluation
Returns:
New signal with the fit evaluated on src2's x-axis
"""
fit_params = extract_fit_params(src1)
dst = dst_2_to_1(src1, src2, "evaluate_fit")
# Evaluate fit on src2's x-axis
x = src2.x
y = fitting.evaluate_fit(x, **fit_params)
dst.set_xydata(x, y)
dst.title = f"Fitted {fit_params['fit_type']}"
# Copy fit parameters to destination metadata
dst.metadata["fit_params"] = fit_params
return dst
|