Holcombe:Psychopy

From OpenWetWare

Revision as of 18:50, 12 September 2010 by Fahed Jbarah (Talk | contribs)
Jump to: navigation, search

Members

Alex Holcombe
Sarah McIntyre
Fahed Jbarah
• Shih-Yu Lo
• Patrick Goodbourn
Lizzy Nguyen
Alumni


Technical

Skills Checklist
Python Programming
Psychopy/VisionEgg Installation Notes
R analysis,plot,stats
Statistics
Buttonbox
Verifying timing
Programming Cheat Sheets



  • WINDOWS: Psychopy installation. It is easier to intall Enthought Python Distribution that contains all the necessary dependencies than to install at hand one by one the dependencies. Using Enthought, however, I found incompatibilities with Visionegg. Installing the dependencies at hand I did not have problems to run both programs in the same computer.
  • OSX

Site packages (like visionegg and psychopy non-standalone version) should reside in a directory given by, at python prompt:

from distutils.sysconfig import *
print get_python_lib() 

OSX confusingly has three places for Python packages, /System/Library/... and /Library/Python/2.5/site-packages and also /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages You probably want to use /Library/Frameworks/... version. (why are silverTow, sarah's iMac, and Kuna laptop all set to /Library/Python and how do I change that? Kuna nevertheless finds packages in /Library/Frameworks) Some python installation instructions, related issue


Everything I didn't want to know about installing python packages

If you want to grab code from the bleeding edge repository version, you better know what's in subversion etc notes Also info there in subversion etc notes about accessing standalone PsychopyIDE libraries from a terminal session.

VisionEgg 1.2.1 Installation experience for Lee on IMac OSX10.6

Python 2.6, Pygame and PyOpenGL were already installed.
1. Install / update XTools (you may have to upgrade MacOSX).
2. Install / update MacPorts
3. Sync MacPorts ( sudo port selfupdate)
You may need to set up proxy through terminal so call Nenad for a free static IP address that you can manually input to bypass the firewall, then use the following commands in terminal:

export http_proxy='proxy:port'
export rsync_proxy='proxy:port'
  • Remember to make sure you revert to a DHCP assigned IP address after you've installed VisionEgg to reinstate the firewall protection.

4. Install libjpeg via terminal

sudo port install jpeg

If MacPorts can't find libjpeg to install, download and unzip the .tar ball and after changing the present working directory interminal to that directory, run the above command.
5. Download PIL1.1.7 from source
6. Extract the PIL tar ball and edit the setup.py file within:

the line starting with JPEG_ROOT should be changed to:
JPEG_ROOT="opt/local/lib/libjpeg.dylib"
  • Just be sure to check that the opt/local/lib/libjpeg.dylib file does indeed exist. If not, find where libjpeg installed the file and input that address between the quotes.

7. After changing to the PIL directory, compile and build it from source:

sudo python2.6 setup.py install
  • Check to make sure you can find a PIL folder in the Python 2.6 'site-packages' directory

8. Download the VisionEgg source tar ball.
9. Change into that directory in terminal and:

sudo python2.6 setup.py install

VisionEgg Installation experience for ShihYu on MacBook OSX10.5

easy_install VisionEgg executes and puts the .egg in /sw/lib/python2.5/site-packages But import VisionEgg still failed. Adding the VisionEgg egg directories to the python path didn't help. When Fahed moved the VisionEgg directory to the site-packages directory where other packages live, it worked!

However, "import pygame" does not work and said we have the wrong version of PyObjC. We downloaded pyobjc-1.4-py2.5-macosx10.4.mpkg.zip from where it was linked to at http://pygame.org/wiki/PyObjC Then pygame worked.

Installation experience of Fahed on Linux

The following error:

 /usr/lib/python2.5/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:20
     ' install scikits.umfpack instead', DeprecationWarning )

can be resolved by downloading this zip file Scikits.umfpack and placing the linsolve file within in the appropriate python directory.

(search scikits.umfpack in google and download the latest).

installation experience with python2.5 on Intel laptop --Alex O. Holcombe 01:58, 23 March 2009 (EDT)

demos/mouse_pygame.py doesn't work because the default window type is pyglet, as revealed by

myWin = visual.Window((600.0,600.0), allowGUI=True, fullscrn=0)
myWin.winType  #gives you pyglet

Pre-python 2.4, pygame is used for mouse functions, sounds, and other things. Could force use of pygame:

myWin = visual.Window((600.0,600.0), allowGUI=True, fullscrn=0, winType="pygame")

However still the way we draw things in our programs doesn't work, not sure why. Ah, apparently going to python2.5 is supposed to use pyglet for everything, which requires different functions for mouse polling (see demo: mouse.py) and maybe other minor changes, see next section:

adapting to pyglet

  • The 'depth=-1' kwarg which I was using for fixation now makes it invisible. Just delete it, we don't seem to need it
  • The functions for polling the mouse have different names. I handle that by giving the functions the same names:

if win.winType == 'pyglet':
  myMouse = event.Mouse(win=win)
  getRelMouseCoords = myMouse.getRel
  getMouseButtons = myMouse.getPressed
else: 
  myMouse = event.mouse #pygame
  getRelMouseCoords = myMouse.get_rel
  getMouseButtons = myMouse.get_pressed

older

I think I didn't use that version (with pyglet extensions) with 2.5 yet. Will try to look into it.

I think it's to do with PsychoPy selecting the wrong openGL to draw to (PyOpenGL and pyglet.GL aren't compatible and require different argument types). I should be able to look into it, but could you let me know which version of Pyglet (if any) you've installed?

cheers, as ever, for the useful feedback, Jon

Alex Holcombe wrote: Hi Jon, We have a new machine and decided to try using psychopy with python2.5. We installed from source PsychoPy-0.93.4 and tried to install the dependencies correctly by going through the list in the dependenciesOSXuniversal package for python2.4, and finding the appropriate packages on the web for python2.5. Unfortunately upon running the psychopy demos we get an error triggered by the visual.Patchstim commands, for example upon running clockface.py we get the following output:


Traceback (most recent call last):

File "clockface.py", line 12, in <module>
  tex=None, mask=minHand,interpolate=False)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/psychopy/visual.py", line 1030, in __init__
  self._setTex(tex)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/psychopy/visual.py", line 1533, in _setTexNoShaders
  GL.glBindTexture(GL.GL_TEXTURE_1D, self.texID)#bind that name to the target

ctypes.ArgumentError: argument 2: <type 'exceptions.TypeError'>: wrong type


We can go back to using psychopy with python2.4 if necessary, but I thought I'd let you know about this as you mentioned on the webpage that you might provide Python2.5 installers if someone asked. Incidentally, even other demo programs not dependent on visual seem to get errors, such as demo_sound.py, which gives the output at the bottom of this email. Anyway no worries if you don't have time for this, thanks for all the code, we're happily using psychopy in conjunction with some visionEgg for all our experiments now.

cheers Alex


Traceback (most recent call last):

File "demo_sound.py", line 4, in <module>
  sound.init(rate=22050, bits=16, stereo=True, buffer=1024)
File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/psychopy/sound.py", line 67, in init
  mixer.init(rate, bits, stereoChans, buffer) #defaults: 22050Hz, 16bit, stereo,

pygame.error: Failed to start CoreAudio: AudioUnitSetProperty (kAudioUnitProperty_StreamFormat)


On 26/02/2008, at 4:50 AM, Jon Peirce wrote:

Hi Alex, two options. This is the code I used just to get thigns going, and tested against a parallel port on winXP. Pyglet sounds can be used alongside pygame for windowing etc... so that you don't need to change too much other code. One thing you should be aware of is the need to dispatch_events() for pyglet.media

Alternatively, the pyglet backend for PsychoPy is nearly there. The only things missing are a set.gamma function for the window (do you need gamma correction?) and controls for the mouse. I'll try and have a new OS X build for you to play with in the next 1/2 hr. Obviously, going this route will need a bit more testing at your end to make sure it

chrs, Jon


  1. test the speed of a keypress detection

import ctypes, numpy from psychopy import event, visual, core, _parallel import pyglet.media, pyglet.media.procedural

class ArraySnd(pyglet.media.procedural.ProceduralSource):

"""
Create a pyglet.StaticSource from a numpy array.
"""
def __init__(self, data, sample_rate=44800, sample_size=16):
    """Array data should be float (-+1.0)
    sample_size (16 or 8) determines the number of bits used for subsequent storage"""
    duration = len(data)/float(sample_rate) #determine duration from data
    super(ArraySnd, self).__init__(duration,sample_rate, sample_size)
    self.sample_rate = sample_rate
          if sample_size==8:          #ubyte
        self.allData = (data*127+127).astype(numpy.uint8)
    elif sample_size==16:      #signed int16
        self.allData = (data*32767).astype(numpy.int16)
      def _generate_data(self, bytes, offset):
    if self._bytes_per_sample == 1:#ubyte
        start = offset
        samples = bytes
    else:                        #signed int16
        start = offset >> 1
        samples = bytes >> 1
    return (self.allData[start:(start+samples)]).tostring()

def makeSine(duration, frequency=440, sample_rate=44800, sample_size=16): step = frequency * (numpy.pi * 2) / sample_rate

samples = sample_rate*duration
snd = ArraySnd(numpy.sin(step*(numpy.arange(samples))), sample_rate, sample_size)
return snd
           win = visual.Window([200,200],winType='pygame')

A = makeSine(1, 220, sample_size=16)

  1. A = pyglet.media.procedural.Sine(1,220)

core.wait(0.1)

LPT1 = 0x378#address for parallel port on many machines pinNumber = 2#choose a pin to write to (2-9). A.play() _parallel.out(LPT1, 2**(pinNumber-2))#sets just this pin to be high (pin2 represent databit 0, pin3=bit1...)

clock = core.Clock() while clock.getTime()<5.0:

pyglet.media.dispatch_events()#have to call this or pyglet sound manager doesn't update its buffer
if len(event.getKeys())>0:
    break

core.wait(0.01)

_parallel.out(LPT1, 0)#sets all pins low
Views
Personal tools