Source code for ClearMap.Analysis.Curves.Resampling

# -*- coding: utf-8 -*-
"""
Resampling
==========

Module with routines for data and curve resampling and smoothing based on splines.
"""
__author__    = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__   = 'GPLv3 - GNU General Pulic License v3 (see LICENSE)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__   = 'http://idisco.info'
__download__  = 'http://www.github.com/ChristophKirst/ClearMap2'


import numpy as np
from scipy.interpolate import splprep,splrep, splev


[docs] def resample_nd(curve, n_points = None, smooth = 0, periodic = False, derivative = 0, order = 5, iterations = 1): """Resample n points using n equidistant points along a curve Arguments --------- curve : mxd array Coordinates for the reference points of the curve. n_points : int Number of equidistant points to evaluate the curve on. smooth : int or float Smoothness factor. periodic : bool If True, assume the curve is a closed loop. derivative : int If > 0, return the n-th derivative of the curve. order : int The spline order to use to interpolate the curve. iterations : int Iterate the resampling process this amount of time. Returns ------- curve : nxd array Resampled curve along n_points equidistant points. """ if n_points is None or n_points is all: n_points = curve.shape[0]; for i in range(iterations): cinterp, u = splprep(curve.T, u=None, s=smooth, per=periodic, k=order); us = np.linspace(u.min(), u.max(), n_points) curve = np.vstack(splev(us, cinterp, der=derivative)).T; return curve;
[docs] def resample_1d(data, n_points = None, smooth = 0, periodic = False, derivative = 0, order = 5, iterations = 0): """Resample 1d data using n equidistant points Arguments --------- curve : mxd array Coordinates for the reference points of the curve. n_points : int Number of equidistant points to evaluate the curve on. smooth : int or float Smoothness factor. periodic : bool If True, assume the curve is a closed loop. derivative : int If > 0, return the n-th derivative of the curve. order : int The spline order to use to interpolate the curve. iterations : int Iterate the resampling process this amount of time. Returns ------- curve : nxd array Resampled curve along n_points equidistant points. """ if n_points is None or n_points is None: n_points = data.shape[0]; u0 = np.linspace(0, 1, data.shape[0]); us = np.linspace(0, 1, n_points); for i in range(iterations): dinterp = splrep(u0, data, s=smooth, per=periodic, k=order); data = splev(us, dinterp, der = derivative); return data;
[docs] def resample(curve, n_points = None, smooth = 0, periodic = False, derivative = 0, order = 5, iterations = 1): """Resample a curve using equidistant points along a curve. Arguments --------- curve : mxd array Coordinates for the reference points of the curve. n_points : int Number of equidistant points to evaluate the curve on. smooth : int or float Smoothness factor. periodic : bool If True, assume the curve is a closed loop. derivative : int If > 0, return the n-th derivative of the curve. order : int The spline order to use to interpolate the curve. iterations : int Iterate the resampling process this amount of time. Returns ------- curve : nxd array Resampled curve along n_points equidistant points. """ if curve.ndim > 1: return resample_nd(curve, n_points, smooth=smooth, periodic=periodic, derivative=derivative, order=order, iterations=iterations); else: return resample_1d(curve, n_points, smooth=smooth, periodic=periodic, derivative=derivative, order=order, iterations=iterations);
[docs] def test(): import numpy as np import matplotlib.pyplot as plt import ClearMap.Analysis.Curves.Resampling as res #reload(res) curve = np.linspace(0,10,50); curve = np.vstack([curve, np.sin(curve)]).T; rcurve = res.resample(curve, n_points=150, smooth=0); plt.figure(1); plt.clf(); plt.plot(rcurve[:,0], rcurve[:,1], 'red'); plt.plot(curve[:,0], curve[:,1], 'blue'); curve1d = np.sin(np.linspace(0,1,50) * 2 * np.pi); rcurve1d = res.resample(curve1d, n_points=150, smooth=0); plt.figure(2); plt.clf(); plt.plot(curve1d); plt.plot(rcurve1d);