Source code for

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Part of the PsychoPy library
# Copyright (C) 2002-2018 Jonathan Peirce (C) 2019-2022 Open Science Tools Ltd.
# Distributed under the terms of the GNU General Public License (GPL).

import os
import re
import ast
import pickle
import time, datetime
import numpy as np
import pandas as pd

from collections import OrderedDict
from pkg_resources import parse_version

from psychopy import logging, exceptions
from import pathToString
from psychopy.localization import _translate

    import openpyxl
    if parse_version(openpyxl.__version__) >= parse_version('2.4.0'):
        # openpyxl moved get_column_letter to utils.cell
        from openpyxl.utils.cell import get_column_letter
        from openpyxl.cell import get_column_letter
    from openpyxl.reader.excel import load_workbook
    haveOpenpyxl = True
except ImportError:
    haveOpenpyxl = False

haveXlrd = False

_nonalphanumeric_re = re.compile(r'\W')  # will match all bad var name chars

def checkValidFilePath(filepath, makeValid=True):
    """Checks whether file path location (e.g. is a valid folder)

    This should also check whether we have write-permissions to the folder
    but doesn't currently do that!

    added in: 1.90.00
    folder = os.path.split(os.path.abspath(filepath))[0]
    if not os.path.isdir(folder):
        os.makedirs(folder)  # spit an error if we fail
    return True

def isValidVariableName(name):
    """Checks whether a certain string could be used as a valid variable.

        OK, msg, translated = isValidVariableName(name)

    >>> isValidVariableName('name')
    (True, '', '')
    >>> isValidVariableName('0name')
    (False, 'Variables cannot begin with numeric character', 'Variabiles non possunt incipere numerorum mores')
    >>> isValidVariableName('first.second')
    (False, 'Variables cannot contain punctuation or spaces', 'Variabiles non habet interpunctionem vel spatia')
    >>> isValidVariableName('first second')
    (False, 'Variables cannot contain punctuation or spaces', 'Variabiles non habet interpunctionem vel spatia')
    >>> isValidVariableName('')
    (False, "Variables cannot be missing, None, or ''", "Variabiles deesse non possunt, nemo, vel ''")
    >>> isValidVariableName(None)
    (False, "Variables cannot be missing, None, or ''", "Variabiles deesse non possunt, nemo, vel ''")
    >>> isValidVariableName(23)
    (False, "Variables must be string-like", "Variabiles debent esse linea-similis")
    >>> isValidVariableName('a_b_c')
    (True, '', '')
    if not name:
        return (
            "Variables cannot be missing, None, or ''",
            _translate("Variables cannot be missing, None, or ''")
    if not isinstance(name, str):
        return (
            "Variables must be string-like",
            _translate("Variables must be string-like")
        name = str(name)  # convert from unicode if possible
    except Exception:
        if type(name) in [str, np.unicode_]:
            raise exceptions.ConditionsImportError(
                "name %s (type %s) contains non-ASCII characters (e.g. accents)" % (name, type(name)),
                translated=_translate("name %s (type %s) contains non-ASCII characters (e.g. accents)") % (name, type(name))
            raise exceptions.ConditionsImportError(
                "name %s (type %s) could not be converted to a string",
                translated=_translate("name %s (type %s) could not be converted to a string") % (name, type(name))

    if name[0].isdigit():
        return (
            "Variables cannot begin with numeric character",
            _translate("Variables cannot begin with numeric character")
        return (
            "Variables cannot contain punctuation or spaces",
            _translate("Variables cannot contain punctuation or spaces")
    return True, '', ''

def _getExcelCellName(col, row):
    """Returns the excel cell name for a row and column (zero-indexed)

    >>> _getExcelCellName(0,0)
    >>> _getExcelCellName(2,1)
    # BEWARE - openpyxl uses indexing at 1, to fit with Excel
    return "%s%i" % (get_column_letter(col + 1), row + 1)

def importTrialTypes(fileName, returnFieldNames=False):
    """importTrialTypes is DEPRECATED (as of v1.70.00)
    Please use `importConditions` for identical functionality.
    logging.warning("importTrialTypes is DEPRECATED (as of v1.70.00). "
                    "Please use `importConditions` for identical "
    return importConditions(fileName, returnFieldNames)

def sliceFromString(sliceString):
    """Convert a text string into a valid slice object
    which can be used as indices for a list or array.

    >>> sliceFromString("0:10")
    >>> sliceFromString("0::3")
    >>> sliceFromString("-8:")
    sliceArgs = []
    for val in sliceString.split(':'):
        if len(val) == 0:
            # nb int(round(float(x))) is needed for x='4.3'
    return slice(*sliceArgs)

def indicesFromString(indsString):
    """Convert a text string into a valid list of indices
    # "6"
        inds = int(round(float(indsString)))
        return [inds]
    except Exception:
    # "-6::2"
        inds = sliceFromString(indsString)
        return inds
    except Exception:
    # "1,4,8"
        inds = list(eval(indsString))
        return inds
    except Exception:

def listFromString(val, excludeEmpties=False):
    """Take a string that looks like a list (with commas and/or [] and make
    an actual python list"""
    # was previously called strToList and str2list might have been an option!
    # I'll leave those here for anyone doing a find-in-path for those
    if type(val) == tuple:
        return list(val)
    elif type(val) == list:
        return list(val)  # nothing to do
    elif type(val) != str:
        raise ValueError("listFromString requires a string as its input not {}"
    # try to evaluate with ast (works for "'yes,'no'" or "['yes', 'no']")
        iterable = ast.literal_eval(val)
        if type(iterable) == tuple:
            iterable = list(iterable)
        return iterable
    except (ValueError, SyntaxError):
        pass  # e.g. "yes, no" won't work. We'll go on and try another way

    val = val.strip()  # in case there are spaces
    if val.startswith(('[', '(')) and val.endswith((']', ')')):
        val = val[1:-1]
    asList = val.split(",")
    if excludeEmpties:
        asList = [this.strip() for this in asList if this]
        asList = [this.strip() for this in asList]
    return asList

[docs]def importConditions(fileName, returnFieldNames=False, selection=""): """Imports a list of conditions from an .xlsx, .csv, or .pkl file The output is suitable as an input to :class:`TrialHandler` `trialList` or to :class:`MultiStairHandler` as a `conditions` list. If `fileName` ends with: - .csv: import as a comma-separated-value file (header + row x col) - .xlsx: import as Excel 2007 (xlsx) files. No support for older (.xls) is planned. - .pkl: import from a pickle file as list of lists (header + row x col) The file should contain one row per type of trial needed and one column for each parameter that defines the trial type. The first row should give parameter names, which should: - be unique - begin with a letter (upper or lower case) - contain no spaces or other punctuation (underscores are permitted) `selection` is used to select a subset of condition indices to be used It can be a list/array of indices, a python `slice` object or a string to be parsed as either option. e.g.: - "1,2,4" or [1,2,4] or (1,2,4) are the same - "2:5" # 2, 3, 4 (doesn't include last whole value) - "-10:2:" # tenth from last to the last in steps of 2 - slice(-10, 2, None) # the same as above - random(5) * 8 # five random vals 0-7 """ def _attemptImport(fileName, sep=',', dec='.'): """Attempts to import file with specified settings and raises ConditionsImportError if fails due to invalid format :param filename: str :param sep: str indicating the separator for cells (',', ';' etc) :param dec: str indicating the decimal point ('.', '.') :return: trialList, fieldNames """ if fileName.endswith(('.csv', '.tsv')): trialsArr = pd.read_csv(fileName, encoding='utf-8-sig', sep=sep, decimal=dec) for col in trialsArr.columns: for row, cell in enumerate(trialsArr[col]): if isinstance(cell, str): tryVal = cell.replace(",", ".") try: trialsArr[col][row] = float(tryVal) except ValueError: pass logging.debug(u"Read csv file with pandas: {}".format(fileName)) elif fileName.endswith(('.xlsx', '.xlsm')): trialsArr = pd.read_excel(fileName, engine='openpyxl') logging.debug(u"Read Excel file with pandas: {}".format(fileName)) elif fileName.endswith('.xls'): trialsArr = pd.read_excel(fileName, engine='xlrd') logging.debug(u"Read Excel file with pandas: {}".format(fileName)) # then try to convert array to trialList and fieldnames unnamed = trialsArr.columns.to_series().str.contains('^Unnamed: ') trialsArr = trialsArr.loc[:, ~unnamed] # clear unnamed cols logging.debug(u"Clearing unnamed columns from {}".format(fileName)) trialList, fieldNames = pandasToDictList(trialsArr) return trialList, fieldNames def _assertValidVarNames(fieldNames, fileName): """screens a list of names as candidate variable names. if all names are OK, return silently; else raise with msg """ fileName = pathToString(fileName) if not all(fieldNames): raise exceptions.ConditionsImportError( "Conditions file %s: Missing parameter name(s); empty cell(s) in the first row?" % fileName, translated=_translate("Conditions file %s: Missing parameter name(s); empty cell(s) in the first row?") % fileName ) for name in fieldNames: OK, msg, translated = isValidVariableName(name) if not OK: # tailor message to importConditions msg = msg.replace('Variables', 'Parameters (column headers)') translated = msg.replace('Variables', 'Parameters (column headers)') raise exceptions.ConditionsImportError( 'Bad name: %s%s"%s"' % (name, os.linesep, msg), translated='Bad name: %s%s"%s"' % (name, os.linesep, translated) ) if fileName in ['None', 'none', None]: if returnFieldNames: return [], [] return [] if not os.path.isfile(fileName): raise exceptions.ConditionsImportError( "Conditions file not found: %s" % fileName, translated=_translate("Conditions file not found: %s") % fileName ) def pandasToDictList(dataframe): """Convert a pandas dataframe to a list of dicts. This helper function is used by csv or excel imports via pandas """ # convert the resulting dataframe to a numpy recarray trialsArr = dataframe.to_records(index=False) # Check for new line characters in strings, and replace escaped characters for record in trialsArr: for idx, element in enumerate(record): if isinstance(element, str): record[idx] = element.replace('\\n', '\n') if trialsArr.shape == (): # convert 0-D to 1-D with one element: trialsArr = trialsArr[np.newaxis] fieldNames = list(trialsArr.dtype.names) _assertValidVarNames(fieldNames, fileName) # convert the record array into a list of dicts trialList = [] for trialN, trialType in enumerate(trialsArr): thisTrial = OrderedDict() for fieldN, fieldName in enumerate(fieldNames): val = trialsArr[trialN][fieldN] if isinstance(val, str): if val.startswith('[') and val.endswith(']'): # val = eval('%s' %unicode(val.decode('utf8'))) val = eval(val) elif type(val) == np.string_: val = str(val.decode('utf-8-sig')) # if it looks like a list, convert it: if val.startswith('[') and val.endswith(']'): # val = eval('%s' %unicode(val.decode('utf8'))) val = eval(val) elif np.isnan(val): val = None thisTrial[fieldName] = val trialList.append(thisTrial) return trialList, fieldNames if (fileName.endswith(('.csv', '.tsv')) or (fileName.endswith(('.xlsx', '.xls', '.xlsm')) and haveXlrd)): if fileName.endswith(('.csv', '.tsv', '.dlm')): # delimited text file for sep, dec in [ (',', '.'), (';', ','), # most common in US, EU ('\t', '.'), ('\t', ','), (';', '.')]: try: trialList, fieldNames = _attemptImport(fileName=fileName, sep=sep, dec=dec) break # seems to have worked except exceptions.ConditionsImportError as e: continue # try a different format else: trialList, fieldNames = _attemptImport(fileName=fileName) elif fileName.endswith(('.xlsx','.xlsm')): # no xlsread so use openpyxl if not haveOpenpyxl: raise exceptions.ConditionsImportError( "openpyxl or xlrd is required for loading excel files, but neither was found.", _translate("openpyxl or xlrd is required for loading excel files, but neither was found.") ) # data_only was added in 1.8 if parse_version(openpyxl.__version__) < parse_version('1.8'): wb = load_workbook(filename=fileName) else: wb = load_workbook(filename=fileName, data_only=True) ws = wb.worksheets[0] logging.debug(u"Read excel file with openpyxl: {}".format(fileName)) try: # in new openpyxl (2.3.4+) get_highest_xx is deprecated nCols = ws.max_column nRows = ws.max_row except Exception: # version openpyxl 1.5.8 (in Standalone 1.80) needs this nCols = ws.get_highest_column() nRows = ws.get_highest_row() # get parameter names from the first row header fieldNames = [] rangeCols = [] for colN in range(nCols): if parse_version(openpyxl.__version__) < parse_version('2.0'): fieldName = ws.cell(_getExcelCellName(col=colN, row=0)).value else: # From 2.0, cells are referenced with 1-indexing: A1 == cell(row=1, column=1) fieldName = ws.cell(row=1, column=colN + 1).value if fieldName: # If column is named, add its name to fieldNames fieldNames.append(fieldName) rangeCols.append(colN) _assertValidVarNames(fieldNames, fileName) # loop trialTypes trialList = [] for rowN in range(1, nRows): # skip header first row thisTrial = {} for rangeColsIndex, colN in enumerate(rangeCols): if parse_version(openpyxl.__version__) < parse_version('2.0'): val = ws.cell(_getExcelCellName(col=colN, row=0)).value else: # From 2.0, cells are referenced with 1-indexing: A1 == cell(row=1, column=1) val = ws.cell(row=rowN + 1, column=colN + 1).value # if it looks like a list or tuple, convert it if (isinstance(val, str) and (val.startswith('[') and val.endswith(']') or val.startswith('(') and val.endswith(')'))): val = eval(val) # if it has any line breaks correct them if isinstance(val, str): val = val.replace('\\n', '\n') # Convert from eu style decimals: replace , with . and try to make it a float if isinstance(val, str): tryVal = val.replace(",", ".") try: val = float(tryVal) except ValueError: pass fieldName = fieldNames[rangeColsIndex] thisTrial[fieldName] = val trialList.append(thisTrial) elif fileName.endswith('.pkl'): f = open(fileName, 'rb') # Converting newline characters. # 'b' is necessary in Python3 because byte object is # returned when file is opened in binary mode. buffer ='\r\n',b'\n').replace(b'\r',b'\n') try: trialsArr = pickle.loads(buffer) except Exception: raise exceptions.ConditionsImportError( 'Could not open %s as conditions' % fileName, translated=_translate('Could not open %s as conditions') % fileName ) f.close() trialList = [] # In Python3, strings returned by pickle() are unhashable so we have to # convert them to str. trialsArr = [[str(item) if isinstance(item, str) else item for item in row] for row in trialsArr] fieldNames = trialsArr[0] # header line first _assertValidVarNames(fieldNames, fileName) for row in trialsArr[1:]: thisTrial = {} for fieldN, fieldName in enumerate(fieldNames): # type is correct, being .pkl thisTrial[fieldName] = row[fieldN] trialList.append(thisTrial) else: raise exceptions.ConditionsImportError( 'Your conditions file should be an xlsx, csv, dlm, tsv or pkl file', translated=_translate('Your conditions file should be an xlsx, csv, dlm, tsv or pkl file') ) # if we have a selection then try to parse it if isinstance(selection, str) and len(selection) > 0: selection = indicesFromString(selection) if not isinstance(selection, slice): for n in selection: try: assert n == int(n) except AssertionError: raise exceptions.ConditionsImportError( "importConditions() was given some `indices` but could not parse them", translated=_translate("importConditions() was given some `indices` but could not parse them") ) # the selection might now be a slice or a series of indices if isinstance(selection, slice): trialList = trialList[selection] elif len(selection) > 0: allConds = trialList trialList = [] print(selection) print(len(allConds)) for ii in selection: trialList.append(allConds[int(ii)]) logging.exp('Imported %s as conditions, %d conditions, %d params' % (fileName, len(trialList), len(fieldNames))) if returnFieldNames: return (trialList, fieldNames) else: return trialList
def createFactorialTrialList(factors): """Create a trialList by entering a list of factors with names (keys) and levels (values) it will return a trialList in which all factors have been factorially combined (so for example if there are two factors with 3 and 5 levels the trialList will be a list of 3*5 = 15, each specifying the values for a given trial Usage:: trialList = createFactorialTrialList(factors) :Parameters: factors : a dictionary with names (keys) and levels (values) of the factors Example:: factors={"text": ["red", "green", "blue"], "letterColor": ["red", "green"], "size": [0, 1]} mytrials = createFactorialTrialList(factors) """ # the first step is to place all the factorial combinations in a list of # lists tempListOfLists = [[]] for key in factors: # this takes the levels of each factor as a set of values # (a list) at a time alist = factors[key] tempList = [] for value in alist: # now we loop over the values in a given list, # and add each value of the other lists for iterList in tempListOfLists: tempList.append(iterList + [key, value]) tempListOfLists = tempList # this second step is so we can return a list in the format of trialList trialList = [] for atrial in tempListOfLists: keys = atrial[0::2] # the even elements are keys values = atrial[1::2] # the odd elements are values atrialDict = {} for i in range(len(keys)): # this combines the key with the value atrialDict[keys[i]] = values[i] # append one trial at a time to the final trialList trialList.append(atrialDict) return trialList
[docs]def bootStraps(dat, n=1): """Create a list of n bootstrapped resamples of the data SLOW IMPLEMENTATION (Python for-loop) Usage: ``out = bootStraps(dat, n=1)`` Where: dat an NxM or 1xN array (each row is a different condition, each column is a different trial) n number of bootstrapped resamples to create out - dim[0]=conditions - dim[1]=trials - dim[2]=resamples """ dat = np.asarray(dat) if len(dat.shape) == 1: # have presumably been given a series of data for one stimulus # adds a dimension (arraynow has shape (1,Ntrials)) dat = np.array([dat]) nTrials = dat.shape[1] # initialise a matrix to store output resamples = np.zeros(dat.shape + (n,), dat.dtype) rand = np.random.rand for stimulusN in range(dat.shape[0]): thisStim = dat[stimulusN, :] # fetch data for this stimulus for sampleN in range(n): indices = np.floor(nTrials * rand(nTrials)).astype('i') resamples[stimulusN, :, sampleN] = np.take(thisStim, indices) return resamples
[docs]def functionFromStaircase(intensities, responses, bins=10): """Create a psychometric function by binning data from a staircase procedure. Although the default is 10 bins Jon now always uses 'unique' bins (fewer bins looks pretty but leads to errors in slope estimation) usage:: intensity, meanCorrect, n = functionFromStaircase(intensities, responses, bins) where: intensities are a list (or array) of intensities to be binned responses are a list of 0,1 each corresponding to the equivalent intensity value bins can be an integer (giving that number of bins) or 'unique' (each bin is made from aa data for exactly one intensity value) intensity a numpy array of intensity values (where each is the center of an intensity bin) meanCorrect a numpy array of mean % correct in each bin n a numpy array of number of responses contributing to each mean """ # convert to arrays try: # concatenate if multidimensional intensities = np.concatenate(intensities) responses = np.concatenate(responses) except Exception: intensities = np.array(intensities) responses = np.array(responses) # sort the responses sort_ii = np.argsort(intensities) sortedInten = np.take(intensities, sort_ii) sortedResp = np.take(responses, sort_ii) binnedResp = [] binnedInten = [] nPoints = [] if bins == 'unique': intensities = np.round(intensities, decimals=8) uniqueIntens = np.unique(intensities) for thisInten in uniqueIntens: theseResps = responses[intensities == thisInten] binnedInten.append(thisInten) binnedResp.append(np.mean(theseResps)) nPoints.append(len(theseResps)) else: pointsPerBin = len(intensities)/bins for binN in range(bins): start = int(round(binN * pointsPerBin)) stop = int(round((binN + 1) * pointsPerBin)) thisResp = sortedResp[start:stop] thisInten = sortedInten[start:stop] binnedResp.append(np.mean(thisResp)) binnedInten.append(np.mean(thisInten)) nPoints.append(len(thisInten)) return binnedInten, binnedResp, nPoints
def getDateStr(format="%Y-%m-%d_%Hh%M.%S.%f", fractionalSecondDigits=3): """Uses ````_ to generate a string based on ISO 8601 but made safe for filename use:: "2022-01-14_18h35.05.386" represents 14th Jan 2022 at 6:35pm with 5 sec and 386 ms This is often useful appended to data filenames to provide unique names. Parameters ---------- format : str See the documentation for `datetime.datetime.strftime` for more information on format syntax: default="%Y-%m-%d_%Hh%M.%S.%f" fractionalSecondDigits : int An integer value 1-6 indicating the number of digits of fractional seconds to include if the `%f` parameter is included in the format. This would normally give 6 digits (microseconds) but to get just milliseconds you can set fractionalSecondDigits=3 """ now = microsecs = now.strftime("%f") nowStr = now.strftime(format) if "%f" in format and ( fractionalSecondDigits < 1 or int(fractionalSecondDigits) != fractionalSecondDigits ): raise TypeError("fractionalSecondDigits argument to getDateStr should " f"be an integer greater than 1, not {fractionalSecondDigits}") elif "%f" in format and fractionalSecondDigits > len(microsecs): logging.warning("fractionalSecondDigits argument to getDateStr requested " f"{fractionalSecondDigits} digits but only {len(microsecs)} " f"are available. Truncating to {len(microsecs)}.") elif "%f" in format: nowStr = nowStr.replace( microsecs, microsecs[:int(fractionalSecondDigits)], ) return nowStr

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