vu-cog-sci/exptools2

Version 2 of exptools (by KnapenLab)

exptools2's Issues

Experiment always crashes after running

Hey guys,

Both demo experiments as well as my own experiments completely run and write log files, but then crash with the following error:

2019-05-26 15:49:47.648 python[15224:110803] -[NSApplication _setup:]: unrecognized selector sent to instance 0x7f93da0281d0
2019-05-26 15:49:47.650 python[15224:110803] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[NSApplication _setup:]: unrecognized selector sent to instance 0x7f93da0281d0'
*** First throw call stack:
(
	0   CoreFoundation                      0x00007fff304be43d __exceptionPreprocess + 256
	1   libobjc.A.dylib                     0x00007fff5c3cb720 objc_exception_throw + 48
	2   CoreFoundation                      0x00007fff3053b255 -[NSObject(NSObject) __retain_OA] + 0
	3   CoreFoundation                      0x00007fff3045dad0 ___forwarding___ + 1486
	4   CoreFoundation                      0x00007fff3045d478 _CF_forwarding_prep_0 + 120
	5   libtk8.6.dylib                      0x0000000121a8831d TkpInit + 413
	6   libtk8.6.dylib                      0x00000001219e017e Initialize + 2622
	7   _tkinter.cpython-36m-darwin.so      0x0000000121808a16 _tkinter_create + 1174
	8   python                              0x000000010ff59068 _PyCFunction_FastCallDict + 200
	9   python                              0x000000011002e61f call_function + 143
	10  python                              0x000000011002c175 _PyEval_EvalFrameDefault + 46837
	11  python                              0x000000011001f8c9 _PyEval_EvalCodeWithName + 425
	12  python                              0x000000011002f2cc _PyFunction_FastCallDict + 364
	13  python                              0x000000010fed7f80 _PyObject_FastCallDict + 320
	14  python                              0x000000010feff5f8 method_call + 136
	15  python                              0x000000010fedf5ce PyObject_Call + 62
	16  python                              0x000000010ff805b5 slot_tp_init + 117
	17  python                              0x000000010ff84af1 type_call + 241
	18  python                              0x000000010fed7ef1 _PyObject_FastCallDict + 177
	19  python                              0x000000010fee0137 _PyObject_FastCallKeywords + 327
	20  python                              0x000000011002e718 call_function + 392
	21  python                              0x000000011002c225 _PyEval_EvalFrameDefault + 47013
	22  python                              0x000000011002e9dc fast_function + 188
	23  python                              0x000000011002e67c call_function + 236
	24  python                              0x000000011002c175 _PyEval_EvalFrameDefault + 46837
	25  python                              0x000000011001f8c9 _PyEval_EvalCodeWithName + 425
	26  python                              0x000000011002f2cc _PyFunction_FastCallDict + 364
	27  python                              0x000000010fed7f80 _PyObject_FastCallDict + 320
	28  python                              0x000000010feff5f8 method_call + 136
	29  python                              0x000000010fedf5ce PyObject_Call + 62
	30  python                              0x000000011002c376 _PyEval_EvalFrameDefault + 47350
	31  python                              0x000000011001f8c9 _PyEval_EvalCodeWithName + 425
	32  python                              0x000000010ff2292d function_call + 125
	33  python                              0x000000010fedf5ce PyObject_Call + 62
	34  python                              0x000000011002c376 _PyEval_EvalFrameDefault + 47350
	35  python                              0x000000011001f8c9 _PyEval_EvalCodeWithName + 425
	36  python                              0x000000011002ea8a fast_function + 362
	37  python                              0x000000011002e67c call_function + 236
	38  python                              0x000000011002c225 _PyEval_EvalFrameDefault + 47013
	39  python                              0x000000011002e9dc fast_function + 188
	40  python                              0x000000011002e67c call_function + 236
	41  python                              0x000000011002c175 _PyEval_EvalFrameDefault + 46837
	42  python                              0x000000011002e9dc fast_function + 188
	43  python                              0x000000011002e67c call_function + 236
	44  python                              0x000000011002c175 _PyEval_EvalFrameDefault + 46837
	45  python                              0x000000011001f8c9 _PyEval_EvalCodeWithName + 425
	46  python                              0x000000011007855c PyRun_FileExFlags + 252
	47  python                              0x0000000110077a34 PyRun_SimpleFileExFlags + 372
	48  python                              0x000000011009e7c6 Py_Main + 3734
	49  python                              0x000000010fecff59 main + 313
	50  libdyld.dylib                       0x00007fff5d499085 start + 1
	51  ???                                 0x0000000000000002 0x0 + 2

Does this look familiar to anyone? Is this a pyschopy/qt-issue?

I use qt 5.9.7 and psychopy 3.1.2, wxpython 4.0.6 with mac os x 10.14.

Also when I follow the psychopy installation instructions exactly, but then replace python 3.5 with 3.6, I get the same errors, even though it uses tk 8.6.8 and wxpython 4.0.4

Error during isntallation: No module named 'distutils.command.bdist_msi'

Having followed the previous installation steps, after running pip install git+https://github.com/VU-Cog-Sci/exptools2/ I am getting the following error:

Collecting pocketsphinx
  Downloading pocketsphinx-0.1.15.tar.gz (29.1 MB)
     ---------------------------------------- 29.1/29.1 MB 13.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\leonb\AppData\Local\Temp\pip-install-ruvaa2uk\pocketsphinx_3b3fbb0f2d674c4f8065bf4bb006163c\setup.py", line 20, in <module>
          from distutils.command.bdist_msi import bdist_msi as _bdist_msi
      ModuleNotFoundError: No module named 'distutils.command.bdist_msi'
      [end of output]

Any suggestions for troubleshooting?

Nr_Frames is not a number and makes experiment crash

I keep getting errors like this at the end of the experiment. Sometimes they happen and sometimes they don't.

Traceback (most recent call last):
  File "main.py", line 124, in <module>
    session.run()
  File "main.py", line 114, in run
    trial.run()
  File "/Users/gilles/git/exptools2/exptools2/core/trial.py", line 237, in run
    self.get_events()
  File "/Users/gilles/git/exptools2/exptools2/core/trial.py", line 150, in get_events
    self.session.close()
  File "/Users/gilles/git/exptools2/exptools2/core/session.py", line 252, in close
    self.global_log.loc[nonresp_idx, 'nr_frames'] = nr_frames.astype(int)
ValueError: cannot convert float NaN to integer

it seems that at that point self.global_log.loc[nonresp_idx, 'nr_frames'].values[1:] is equal to [nan nan] (or longer, like [nan nan nan nan nan nan nan nan nan nan nan nan nan nan]) and self.nr_frames is a proper number (e.g., 358 in this case).

Can someone explain this line of code?

exptools2/exptools2/core/session.py

Line 250 in 723454f

nr_frames = np.append(self.global_log.loc[nonresp_idx, 'nr_frames'].values[1:], self.nr_frames)

Some errors when putting event files produced by exptools2 through BIDS validator (BIDS 1.2.0)

As from title. I note that these files were produced when i did the pilot so this might have already been addressed in a more recent exptools2 version. Delete issue if that is the case!

Error 1: [Code 20] EVENTS_COLUMN_ONSET
First column of the events file must be named 'onset'

Error 2: [Code 21] EVENTS_COLUMN_DURATION
Second column of the events file must be named 'duration'

Error 3: [Code 22] TSV_EQUAL_ROWS
All rows must have the same number of columns as there are headers.

Error 4: [Code 23] TSV_EMPTY_CELL
Empty cell in TSV file detected: The proper way of labeling missing values is "n/a".

Warning 1: [Code 82] CUSTOM_COLUMN_WITHOUT_DESCRIPTION
Tabular file contains custom columns not described in a data dictionary

closing session crashes when frames are dropped

Hey,

I'm designing a stimuli that has fairly fast flickering, and I want the trial to stop upon a keypress.

I noticed that the code would crash when defining and saving the global_log with the message:

File "/Users/verissimo/anaconda3/envs/i36/lib/python3.6/site-packages/exptools2-0.1.dev0-py3.6.egg/exptools2/core/session.py", line 251, in close
    self.global_log.loc[nonresp_idx, 'nr_frames'] = nr_frames.astype(int)
ValueError: cannot convert float NaN to integer

I think it's because of frames dropping throughout the trial. I solved it by replacing this line

exptools2/exptools2/core/session.py

Line 251 in b41407a

self.global_log.loc[nonresp_idx, 'nr_frames'] = nr_frames.astype(int)

with:
self.global_log.loc[nonresp_idx, 'nr_frames'] = nr_frames.astype(np.float).astype('Int32')

Note to self: bug when merging custom settings + default

Is not recursive, but should be.

Hard to overload get_events()

When developing an experiment, I noticed that I can't overload the get_events()-method of the Trial-class, without repeating the logging part etc entirely: If you use super().get_events(), that method flushes the event buffer using psychopy.events.getKeys(), which means I can't access the events/keys that were pressed.

I propose that we let Trial.get_events() also return events, so that overloaded methods can act on it, without repeating/rewriting the logging part. So you could do:

My Trial(...):
    def get_events():
        events = super().get_events()
        if 'y' in events:
            print("yo")

And still everything get logged.

Any ideas?

Note to self: create logdir if not exists yet

Minor issue: window size

It appears the size of the window obtained from session.win is not the same size set through the parameter file. Looks like a psychopy issue, or maybe only my system.

PyWinHook requires swig and Microsoft Visual C++ 14

Some requirements aren't listed in the readme. Microsoft Visual C++ 14 or higher and swig are necessary.

When following the steps described in 'Installation using conda', we ran in to

ERROR: Failed building wheel for pywinhook  
...
error: command 'swig.exe' failed: None                       [end of output]    

After installing swig using pip install swig, the above was solved. It was then followed by

error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/  

After installing Visual Studio Build Tools 2022 (17.5.1) using the Visual Studio Installer, Microsoft Visual C++ 14.35.31938 was installed (2015-2022 Redistributable).

This allowed pip install pywinhook to complete successfully.

Suggested to update this in the readme!

Kind regards,

FGB Brain and Behavior Lab Team

Error during installation - ValueError: list.remove(x): x not in list

Hi,

I am trying to install exptools2 in an Anaconda environment and followed the instructions of the readme. When running the command pip install zmq json-tricks pyparallel sounddevice pygame pysoundcard psychopy_ext psychopy I get an error when Collecting Psychopy:

Downloading PsychoPy-2022.2.3.zip (26.2 MB)
     |████████████████████████████████| 26.2 MB 6.8 MB/s
  Downloading PsychoPy-2022.2.2.zip (26.2 MB)
     |████████████████████████████████| 26.2 MB 104 kB/s
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\leonb\anaconda3\envs\exptools2\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\leonb\\AppData\\Local\\Temp\\pip-install-uu_o5bu8\\psychopy_84a574850b85419a8e4bb9ab601178bf\\setup.py'"'"'; __file__='"'"'C:\\Users\\leonb\\AppData\\Local\\Temp\\pip-install-uu_o5bu8\\psychopy_84a574850b85419a8e4bb9ab601178bf\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\leonb\AppData\Local\Temp\pip-pip-egg-info-tl9klxdl'
         cwd: C:\Users\leonb\AppData\Local\Temp\pip-install-uu_o5bu8\psychopy_84a574850b85419a8e4bb9ab601178bf\
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\leonb\AppData\Local\Temp\pip-install-uu_o5bu8\psychopy_84a574850b85419a8e4bb9ab601178bf\setup.py", line 41, in <module>
        required.remove('pyqt5; python_version >= "3"')
    ValueError: list.remove(x): x not in list
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/b9/91/7a2f0acb1c9ed4e4f03aab2e1e349d33e97e6904f2436ad36f4dccfbe116/PsychoPy-2022.2.2.zip#sha256=8bbb058e12674a83ca3266a894d7cb856c36876f690f455630f353f0dda2f4f8 (from https://pypi.org/simple/psychopy/) (requires-python:>=3.6). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

This error repeats for the next download (Downloading PsychoPy-2022.2.0.zip (27.3 MB)).

Proper releases

Hey guys,

Great work.

I'm starting a new project and developing an experiment from scratch . Since a year or two I try to do everything properly with with fixed Docker images and conda environments, but I keep spending a good portion of my precious postdoc time on duck taping backward compatibility issues of different Python packages. I think it would be super helpful if we could make different releases of exptools2 (rather than, e.g., commits) that we can use, so it's super clear with what exptools-code a given experiment was put together.

Github has a nice lemma on this:
https://help.github.com/en/articles/creating-releases

Cheers,
Gilles

Issues during installation in conda environment

Some issues I encountered when installing for the first time and trying to get the basic Stroop example to work.

wxpython & xlrd

• these packages require Python version <3.8.0a0
• they are not required to get the Stroop example to run and I did not include them in the conda install

psychopy-sounddevice and psychopy-mri-emulator

• These seem to be required for from psychopy.hardware.emulator import SyncGenerator in exptools2.core.session
• I installed them using pip:

pip install psychopy-sounddevice pscyhopy-mri-emulator

Recommended updated installation instruction

• In summary, I did not include wxpython and xlrd, and installed psychopy-sounddevice and psychopy-mri-emulator
• Put together this would result in the following update to the installation instruction

conda create -n exptools2 python=3.9
conda activate exptools2
conda install numpy scipy matplotlib pandas pyopengl pillow lxml openpyxl configobj pyyaml gevent greenlet msgpack-python psutil pytables requests[security] cffi seaborn cython pyzmq pyserial qt pyqt
conda install -c conda-forge pyglet pysoundfile python-bidi moviepy pyosf
pip install zmq json-tricks pyparallel sounddevice pygame pysoundcard psychopy_ext psychopy psychopy-sounddevice psychopy-mri-emulator
pip install git+https://github.com/VU-Cog-Sci/exptools2/

Hope this helps someone :)