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utils.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-09-19 22:30:46
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-09-25 18:03:00
""" Definition of generic utility functions used in other modules """
import operator
import os
import pickle
import tkinter as tk
from tkinter import filedialog
import numpy as np
import colorlog
from scipy.interpolate import interp1d
def setLogger():
log_formatter = colorlog.ColoredFormatter(
'%(log_color)s %(asctime)s %(message)s',
datefmt='%d/%m/%Y %H:%M:%S:',
reset=True,
log_colors={
'DEBUG': 'green',
'INFO': 'white',
'WARNING': 'yellow',
'ERROR': 'red',
'CRITICAL': 'red,bg_white',
},
style='%'
)
log_handler = colorlog.StreamHandler()
log_handler.setFormatter(log_formatter)
color_logger = colorlog.getLogger('PySONIC')
color_logger.addHandler(log_handler)
return color_logger
# Get package logger
logger = setLogger()
# SI units prefixes
si_prefixes = {
'y': 1e-24, # yocto
'z': 1e-21, # zepto
'a': 1e-18, # atto
'f': 1e-15, # femto
'p': 1e-12, # pico
'n': 1e-9, # nano
'u': 1e-6, # micro
'm': 1e-3, # mili
'': 1e0, # None
'k': 1e3, # kilo
'M': 1e6, # mega
'G': 1e9, # giga
'T': 1e12, # tera
'P': 1e15, # peta
'E': 1e18, # exa
'Z': 1e21, # zetta
'Y': 1e24, # yotta
}
def si_format(x, precision=0, space=''):
''' Format a float according to the SI unit system, with the appropriate prefix letter. '''
if isinstance(x, float) or isinstance(x, int) or isinstance(x, np.float) or\
isinstance(x, np.int32) or isinstance(x, np.int64):
if x == 0:
factor = 1e0
prefix = ''
else:
sorted_si_prefixes = sorted(si_prefixes.items(), key=operator.itemgetter(1))
vals = [tmp[1] for tmp in sorted_si_prefixes]
# vals = list(si_prefixes.values())
ix = np.searchsorted(vals, np.abs(x)) - 1
if np.abs(x) == vals[ix + 1]:
ix += 1
factor = vals[ix]
prefix = sorted_si_prefixes[ix][0]
# prefix = list(si_prefixes.keys())[ix]
return '{{:.{}f}}{}{}'.format(precision, space, prefix).format(x / factor)
elif isinstance(x, list) or isinstance(x, tuple):
return [si_format(item, precision, space) for item in x]
elif isinstance(x, np.ndarray) and x.ndim == 1:
return [si_format(float(item), precision, space) for item in x]
else:
print(type(x))
def pow10_format(number, precision=2):
''' Format a number in power of 10 notation. '''
ret_string = '{0:.{1:d}e}'.format(number, precision)
a, b = ret_string.split("e")
a = float(a)
b = int(b)
return '{}10^{{{}}}'.format('{} * '.format(a) if a != 1. else '', b)
def rmse(x1, x2):
""" Compute the root mean square error between two 1D arrays """
return np.sqrt(((x1 - x2) ** 2).mean())
def rsquared(x1, x2):
''' compute the R-squared coefficient between two 1D arrays '''
residuals = x1 - x2
ss_res = np.sum(residuals**2)
ss_tot = np.sum((x1 - np.mean(x1))**2)
return 1 - (ss_res / ss_tot)
def Pressure2Intensity(p, rho=1075.0, c=1515.0):
""" Return the spatial peak, pulse average acoustic intensity (ISPPA)
associated with the specified pressure amplitude.
:param p: pressure amplitude (Pa)
:param rho: medium density (kg/m3)
:param c: speed of sound in medium (m/s)
:return: spatial peak, pulse average acoustic intensity (W/m2)
"""
return p**2 / (2 * rho * c)
def Intensity2Pressure(I, rho=1075.0, c=1515.0):
""" Return the pressure amplitude associated with the specified
spatial peak, pulse average acoustic intensity (ISPPA).
:param I: spatial peak, pulse average acoustic intensity (W/m2)
:param rho: medium density (kg/m3)
:param c: speed of sound in medium (m/s)
:return: pressure amplitude (Pa)
"""
return np.sqrt(2 * rho * c * I)
def OpenFilesDialog(filetype, dirname=''):
""" Open a FileOpenDialogBox to select one or multiple file.
The default directory and file type are given.
:param dirname: default directory
:param filetype: default file type
:return: tuple of full paths to the chosen filenames
"""
root = tk.Tk()
root.withdraw()
filenames = filedialog.askopenfilenames(filetypes=[(filetype + " files", '.' + filetype)],
initialdir=dirname)
if filenames:
par_dir = os.path.abspath(os.path.join(filenames[0], os.pardir))
else:
par_dir = None
return (filenames, par_dir)
def selectDirDialog():
""" Open a dialog box to select a directory.
:return: full path to selected directory
"""
root = tk.Tk()
root.withdraw()
return filedialog.askdirectory()
def SaveFileDialog(filename, dirname=None, ext=None):
''' Open a dialog box to save file.
:param filename: filename
:param dirname: initial directory
:param ext: default extension
:return: full path to the chosen filename
'''
root = tk.Tk()
root.withdraw()
filename_out = filedialog.asksaveasfilename(
defaultextension=ext, initialdir=dirname, initialfile=filename)
return filename_out
def downsample(t_dense, y, nsparse):
""" Decimate periodic signals to a specified number of samples."""
if(y.ndim) > 1:
nsignals = y.shape[0]
else:
nsignals = 1
y = np.array([y])
# determine time step and period of input signal
T = t_dense[-1] - t_dense[0]
dt_dense = t_dense[1] - t_dense[0]
# resample time vector linearly
t_ds = np.linspace(t_dense[0], t_dense[-1], nsparse)
# create MAV window
nmav = int(0.03 * T / dt_dense)
if nmav % 2 == 0:
nmav += 1
mav = np.ones(nmav) / nmav
# determine signals padding
npad = int((nmav - 1) / 2)
# determine indexes of sampling on convolved signals
ids = np.round(np.linspace(0, t_dense.size - 1, nsparse)).astype(int)
y_ds = np.empty((nsignals, nsparse))
# loop through signals
for i in range(nsignals):
# pad, convolve and resample
pad_left = y[i, -(npad + 2):-2]
pad_right = y[i, 1:npad + 1]
y_ext = np.concatenate((pad_left, y[i, :], pad_right), axis=0)
y_mav = np.convolve(y_ext, mav, mode='valid')
y_ds[i, :] = y_mav[ids]
if nsignals == 1:
y_ds = y_ds[0, :]
return (t_ds, y_ds)
def rescale(x, lb=None, ub=None, lb_new=0, ub_new=1):
''' Rescale a value to a specific interval by linear transformation. '''
if lb is None:
lb = x.min()
if ub is None:
ub = x.max()
xnorm = (x - lb) / (ub - lb)
return xnorm * (ub_new - lb_new) + lb_new
def extractCompTimes(filenames):
''' Extract computation times from a list of simulation files. '''
tcomps = np.empty(len(filenames))
for i, fn in enumerate(filenames):
logger.info('Loading data from "%s"', fn)
with open(fn, 'rb') as fh:
frame = pickle.load(fh)
meta = frame['meta']
tcomps[i] = meta['tcomp']
return tcomps
def getNeuronLookupsFile(mechname):
return os.path.join(
os.path.split(__file__)[0],
'neurons',
'{}_lookups.pkl'.format(mechname))
def getLookups2D(mechname, a, Fdrive):
''' Retrieve appropriate 2D lookup tables and reference vectors
for a given membrane mechanism, sonophore diameter and US frequency.
:param mechname: name of membrane density mechanism
:param a: sonophore diameter (m)
:param Fdrive: US frequency (Hz)
:return: 3-tuple with 1D numpy arrays of reference acoustic amplitudes and charge densities,
and a dictionary of 2D lookup numpy arrays
'''
# Check lookup file existence
lookup_path = getNeuronLookupsFile(mechname)
if not os.path.isfile(lookup_path):
raise FileNotFoundError('Missing lookup file: "{}"'.format(lookup_path))
# Load lookups dictionary
logger.debug('Loading lookup table')
with open(lookup_path, 'rb') as fh:
lookups4D = pickle.load(fh)
# Retrieve 1D inputs from lookups dictionary
aref = lookups4D.pop('a')
Fref = lookups4D.pop('f')
Aref = lookups4D.pop('A')
Qref = lookups4D.pop('Q')
# Check that sonophore diameter is within lookup range
arange = (aref.min() - 1e-12, aref.max() + 1e-12)
if a < arange[0] or a > arange[1]:
raise ValueError('Invalid sonophore diameter: {}m (must be within {}m - {}m lookup interval)'
.format(*si_format([a, *arange], precision=2, space=' ')))
# Check that US frequency is within lookup range
Frange = (Fref.min() - 1e-9, Fref.max() + 1e-9)
if Fdrive < Frange[0] or Fdrive > Frange[1]:
raise ValueError('Invalid frequency: {}Hz (must be within {}Hz - {}Hz lookup interval)'
.format(*si_format([Fdrive, *Frange], precision=2, space=' ')))
# Interpolate 4D lookups at sonophore diameter and then at US frequency
logger.debug('Interpolating lookups at a = {}m'.format(si_format(a, space=' ')))
lookups3D = {key: interp1d(aref, y4D, axis=0)(a) for key, y4D in lookups4D.items()}
logger.debug('Interpolating lookups at f = {}Hz'.format(si_format(Fdrive, space=' ')))
lookups2D = {key: interp1d(Fref, y3D, axis=0)(Fdrive) for key, y3D in lookups3D.items()}
return Aref, Qref, lookups2D

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