Source code for psychopy.data.experiment

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

from __future__ import absolute_import, print_function

# from future import standard_library
# standard_library.install_aliases()
from builtins import str
import sys
import copy
import pickle
import atexit

from psychopy import logging
from psychopy.tools.filetools import (openOutputFile, genDelimiter,
                                      genFilenameFromDelimiter)
from .utils import checkValidFilePath
from .base import _ComparisonMixin


[docs]class ExperimentHandler(_ComparisonMixin): """A container class for keeping track of multiple loops/handlers Useful for generating a single data file from an experiment with many different loops (e.g. interleaved staircases or loops within loops :usage: exp = data.ExperimentHandler(name="Face Preference",version='0.1.0') """ def __init__(self, name='', version='', extraInfo=None, runtimeInfo=None, originPath=None, savePickle=True, saveWideText=True, dataFileName='', autoLog=True, appendFiles=False): """ :parameters: name : a string or unicode As a useful identifier later version : usually a string (e.g. '1.1.0') To keep track of which version of the experiment was run extraInfo : a dictionary Containing useful information about this run (e.g. {'participant':'jwp','gender':'m','orientation':90} ) runtimeInfo : :class:`psychopy.info.RunTimeInfo` Containining information about the system as detected at runtime originPath : string or unicode The path and filename of the originating script/experiment If not provided this will be determined as the path of the calling script. dataFileName : string This is defined in advance and the file will be saved at any point that the handler is removed or discarded (unless .abort() had been called in advance). The handler will attempt to populate the file even in the event of a (not too serious) crash! savePickle : True (default) or False saveWideText : True (default) or False autoLog : True (default) or False """ self.loops = [] self.loopsUnfinished = [] self.name = name self.version = version self.runtimeInfo = runtimeInfo if extraInfo is None: self.extraInfo = {} else: self.extraInfo = extraInfo self.originPath = originPath self.savePickle = savePickle self.saveWideText = saveWideText self.dataFileName = dataFileName self.thisEntry = {} self.entries = [] # chronological list of entries self._paramNamesSoFar = [] self.dataNames = [] # names of all the data (eg. resp.keys) self.autoLog = autoLog self.appendFiles = appendFiles if dataFileName in ['', None]: logging.warning('ExperimentHandler created with no dataFileName' ' parameter. No data will be saved in the event ' 'of a crash') else: # fail now if we fail at all! checkValidFilePath(dataFileName, makeValid=True) atexit.register(self.close) def __del__(self): self.close()
[docs] def addLoop(self, loopHandler): """Add a loop such as a :class:`~psychopy.data.TrialHandler` or :class:`~psychopy.data.StairHandler` Data from this loop will be included in the resulting data files. """ self.loops.append(loopHandler) self.loopsUnfinished.append(loopHandler) # keep the loop updated that is now owned loopHandler.setExp(self)
[docs] def loopEnded(self, loopHandler): """Informs the experiment handler that the loop is finished and not to include its values in further entries of the experiment. This method is called by the loop itself if it ends its iterations, so is not typically needed by the user. """ if loopHandler in self.loopsUnfinished: self.loopsUnfinished.remove(loopHandler)
[docs] def _getAllParamNames(self): """Returns the attribute names of loop parameters (trialN etc) that the current set of loops contain, ready to build a wide-format data file. """ names = copy.deepcopy(self._paramNamesSoFar) # get names (or identifiers) for all contained loops for thisLoop in self.loops: theseNames, vals = self._getLoopInfo(thisLoop) for name in theseNames: if name not in names: names.append(name) return names
[docs] def _getExtraInfo(self): """Get the names and vals from the extraInfo dict (if it exists) """ if type(self.extraInfo) != dict: names = [] vals = [] else: names = list(self.extraInfo) vals = list(self.extraInfo.values()) return names, vals
[docs] def _getLoopInfo(self, loop): """Returns the attribute names and values for the current trial of a particular loop. Does not return data inputs from the subject, only info relating to the trial execution. """ names = [] vals = [] name = loop.name # standard attributes for attr in ('thisRepN', 'thisTrialN', 'thisN', 'thisIndex', 'stepSizeCurrent'): if hasattr(loop, attr): attrName = name + '.' + attr.replace('Current', '') # append the attribute name and the current value names.append(attrName) vals.append(getattr(loop, attr)) # method of constants if hasattr(loop, 'thisTrial'): trial = loop.thisTrial if hasattr(trial, 'items'): # is a TrialList object or a simple dict for attr, val in list(trial.items()): if attr not in self._paramNamesSoFar: self._paramNamesSoFar.append(attr) names.append(attr) vals.append(val) # single StairHandler elif hasattr(loop, 'intensities'): names.append(name + '.intensity') if len(loop.intensities) > 0: vals.append(loop.intensities[-1]) else: vals.append(None) return names, vals
[docs] def addData(self, name, value): """Add the data with a given name to the current experiment. Typically the user does not need to use this function; if you added your data to the loop and had already added the loop to the experiment then the loop will automatically inform the experiment that it has received data. Multiple data name/value pairs can be added to any given entry of the data file and is considered part of the same entry until the nextEntry() call is made. e.g.:: # add some data for this trial exp.addData('resp.rt', 0.8) exp.addData('resp.key', 'k') # end of trial - move to next line in data output exp.nextEntry() """ if name not in self.dataNames: self.dataNames.append(name) # could just copy() every value, but not always needed, so check: try: hash(value) except TypeError: # unhashable type (list, dict, ...) == mutable, so need a copy() value = copy.deepcopy(value) self.thisEntry[name] = value
[docs] def nextEntry(self): """Calling nextEntry indicates to the ExperimentHandler that the current trial has ended and so further addData() calls correspond to the next trial. """ this = self.thisEntry # fetch data from each (potentially-nested) loop for thisLoop in self.loopsUnfinished: names, vals = self._getLoopInfo(thisLoop) for n, name in enumerate(names): this[name] = vals[n] # add the extraInfo dict to the data if type(self.extraInfo) == dict: this.update(self.extraInfo) self.entries.append(this) self.thisEntry = {}
[docs] def getAllEntries(self): """Fetches a copy of all the entries including a final (orphan) entry if that exists. This allows entries to be saved even if nextEntry() is not yet called. :return: copy (not pointer) to entries """ # check for orphan final data (not committed as a complete entry) entries = copy.copy(self.entries) if self.thisEntry: # thisEntry is not empty entries.append(self.thisEntry) return entries
[docs] def saveAsWideText(self, fileName, delim=None, matrixOnly=False, appendFile=None, encoding='utf-8-sig', fileCollisionMethod='rename', sortColumns=False): """Saves a long, wide-format text file, with one line representing the attributes and data for a single trial. Suitable for analysis in R and SPSS. If `appendFile=True` then the data will be added to the bottom of an existing file. Otherwise, if the file exists already it will be overwritten If `matrixOnly=True` then the file will not contain a header row, which can be handy if you want to append data to an existing file of the same format. :Parameters: fileName: if extension is not specified, '.csv' will be appended if the delimiter is ',', else '.tsv' will be appended. Can include path info. delim: allows the user to use a delimiter other than the default tab ("," is popular with file extension ".csv") matrixOnly: outputs the data with no header row. appendFile: will add this output to the end of the specified file if it already exists. encoding: The encoding to use when saving a the file. Defaults to `utf-8-sig`. fileCollisionMethod: Collision method passed to :func:`~psychopy.tools.fileerrortools.handleFileCollision` sortColumns: will sort columns alphabetically by header name if True """ # set default delimiter if none given if delim is None: delim = genDelimiter(fileName) if appendFile is None: appendFile = self.appendFiles # create the file or send to stdout fileName = genFilenameFromDelimiter(fileName, delim) f = openOutputFile(fileName, append=appendFile, fileCollisionMethod=fileCollisionMethod, encoding=encoding) names = self._getAllParamNames() names.extend(self.dataNames) # names from the extraInfo dictionary names.extend(self._getExtraInfo()[0]) # sort names if requested if sortColumns: names.sort() # write a header line if not matrixOnly: for heading in names: f.write(u'%s%s' % (heading, delim)) f.write('\n') # write the data for each entry for entry in self.getAllEntries(): for name in names: if name in entry: ename = str(entry[name]) if ',' in ename or '\n' in ename: fmt = u'"%s"%s' else: fmt = u'%s%s' f.write(fmt % (entry[name], delim)) else: f.write(delim) f.write('\n') if f != sys.stdout: f.close() logging.info('saved data to %r' % f.name)
[docs] def saveAsPickle(self, fileName, fileCollisionMethod='rename'): """Basically just saves a copy of self (with data) to a pickle file. This can be reloaded if necessary and further analyses carried out. :Parameters: fileCollisionMethod: Collision method passed to :func:`~psychopy.tools.fileerrortools.handleFileCollision` """ # Store the current state of self.savePickle and self.saveWideText # for later use: # We are going to set both to False before saving, # so PsychoPy won't try to save again after loading the pickled # .psydat file from disk. # # After saving, the initial state of self.savePickle and # self.saveWideText is restored. # # See # https://groups.google.com/d/msg/psychopy-dev/Z4m_UX88q8U/UGuh1eeyjMEJ savePickle = self.savePickle saveWideText = self.saveWideText self.savePickle = False self.saveWideText = False origEntries = self.entries self.entries = self.getAllEntries() # otherwise use default location if not fileName.endswith('.psydat'): fileName += '.psydat' with openOutputFile(fileName=fileName, append=False, fileCollisionMethod=fileCollisionMethod) as f: pickle.dump(self, f) if (fileName is not None) and (fileName != 'stdout'): logging.info('saved data to %s' % f.name) self.entries = origEntries # revert list of completed entries post-save self.savePickle = savePickle self.saveWideText = saveWideText
[docs] def close(self): if self.dataFileName not in ['', None]: if self.autoLog: msg = 'Saving data for %s ExperimentHandler' % self.name logging.debug(msg) if self.savePickle: self.saveAsPickle(self.dataFileName) if self.saveWideText: self.saveAsWideText(self.dataFileName + '.csv') self.abort() self.autoLog = False
[docs] def abort(self): """Inform the ExperimentHandler that the run was aborted. Experiment handler will attempt automatically to save data (even in the event of a crash if possible). So if you quit your script early you may want to tell the Handler not to save out the data files for this run. This is the method that allows you to do that. """ self.savePickle = False self.saveWideText = False

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