Staircase_analyse.py

This script will take a 'pickle' data file from a staircase experiment (or will even combine pickles from multiple runs) and fit a full psychometric function to it. It works by binning the intensity values and the responses from all the way through the staircase. This way the subject's threshold is calculated from all of their data rather than just the intensity at the final 4 reversals.

#This analysis script takes one or more staircase datafiles as input from a GUI
#It then plots the staircases on top of each other on the left 
#and a combined psychometric function from the same data
#on the right
#

from psychopy import data, gui, misc, core
import pylab

files = gui.fileOpenDlg('.')
if not files:
    core.quit()

#get the data from all the files
allIntensities, allResponses = [],[]
for thisFileName in files:
    thisDat = misc.fromFile(thisFileName)
    allIntensities.append( thisDat.intensities )
    allResponses.append( thisDat.data )

#plot each staircase
pylab.subplot(121)
colors = 'brgkcmbrgkcm'
lines, names = [],[]
for fileN, thisStair in enumerate(allIntensities):
    #lines.extend(pylab.plot(thisStair))
    #names = files[fileN]
    pylab.plot(thisStair, label=files[fileN])
#pylab.legend()

#get combined data
combinedInten, combinedResp, combinedN = \
             data.functionFromStaircase(allIntensities, allResponses, 5)
#fit curve
fit = data.FitFunction('weibullTAFC',combinedInten, combinedResp, guess=[0.2, 0.5])
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.8)
print thresh

#plot curve
pylab.subplot(122)
pylab.plot(smoothInt, smoothResp, '-')
pylab.plot([thresh, thresh],[0,0.8],'--'); pylab.plot([0, thresh],[0.8,0.8],'--')
pylab.title('threshold = %0.3f' %(thresh))
#plot points
pylab.plot(combinedInten, combinedResp, 'o')
pylab.ylim([0,1])

pylab.show()