Source code for hpvsim.misc

Miscellaneous functions that do not belong anywhere else

import re
import inspect
import warnings
import numpy as np
import pandas as pd
import pylab as pl
import sciris as sc
import collections as co
from pathlib import Path
from distutils.version import LooseVersion # TODO: deprecated, remove
from . import version as hpv
from . import data as hpdata
from .settings import options as hpo

#%% Convenience imports from Sciris

__all__ = ['date', 'day', 'daydiff', 'date_range']

date       =
day        =
daydiff    = sc.daydiff
date_range = sc.daterange

#%% Loading/saving functions

__all__ += ['load_data', 'load', 'save', 'savefig']

[docs] def load_data(datafile, check_date=False, header='infer', calculate=True, **kwargs): ''' Load data for comparing to the model output, either from file or from a dataframe. Data is expected to be in wide format, with each row representing a year and columns for each variable by genotype/age/sex. Args: datafile (str/df): if a string, the name of the file to load (either Excel or CSV); if a dataframe, use directly start_year (int): first year with data available kwargs (dict): passed to pd.read_excel() Returns: data (dataframe): pandas dataframe of the loaded data ''' # Load data if isinstance(datafile, Path): # Convert to a string datafile = str(datafile) if isinstance(datafile, str): df_lower = datafile.lower() full_df = sc.makefilepath(datafile) if df_lower.endswith('csv'): data = pd.read_csv(full_df, header=header, **kwargs) elif df_lower.endswith('xlsx') or df_lower.endswith('xls'): data = pd.read_excel(full_df, **kwargs) else: errormsg = f'Currently loading is only supported from .csv, .xls, and .xlsx files, not "{datafile}"' raise NotImplementedError(errormsg) elif isinstance(datafile, pd.DataFrame): data = datafile else: # pragma: no cover errormsg = f'Could not interpret data {type(datafile)}: must be a string or a dataframe' raise TypeError(errormsg) # Set the index to be the years if check_date: if 'year' not in data.columns: errormsg = f'Required column "year" not found; columns are {data.columns}' raise ValueError(errormsg) data.set_index('year', inplace=True, drop=False) return data
[docs] def load(*args, update=True, verbose=True, **kwargs): ''' Convenience method for sc.loadobj() and equivalent to hpv.Sim.load() or hpv.Scenarios.load(). Args: filename (str): file to load do_migrate (bool): whether to migrate if loading an old object update (bool): whether to modify the object to reflect the new version verbose (bool): whether to print migration information args (list): passed to sc.loadobj() kwargs (dict): passed to sc.loadobj() Returns: Loaded object **Examples**:: sim = hpv.load('calib.sim') # Equivalent to hpv.Sim.load('calib.sim') scens = hpv.load(filename='school-closures.scens', folder='schools') ''' obj = sc.loadobj(*args, **kwargs) if hasattr(obj, 'version'): v_curr = hpv.__version__ v_obj = obj.version cmp = check_version(v_obj, verbose=False) if cmp != 0: print(f'Note: you have HPVsim v{v_curr}, but are loading an object from v{v_obj}') return obj
[docs] def save(*args, **kwargs): ''' Convenience method for sc.saveobj() and equivalent to or Args: filename (str): file to save to obj (object): object to save args (list): passed to sc.saveobj() kwargs (dict): passed to sc.saveobj() Returns: Filename the object is saved to **Examples**::'calib.sim', sim) # Equivalent to'calib.sim')'school-closures.scens', folder='schools', obj=scens) ''' filepath = sc.saveobj(*args, **kwargs) return filepath
[docs] def savefig(filename=None, comments=None, fig=None, **kwargs): ''' Wrapper for Matplotlib's ``pl.savefig()`` function which automatically stores HPVsim metadata in the figure. By default, saves (git) information from both the HPVsim version and the calling function. Additional comments can be added to the saved file as well. These can be retrieved via ``hpv.get_png_metadata()`` (or :py:func:`sciris.sc_plotting.loadmetadata`). Metadata can also be stored for PDF, but cannot be automatically retrieved. Args: filename (str/list): name of the file to save to (default, timestamp); can also be a list of names comments (str/dict): additional metadata to save to the figure fig (fig/list): figure to save (by default, current one); can also be a list of figures kwargs (dict): passed to ``fig.savefig()`` **Example**:: hpv.Sim().run().plot() hpv.savefig() ''' # Handle inputs dpi = kwargs.pop('dpi', 150) metadata = kwargs.pop('metadata', {}) if fig is None: fig = pl.gcf() figlist = sc.tolist(fig) if filename is None: # pragma: no cover now = sc.getdate(dateformat='%Y-%b-%d_%H.%M.%S') filename = f'hpvsim_{now}.png' filenamelist = sc.tolist(filename) if len(figlist) != len(filenamelist): errormsg = f'You have supplied {len(figlist)} figures and {len(filenamelist)} filenames: these must be the same length' raise ValueError(errormsg) metadata = {} metadata['hpvsim version'] = hpv.__version__ gitinfo = git_info() for key,value in gitinfo['hpvsim'].items(): metadata[f'HPVsim {key}'] = value for key,value in gitinfo['called_by'].items(): metadata[f'HPVsim caller {key}'] = value metadata['HPVsim current time'] = sc.getdate() metadata['HPVsim calling file'] = sc.getcaller() if comments: metadata['HPVsim comments'] = comments # Loop over the figures (usually just one) for thisfig, thisfilename in zip(figlist, filenamelist): # Handle different formats lcfn = thisfilename.lower() # Lowercase filename if lcfn.endswith('pdf') or lcfn.endswith('svg'): metadata = {'Keywords':str(metadata)} # PDF and SVG doesn't support storing a dict # Save the figure thisfig.savefig(thisfilename, dpi=dpi, metadata=metadata, **kwargs) return filename
#%% Versioning functions __all__ += ['git_info', 'check_version', 'check_save_version', 'get_version_pars', 'get_png_metadata']
[docs] def git_info(filename=None, check=False, comments=None, old_info=None, die=False, indent=2, verbose=True, frame=2, **kwargs): ''' Get current git information and optionally write it to disk. Simplest usage is hpv.git_info(__file__) Args: filename (str): name of the file to write to or read from check (bool): whether or not to compare two git versions comments (dict): additional comments to include in the file old_info (dict): dictionary of information to check against die (bool): whether or not to raise an exception if the check fails indent (int): how many indents to use when writing the file to disk verbose (bool): detail to print frame (int): how many frames back to look for caller info kwargs (dict): passed to sc.loadjson() (if check=True) or sc.savejson() (if check=False) **Examples**:: hpv.git_info() # Return information hpv.git_info(__file__) # Writes to disk hpv.git_info('hpvsim_version.gitinfo') # Writes to disk hpv.git_info('hpvsim_version.gitinfo', check=True) # Checks that current version matches saved file ''' # Handle the case where __file__ is supplied as the argument if isinstance(filename, str) and filename.endswith('.py'): filename = filename.replace('.py', '.gitinfo') # Get git info calling_file = sc.makefilepath(sc.getcaller(frame=frame, tostring=False)['filename']) hpv_info = {'version':hpv.__version__} hpv_info.update(sc.gitinfo(__file__, verbose=False)) caller_info = sc.gitinfo(calling_file, verbose=False) caller_info['filename'] = calling_file info = {'hpvsim':hpv_info, 'called_by':caller_info} if comments: info['comments'] = comments # Just get information and optionally write to disk if not check: if filename is not None: output = sc.savejson(filename, info, indent=indent, **kwargs) else: output = info return output # Check if versions match, and optionally raise an error else: if filename is not None: old_info = sc.loadjson(filename, **kwargs) string = '' old_hpv_info = old_info['hpvsim'] if 'hpvsim' in old_info else old_info if hpv_info != old_hpv_info: # pragma: no cover string = f'Git information differs: {hpv_info} vs. {old_hpv_info}' if die: raise ValueError(string) elif verbose: print(string) return
[docs] def check_version(expected, die=False, verbose=True): ''' Get current git information and optionally write it to disk. The expected version string may optionally start with '>=' or '<=' (== is implied otherwise), but other operators (e.g. ~=) are not supported. Note that e.g. '>' is interpreted to mean '>='. Args: expected (str): expected version information die (bool): whether or not to raise an exception if the check fails **Example**:: hpv.check_version('>=1.7.0', die=True) # Will raise an exception if an older version is used ''' if expected.startswith('>'): valid = 1 elif expected.startswith('<'): valid = -1 else: valid = 0 # Assume == is the only valid comparison expected = expected.lstrip('<=>') # Remove comparator information version = hpv.__version__ compare = sc.compareversions(version, expected) # Returns -1, 0, or 1 relation = ['older', '', 'newer'][compare+1] # Picks the right string if relation: # Versions mismatch, print warning or raise error string = f'Note: HPVsim is {relation} than expected ({version} vs. {expected})' if die and compare != valid: raise ValueError(string) elif verbose: print(string) return compare
[docs] def check_save_version(expected=None, filename=None, die=False, verbose=True, **kwargs): ''' A convenience function that bundles check_version with git_info and saves automatically to disk from the calling file. The idea is to put this at the top of an analysis script, and commit the resulting file, to keep track of which version of HPVsim was used. Args: expected (str): expected version information filename (str): file to save to; if None, guess based on current file name kwargs (dict): passed to git_info(), and thence to sc.savejson() **Examples**:: hpv.check_save_version() hpv.check_save_version('1.3.2', filename='script.gitinfo', comments='This is the main analysis script') hpv.check_save_version('1.7.2', folder='gitinfo', comments={'SynthPops':sc.gitinfo(sp.__file__)}) ''' # First, check the version if supplied if expected: check_version(expected, die=die, verbose=verbose) # Now, check and save the git info if filename is None: filename = sc.getcaller(tostring=False)['filename'] git_info(filename=filename, frame=3, **kwargs) return
[docs] def get_version_pars(version, verbose=True): ''' Function for loading parameters from the specified version. Parameters will be loaded for HPVsim 'as at' the requested version i.e. the most recent set of parameters that is <= the requested version. Available parameter values are stored in the regression folder. If parameters are available for versions 1.3, and 1.4, then this function will return the following - If parameters for version '1.3' are requested, parameters will be returned from '1.3' - If parameters for version '1.3.5' are requested, parameters will be returned from '1.3', since HPVsim at version 1.3.5 would have been using the parameters defined at version 1.3. - If parameters for version '1.4' are requested, parameters will be returned from '1.4' Args: version (str): the version to load parameters from Returns: Dictionary of parameters from that version ''' # Construct a sorted list of available parameters based on the files in the regression folder regression_folder = sc.thisdir(__file__, 'regression', aspath=True) available_versions = [x.stem.replace('pars_v','') for x in regression_folder.iterdir() if x.suffix=='.json'] available_versions = sorted(available_versions, key=LooseVersion) # Find the highest parameter version that is <= the requested version version_comparison = [sc.compareversions(version, v)>=0 for v in available_versions] try: target_version = available_versions[sc.findlast(version_comparison)] except IndexError: errormsg = f"Could not find a parameter version that was less than or equal to '{version}'. Available versions are {available_versions}" raise ValueError(errormsg) # Load the parameters pars = sc.loadjson(filename=regression_folder/f'pars_v{target_version}.json', folder=regression_folder) if verbose: print(f'Loaded parameters from {target_version}') return pars
[docs] def get_png_metadata(filename, output=False): ''' Read metadata from a PNG file. For use with images saved with hpv.savefig(). Requires pillow, an optional dependency. Metadata retrieval for PDF and SVG is not currently supported. Args: filename (str): the name of the file to load the data from **Example**:: hpv.Sim().run(do_plot=True) hpv.savefig('hpvsim.png') hpv.get_png_metadata('hpvsim.png') ''' try: import PIL except ImportError as E: # pragma: no cover errormsg = f'Pillow import failed ({str(E)}), please install first (pip install pillow)' raise ImportError(errormsg) from E im = metadata = {} for key,value in if key.startswith('HPVsim'): metadata[key] = value if not output: print(f'{key}: {value}') if output: return metadata else: return
#%% Simulation/statistics functions __all__ += ['get_doubling_time', 'compute_gof']
[docs] def get_doubling_time(sim, series=None, interval=None, start_day=None, end_day=None, moving_window=None, exp_approx=False, max_doubling_time=100, eps=1e-3, verbose=None): ''' Alternate method to calculate doubling time (one is already implemented in the sim object). **Examples**:: hpv.get_doubling_time(sim, interval=[3,30]) # returns the doubling time over the given interval (single float) hpv.get_doubling_time(sim, interval=[3,30], moving_window=3) # returns doubling times calculated over moving windows (array) ''' # Set verbose level if verbose is None: verbose = sim['verbose'] # Validate inputs: series if series is None or isinstance(series, str): if not sim.results_ready: # pragma: no cover raise Exception("Results not ready, cannot calculate doubling time") else: if series is None or series not in sim.result_keys(): sc.printv("Series not supplied or not found in results; defaulting to use cumulative exposures", 1, verbose) series='cum_infections' series = sim.results[series].values else: series = sc.promotetoarray(series) # Validate inputs: interval if interval is not None: if len(interval) != 2: # pragma: no cover sc.printv(f"Interval should be a list/array/tuple of length 2, not {len(interval)}. Resetting to length of series.", 1, verbose) interval = [0,len(series)] start_day, end_day = interval[0], interval[1] if len(series) < end_day: sc.printv(f"End day {end_day} is after the series ends ({len(series)}). Resetting to length of series.", 1, verbose) end_day = len(series) int_length = end_day - start_day # Deal with moving window if moving_window is not None: if not sc.isnumber(moving_window): # pragma: no cover sc.printv("Moving window should be an integer; ignoring and calculating single result", 1, verbose) doubling_time = get_doubling_time(sim, series=series, start_day=start_day, end_day=end_day, moving_window=None, exp_approx=exp_approx) else: if not isinstance(moving_window,int): # pragma: no cover sc.printv(f"Moving window should be an integer; recasting {moving_window} the nearest integer... ", 1, verbose) moving_window = int(moving_window) if moving_window < 2: sc.printv(f"Moving window should be greater than 1; recasting {moving_window} to 2", 1, verbose) moving_window = 2 doubling_time = [] for w in range(int_length-moving_window+1): this_start = start_day + w this_end = this_start + moving_window this_doubling_time = get_doubling_time(sim, series=series, start_day=this_start, end_day=this_end, exp_approx=exp_approx) doubling_time.append(this_doubling_time) # Do calculations else: if not exp_approx: try: import statsmodels.api as sm except ModuleNotFoundError as E: # pragma: no cover errormsg = f'Could not import statsmodels ({E}), falling back to exponential approximation' print(errormsg) exp_approx = True if exp_approx: if series[start_day] > 0: r = series[end_day] / series[start_day] if r > 1: doubling_time = int_length * np.log(2) / np.log(r) doubling_time = min(doubling_time, max_doubling_time) # Otherwise, it's unbounded else: # pragma: no cover raise ValueError("Can't calculate doubling time with exponential approximation when initial value is zero.") else: if np.any(series[start_day:end_day]): # Deal with zero values if possible nonzero = np.nonzero(series[start_day:end_day])[0] if len(nonzero) >= 2: exog = sm.add_constant(np.arange(len(nonzero))) endog = np.log2((series[start_day:end_day])[nonzero]) model = sm.OLS(endog, exog) doubling_rate =[1] if doubling_rate > eps: doubling_time = 1.0 / doubling_rate else: doubling_time = max_doubling_time else: # pragma: no cover raise ValueError(f"Can't calculate doubling time for series {series[start_day:end_day]}. Check whether series is growing.") else: # pragma: no cover raise ValueError(f"Can't calculate doubling time for series {series[start_day:end_day]}. Check whether series is growing.") return doubling_time
[docs] def compute_gof(actual, predicted, normalize=True, use_frac=False, use_squared=False, as_scalar='none', eps=1e-9, skestimator=None, estimator=None, **kwargs): ''' Calculate the goodness of fit. By default use normalized absolute error, but highly customizable. For example, mean squared error is equivalent to setting normalize=False, use_squared=True, as_scalar='mean'. Args: actual (arr): array of actual (data) points predicted (arr): corresponding array of predicted (model) points normalize (bool): whether to divide the values by the largest value in either series use_frac (bool): convert to fractional mismatches rather than absolute use_squared (bool): square the mismatches as_scalar (str): return as a scalar instead of a time series: choices are sum, mean, median eps (float): to avoid divide-by-zero skestimator (str): if provided, use this scikit-learn estimator instead estimator (func): if provided, use this custom estimator instead kwargs (dict): passed to the scikit-learn or custom estimator Returns: gofs (arr): array of goodness-of-fit values, or a single value if as_scalar is True **Examples**:: x1 = np.cumsum(np.random.random(100)) x2 = np.cumsum(np.random.random(100)) e1 = compute_gof(x1, x2) # Default, normalized absolute error e2 = compute_gof(x1, x2, normalize=False, use_frac=False) # Fractional error e3 = compute_gof(x1, x2, normalize=False, use_squared=True, as_scalar='mean') # Mean squared error e4 = compute_gof(x1, x2, skestimator='mean_squared_error') # Scikit-learn's MSE method e5 = compute_gof(x1, x2, as_scalar='median') # Normalized median absolute error -- highly robust ''' # Handle inputs actual = np.array(sc.dcp(actual), dtype=float) predicted = np.array(sc.dcp(predicted), dtype=float) # Scikit-learn estimator is supplied: use that if skestimator is not None: # pragma: no cover try: import sklearn.metrics as sm sklearn_gof = getattr(sm, skestimator) # Shortcut to e.g. sklearn.metrics.max_error except ImportError as E: raise ImportError(f'You must have scikit-learn >=0.22.2 installed: {str(E)}') except AttributeError: raise AttributeError(f'Estimator {skestimator} is not available; see for options') gof = sklearn_gof(actual, predicted, **kwargs) return gof # Custom estimator is supplied: use that if estimator is not None: try: gof = estimator(actual, predicted, **kwargs) except Exception as E: errormsg = f'Custom estimator "{estimator}" must be a callable function that accepts actual and predicted arrays, plus optional kwargs' raise RuntimeError(errormsg) from E return gof # Default case: calculate it manually else: # Key step -- calculate the mismatch! gofs = abs(np.array(actual) - np.array(predicted)) if normalize and not use_frac: actual_max = abs(actual).max() if actual_max>0: gofs /= actual_max if use_frac: if (actual<0).any() or (predicted<0).any(): print('Warning: Calculating fractional errors for non-positive quantities is ill-advised!') else: maxvals = np.maximum(actual, predicted) + eps gofs /= maxvals if use_squared: gofs = gofs**2 if as_scalar == 'sum': gofs = np.sum(gofs) elif as_scalar == 'mean': gofs = np.mean(gofs) elif as_scalar == 'median': gofs = np.median(gofs) return gofs
#%% Help and warnings __all__ += ['help']
[docs] def help(pattern=None, source=False, ignorecase=True, flags=None, context=False, output=False): ''' Get help on HPVsim in general, or search for a word/expression. Args: pattern (str): the word, phrase, or regex to search for source (bool): whether to search source code instead of docstrings for matches ignorecase (bool): whether to ignore case (equivalent to ``flags=re.I``) flags (list): additional flags to pass to ``re.findall()`` context (bool): whether to show the line(s) of matches output (bool): whether to return the dictionary of matches **Examples**::'vaccine')'contact', ignorecase=False, context=True)'lognormal', source=True, context=True) | New in version 3.1.2. ''' defaultmsg = ''' For general help using HPVsim, the best place to start is the docs: To search for a keyword/phrase/regex in HPVsim's docstrings, use e.g.: >>>'vaccine') See help( for more information. For help on HPVsim options, see ''' # No pattern is provided, print out default help message if pattern is None: print(defaultmsg) else: import hpvsim as hpv # Here to avoid circular import # Handle inputs flags = sc.promotetolist(flags) if ignorecase: flags.append(re.I) def func_ok(fucname, func): ''' Skip certain functions ''' excludes = [ fucname.startswith('_'), fucname in ['help', 'options', 'default_float', 'default_int'], inspect.ismodule(func), ] ok = not(any(excludes)) return ok # Get available functions/classes funcs = [funcname for funcname in dir(hpv) if func_ok(funcname, getattr(hpv, funcname))] # Skip dunder methods and modules # Get docstrings or full source code docstrings = dict() for funcname in funcs: f = getattr(hpv, funcname) if source: string = inspect.getsource(f) else: string = f.__doc__ docstrings[funcname] = string # Find matches matches = co.defaultdict(list) linenos = co.defaultdict(list) for k,docstring in docstrings.items(): for l,line in enumerate(docstring.splitlines()): if re.findall(pattern, line, *flags): linenos[k].append(str(l)) matches[k].append(line) # Assemble output if not len(matches): string = f'No matches for "{pattern}" found among {len(docstrings)} available functions.' else: string = f'Found {len(matches)} matches for "{pattern}" among {len(docstrings)} available functions:\n' maxkeylen = 0 for k in matches.keys(): maxkeylen = max(len(k), maxkeylen) for k,match in matches.items(): if not context: keystr = f' {k:>{maxkeylen}s}' else: keystr = k matchstr = f'{keystr}: {len(match):>2d} matches' if context: matchstr = sc.heading(matchstr, output=True) else: matchstr += '\n' string += matchstr if context: lineno = linenos[k] maxlnolen = max([len(l) for l in lineno]) for l,m in zip(lineno, match): string += sc.colorize(string=f' {l:>{maxlnolen}s}: ', fg='cyan', output=True) string += f'{m}\n' string += '—'*60 + '\n' # Print result and return print(string) if output: return string else: return
def warn(msg, category=None, verbose=None, die=None): ''' Helper function to handle warnings -- not for the user ''' # Handle inputs warnopt = hpo.warnings if not die else 'error' if category is None: category = RuntimeWarning if verbose is None: verbose = hpo.verbose # Handle the different options if warnopt in ['error', 'errors']: # Include alias since hard to remember raise category(msg) elif warnopt == 'warn': msg = '\n' + msg warnings.warn(msg, category=category, stacklevel=2) elif warnopt == 'print': if verbose: msg = 'Warning: ' + msg print(msg) elif warnopt == 'ignore': pass else: options = ['error', 'warn', 'print', 'ignore'] errormsg = f'Could not understand "{warnopt}": should be one of {options}' raise ValueError(errormsg) return