ioHub: object has no attribute 'run'

[Sabrina Hoppe]

Hi everyone,

I'm using Psychopy 1.78.01  on Ubuntu 14.04 with Python 2.7 and would like to connect my experiment to a Tobii TX300 Eye Tracker. However, my own scripts as well as the examples I could find online (e.g. http://www.isolver-solutions.com/iohubdocs/iohub/quickstart.html#converting-psychopy-s-mouse-py-demo-to-use-iohub, or workshop ressources from the psychopy webpage) all result in the following error:

Error occurred during ioServer.start(): 'module' object has no attribute 'run'
<type 'exceptions.AttributeError'>
AttributeError("'module' object has no attribute 'run'",)
['  File "/usr/lib/pymodules/python2.7/psychopy/iohub/launchHubProcess.py", line 55, in run\n    gevent.run()\n']
------------------------------
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/datastore/__init__.py", line 466, in close_open_data_files
    for fileh in open_files.keys():
AttributeError: '_FileRegistry' object has no attribute 'keys'
Error in sys.exitfunc:
Traceback (most recent call last):
  File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/datastore/__init__.py", line 466, in close_open_data_files
    for fileh in open_files.keys():
AttributeError: '_FileRegistry' object has no attribute 'keys'

Does someone have any thoughts on this?

I know I'm not using the latest version of Psychopy - that's because I had trouble to use an existing experiment with the latest version. I briefly tested the iohub functionality on the latest psychopy version though and got the same error.

Thanks in advance,

Sabrina 

[Sol Simpson]

 My own scripts as well as the examples I could find online [(..., or workshop resources from the psychopy webpage) .... ]  all result in the [...] error

What version of the gevent package are you running?

If you are going to use 1.78.01 then you also need to use an older version of the gevent 1.0 package, '1.0b3' I /think/. Versions of gevent after that have an api change, removing the gevent.run() function that was being used by iohub in 1.78.01. 

If you upgrade to 1.81.x then iohub works with the newer gevent package releases, as well as the beta / release candidate versions of gevent 1.0. 

Note that if you upgrade to the latest psychopy source, you should also only use the demos/coder/iohub examples that come with the psychopy source package. Many older examples, and those from the workshop, will no longer work because of changes made to the iohub keyboard device api.

 

 I briefly tested the iohub functionality on the latest psychopy version though and got the same error.

Are you sure you got the /actual same/ error vs. some other error?  If you can use the latest psychopy, please retest with a recent demo. If you are still getting an error send the details along please.

I know I'm not using the latest version of Psychopy - that's because I had trouble to use an existing experiment with the latest version. 

Maybe we can help determine why the old experiment does not work if more info on the issue / error is provided.

Thanks again.

[Sabrina Hoppe]

Am Montag, 1. Dezember 2014 21:35:42 UTC+1 schrieb Sol Simpson:

 My own scripts as well as the examples I could find online [(..., or workshop resources from the psychopy webpage) .... ]  all result in the [...] error

What version of the gevent package are you running?

If you are going to use 1.78.01 then you also need to use an older version of the gevent 1.0 package, '1.0b3' I /think/. Versions of gevent after that have an api change, removing the gevent.run() function that was being used by iohub in 1.78.01. 

Thanks, this was indeed the problem. I replaced gevent 1.0 by gevent 1.0b3 and at least the program is running now. However, I ran into a new problem:

/usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning: /home/sabrina/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)
/usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning: /home/sabrina/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)
Xfixes DLL could not be loaded. Cursor visiblity support is unavailable.
Exception in thread Thread-1:

Traceback (most recent call last):

  File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/devices/pyXHook.py", line 140, in run
    self.record_dpy.record_enable_context(self.ctx, self.processevents)
  File "/usr/lib/python2.7/dist-packages/Xlib/ext/record.py", line 238, in enable_context
    context = context)
  File "/usr/lib/python2.7/dist-packages/Xlib/ext/record.py", line 215, in __init__
    rq.ReplyRequest.__init__(self, *args, **keys)
  File "/usr/lib/python2.7/dist-packages/Xlib/protocol/rq.py", line 1478, in __init__
    self.reply()
  File "/usr/lib/python2.7/dist-packages/Xlib/protocol/rq.py", line 1490, in reply
    self._display.send_and_recv(request = self._serial)
  File "/usr/lib/python2.7/dist-packages/Xlib/protocol/display.py", line 556, in send_and_recv
    gotreq = self.parse_response(request)
  File "/usr/lib/python2.7/dist-packages/Xlib/protocol/display.py", line 643, in parse_response
    gotreq = self.parse_request_response(request) or gotreq
  File "/usr/lib/python2.7/dist-packages/Xlib/protocol/display.py", line 729, in parse_request_response
    req._parse_response(self.data_recv[:self.request_length])
  File "/usr/lib/python2.7/dist-packages/Xlib/ext/record.py", line 219, in _parse_response
    self._callback(r)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/devices/pyXHook.py", line 196, in processevents
    hookevent = self.keypressevent(event)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/devices/pyXHook.py", line 241, in keypressevent
    return self.makekeyhookevent(keysym, event)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/devices/pyXHook.py", line 390, in makekeyhookevent
    int(storewm["handle"], base=16)
ValueError: invalid literal for int() with base 16: ".Window'>("

 
Do you have any idea where this problem could come from?

 

 I briefly tested the iohub functionality on the latest psychopy version though and got the same error.

Are you sure you got the /actual same/ error vs. some other error?  If you can use the latest psychopy, please retest with a recent demo. If you are still getting an error send the details along please.

No, I'm not entirely sure about these details anymore. I've done these tests on a colleague's machine while he didn't need it, so I can't reproduce it right now. But I will test it at some point and let you know if I can't get it work.
 

I know I'm not using the latest version of Psychopy - that's because I had trouble to use an existing experiment with the latest version. 

Maybe we can help determine why the old experiment does not work if more info on the issue / error is provided. 

Essentially, I could not change the color of elementarraystim objects (at least not individually). However, I also cannot reproduce these problems right now, because the according packages are no longer installed on my computer. Maybe we can make it work with the old versions; otherwise I'll reinstall the latest version and ask about this again.

Thanks for your help!

[Sabrina Hoppe]

Probably, I should have mentioned what code I was trying to execute:
the demo "iohub_basic/iohub_mouse.py" that came with the 1.78.01 psychopy distribution. I get the same errors about the invalid literal for int() with base 16 if I run either the "iohub_basic/iohub_keyboard" sample or the "iohub_extended/eye_tracker" example.
(By the way, to make the eye tracker sample code run, the file 'iohub_config.yaml' needs to be renamed to 'ioHub_config.yaml' - note the capital H)

Another error that occured in my tests, but typically after I tried to exit the program is the following:

Error in atexit._run_exitfuncs:

Traceback (most recent call last):

  File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/datastore/__init__.py", line 466, in close_open_data_files
    for fileh in open_files.keys():
AttributeError: '_FileRegistry' object has no attribute 'keys'
Error in sys.exitfunc:

Traceback (most recent call last):

  File "/usr/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/usr/lib/pymodules/python2.7/psychopy/iohub/datastore/__init__.py", line 466, in close_open_data_files
    for fileh in open_files.keys():
AttributeError: '_FileRegistry' object has no attribute 'keys'

Do you have any idea what else could be wrong here? Thanks!

[Sol Simpson]

All the issues you are running into (other than the case sensitivity in the iohub_config file name), are caused from newer 3rd party package versions not working with the old 1.78 iohub code. I worry that we will be going around in circles here and that it would be most time efficient to upgrade your psychopy to the latest psychopy source from github and then work from there. More info on each error below.

Thanks again.

(By the way, to make the eye tracker sample code run, the file 'iohub_config.yaml' needs to be renamed to 'ioHub_config.yaml' - note the capital H)

Thanks for pointing this issue out; on Windows case does not matter and that is what I test on 90% of the time. Will fix the issue.

 

  File "/usr/lib/pymodules/python2.7/psychopy/iohub/devices/pyXHook.py", line 390, in makekeyhookevent
    int(storewm["handle"], base=16)

ValueError: invalid literal for int() with base 16: ".Window'>("

This is an issue between versions of the pyxlib module. It is handled in newer versions of iohub.

  File "/usr/lib/pymodules/python2.7/psychopy/iohub/datastore/__init__.py", line 466, in close_open_data_files
    for fileh in open_files.keys():
AttributeError: '_FileRegistry' object has no attribute 'keys'

This error is from the pytables module you are using being too recent for the old version of the iohub code. The pytables api changed. You will need to downgrade to an earlier version of pytables (I forget which version though, sorry).

[Sabrina Hoppe]

Hi again,

ok, thanks for these insights. I decided to take your advice and just set up everything using the latest versions again (i.e. Psychopy 1.81 and its requirements). Taking more care of which exact libraries to install, I got a connection to the eye tracker now. However, if I run the coder/iohub/eyetracker example, the GUI opens and I can see the bars on the bottom of the screen reacting to the way I move my eyes/head, but keyboard or mouse events are not detected. Instead, I get the following error:

Error saving event: [1L, 4, 0, 253, 23, 706.549, 6.715169906616211, 6.715169906616211, 0.0, 0.0, 0, None, 65, 32L, 0, ' ', 8192, 67108872, ' ', 0.11952090263366699, 244]

<type 'exceptions.TypeError'>

TypeError("long() argument must be a string or a number, not 'NoneType'",)

['  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.01-py2.7.egg/psychopy/iohub/datastore/__init__.py", line 435, in _handleEvent\n    np_array= N.array([tuple(event),],dtype=eventClass.NUMPY_DTYPE)\n']

Error saving event: [1L, 4, 0, 389, 23, 708.821, 8.987269878387451, 8.987269878387451, 0.0, 0.0, 0, None, 9, 65307L, 0, 'escape', 8192, 67108872, '', 0.07965397834777832, 384]

<type 'exceptions.TypeError'>

TypeError("long() argument must be a string or a number, not 'NoneType'",)

['  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.01-py2.7.egg/psychopy/iohub/datastore/__init__.py", line 435, in _handleEvent\n    np_array= N.array([tuple(event),],dtype=eventClass.NUMPY_DTYPE)\n']

Traceback (most recent call last):

  File "validation.py", line 106, in <module>

    results_in_degrees=True

  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.01-py2.7.egg/psychopy/iohub/util/targetpositionsequence.py", line 1217, in __init__

    self.display_size=win.size

AttributeError: 'TargetStim' object has no attribute 'size'

AL lib: ReleaseALC: 1 device not closed

AL lib: ReleaseALC: 1 device not closed

Do you have any idea what goes wrong here?

Additionally, I got this ReleaseALC lib warning in my own old code as well. What does it mean? And which device could it refer to?

( Two more comments on the installation process that I went through again today:

I noticed that the instruction on http://www.psychopy.org/installation.html to "follow the ‘Package authentification’ procedure described in http://neuro.debian.net/" might be out of date. At least I could not find such a procedure described on the website you refer to. 

Also, it is important to install psutil version 2.2.0 - using the psutil from the ubuntu repositories (1.2.1) causes an error when cpu_count() is requested. So maybe you would like to add this in the requirement section of the installation webpage.)

Thanks,

Sabrina

[Sol Simpson]

Are you using the latest psychopy source from www.github.com/psychopy/psychopy? The error you are getting from the ioHub Tobii calibration graphics should be fixed in that source.

Also, please delete any .hdf5 files from the demo folder before you start it again.

Please let me know.

Thanks,

Sol

[Sabrina Hoppe]

Thanks. Indeed I was not using the latest source from github (but the latest download available from the psychopy website). However, after installing version 1.81.03 from github, I still get similar errors running the eye tracking demos:

• iohub/eyetracking/gcCursor:

Traceback (most recent call last):

  File "run.py", line 315, in <module>

    runtime=ExperimentRuntime(module_directory(ExperimentRuntime.run), "experiment_config.yaml")

  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/client/__init__.py", line 1615, in __init__

    self.hub = self._initalizeConfiguration()

  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/client/__init__.py", line 1867, in _initalizeConfiguration

    self.hub = ioHubConnection(None, ioHubConfigAbsPath)

  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/client/__init__.py", line 286, in __init__

    self.iohub_status = self._startServer(ioHubConfig, ioHubConfigAbsPath)

  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/client/__init__.py", line 869, in _startServer

    ioHubConfig=load(file(ioHubConfigAbsPath,u'r'), Loader=Loader)

  File "/usr/lib/python2.7/dist-packages/yaml/__init__.py", line 71, in load

    return loader.get_single_data()

  File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 37, in get_single_data

    node = self.get_single_node()

  File "_yaml.pyx", line 707, in _yaml.CParser.get_single_node (ext/_yaml.c:8309)

  File "_yaml.pyx", line 725, in _yaml.CParser._compose_document (ext/_yaml.c:8582)

  File "_yaml.pyx", line 776, in _yaml.CParser._compose_node (ext/_yaml.c:9307)

  File "_yaml.pyx", line 892, in _yaml.CParser._compose_mapping_node (ext/_yaml.c:10869)

  File "_yaml.pyx", line 905, in _yaml.CParser._parse_next_event (ext/_yaml.c:11046)

yaml.parser.ParserError: while parsing a block mapping

  in "/home/sabrina/Desktop/demos/coder/iohub/eyetracking/gcCursor/iohub_config.yaml", line 1, column 1

did not find expected key

  in "/home/sabrina/Desktop/demos/coder/iohub/eyetracking/gcCursor/iohub_config.yaml", line 111, column 2

 

• iohub/eyetracking/selectTracker:

Error saving event: [1, 1, 0, 288, 23, 243.865, 11.52069902420044, 11.52069902420044, 0.0, 0.0, 0, None, 65, 32L, 0, ' ', 8192, 67108872, ' ', 0.13553094863891602, 271]

<type 'exceptions.TypeError'>

TypeError("long() argument must be a string or a number, not 'NoneType'",)

['  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/datastore/__init__.py", line 435, in _handleEvent\n    np_array= N.array([tuple(event),],dtype=eventClass.NUMPY_DTYPE)\n']

[.... this type error occurs several times...]

AL lib: ReleaseALC: 1 device not closed

ioHub Server Process Completed With Code:  0

Exception TypeError: "'NoneType' object is not callable" in <bound method Window.__del__ of <psychopy.visual.window.Window object at 0xaddd80ec>> ignored

AL lib: ReleaseALC: 1 device not closed

• the same error ("long() argument must be a string or a number") also occurs when running the iohub/eyetracking/validation demo.

Despite these errors, the hdf5 file seems to contain gaze points, so I'm not sure how relevant these events are.

Thanks!

[Sol Simpson]

• iohub/eyetracking/gcCursor:

Traceback (most recent call last):
  File "run.py", line 315, in <module>
    runtime=ExperimentRuntime(module_directory(ExperimentRuntime.run), "experiment_config.yaml")

Did you modify the experiment_config.yaml file in the script directory you are running? This error indicates the file is no longer in valid YAML format. If you did edit it, you can send it and I can point out what the issue is. 

If you did not, let me know.

Error saving event: [1, 1, 0, 288, 23, 243.865, 11.52069902420044, 11.52069902420044, 0.0, 0.0, 0, None, 65, 32L, 0, ' ', 8192, 67108872, ' ', 0.13553094863891602, 271]

• the same error ("long() argument must be a string or a number") also occurs when running the iohub/eyetracking/validation demo.

This seems to be coming from keyboard release events. The field that is None is the 'auto_repeated' event field, which should be 0 for any keyboard release, so this is a bug. 

Can you remind me what OS you are using and i will look at fixing whatever the issue is.

If you are using Linux, I think I see the issue and will submit a bug fix for it today. Thanks!

[Sabrina Hoppe]

• iohub/eyetracking/gcCursor:

Traceback (most recent call last):
  File "run.py", line 315, in <module>
    runtime=ExperimentRuntime(module_directory(ExperimentRuntime.run), "experiment_config.yaml")

Did you modify the experiment_config.yaml file in the script directory you are running? This error indicates the file is no longer in valid YAML format. If you did edit it, you can send it and I can point out what the issue is. 

If you did not, let me know.

 

I don't think I changed it... this is what it looks like now:
# experiment_config.yaml: settings related to the experiment being run when the run.py script is launched,
# any custom session variables you want displayed in a dialog for input at the start of the experiment

title: smiTrackerTest
code: smi_t1
version: '1.0'
description: User looks at an image and program counts fixations and dwell times.
session_defaults:
name: Session Name
code: E1S01
comments: None
user_variables:
participant_age: Unknown
participant_gender: [ Select, Male, Female ]
glasses: [Select, Yes, No ]
contacts: [Select, Yes, No ]
eye_color: Unknown
session_variable_order: [ name, code, comments, participant_age, participant_gender, glasses, contacts, eye_color ]
event_buffer_length: 2048
process_affinity: []
remaining_processes_affinity: []
ioHub:
enable: True
process_affinity: []
config: iohub_config.yaml

Error saving event: [1, 1, 0, 288, 23, 243.865, 11.52069902420044, 11.52069902420044, 0.0, 0.0, 0, None, 65, 32L, 0, ' ', 8192, 67108872, ' ', 0.13553094863891602, 271]

• the same error ("long() argument must be a string or a number") also occurs when running the iohub/eyetracking/validation demo.

This seems to be coming from keyboard release events. The field that is None is the 'auto_repeated' event field, which should be 0 for any keyboard release, so this is a bug. 

Can you remind me what OS you are using and i will look at fixing whatever the issue is.

If you are using Linux, I think I see the issue and will submit a bug fix for it today. Thanks!

Yes, I use Linux indeed (Ubuntu 14.04). Thanks!

[Sol Simpson]

I submitted a BF to psychopy/psychopy master stream that should fix the keyboard release issue you were seeing. Please let me know if it does not.

Re the yaml file, can you attach the file? The indentation matters for YAML similar to how it does for Python.

Thanks

[Sabrina Hoppe]

Am Montag, 15. Dezember 2014 19:37:37 UTC+1 schrieb Sol Simpson:

I submitted a BF to psychopy/psychopy master stream that should fix the keyboard release issue you were seeing. Please let me know if it does not.

I'll test it and let you know soon.

 

Re the yaml file, can you attach the file? The indentation matters for YAML similar to how it does for Python.

 
Oh sorry, I wasn't aware of that. It's attached now.

Thank you!

[Sabrina Hoppe]

I submitted a BF to psychopy/psychopy master stream that should fix the keyboard release issue you were seeing. Please let me know if it does not.

I'll test it and let you know soon.

I get a different error now:

Error saving event: [1L, 40, 0, 1950, 23, 1528.882, 27.037971019744873, 27.037971019744873, 0.0, 0.0, 0, None, 24, 113L, 0, 'q', 8192, 62914568, 'q', 0.09567904472351074, 1936]

<type 'exceptions.TypeError'>

TypeError("long() argument must be a string or a number, not 'NoneType'",)

['  File "/usr/local/lib/python2.7/dist-packages/PsychoPy-1.81.03-py2.7.egg/psychopy/iohub/datastore/__init__.py", line 435, in _handleEvent\n    np_array= N.array([tuple(event),],dtype=eventClass.NUMPY_DTYPE)\n']

By the way, the YAML parser error message is gone as well (have no idea why though).

Thanks a lot!

[Sabrina Hoppe]

By the way, the YAML parser error message is gone as well (have no idea why though).

 

Sorry, this was just my confusion. The error does not occur when running my own project, but it still does come up for the gcCursor demo. However, now I can be sure the experiment_config.yaml is not changed as I just downloaded it again today when upgrading to the latest version of PsychoPy.

[Sabrina Hoppe]

I think I found the yaml error, it's just a typo in the demo: 

in line 156 of the iohub_config.yaml, there should be a ':' instead of the '.' at the end of the line.

This seems to fix the issue.

[Sol Simpson]

Thank you for the updates.

The change that fixes the "Error saving event:..." exception has not yet been accepted into psychopy/psychopy. 

For now, you can get the update from isolver/psychopy if you want to test it out.

I think I found the yaml error, it's just a typo in the demo: 
in line 156 of the iohub_config.yaml, there should be a ':' instead of the '.' at the end of the line.
This seems to fix the issue.

Is this for the latest version of the gccursor demo, in demos.coder.iohub.eyetracking ? Line 156 of the iohub_config file I have (which seems to be what is on psychopy/psychopy) is a commented out line, and the demo runs without any parsing errors. Could you let me know where you are downloading the source files from?

Thanks very much,

Sol

I'm 

[Sabrina Hoppe]

I think I found the yaml error, it's just a typo in the demo: 
in line 156 of the iohub_config.yaml, there should be a ':' instead of the '.' at the end of the line.
This seems to fix the issue.

Is this for the latest version of the gccursor demo, in demos.coder.iohub.eyetracking ? Line 156 of the iohub_config file I have (which seems to be what is on psychopy/psychopy) is a commented out line, and the demo runs without any parsing errors. Could you let me know where you are downloading the source files from?

Sorry, I was unclear here. I'm talking about this file. Line 156 is indeed commented, but in order to use the sample, you need to uncomment the section corresponding to your eye tracker. So I uncommented lines 111-173 as I use a Tobii tracker. The error is then thrown after uncommenting, because the line in question contains  'target_attributes.' instead of 'target_attributes:'.

[Sol Simpson]

Good catch. Thanks again for pointing out the issue. The file has been updated and should hit psychopy/psychopy master in the next few days.