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A QUEST+ implementation in Python.

License: GNU General Public License v3.0

Python 100.00%

psychophysics psychology

questplus's Introduction

A QUEST+ implementation in Python

This is a simple implementation of the QUEST+ algorithm in Python.

Documentation

Please find the documentation at questplus.readthedocs.io.

questplus's People

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gjcooper psychonomic ngurkan aforren1 tetsuzawa histedlab sumeetgohil steffejr adrianbunk

questplus's Issues

Please upload the latest version of the library to PyPI.

Hello. I am using the 2019.4 version of the QUEST+ library for my psychometric experiments.

However, I am having trouble with a bug in the psychometric function (norm_pdf).

This bug seems to have been resolved in the latest commit (9e1d0b8), so I would like you to upload this version of the QUEST+ library to PyPI.

Thank you for implementing this great software.

Add formulas of psychometric functions to docstrings

Add references to docstrings

Add references to Watson (2017), King-Smith et al. (1994), etc.

bug: 'linear' stimScale does not work with negative numbers (xarray RuntimeWarning)

Hi, thanks for this package! I am using it in psychopy :) unfortunately the 'linear' stimScale does not behave as expected for negative intensityVals/thresholdVals as it results in a RuntimeWarning. Maybe it's just my code, but "linear" with positive values works great and using "log10" with negative intensity values also gives a good estimate.

Please let me know if you need more information to debug or decide if this is a bug. Thank you!

[/lib/python3.8/site-packages/xarray/core/computation.py:771](/lib/python3.8/site-packages/xarray/core/computation.py:771): RuntimeWarning: invalid value encountered in log result_data = func(*input_data)

Example using 'linear'-scale and negative intensity values:

Switch CI to GH actions

Add support for inverse function

Hi, for our project we adjusted the code to use an inverse function. I think this could be helpful for some others. Please let me know if you want a reproducible example or a pull request :)

Adjust line 111 in questplus/psychometric_function.py:

- return p
+ return (1 + lower_asymptote - lapse_rate) - p

Example plot:

xarray’s expand_dims() has been removed

http://xarray.pydata.org/en/stable/whats-new.html#v0-13-0-17-sep-2019

Add demos

Should include some simulations and plotting.

Simplify retrieval of marginal posterior PDFs

Re-enable min_n_entropy stimulus selection option

Draft PyPI and conda-forge releases

Turn QuestPlus class into an iterator?

Potentially transform class into an iterator, so users would be able to iterate over it e.g. using a for loop:

q = QuestPlus(...)
for stimulus in q:
    ...

from questplus import QuestPlus
import numpy as np

thresholds = np.arange(-40, 0 + 1)
slope, guess, lapse = 3.5, 0.5, 0.02
contrasts = thresholds.copy()

threshold_prior_vals = np.random.randint(low=1, high=10,
                                        size=len(thresholds))
threshold_prior_vals = threshold_prior_vals / threshold_prior_vals.sum()
prior = dict(threshold=threshold_prior_vals)
q = QuestPlusHandler(
    nTrials=20,
    intensityVals=contrasts,
    thresholdVals=thresholds,
    slopeVals=slope,
    lowerAsymptoteVals=guess,
    lapseRateVals=lapse,
    prior=prior)
print (q)

results in this error with numpy 1.24 but succeeds in numpy <=1.23

Traceback (most recent call last):
  File "/Applications/PyCharm CE.app/Contents/plugins/python-ce/helpers/pydev/pydevd.py", line 1483, in _exec
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "/Applications/PyCharm CE.app/Contents/plugins/python-ce/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/Users/lpzjwp/Desktop/questplus_test.py", line 14, in <module>
    q = QuestPlusHandler(
  File "/Users/lpzjwp/code/psychopy/git/psychopy/data/staircase.py", line 1575, in __init__
    self._qp = qp.QuestPlusWeibull(
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/questplus/qp.py", line 489, in __init__
    super().__init__(stim_domain=dict(intensity=intensities),
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/questplus/qp.py", line 86, in __init__
    self.prior = self._gen_prior(prior=prior)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/questplus/qp.py", line 175, in _gen_prior
    prior_grid = np.meshgrid(*list(prior_orig.values()),
  File "<__array_function__ internals>", line 200, in prod
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 3076, in prod
    return _wrapreduction(a, np.multiply, 'prod', axis, dtype, out,
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (4,) + inhomogeneous part.

Add Sphinx documentation and publish on readthedocs

Sphinx support
RTD builds

Installing on a fresh Ubuntu18.04 using pip3

I get the following output

Collecting questplus
  Using cached https://files.pythonhosted.org/packages/ec/a4/8d47d76a484e0f7080cd43b3141063efd938a7aceb8a2bc39fe2dc08685a/questplus-0.0.5.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-llc0eh02/questplus/setup.py", line 12, in <module>
        version=versioneer.get_version(),
      File "/tmp/pip-build-llc0eh02/questplus/versioneer.py", line 1480, in get_version
        return get_versions()["version"]
      File "/tmp/pip-build-llc0eh02/questplus/versioneer.py", line 1412, in get_versions
        cfg = get_config_from_root(root)
      File "/tmp/pip-build-llc0eh02/questplus/versioneer.py", line 344, in get_config_from_root
        parser.readfp(f)
      File "/usr/lib/python3.6/configparser.py", line 763, in readfp
        self.read_file(fp, source=filename)
      File "/usr/lib/python3.6/configparser.py", line 718, in read_file
        self._read(f, source)
      File "/usr/lib/python3.6/configparser.py", line 1015, in _read
        for lineno, line in enumerate(fp, start=1):
      File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
        return codecs.ascii_decode(input, self.errors)[0]
    UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 46: ordinal not in range(128)
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-llc0eh02/questplus/