diff --git a/PySONIC/core/lookups.py b/PySONIC/core/lookups.py index eb1992b..18b0b86 100644 --- a/PySONIC/core/lookups.py +++ b/PySONIC/core/lookups.py @@ -1,511 +1,511 @@ # -*- coding: utf-8 -*- # @Author: Theo Lemaire # @Email: theo.lemaire@epfl.ch # @Date: 2019-06-27 13:59:02 # @Last Modified by: Theo Lemaire -# @Last Modified time: 2020-03-18 16:02:03 +# @Last Modified time: 2020-06-04 22:02:48 import os from sys import getsizeof import json import pickle import re import numpy as np from scipy.interpolate import interp1d from ..utils import isWithin, isIterable, moveItem class Lookup: ''' Multidimensional lookup object allowing to store, project, interpolate and retrieve several lookup tables along multiple reference input vectors. ''' interp_choices = ('linear', 'quadratic', 'cubic', 'poly1', 'poly2', 'poly3') def __init__(self, refs, tables, interp_method='linear', extrapolate=False): ''' Constructor. :param refs: dictionary of reference one-dimensional input vectors. :param tables: dictionary of multi-dimensional lookup tables :param interp_method: interpolation method :param extrapolate: boolean stating whether tables can be extrapolated outside of reference bounds ''' self.refs = refs self.tables = tables self.interp_method = interp_method self.extrapolate = extrapolate for k, v in self.items(): if v.shape != self.dims: raise ValueError( f'{k} Table dimensions {v.shape} does not match references {self.dims}') # If no dimension, make sure tables contain scalars if self.ndims == 0 and isinstance(self.tables[self.outputs[0]], np.ndarray): self.tables = {k: v.item(0) for k, v in self.items()} # If single input, mark it as sole ref if self.ndims == 1: self.refkey = self.inputs[0] self.ref = self.refs[self.refkey] def __repr__(self): ref_str = ', '.join([f'{x[0]}: {x[1]}' for x in zip(self.inputs, self.dims)]) tables_str = ', '.join(self.outputs) return f'{self.__class__.__name__}{self.ndims}D({ref_str})[{tables_str}]' def __getitem__(self, key): ''' simplified lookup table getter. ''' return self.tables[key] def __delitem__(self, key): ''' simplified lookup table suppressor. ''' del self.tables[key] def __setitem__(self, key, value): ''' simplified lookup table setter. ''' self.tables[key] = value def __sizeof__(self): ''' Return the size of the lookup in bytes. ''' s = getsizeof(self.refs) + getsizeof(self.tables) for k, v in self.refitems(): s += v.nbytes for k, v in self.items(): s += v.nbytes return s def keys(self): return self.tables.keys() def values(self): return self.tables.values() def items(self): return self.tables.items() def refitems(self): return self.refs.items() def pop(self, key): x = self.tables[key] del self.tables[key] return x def rename(self, key1, key2): self.tables[key2] = self.tables.pop(key1) @property def dims(self): ''' Tuple indicating the size of each input vector. ''' return tuple([x.size for x in self.refs.values()]) @property def ndims(self): ''' Number of dimensions in lookup. ''' return len(self.refs) @property def inputs(self): ''' Names of reference input vectors. ''' return list(self.refs.keys()) @property def outputs(self): ''' Names of the different output tables. ''' return list(self.keys()) @property def interp_method(self): return self._interp_method @interp_method.setter def interp_method(self, value): if value not in self.interp_choices: raise ValueError(f'interpolation method must be one of {self.interp_choices}') if self.isPolynomialMethod(value) and self.ndims > 1: raise ValueError(f'polynomial interpolation only available for 1D lookups') self._interp_method = value @property def extrapolate(self): return self._extrapolate @extrapolate.setter def extrapolate(self, value): if not isinstance(value, bool): raise ValueError(f'extrapolate: expected boolean') self._extrapolate = value @property def kwattrs(self): return { 'interp_method': self.interp_method, 'extrapolate': self.extrapolate} def checkAgainst(self, other): ''' Check self object against another lookup object for compatibility. ''' if self.inputs != other.inputs: raise ValueError(f'Differing lookups (references names do not match)') if self.dims != other.dims: raise ValueError(f'Differing lookup dimensions ({self.dims} - {other.dims})') for k, v in self.refitems(): if (other.refs[k] != v).any(): raise ValueError(f'Differing {k} lookup reference') if self.outputs != other.outputs: raise ValueError(f'Differing lookups (table names do not match)') def operate(self, other, op): ''' Generic arithmetic operator. ''' if isinstance(other, int): other = float(other) if isinstance(other, self.__class__): self.checkAgainst(other) tables = {k: getattr(v, op)(other[k]) for k, v in self.items()} elif isinstance(other, float): tables = {k: getattr(v, op)(other) for k, v in self.items()} else: raise ValueError(f'Cannot {op} {self.__class__} object with {type(other)} variable') return self.__class__(self.refs, tables, **self.kwattrs) def __add__(self, other): ''' Addition operator. ''' return self.operate(other, '__add__') def __sub__(self, other): ''' Subtraction operator. ''' return self.operate(other, '__sub__') def __mul__(self, other): ''' Multiplication operator. ''' return self.operate(other, '__mul__') - def __div__(self, other): + def __truediv__(self, other): ''' Division operator. ''' - return self.operate(other, '__div__') + return self.operate(other, '__truediv__') def squeeze(self): ''' Return a new lookup object in which all lookup dimensions that only contain a single value have been removed ''' new_tables = {k: v.squeeze() for k, v in self.items()} new_refs = {} for k, v in self.refitems(): if v.size > 1: new_refs[k] = v return self.__class__(new_refs, new_tables, **self.kwattrs) def getAxisIndex(self, key): ''' Get the axis index of a specific input key. ''' assert key in self.inputs, f'Unkown input dimension: {key}' return self.inputs.index(key) def copy(self): ''' Return a copy of the current lookup object. ''' return self.__class__(self.refs, self.tables, **self.kwattrs) def checkInterpMethod(self, interp_method): if interp_method not in self.interp_choices: raise ValueError(f'interpolation method must be one of {self.interp_choices}') @staticmethod def isPolynomialMethod(method): return method.startswith('poly') def getInterpolationDegree(self): return int(self.interp_method[-1]) def getInterpolator(self, ref_key, table_key, axis=-1): ''' Return 1D interpolator function along a given reference vector for a specific table .''' if self.isPolynomialMethod(self.interp_method): return np.poly1d(np.polyfit(self.refs[ref_key], self.tables[table_key], self.getInterpolationDegree())) else: fill_value = 'extrapolate' if self.kwattrs['extrapolate'] else np.nan return interp1d(self.refs[ref_key], self.tables[table_key], axis=axis, kind=self.interp_method, assume_sorted=True, fill_value=fill_value) def project(self, key, value): ''' Return a new lookup object in which tables are interpolated at one/several specific value(s) along a given dimension. :param key: input key :param value: value(s) to interpolate lookup tables at :return: new interpolated lookup object with adapted dimensions ''' # Check if value is 0 or 1-dimensional if not isIterable(value): delete_input_dim = True else: delete_input_dim = False value = np.asarray(value) # Check that value is within the bounds of the reference vector if not self.kwattrs['extrapolate']: value = isWithin(key, value, (self.refs[key].min(), self.refs[key].max())) # Get the axis index of the reference vector axis = self.getAxisIndex(key) # print(f'interpolating lookup along {key} (axis {axis}) at {value}') # Construct new tables dictionary if self.refs[key].size == 1: # If reference vector has only 1 value, take the mean along corresponding dimension new_tables = {k: v.mean(axis=axis) for k, v in self.items()} else: # Otherwise, interpolate lookup tables appropriate value(s) along the reference vector new_tables = {k: self.getInterpolator(key, k, axis=axis)(value) for k in self.keys()} # Construct new refs dictionary, deleting new_refs = self.refs.copy() if delete_input_dim: # If interpolation value is a scalar, remove the corresponding input vector del new_refs[key] else: # Otherwise, update the input vector at the interpolation values new_refs[key] = value # Construct and return a lookup object with the updated refs and tables return self.__class__(new_refs, new_tables, **self.kwattrs) def projectN(self, projections): ''' Project along multiple dimensions simultaneously. :param projections: dictionary of input keys and corresponding interpolation value(s) :return: new interpolated lookup object with adapted dimensions ''' # Construct a copy of the current lookup object lkp = self.copy() # Apply successive projections, overwriting the lookup object at each step for k, v in projections.items(): lkp = lkp.project(k, v) # Return updated lookup object return lkp def move(self, key, index): ''' Move a specific input to a new index and re-organize lookup object accordingly. :param key: input key :param index: target index ''' # Get absolute target axis index if index == -1: index = self.ndims - 1 # Get reference axis index iref = self.getAxisIndex(key) # Re-organize all lookup tables, moving the reference axis to the target index for k in self.keys(): self.tables[k] = np.moveaxis(self.tables[k], iref, index) # Re-order refs dictionary such that key falls at the appropriate index self.refs = {k: self.refs[k] for k in moveItem(list(self.refs.keys()), key, index)} def interpVar1D(self, ref_value, var_key): ''' Interpolate a specific lookup vector at one/several specific value(s) along the reference input vector. :param ref_value: specific input value :param var_key: output table key :return: interpolated value(s) .. warning:: This method can only be used for 1 dimensional lookups. ''' assert self.ndims == 1, 'Cannot interpolate multi-dimensional object' return np.interp(ref_value, self.ref, self.tables[var_key], left=np.nan, right=np.nan) def interpolate1D(self, value): ''' Interpolate all lookup vectors variable at one/several specific value(s) along the reference input vector. :param value: specific input value :return: dictionary of output keys: interpolated value(s) .. warning:: This method can only be used for 1 dimensional lookups. ''' return {k: self.interpVar1D(value, k) for k in self.outputs} def tile(self, ref_name, ref_values): ''' Return a new lookup object in which tables are tiled along a new input dimension. :param ref_name: input name :param ref_values: input vector :return: lookup object with additional input vector and tiled tables ''' itiles = range(ref_values.size) tables = {k: np.array([v for i in itiles]) for k, v in self.items()} refs = {**{ref_name: ref_values}, **self.refs} return self.__class__(refs, tables, **self.kwattrs) def toDict(self): ''' Translate self object into a dictionary. ''' return { 'refs': {k: v.tolist() for k, v in self.refs.items()}, 'tables': {k: v.tolist() for k, v in self.tables.items()}, } @classmethod def fromDict(cls, d): ''' Construct lookup instance from dictionary. ''' refs = {k: np.array(v) for k, v in d['refs'].items()} tables = {k: np.array(v) for k, v in d['tables'].items()} return cls(refs, tables) def toJson(self, fpath): ''' Save self object to a JSON file. ''' with open(fpath, 'w') as fh: json.dump(self.toDict(), fh) @classmethod def fromJson(cls, fpath): ''' Construct lookup instance from JSON file. ''' cls.checkForExistence(fpath) with open(fpath) as fh: d = json.load(fh) return cls.fromDict(d) def toPickle(self, fpath): ''' Save self object to a PKL file. ''' with open(fpath, 'wb') as fh: pickle.dump({'refs': self.refs, 'tables': self.tables}, fh) @classmethod def fromPickle(cls, fpath): ''' Construct lookup instance from PKL file. ''' cls.checkForExistence(fpath) with open(fpath, 'rb') as fh: d = pickle.load(fh) return cls(d['refs'], d['tables']) @staticmethod def checkForExistence(fpath): ''' Raise an error if filepath does not correspond to an existing file. ''' if not os.path.isfile(fpath): raise FileNotFoundError(f'Missing lookup file: "{fpath}"') class EffectiveVariablesLookup(Lookup): ''' Lookup object with added functionality to handle effective variables, namely: - a special EffectiveVariablesDict wrapper around the output tables - projectOff and projectDC methods allowing for smart projections. ''' def __init__(self, refs, tables, **kwargs): if not isinstance(tables, EffectiveVariablesDict): tables = EffectiveVariablesDict(tables) super().__init__(refs, tables, **kwargs) def interpolate1D(self, value): return EffectiveVariablesDict(super().interpolate1D(value)) def projectOff(self): ''' Project for OFF periods (zero amplitude). ''' # Interpolate at zero amplitude lkp0 = self.project('A', 0.) # Move charge axis to end in all tables Qaxis = lkp0.getAxisIndex('Q') for k, v in lkp0.items(): lkp0.tables[k] = np.moveaxis(v, Qaxis, -1) # Iterate along dimensions and take first value along corresponding axis for i in range(lkp0.ndims - 1): for k, v in lkp0.items(): lkp0.tables[k] = v[0] # Keep only charge vector in references lkp0.refs = {'Q': lkp0.refs['Q']} return lkp0 def projectDC(self, amps=None, DC=1.): ''' Project lookups at a given duty cycle.''' # Assign default values if amps is None: amps = self.refs['A'] elif not isIterable(amps): amps = np.array([amps]) # project lookups at zero and defined amps lkp0 = self.project('A', 0.) lkps_ON = self.project('A', amps) # Retrieve amplitude axis index, and move amplitude to first axis A_axis = lkps_ON.getAxisIndex('A') lkps_ON.move('A', 0) # Tile the zero-amplitude lookup to match the lkps_ON dimensions lkps_OFF = lkp0.tile('A', lkps_ON.refs['A']) # Compute a DC averaged lookup lkp = lkps_ON * DC + lkps_OFF * (1 - DC) # Move amplitude back to its original axis lkp.move('A', A_axis) return lkp class EffectiveVariablesDict(): ''' Wrapper around a dictionary object, allowing to return derived effetive variables for special keys. ''' # Key patterns suffix_pattern = '[A-Za-z0-9_]+' xinf_pattern = re.compile(f'^({suffix_pattern})inf$') taux_pattern = re.compile(f'^tau({suffix_pattern})$') def __init__(self, d): self.d = d def __repr__(self): return self.__class__.__name__ + '(' + ', '.join(self.d.keys()) + ')' def items(self): return self.d.items() def keys(self): return self.d.keys() def values(self): return self.d.values() def alphax(self, x): return self.d[f'alpha{x}'] def betax(self, x): return self.d[f'beta{x}'] def taux(self, x): return 1 / (self.alphax(x) + self.betax(x)) def xinf(self, x): return self.alphax(x) * self.taux(x) def __getitem__(self, key): if key in self.d: return self.d[key] else: m = self.taux_pattern.match(key) if m is not None: return self.taux(m.group(1)) else: m = self.xinf_pattern.match(key) if m is not None: return self.xinf(m.group(1)) else: raise KeyError(key) def __setitem__(self, key, value): self.d[key] = value def __delitem__(self, key): del self.d[key] def pop(self, key): return self.d.pop(key) diff --git a/PySONIC/utils.py b/PySONIC/utils.py index 8ebcc71..f8cb8d2 100644 --- a/PySONIC/utils.py +++ b/PySONIC/utils.py @@ -1,1096 +1,1096 @@ # -*- coding: utf-8 -*- # @Author: Theo Lemaire # @Email: theo.lemaire@epfl.ch # @Date: 2016-09-19 22:30:46 # @Last Modified by: Theo Lemaire -# @Last Modified time: 2020-06-03 16:54:41 +# @Last Modified time: 2020-06-04 22:02:35 ''' Definition of generic utility functions used in other modules ''' import csv from functools import wraps import operator import time from inspect import signature import os from shutil import get_terminal_size import lockfile import math import pickle import json from tqdm import tqdm import logging import tkinter as tk from tkinter import filedialog import base64 import datetime import numpy as np import pandas as pd from scipy.optimize import brentq from scipy.interpolate import interp1d from scipy import linalg import colorlog from pushbullet import Pushbullet # Package logger my_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='%') def setHandler(logger, handler): for h in logger.handlers: logger.removeHandler(h) logger.addHandler(handler) return logger def setLogger(name, formatter): handler = colorlog.StreamHandler() handler.setFormatter(formatter) logger = colorlog.getLogger(name) logger.addHandler(handler) return logger class TqdmHandler(logging.StreamHandler): def __init__(self, formatter): logging.StreamHandler.__init__(self) self.setFormatter(formatter) def emit(self, record): msg = self.format(record) tqdm.write(msg) logger = setLogger('PySONIC', my_log_formatter) def fillLine(text, char='-', totlength=None): ''' Surround a text with repetitions of a specific character in order to fill a line to a given total length. :param text: text to be surrounded :param char: surrounding character :param totlength: target number of characters in filled text line :return: filled text line ''' if totlength is None: totlength = get_terminal_size().columns - 1 ndashes = totlength - len(text) - 2 if ndashes < 2: return text else: nside = ndashes // 2 nleft, nright = nside, nside if ndashes % 2 == 1: nright += 1 return f'{char * nleft} {text} {char * nright}' # 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 } sorted_si_prefixes = sorted(si_prefixes.items(), key=operator.itemgetter(1)) def getSIpair(x, scale='lin'): ''' Get the correct SI factor and prefix for a floating point number. ''' if isIterable(x): # If iterable, get a representative number of the distribution x = np.asarray(x) x = x.prod()**(1.0 / x.size) if scale == 'log' else np.mean(x) if x == 0: return 1e0, '' else: vals = [tmp[1] for tmp in sorted_si_prefixes] ix = np.searchsorted(vals, np.abs(x)) - 1 if np.abs(x) == vals[ix + 1]: ix += 1 return vals[ix], sorted_si_prefixes[ix][0] 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): factor, prefix = getSIpair(x) return f'{x / factor:.{precision}f}{space}{prefix}' 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: raise ValueError(f'cannot si_format {type(x)} objects') def pow10_format(number, precision=2): ''' Format a number in power of 10 notation. ''' sci_string = f'{number:.{precision}e}' value, exponent = sci_string.split("e") value, exponent = float(value), int(exponent) val_str = f'{value} * ' if value != 1. else '' return f'{val_str}10^{{{exponent}}}' def rmse(x1, x2, axis=None): ''' Compute the root mean square error between two 1D arrays ''' return np.sqrt(((x1 - x2) ** 2).mean(axis=axis)) 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 convertPKL2JSON(): for pkl_filepath in OpenFilesDialog('pkl')[0]: logger.info(f'Processing {pkl_filepath} ...') json_filepath = f'{os.path.splitext(pkl_filepath)[0]}.json' with open(pkl_filepath, 'rb') as fpkl, open(json_filepath, 'w') as fjson: data = pickle.load(fpkl) json.dump(data, fjson, ensure_ascii=False, sort_keys=True, indent=4) logger.info('All done!') 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 len(filenames) == 0: raise ValueError('no input file selected') par_dir = os.path.abspath(os.path.join(filenames[0], os.pardir)) return filenames, par_dir def selectDirDialog(title='Select directory'): ''' Open a dialog box to select a directory. :return: full path to selected directory ''' root = tk.Tk() root.withdraw() directory = filedialog.askdirectory(title=title) if directory == '': raise ValueError('no directory selected') return directory 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) if len(filename_out) == 0: raise ValueError('no output filepath selected') return filename_out def loadData(fpath, frequency=1): ''' Load dataframe and metadata dictionary from pickle file. ''' logger.info('Loading data from "%s"', os.path.basename(fpath)) with open(fpath, 'rb') as fh: frame = pickle.load(fh) df = frame['data'].iloc[::frequency] meta = frame['meta'] return df, meta 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 expandRange(xmin, xmax, exp_factor=2): if xmin > xmax: raise ValueError('values must be provided in (min, max) order') xptp = xmax - xmin xmid = (xmin + xmax) / 2 xdev = xptp * exp_factor / 2 return (xmid - xdev, xmin + xdev) def isIterable(x): for t in [list, tuple, np.ndarray]: if isinstance(x, t): return True return False def isWithin(name, val, bounds, rel_tol=1e-9, raise_warning=True): ''' Check if a floating point number is within an interval. If the value falls outside the interval, an error is raised. If the value falls just outside the interval due to rounding errors, the associated interval bound is returned. :param val: float value :param bounds: interval bounds (float tuple) :return: original or corrected value ''' if isIterable(val): return np.array([isWithin(name, v, bounds, rel_tol, raise_warning) for v in val]) if val >= bounds[0] and val <= bounds[1]: return val elif val < bounds[0] and math.isclose(val, bounds[0], rel_tol=rel_tol): if raise_warning: logger.warning( 'Rounding %s value (%s) to interval lower bound (%s)', name, val, bounds[0]) return bounds[0] elif val > bounds[1] and math.isclose(val, bounds[1], rel_tol=rel_tol): if raise_warning: logger.warning( 'Rounding %s value (%s) to interval upper bound (%s)', name, val, bounds[1]) return bounds[1] else: raise ValueError(f'{name} value ({val}) out of [{bounds[0]}, {bounds[1]}] interval') def getDistribution(xmin, xmax, nx, scale='lin'): if scale == 'log': xmin, xmax = np.log10(xmin), np.log10(xmax) return {'lin': np.linspace, 'log': np.logspace}[scale](xmin, xmax, nx) def getDistFromList(xlist): if not isinstance(xlist, list): raise TypeError('Input must be a list') if len(xlist) != 4: raise ValueError('List must contain exactly 4 arguments ([type, min, max, n])') scale = xlist[0] if scale not in ('log', 'lin'): raise ValueError('Unknown distribution type (must be "lin" or "log")') xmin, xmax = [float(x) for x in xlist[1:-1]] if xmin >= xmax: raise ValueError('Specified minimum higher or equal than specified maximum') nx = int(xlist[-1]) if nx < 2: raise ValueError('Specified number must be at least 2') return getDistribution(xmin, xmax, nx, scale=scale) def getIndex(container, value): ''' Return the index of a float / string value in a list / array :param container: list / 1D-array of elements :param value: value to search for :return: index of value (if found) ''' if isinstance(value, float): container = np.array(container) imatches = np.where(np.isclose(container, value, rtol=1e-9, atol=1e-16))[0] if len(imatches) == 0: raise ValueError(f'{value} not found in {container}') return imatches[0] elif isinstance(value, str): return container.index(value) def funcSig(func, args, kwargs): args_repr = [repr(a) for a in args] kwargs_repr = [f"{k}={v!r}" for k, v in kwargs.items()] return f'{func.__name__}({", ".join(args_repr + kwargs_repr)})' def debug(func): ''' Print the function signature and return value. ''' @wraps(func) def wrapper_debug(*args, **kwargs): print(f'Calling {funcSig(func, args, kwargs)}') value = func(*args, **kwargs) print(f"{func.__name__!r} returned {value!r}") return value return wrapper_debug def timer(func): ''' Monitor and return the runtime of the decorated function. ''' @wraps(func) def wrapper(*args, **kwargs): start_time = time.perf_counter() value = func(*args, **kwargs) end_time = time.perf_counter() run_time = end_time - start_time return value, run_time return wrapper def alignWithFuncDef(func, args, kwargs): ''' Align a set of provided positional and keyword arguments with the arguments signature in a specific function definition. :param func: function object :param args: list of provided positional arguments :param kwargs: dictionary of provided keyword arguments :return: 2-tuple with the modified arguments and ''' # Get positional and keyword arguments from function signature sig_params = {k: v for k, v in signature(func).parameters.items()} sig_args = list(filter(lambda x: x.default == x.empty, sig_params.values())) sig_kwargs = {k: v.default for k, v in sig_params.items() if v.default != v.empty} sig_nargs = len(sig_args) kwarg_keys = list(sig_kwargs.keys()) # Restrain provided positional arguments to those that are also positional in signature new_args = args[:sig_nargs] # Construct hybrid keyword arguments dictionary from: # - remaining positional arguments # - provided keyword arguments # - default keyword arguments new_kwargs = sig_kwargs for i, x in enumerate(args[sig_nargs:]): new_kwargs[kwarg_keys[i]] = x for k, v in kwargs.items(): new_kwargs[k] = v return new_args, new_kwargs def alignWithMethodDef(method, args, kwargs): args, kwargs = alignWithFuncDef(method, [None] + list(args), kwargs) return tuple(args[1:]), kwargs def logCache(fpath, delimiter='\t', out_type=float): ''' Add an extra IO memoization functionality to a function using file caching, to avoid repetitions of tedious computations with identical inputs. ''' def wrapper_with_args(func): @wraps(func) def wrapper(*args, **kwargs): # If function has history -> do not log if 'history' in kwargs: return func(*args, **kwargs) # Modify positional and keyword arguments to match function signature, if needed args, kwargs = alignWithFuncDef(func, args, kwargs) # Translate args and kwargs into string signature fsignature = funcSig(func, args, kwargs) # If entry present in log, return corresponding output if os.path.isfile(fpath): with open(fpath, 'r', newline='') as f: reader = csv.reader(f, delimiter=delimiter) for row in reader: if row[0] == fsignature: logger.debug(f'entry found in "{os.path.basename(fpath)}"') return out_type(row[1]) # Otherwise, compute output and log it into file before returning out = func(*args, **kwargs) lock = lockfile.FileLock(fpath) lock.acquire() with open(fpath, 'a', newline='') as csvfile: writer = csv.writer(csvfile, delimiter=delimiter) writer.writerow([fsignature, str(out)]) lock.release() return out return wrapper return wrapper_with_args def fileCache(root, fcode_func, ext='json'): def wrapper_with_args(func): @wraps(func) def wrapper(*args, **kwargs): # Get load and dump functions from file extension try: load_func = { 'json': json.load, 'pkl': pickle.load, 'csv': lambda f: np.loadtxt(f, delimiter=',') }[ext] dump_func = { 'json': json.dump, 'pkl': pickle.dump, 'csv': lambda x, f: np.savetxt(f, x, delimiter=',') }[ext] except KeyError: raise ValueError('Unknown file extension') # Get read and write mode (text or binary) from file extension mode = 'b' if ext == 'pkl' else '' # Get file path from root and function arguments, using fcode function if callable(fcode_func): fcode = fcode_func(*args) else: fcode = fcode_func fpath = os.path.join(os.path.abspath(root), f'{fcode}.{ext}') # If file exists, load output from it if os.path.isfile(fpath): logger.info(f'loading data from "{fpath}"') with open(fpath, 'r' + mode) as f: out = load_func(f) # Otherwise, execute function and create the file to dump the output else: logger.warning(f'reference data file not found: "{fpath}"') out = func(*args, **kwargs) logger.info(f'dumping data in "{fpath}"') lock = lockfile.FileLock(fpath) lock.acquire() with open(fpath, 'w' + mode) as f: dump_func(out, f) lock.release() return out return wrapper return wrapper_with_args def derivative(f, x, eps, method='central'): ''' Compute the difference formula for f'(x) with perturbation size eps. :param dfunc: derivatives function, taking an array of states and returning an array of derivatives :param x: states vector :param method: difference formula: 'forward', 'backward' or 'central' :param eps: perturbation vector (same size as states vector) :return: numerical approximation of the derivative around the fixed point ''' if isIterable(x): if not isIterable(eps) or len(eps) != len(x): raise ValueError('eps must be the same size as x') elif np.sum(eps != 0.) != 1: raise ValueError('eps must be zero-valued across all but one dimensions') eps_val = np.sum(eps) else: eps_val = eps if method == 'central': df = (f(x + eps) - f(x - eps)) / 2 elif method == 'forward': df = f(x + eps) - f(x) elif method == 'backward': df = f(x) - f(x - eps) else: raise ValueError("Method must be 'central', 'forward' or 'backward'.") return df / eps_val def jacobian(dfunc, x, rel_eps=None, abs_eps=None, method='central'): ''' Evaluate the Jacobian maatrix of a (time-invariant) system, given a states vector and derivatives function. :param dfunc: derivatives function, taking an array of n states and returning an array of n derivatives :param x: n-states vector :return: n-by-n square Jacobian matrix ''' if sum(e is not None for e in [abs_eps, rel_eps]) != 1: raise ValueError('one (and only one) of "rel_eps" or "abs_eps" parameters must be provided') # Determine vector size x = np.asarray(x) n = x.size # Initialize Jacobian matrix J = np.empty((n, n)) # Create epsilon vector if rel_eps is not None: mode = 'relative' eps_vec = rel_eps else: mode = 'absolute' eps_vec = abs_eps if not isIterable(eps_vec): eps_vec = np.array([eps_vec] * n) if mode == 'relative': eps = x * eps_vec else: eps = eps_vec # Perturb each state by epsilon on both sides, re-evaluate derivatives # and assemble Jacobian matrix ei = np.zeros(n) for i in range(n): ei[i] = 1 J[:, i] = derivative(dfunc, x, eps * ei, method=method) ei[i] = 0 return J def classifyFixedPoint(x, dfunc): ''' Characterize the stability of a fixed point by numerically evaluating its Jacobian matrix and evaluating the sign of the real part of its associated eigenvalues. :param x: n-states vector :param dfunc: derivatives function, taking an array of n states and returning an array of n derivatives ''' # Compute Jacobian numerically # print(f'x = {x}, dfunx(x) = {dfunc(x)}') eps_machine = np.sqrt(np.finfo(float).eps) J = jacobian(dfunc, x, rel_eps=eps_machine, method='forward') # Compute eigenvalues and eigenvectors eigvals, eigvecs = linalg.eig(J) logger.debug(f"eigenvalues = {[f'({x.real:.2e} + {x.imag:.2e}j)' for x in eigvals]}") # Determine fixed point stability based on eigenvalues is_neg_eigvals = eigvals.real < 0 if is_neg_eigvals.all(): # all real parts negative -> stable key = 'stable' elif is_neg_eigvals.any(): # both posivie and negative real parts -> saddle key = 'saddle' else: # all real parts positive -> unstable key = 'unstable' return eigvals, key def findModifiedEq(x0, dfunc, *args): ''' Find an equilibrium variable in a modified system by searching for its derivative root within an interval around its original equilibrium. :param x0: equilibrium value in original system. :param func: derivative function, taking the variable as first parameter. :param *args: remaining arguments needed for the derivative function. :return: variable equilibrium value in modified system. ''' is_iterable = [isIterable(arg) for arg in args] if any(is_iterable): if not all(is_iterable): raise ValueError('mix of iterables and non-iterables') lengths = [len(arg) for arg in args] if not all(n == lengths[0] for n in lengths): raise ValueError(f'inputs are not of the same size: {lengths}') n = lengths[0] res = [] for i in range(n): x = [arg[i] for arg in args] res.append(findModifiedEq(x0, dfunc, *x)) return np.array(res) else: return brentq(lambda x: dfunc(x, *args), x0 * 1e-4, x0 * 1e3, xtol=1e-16) def swapFirstLetterCase(s): if s[0].islower(): return s.capitalize() else: return s[0].lower() + s[1:] def getPow10(x, direction='up'): ''' Get the power of 10 that is closest to a number, in either direction("down" or "up"). ''' round_method = {'up': np.ceil, 'down': np.floor}[direction] return np.power(10, round_method(np.log10(x))) def rotAroundPoint2D(x, theta, p): ''' Rotate a 2D vector around a center point by a given angle. :param x: 2D coordinates vector :param theta: rotation angle (in rad) :param p: 2D center point coordinates :return: 2D rotated coordinates vector ''' n1, n2 = x.shape if n1 != 2: if n2 == 2: x = x.T else: raise ValueError('x should be a 2-by-n vector') # Rotation matrix R = np.array([ [np.cos(theta), -np.sin(theta)], [np.sin(theta), np.cos(theta)], ]) # Broadcast center point to input vector ptile = np.tile(p, (x.shape[1], 1)).T # Subtract, rotate and add return R.dot(x - ptile) + ptile def getKey(keyfile='pushbullet.key'): dir_path = os.path.dirname(os.path.realpath(__file__)) package_root = os.path.abspath(os.path.join(dir_path, os.pardir)) fpath = os.path.join(package_root, keyfile) if not os.path.isfile(fpath): raise FileNotFoundError('pushbullet API key file not found') with open(fpath) as f: encoded_key = f.readlines()[0] return base64.b64decode(str.encode(encoded_key)).decode() def sendPushNotification(msg): try: key = getKey() pb = Pushbullet(key) dt = datetime.datetime.now() s = dt.strftime('%Y-%m-%d %H:%M:%S') pb.push_note('Code Messenger', f'{s}\n{msg}') except FileNotFoundError: logger.error(f'Could not send push notification: "{msg}"') def alert(func): ''' Run a function, and send a push notification upon completion, or if an error is raised during its execution. ''' @wraps(func) def wrapper(*args, **kwargs): try: out = func(*args, **kwargs) sendPushNotification(f'completed "{func.__name__}" execution successfully') return out except BaseException as e: sendPushNotification(f'error during "{func.__name__}" execution: {e}') raise e return wrapper def sunflower(n, radius=1, alpha=1): ''' Generate a population of uniformly distributed 2D data points in a unit circle. :param n: number of data points :param alpha: coefficient determining evenness of the boundary :return: 2D matrix of Cartesian (x, y) positions ''' nbounds = np.round(alpha * np.sqrt(n)) # number of boundary points phi = (np.sqrt(5) + 1) / 2 # golden ratio k = np.arange(1, n + 1) # index vector theta = 2 * np.pi * k / phi**2 # angle vector r = np.sqrt((k - 1) / (n - nbounds - 1)) # radius vector r[r > 1] = 1 x = r * np.cos(theta) y = r * np.sin(theta) return radius * np.vstack((x, y)) def filecode(model, *args): ''' Generate file code given a specific combination of model input parameters. ''' # If meta dictionary was passed, generate inputs list from it if len(args) == 1 and isinstance(args[0], dict): meta = args[0].copy() if meta['simkey'] == 'ASTIM' and 'fs' not in meta: meta['fs'] = meta['model']['fs'] meta['method'] = meta['model']['method'] meta['qss_vars'] = None for k in ['simkey', 'model', 'tcomp', 'dt', 'atol']: if k in meta: del meta[k] args = list(meta.values()) # Otherwise, transform args tuple into list else: args = list(args) # If any argument is an iterable -> transform it to a continous string for i in range(len(args)): if isIterable(args[i]): args[i] = ''.join([str(x) for x in args[i]]) # Create file code by joining string-encoded inputs with underscores codes = model.filecodes(*args).values() return '_'.join([x for x in codes if x is not None]) def simAndSave(model, *args, **kwargs): ''' Simulate the model and save the results in a specific output directory. :param *args: list of arguments provided to the simulation function :param **kwargs: optional arguments dictionary :return: output filepath ''' # Extract output directory and overwrite boolean from keyword arguments. outputdir = kwargs.pop('outputdir', '.') overwrite = kwargs.pop('overwrite', True) # Set data and meta to None data, meta = None, None # Extract drive object from args drive, *other_args = args # If drive is searchable and not fully resolved if drive.is_searchable: if not drive.is_resolved: # Call simulate to perform titration out = model.simulate(*args) # If titration yields nothing -> no file produced -> return None if out is None: logger.warning('returning None') return None # Store data and meta data, meta = out # Update args list with resovled drive try: args = (meta['drive'], *other_args) except KeyError: args = (meta['source'], *other_args) # Check if a output file corresponding to sim inputs is found in the output directory # That check is performed prior to running the simulation, such that # it is not run if the file is present and overwrite is set ot false. fname = f'{model.filecode(*args)}.pkl' fpath = os.path.join(outputdir, fname) existing_file_msg = f'File "{fname}" already present in directory "{outputdir}"' existing_file = os.path.isfile(fpath) # If file exists and overwrite is set ot false -> return if existing_file and not overwrite: logger.warning(f'{existing_file_msg} -> preserving') return fpath # Run simulation if not already done (for titration cases) if data is None: data, meta = model.simulate(*args) # Raise warning if an existing file is overwritten if existing_file: logger.warning(f'{existing_file_msg} -> overwriting') # Save output file and return output filepath with open(fpath, 'wb') as fh: pickle.dump({'meta': meta, 'data': data}, fh) logger.debug('simulation data exported to "%s"', fpath) return fpath def moveItem(l, value, itarget): ''' Move a list item to a specific target index. :param l: list object :param value: value of the item to move :param itarget: target index :return: re-ordered list. ''' # Get absolute target index if itarget < 0: itarget += len(l) assert itarget < len(l), f'target index {itarget} exceeds list size ({len(l)})' # Get index corresponding to element and delete entry from list iref = l.index(value) new_l = l.copy() del new_l[iref] # Return re-organized list return new_l[:itarget] + [value] + new_l[itarget:] def gaussian(x, mu=0., sigma=1., A=1.): return A * np.exp(-((x - mu) / sigma)**2) def isPickable(obj): try: pickle.dumps(obj) except Exception: return False return True def resolveFuncArgs(func, *args, **kwargs): ''' Return a dictionary of positional and keyword arguments upon function call, adding defaults from simfunc signature if not provided at call time. ''' bound_args = signature(func).bind(*args, **kwargs) bound_args.apply_defaults() return dict(bound_args.arguments) def getMeta(model, simfunc, *args, **kwargs): ''' Construct an informative dictionary about the model and simulation parameters. ''' # Retrieve function call arguments args_dict = resolveFuncArgs(simfunc, model, *args, **kwargs) # Construct meta dictionary meta = {'simkey': model.simkey} for k, v in args_dict.items(): if k == 'self': meta['model'] = v.meta else: meta[k] = v return meta def bounds(arr): ''' Return the bounds or a numpy array / list. ''' return (np.nanmin(arr), np.nanmax(arr)) def addColumn(df, key, arr, preceding_key=None): ''' Add a new column to a dataframe, right after a specific column. ''' df[key] = arr if preceding_key is not None: cols = df.columns.tolist()[:-1] preceding_index = cols.index(preceding_key) df = df[cols[:preceding_index + 1] + [key] + cols[preceding_index + 1:]] return df def integerSuffix(n): return 'th' if 4 <= n % 100 <= 20 else {1: 'st', 2: 'nd', 3: 'rd'}.get(n % 10, 'th') def customStrftime(fmt, dt_obj): return dt_obj.strftime(fmt).replace('{S}', str(dt_obj.day) + integerSuffix(dt_obj.day)) def friendlyLogspace(xmin, xmax, bases=None): ''' Define a "friendly" logspace between two bounds. ''' if bases is None: bases = [1, 2, 5] bases = np.asarray(bases) bounds = np.array([xmin, xmax]) logbounds = np.log10(bounds) bounds_orders = np.floor(logbounds) orders = np.arange(bounds_orders[0], bounds_orders[1] + 1) factors = np.power(10., np.floor(orders)) seq = np.hstack([bases * f for f in factors]) if xmax > seq.max(): seq = np.hstack((seq, xmax)) seq = seq[np.logical_and(seq >= xmin, seq <= xmax)] if xmin not in seq: seq = np.hstack((xmin, seq)) if xmax not in seq: seq = np.hstack((seq, xmax)) return seq def differing(d1, d2, subdkey=None, diff=None): ''' Find differences in values across two dictionaries (recursively). :param d1: first dictionary :param d2: second dictionary :param subdkey: specific sub-dictionary attribute key for objects :param diff: existing diff list to append to :return: list of (key, value1, value2) tuples for each differing values ''' # Initilize diff list if diff is None: diff = [] # Check that the two dicts have the same structure if sorted(list(d1.keys())) != sorted(list(d2.keys())): raise ValueError('inconsistent inputs') # For each key - values triplet for k in d1.keys(): # If values are dicts themselves, loop recursively through them if isinstance(d1[k], dict): diff = differing(d1[k], d2[k], subdkey=subdkey, diff=diff) # If values are objects with a specific sub-dictionary attribute, # loop recursively through them elif hasattr(d1[k], subdkey): diff = differing(getattr(d1[k], subdkey), getattr(d2[k], subdkey), subdkey=subdkey, diff=diff) # Otherwise else: # If values differ, add the key - values triplet to the diff list if d1[k] != d2[k]: diff.append((k, d1[k], d2[k])) # Return the diff list return diff def extractCommonPrefix(labels): ''' Extract a common prefix and a list of suffixes from a list of labels. ''' prefix = os.path.commonprefix(labels) if len(prefix) == 0: return None return prefix, [s.split(prefix)[1] for s in labels] class TimeSeries(pd.DataFrame): ''' Wrapper around pandas DataFrame to store timeseries data. ''' time_key = 't' stim_key = 'stimstate' def __init__(self, t, stim, dout): super().__init__(data={ self.time_key: t, self.stim_key: stim, **dout }) @property def time(self): return self[self.time_key].values @property def tbounds(self): return self.time.min(), self.time.max() @property def stim(self): return self[self.stim_key].values @property def inputs(self): return [self.time_key, self.stim_key] @property def outputs(self): return list(set(self.columns.values) - set(self.inputs)) def interpCol(self, t, k, kind): ''' Interpolate a column according to a new time vector. ''' kind = 'nearest' if k == self.stim_key else 'linear' self[k] = interp1d(self.time, self[k].values, kind=kind)(t) def interp1d(self, t): ''' Interpolate the entire dataframe according to a new time vector. ''' for k in self.outputs: self.interpCol(t, k, 'linear') self.interpCol(t, self.stim_key, 'nearest') self[self.time_key] = t def resample(self, dt): ''' Resample dataframe at regular time step. ''' tmin, tmax = self.tbounds n = int((tmax - tmin) / dt) + 1 self.interp1d(np.linspace(tmin, tmax, n)) def prepend(self, t0=0): ''' Repeat first row outputs for a preceding time. ''' if t0 > self.time.min(): raise ValueError('t0 greater than minimal time value') self.loc[-1] = self.iloc[0] # repeat first row self.index = self.index + 1 # shift index self.sort_index(inplace=True) self[self.time_key][0] = t0 self[self.stim_key][0] = 0 def bound(self, tbounds): ''' Restrict all columns of dataframe to indexes corresponding to time values within specific bounds. ''' tmin, tmax = tbounds return self[np.logical_and(self.time >= tmin, self.time <= tmax)].reset_index(drop=True) def checkAgainst(self, other): assert isinstance(other, self.__class__), 'classes do not match' assert all(self.keys() == other.keys()), 'differing keys' for k in self.inputs: assert all(self[k].values == other[k].values), f'{k} vectors do not match' def operate(self, other, op): ''' Generic arithmetic operator. ''' self.checkAgainst(other) return self.__class__( self.time, self.stim, {k: getattr(self[k].values, op)(other[k].values) for k in self.outputs} ) def __add__(self, other): ''' Addition operator. ''' return self.operate(other, '__add__') def __sub__(self, other): ''' Subtraction operator. ''' return self.operate(other, '__sub__') def __mul__(self, other): ''' Multiplication operator. ''' return self.operate(other, '__mul__') - def __div__(self, other): + def __truediv__(self, other): ''' Division operator. ''' - return self.operate(other, '__div__') + return self.operate(other, '__truediv__')