Alexey Velikiy
7 years ago
9 changed files with 139 additions and 338 deletions
@ -1,5 +1,5 @@
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from detectors.general_detector import GeneralDetector |
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from detectors.pattern_detection_model import PatternDetectionModel |
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from detectors.pattern_detector import PatternDetector |
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from detectors.peaks_detector import PeaksDetector |
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from detectors.step_detector import StepDetector |
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from detectors.jump_detector import Jumpdetector |
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@ -1,231 +0,0 @@
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""" |
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Thomas Kahn |
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thomas.b.kahn@gmail.com |
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""" |
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from __future__ import absolute_import |
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from math import sqrt |
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import multiprocessing as mp |
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import numpy as np |
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from six.moves import range |
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from six.moves import zip |
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def t_scan(L, window = 1e3, num_workers = -1): |
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""" |
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Computes t statistic for i to i+window points versus i-window to i |
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points for each point i in input array. Uses multiple processes to |
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do this calculation asynchronously. Array is decomposed into window |
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number of frames, each consisting of points spaced at window |
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intervals. This optimizes the calculation, as the drone function |
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need only compute the mean and variance for each set once. |
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Parameters |
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---------- |
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L : numpy array |
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1 dimensional array that represents time series of datapoints |
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window : int / float |
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Number of points that comprise the windows of data that are |
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compared |
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num_workers : int |
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Number of worker processes for multithreaded t_stat computation |
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Defult value uses num_cpu - 1 workers |
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Returns |
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------- |
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t_stat : numpy array |
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Array which holds t statistic values for each point. The first |
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and last (window) points are replaced with zero, since the t |
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statistic calculation cannot be performed in that case. |
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""" |
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size = L.size |
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window = int(window) |
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frames = list(range(window)) |
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n_cols = (size // window) - 1 |
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t_stat = np.zeros((window, n_cols)) |
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if num_workers == 1: |
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results = [_t_scan_drone(L, n_cols, frame, window) for frame in frames] |
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else: |
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if num_workers == -1: |
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num_workers = mp.cpu_count() - 1 |
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pool = mp.Pool(processes = num_workers) |
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results = [pool.apply_async(_t_scan_drone, args=(L, n_cols, frame, window)) for frame in frames] |
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results = [r.get() for r in results] |
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pool.close() |
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for index, row in results: |
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t_stat[index] = row |
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t_stat = np.concatenate(( |
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np.zeros(window), |
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t_stat.transpose().ravel(order='C'), |
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np.zeros(size % window) |
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)) |
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return t_stat |
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def _t_scan_drone(L, n_cols, frame, window=1e3): |
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""" |
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Drone function for t_scan. Not Intended to be called manually. |
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Computes t_scan for the designated frame, and returns result as |
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array along with an integer tag for proper placement in the |
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aggregate array |
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""" |
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size = L.size |
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window = int(window) |
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root_n = sqrt(window) |
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output = np.zeros(n_cols) |
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b = L[frame:window+frame] |
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b_mean = b.mean() |
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b_var = b.var() |
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for i in range(window+frame, size-window, window): |
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a = L[i:i+window] |
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a_mean = a.mean() |
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a_var = a.var() |
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output[i // window - 1] = root_n * (a_mean - b_mean) / sqrt(a_var + b_var) |
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b_mean, b_var = a_mean, a_var |
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return frame, output |
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def mz_fwt(x, n=2): |
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""" |
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Computes the multiscale product of the Mallat-Zhong discrete forward |
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wavelet transform up to and including scale n for the input data x. |
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If n is even, the spikes in the signal will be positive. If n is odd |
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the spikes will match the polarity of the step (positive for steps |
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up, negative for steps down). |
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This function is essentially a direct translation of the MATLAB code |
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provided by Sadler and Swami in section A.4 of the following: |
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http://www.dtic.mil/dtic/tr/fulltext/u2/a351960.pdf |
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Parameters |
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---------- |
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x : numpy array |
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1 dimensional array that represents time series of data points |
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n : int |
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Highest scale to multiply to |
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Returns |
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------- |
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prod : numpy array |
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The multiscale product for x |
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""" |
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N_pnts = x.size |
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lambda_j = [1.5, 1.12, 1.03, 1.01][0:n] |
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if n > 4: |
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lambda_j += [1.0]*(n-4) |
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H = np.array([0.125, 0.375, 0.375, 0.125]) |
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G = np.array([2.0, -2.0]) |
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Gn = [2] |
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Hn = [3] |
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for j in range(1,n): |
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q = 2**(j-1) |
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Gn.append(q+1) |
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Hn.append(3*q+1) |
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S = np.concatenate((x[::-1], x)) |
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S = np.concatenate((S, x[::-1])) |
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prod = np.ones(N_pnts) |
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for j in range(n): |
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n_zeros = 2**j - 1 |
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Gz = _insert_zeros(G, n_zeros) |
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Hz = _insert_zeros(H, n_zeros) |
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current = (1.0/lambda_j[j])*np.convolve(S,Gz) |
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current = current[N_pnts+Gn[j]:2*N_pnts+Gn[j]] |
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prod *= current |
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if j == n-1: |
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break |
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S_new = np.convolve(S, Hz) |
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S_new = S_new[N_pnts+Hn[j]:2*N_pnts+Hn[j]] |
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S = np.concatenate((S_new[::-1], S_new)) |
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S = np.concatenate((S, S_new[::-1])) |
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return prod |
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def _insert_zeros(x, n): |
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""" |
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Helper function for mz_fwt. Splits input array and adds n zeros |
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between values. |
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""" |
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newlen = (n+1)*x.size |
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out = np.zeros(newlen) |
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indices = list(range(0, newlen-n, n+1)) |
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out[indices] = x |
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return out |
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def find_steps(array, threshold): |
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""" |
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Finds local maxima by segmenting array based on positions at which |
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the threshold value is crossed. Note that this thresholding is |
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applied after the absolute value of the array is taken. Thus, |
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the distinction between upward and downward steps is lost. However, |
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get_step_sizes can be used to determine directionality after the |
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fact. |
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Parameters |
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---------- |
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array : numpy array |
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1 dimensional array that represents time series of data points |
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threshold : int / float |
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Threshold value that defines a step |
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Returns |
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------- |
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steps : list |
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List of indices of the detected steps |
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""" |
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steps = [] |
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array = np.abs(array) |
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above_points = np.where(array > threshold, 1, 0) |
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ap_dif = np.diff(above_points) |
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cross_ups = np.where(ap_dif == 1)[0] |
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cross_dns = np.where(ap_dif == -1)[0] |
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for upi, dni in zip(cross_ups,cross_dns): |
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steps.append(np.argmax(array[upi:dni]) + upi) |
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return steps |
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def get_step_sizes(array, indices, window=1000): |
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""" |
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Calculates step size for each index within the supplied list. Step |
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size is determined by averaging over a range of points (specified |
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by the window parameter) before and after the index of step |
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occurrence. The directionality of the step is reflected by the sign |
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of the step size (i.e. a positive value indicates an upward step, |
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and a negative value indicates a downward step). The combined |
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standard deviation of both measurements (as a measure of uncertainty |
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in step calculation) is also provided. |
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Parameters |
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---------- |
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array : numpy array |
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1 dimensional array that represents time series of data points |
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indices : list |
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List of indices of the detected steps (as provided by |
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find_steps, for example) |
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window : int, optional |
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Number of points to average over to determine baseline levels |
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before and after step. |
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Returns |
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------- |
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step_sizes : list |
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List of the calculated sizes of each step |
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step_error : list |
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""" |
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step_sizes = [] |
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step_error = [] |
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indices = sorted(indices) |
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last = len(indices) - 1 |
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for i, index in enumerate(indices): |
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if i == 0: |
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q = min(window, indices[i+1]-index) |
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elif i == last: |
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q = min(window, index - indices[i-1]) |
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else: |
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q = min(window, index-indices[i-1], indices[i+1]-index) |
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a = array[index:index+q] |
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b = array[index-q:index] |
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step_sizes.append(a.mean() - b.mean()) |
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step_error.append(sqrt(a.var()+b.var())) |
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return step_sizes, step_error |
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