Welcome to pphelper’s documentation!

About pphelper

pphelper is a collection of tools that can be used for the analysis of psychophysical data.

The racemodel Module

Race model inequality analysis implementation, based on Ulrich, Miller, and Schröter (2007): ‘Testing the race model inequality: An algorithm and computer programs’, published in Behavior Research Methods 39 (2), pp. 291-302.

Provides

  • gen_cdf : Estimate the cumulative distribution function from response time data.
  • gen_cdfs_from_list : Convenience function: Applys gen_cdf to a list of data sets.
  • gen_percentiles : Calculate equally spaced percentiles values.
  • get_percentiles_from_cdf : Get the values (response times) of a cumulative distribution function at the specified percentiles.
  • gen_step_fun : Generate a step function from a set of observed response times.
pphelper.racemodel.gen_cdf(rts, t_max=None)

Estimate the cumulative frequency polygon from response time data.

Parameters:
  • rts (array_like) – The raw response time data. Data does not need to be ordered and may contain duplicate values.
  • t_max (int, optional) – Up to which time point (in milliseconds) the model should be calculated. If not specified, the maximum value of the supplied input data will be used.
Returns:

A Series containing the estimated cumulative frequency polygon, indexed by the time points in ms.
Return type:

DataFrame or Series

See also

gen_cdfs_from_dataframe(), gen_cdfs_from_list(), get_percentiles_from_cdf(), gen_step_fun()

Notes

Response times will be rounded to 1 millisecond. The algorithm is heavily adapted from the one described by Ulrich, Miller, and Schröter (2007): ‘Testing the race model inequality: An algorithm and computer programs’, published in Behavior Research Methods 39 (2), pp. 291-302.

Examples

>>> from pphelper.racemodel import gen_cdf
>>> import numpy as np
>>> RTs = np.array([234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270, 280])
>>> gen_cdf(RTs, t_max=RTs.max())
t
0     0
1     0
2     0
3     0
4     0
5     0
6     0
7     0
8     0
9     0
10    0
11    0
12    0
13    0
14    0
...
266    0.856643
267    0.863636
268    0.870629
269    0.877622
270    0.884615
271    0.892308
272    0.900000
273    0.907692
274    0.915385
275    0.923077
276    0.930769
277    0.938462
278    0.946154
279    0.953846
280    1.000000
Length: 281, dtype: float64
pphelper.racemodel.gen_cdfs_from_dataframe(data, rt_column=u'RT', modality_column=u'Modality', names=None)

Create cumulative distribution functions (CDFs) for response time data.

Parameters:
  • data (DataFrame) – A DataFrame with containing at least two columns: one with response times, and another one specifying the corresponding modalities.
  • rt_column (string, optional) – The name of the column containing the response times. Defaults to RT.
  • modality_column (string, optional) – The name of the column containing the modalities corresponding to the response times. Defaults to Modality.
  • names (list, optional) – A list of length 4, supplying the names of the modalities. The first three elements specify the modalities in the input data to consider. These three and the fourth argument are also used to label the columns in the returned DataFrame. If this argument is not supplied, a default list ['A', 'B', 'AB'] will be used.
Returns:

results – A DataFrame containing the empirical cumulative distribution functions generated from the input, one CDF per column. The number of columns depends on the number of unique values in the modality_column or on the names argument,
Return type:

DataFrame

See also

gen_cdf(), gen_cdfs_from_list(), gen_step_fun(), get_percentiles_from_cdf()

Notes

This function internally calls gen_cdf. Please see this function to find out about additional optional keyword arguments.

Examples

>>> from pphelper.racemodel import gen_cdfs_from_dataframe
>>> import pandas as pd
>>> import numpy as np
>>> data = pd.DataFrame({'RT': np.array([244, 249, 257, 260, 264, 268, 271, 274, 277, 291,
... 245, 246, 248, 250, 251, 252, 253, 254, 255, 259, 263, 265, 279, 282, 284, 319,
... 234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270, 280]),
... 'Modality': ['x', 'x', 'x', 'x', 'x', 'x', 'x', 'x', 'x', 'x',
... 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y',
... 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', 'z', ]})
>>> gen_cdfs_from_dataframe(data)
            x         y  z
t
0    0.000000  0.000000  0
1    0.000000  0.000000  0
2    0.000000  0.000000  0
3    0.000000  0.000000  0
4    0.000000  0.000000  0
5    0.000000  0.000000  0
6    0.000000  0.000000  0
7    0.000000  0.000000  0
8    0.000000  0.000000  0
9    0.000000  0.000000  0
10   0.000000  0.000000  0
11   0.000000  0.000000  0
12   0.000000  0.000000  0
13   0.000000  0.000000  0
14   0.000000  0.000000  0
15   0.000000  0.000000  0
16   0.000000  0.000000  0
17   0.000000  0.000000  0
18   0.000000  0.000000  0
19   0.000000  0.000000  0
20   0.000000  0.000000  0
21   0.000000  0.000000  0
22   0.000000  0.000000  0
23   0.000000  0.000000  0
24   0.000000  0.000000  0
25   0.000000  0.000000  0
26   0.000000  0.000000  0
27   0.000000  0.000000  0
28   0.000000  0.000000  0
29   0.000000  0.000000  0
..        ...       ... ..
290  0.942857  0.916964  1
291  1.000000  0.918750  1
292  1.000000  0.920536  1
293  1.000000  0.922321  1
294  1.000000  0.924107  1
295  1.000000  0.925893  1
296  1.000000  0.927679  1
297  1.000000  0.929464  1
298  1.000000  0.931250  1
299  1.000000  0.933036  1
300  1.000000  0.934821  1
301  1.000000  0.936607  1
302  1.000000  0.938393  1
303  1.000000  0.940179  1
304  1.000000  0.941964  1
305  1.000000  0.943750  1
306  1.000000  0.945536  1
307  1.000000  0.947321  1
308  1.000000  0.949107  1
309  1.000000  0.950893  1
310  1.000000  0.952679  1
311  1.000000  0.954464  1
312  1.000000  0.956250  1
313  1.000000  0.958036  1
314  1.000000  0.959821  1
315  1.000000  0.961607  1
316  1.000000  0.963393  1
317  1.000000  0.965179  1
318  1.000000  0.966964  1
319  1.000000  1.000000  1

[320 rows x 3 columns]

pphelper.racemodel.gen_cdfs_from_list(data, t_max=None, names=None, return_type=u'dataframe')

Estimate the empirical CDFs for a list of arrays.

The is a convenience function that wraps gen_cdf.

Parameters:
  • data (list of array_like objects) – A list of raw response time arrays. The RTs do not have to be ordered and may contain duplicate values.
  • t_max (int, optional) – Up to which time point (in milliseconds) the model should be calculated. If not specified, the maximum value of the supplied input data will be used.
  • return_type ({‘dataframe’, ‘list’}) – The format of the returned object. dataframe returns a DataFrame, list returns a list of Series.
Returns:

The estimated empirical CDFs as columns of a DataFrame (default) or as a list of Series (if return_type=’list’).
Return type:

DataFrame or list of Series
Raises:

ValueError – If the name parameter does not have the same lengths as the data list.

See also

gen_cdf(), gen_cdfs_from_dataframe(), get_percentiles_from_cdf(), gen_step_fun()

Examples

>>> from pphelper.racemodel import gen_cdfs_from_list
>>> import numpy as np
>>> RTs = [np.array([234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270,
 280]), np.array([244, 249, 257, 260, 264, 268, 271, 274, 277, 291])]
>>> gen_cdfs_from_list(RTs, names=['CondA', 'CondB'])
        CondA     CondB
t
0    0.000000  0.000000
1    0.000000  0.000000
2    0.000000  0.000000
3    0.000000  0.000000
4    0.000000  0.000000
5    0.000000  0.000000
6    0.000000  0.000000
7    0.000000  0.000000
8    0.000000  0.000000
9    0.000000  0.000000
10   0.000000  0.000000
11   0.000000  0.000000
12   0.000000  0.000000
13   0.000000  0.000000
14   0.000000  0.000000
15   0.000000  0.000000
16   0.000000  0.000000
17   0.000000  0.000000
18   0.000000  0.000000
19   0.000000  0.000000
20   0.000000  0.000000
21   0.000000  0.000000
22   0.000000  0.000000
23   0.000000  0.000000
24   0.000000  0.000000
25   0.000000  0.000000
26   0.000000  0.000000
27   0.000000  0.000000
28   0.000000  0.000000
29   0.000000  0.000000
..        ...       ...
262  0.828671  0.400000
263  0.835664  0.425000
264  0.842657  0.450000
265  0.849650  0.475000
266  0.856643  0.500000
267  0.863636  0.525000
268  0.870629  0.550000
269  0.877622  0.583333
270  0.884615  0.616667
271  0.892308  0.650000
272  0.900000  0.683333
273  0.907692  0.716667
274  0.915385  0.750000
275  0.923077  0.783333
276  0.930769  0.816667
277  0.938462  0.850000
278  0.946154  0.857143
279  0.953846  0.864286
280  1.000000  0.871429
281  1.000000  0.878571
282  1.000000  0.885714
283  1.000000  0.892857
284  1.000000  0.900000
285  1.000000  0.907143
286  1.000000  0.914286
287  1.000000  0.921429
288  1.000000  0.928571
289  1.000000  0.935714
290  1.000000  0.942857
291  1.000000  1.000000

[292 rows x 2 columns]

pphelper.racemodel.gen_percentiles(n=10)

Calculate n equally spaced percentiles.

Parameters:n (int, optional) – The number of percentiles to generate. Defaults to 10. Floats will be rounded.
Returns:p – 1-dimensional array of the calculated percentiles.
Return type:ndarray
Raises:TypeError – If the supplied percentile number could not be converted to a rounded integer.

See also

get_percentiles_from_cdf()

Examples

>>> from pphelper.racemodel import gen_percentiles
>>> gen_percentiles()
array([ 0.05,  0.15,  0.25,  0.35,  0.45,  0.55,  0.65,  0.75,  0.85,  0.95])
pphelper.racemodel.gen_step_fun(rts)

Generate a step function from an observed response time distribution.

Parameters:rts (array_like) – The input data (usually response times) to generate a step function from. Does not have to be ordered and may contain duplicates.
Returns:A Series of the ordered response times (smallest to largest), indexed by their respective percentiles.
Return type:Series

See also

gen_cdf(), gen_cdfs_from_dataframe(), gen_cdfs_from_list()

Examples

>>> from pphelper.racemodel import gen_step_fun
>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> RTs = np.array([234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270, 280])
>>> sf = gen_step_fun(RTs)
>>> plt.step(sf, sf.index, where='post'); plt.show()
pphelper.racemodel.get_percentiles_from_cdf(cdf, p=None, num_p=10, time_index=u't')

Interpolate the percentile boundaries.

Parameters:
  • cdf (Series) – The cumulative distribution polygon. Usually generated by gen_cdf().
  • p (array_like, optional) – The percentiles for which to get values from the polygon. Usually generated by gen_percentiles(). If this is supplied, the num_p argument will be ignored.
  • num_p (int, optional) – The number of equally spaced percentiles to generate. Will be ignored if p is supplied. Defaults to 10.
  • time_index (str, optional) – The name of the index storing the time (in milliseconds). This will only be used if the supplied CDF is a pandas Series with a MultiIndex. Defaults to t.
Returns:

Returns a Series of interpolated percentile boundaries (fictive response times).
Return type:

Series
Raises:

TypeError – If the supplied percentile object could not be cast into an array, or if the CDF object is not a Series.

See also

gen_cdf(), gen_cdfs_from_list(), gen_cdfs_from_dataframe(), gen_percentiles()

Examples

>>> from pphelper.racemodel import gen_cdf, gen_percentiles, get_percentiles_from_cdf
>>> import numpy as np
>>> RTs = np.array([234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270, 280])
>>> cdf = gen_cdf(RTs)
>>> percentiles = gen_percentiles(5)
>>> get_percentiles_from_cdf(cdf, percentiles)
p
0.1    237.20
0.3    241.35
0.5    245.00
0.7    255.20
0.9    272.00
dtype: float64
pphelper.racemodel.sum_cdfs(cdfs)

Calculate the sum of multiple cumulative distribution functions.

Parameters:

cdfs (list) – A list of CDFs generated with gen_cdf, gen_cdfs_from_list, or gen_cdfs_from_dataframe.
Returns:

The sum of the CDFs in the interval [0, 1], indexed by the time in milliseconds.
Return type:

Series
Raises:
  • ValueError – If the supplied CDFs have unequal lengths.
  • IndexError – If the indices of the supplied CDF Series objects do not match.

Notes

First calculates the sum of the CDFs, and returns the element-wise minima min[(sum, 1).

See also

gen_cdf(), gen_cdfs_from_dataframe(), gen_cdfs_from_list()

Examples

>>> from pphelper.racemodel import gen_cdfs_from_list, sum_cdfs
>>> import numpy as np
>>> RTs = [np.array([234, 238, 240, 240, 243, 243, 245, 251, 254, 256, 259, 270, 280]), np.array([244, 249, 257, 260, 264, 268, 271, 274, 277, 291])]
>>> cdfs = gen_cdfs_from_list(RTs, names=['A', 'B'])
>>> sum_cdfs([cdfs['A'], cdfs['B']])
t
0     0
1     0
2     0
3     0
4     0
5     0
6     0
7     0
8     0
9     0
10    0
11    0
12    0
13    0
14    0
...
277    1
278    1
279    1
280    1
281    1
282    1
283    1
284    1
285    1
286    1
287    1
288    1
289    1
290    1
291    1
Length: 292, dtype: float64

The utils Module

Some functions that come in handy when working with psychophysics datasets.

Provides

  • d_prime : Calculate the sensitivity index d’ (“d-prime”).
  • criterion : Calculate the decision criterion C.
pphelper.sdt.a_prime(hits, false_alarms, n, nafc=1)

Calculate the sensitivity index A’.

Parameters:
  • hits (float) – The number of hits when detecting a signal.
  • false_alarms (float) – The number of false alarms.
  • n (int) – The number of trials in target and no-target trials.
  • nafc (int, optional) – The number of alternative choices in the task. A value of 1 implies a Yes/No task. Defaults to 1.
Returns:

A – The calculated A’.
Return type:

float

Example

>>> from pphelper import sdt
>>> sdt.A_prime(20, 10, 25)
0.79166666666666674
pphelper.sdt.criterion(hits, false_alarms, n, nafc=1)

Calculate the decision criterion C.

Parameters:
  • hits (float) – The number of hits when detecting a signal.
  • false_alarms (float) – The number of false alarms.
  • n (int) – The number of trials in target and no-target trials.
  • nafc (int, optional) – The number of alternative choices in the task. A value of 1 implies a Yes/No task. Defaults to 1.
Returns:

C – The decision criterion. This will be zero for an unbiased observer, and non-zero otherwise. In a 1-AFC (Yes/No) task, a value smaller than 0 implies a bias to responding “Yes”, and a value greater than 0 a bias to responding “No”.
Return type:

float

Example

>>> from pphelper import sdt
>>> sdt.criterion(20, 10, 25)
-0.29413706521855731
pphelper.sdt.d_prime(hits, false_alarms, n, nafc=1)

Calculate the sensitivity index d’ (“d-prime”).

Parameters:
  • hits (float) – The number of hits when detecting a signal.
  • false_alarms (float) – The number of false alarms.
  • n (int) – The number of trials in target and no-target trials.
  • nafc (int, optional) – The number of alternative choices in the task. A value of 1 implies a Yes/No task. Defaults to 1.
Returns:

d – The calculated d’ value, z(hit_rate) - z(fa_rate).
Return type:

float

Example

>>> from pphelper import sdt
>>> sdt.d_prime(20, 10, 25)
1.094968336708714

The hardware Module

Olfactometer

class pphelper.hardware.Olfactometer(ni_lines=u'Dev1/port0/line0:7', ni_trigger_line=None, ni_task_name=u'Olfactometer', use_threads=True)

Bases: pphelper.hardware._StimulationApparatus

Provides an interface to the ValveLink devices used to control olfactometers.

add_stimulus(name, bitmask, duration=1, bitmask_offset=None, trigger_time=None, replace=False, **kwargs)

Add a stimulus to the stimulus set of this apparatus.

Parameters:
  • name (string) – A unique identifier of the stimulus to add.
  • bitmask (array_like) – The bitmask specifying the valve positions required to present this stimulus.
  • duration (float, optional) – The duration of the stimulation, specified in seconds. Defaults to 1 second.
  • bitmask_offset (array_like, optional) – The bitmask specifying the valve positions after the stimulation has finished. If not specified, all valves will be closed at the end of the stimulation.
  • trigger_time (float, optional) – The time (in terms of the psychopy.core.getTime timebase) at which the stimulation should be triggered. If None, trigger immediately. Defaults to None.
  • replace (bool, optional) – Whether an already existing stimulus of the same name should be replaced or not. Defaults to False.

Notes

Any additional keyword arguments will be added as additional stimulus properties.

See also

remove_stimulus(), select_stimulus(), stimulate()

remove_stimulus(name)

Remove the specified stimulus, identified by its unique name, from the stimulus list.

Parameters:name (string) – The unique name of the stimulus to remove.
select_stimulus(name)

Select the specified stimulus for the next stimulation.

Parameters:name (string) – The unique name of the stimulus to select.
stimulate(blocking_wait=False)

Start the stimulation with the currently selected stimulus.

The trigger pulse will open the valves. They are then left open for the intended duration of the stimulus. After that, they will be switched to the offset state specified by the stimulus.

Parameters:blocking_wait (bool, optional) – Specifies whether the stimulation thread should be joined or not, i.e. whether we should wait for it to finish (blocking other operations), or return immediately. This parameter will be ignored if threads are not used for stimulation. Defaults to False, i.e. non-blocking behavior.

See also

add_stimulus(), select_stimulus()

Notes

stimulate invokes _stimulate, which itself unsets the currently selected stimulus at the end of the stimulation. You have to invoke select_stimulus again before you can call stimulate again.

stimuli

A list of all stimuli added to this stimulation apparatus.

See also

add_stimulus, remove_stimulus

stimulus

The currently selected stimulus.

This stimulus will be presented when invoking stimulate. It can be set using select_stimulus.

See also

select_stimulus, stimulate

AnalogInput

class pphelper.hardware.AnalogInput(ni_input_line=u'Dev1/ai0', ni_trigger_line=None, sampling_duration=3, sampling_rate=2000, ni_task_name=u'AnalogInput')

Analog data acquisition using a National Instruments board.

get_data()

Return the acquired data.

If the acquisition is not finished by the time this method is called, it will first wait until finished (blocking other processing) and then return the data.

samples_to_acquire

The number of samples to acquire in the acquisition. This is the product of the sampling rate and the sampling duration.

sampling_duration

The duration (in seconds) of data acquisition.

sampling_rate

The sampling rate (in Hz) of the analog data acquisition.

trigger()

Return the acquired data.

If the acquisition is not finished by the time this method is called, it will first wait until finished (blocking other processing) and then return the data.

Gustometer

class pphelper.hardware.Gustometer(pulse_duration=0.1, pause_duration=0.2, gusto_ip=u'192.168.0.1', gusto_port=40175, local_ip=u'192.168.0.10', local_port=40176, ni_trigger_out_line=u'Dev1/PFI1', ni_trigger_in_line=u'Dev1/ctr0', ni_trigger_out_task_name=u'GustometerOut', ni_trigger_in_task_name=u'GustometerIn', use_threads=True)

Provide an interface to the Burghart GU002 gustometer.

add_stimulus(name, classnum, trigger_time=None, replace=False, **kwargs)

Add a stimulus to the stimulus set of this apparatus.

Parameters:
  • name (string) – A unique identifier of the stimulus to add.
  • classnum (int) – The stimulus class number, as defined in the Gusto Control software.
  • trigger_time (float, optional) – The time (in terms of the psychopy.core.getTime timebase) at which the stimulation should be triggered. If None, trigger immediately. Defaults to None.
  • replace (bool, optional) – Whether an already existing stimulus of the same name should be replaced or not. Defaults to False.

Notes

Any additional keyword arguments will be added as additional stimulus properties.

See also

select_stimulus(), remove_stimulus(), stimulate()

load_classfile(filename)

Load a classes file in the Gusto Control software.

Parameters:filename (string) – The filename of the classes file to be loaded, including the file extension (typically .cla).
remove_stimulus(name)

Remove the specified stimulus, identified by its unique name, from the stimulus list.

Parameters:name (string) – The unique name of the stimulus to remove.
select_stimulus(name)

Select the specified stimulus for the next stimulation.

Parameters:name (string) – The unique name of the stimulus to select.
stimulate(blocking_wait=False)

Start the stimulation with the currently selected stimulus.

The trigger pulse will open the valves. They are then left open for the intended duration of the stimulus. After that, they will be switched to the offset state specified by the stimulus.

Parameters:blocking_wait (bool, optional) – Specifies whether the stimulation thread should be joined or not, i.e. whether we should wait for it to finish (blocking other operations), or return immediately. This parameter will be ignored if threads are not used for stimulation. Defaults to False, i.e. non-blocking behavior.

See also

add_stimulus(), select_stimulus()

Notes

stimulate invokes _stimulate, which itself unsets the currently selected stimulus at the end of the stimulation. You have to invoke select_stimulus again before you can call stimulate again.

stimuli

A list of all stimuli added to this stimulation apparatus.

See also

add_stimulus, remove_stimulus

stimulus

The currently selected stimulus.

This stimulus will be presented when invoking stimulate. It can be set using select_stimulus.

See also

select_stimulus, stimulate

trigger_conf(duration=0.9, int_taste=100, int_bg=100)

Configure the trigger on the gusto.

Parameters:
  • duration (int, optional) – Trigger duration (stimulation duration) in seconds. Defaults to 0.9s.
  • int_taste (int) – Taste intensity in percent. Defaults to 100%.
  • int_bg (int) – Background intensity in percent. Defaults to 100%.

The image Module

pphelper.image

Provides

  • fft_image : Perform an FFT on the supplied image array.

  • lowpass_filter_image : Load an image from a file, and low-pass

    filter via a Gaussian kernel.

pphelper.image.fft_image(image)

Perform an FFT on the supplied image array.

Parameters:image (ndarray) – An array of the image
Returns:A namedtuple containing the the fast-fourier transform, the amplitude and phase.
Return type:namedtuple
pphelper.image.lowpass_filter_image(image=None, filename=None, flatten=False, sigma=3)

Load an image from a file, and low-pass filter via a Gaussian kernel.

Parameters:
  • image (ndarray, optional) – The image to be processed. This will usually have been created using scipy.misc.imread or a similar function. If this argument is present, filename will be ignored.
  • filename (string, optional) – The name of the image file to load and process. Will be ignored is image_array is not None.
  • flatten (bool, optional) – Whether to “flatten” the image before filtering, i.e. convert it to grayscale.
  • sigma (scalar, optional) – The standard deviation for Gaussian kernel. See scipy.ndimage.filters.gaussian_filter.
Returns:

The lowpass-filtered image.
Return type:

ndarray

See also

scipy.ndimage.gaussian_filter()

The utils Module

Some functions that come in handy when working with psychophysics datasets.

Provides

  • add_zero_padding : Convert numbers (typically participant IDs) to strings of specific length, with leading zeros where necessary.
  • get_max_from_list : Return the maximum value from a list or a list of lists.
pphelper.utils.add_zero_padding(data, length=3, return_series=True)

Convert input values to strings and add a zero-padding.

Parameters:
  • data (array_like) – The data to process.
  • length (int, optional) – The desired length of the padded output values.
  • return_series (bool, optional) – If True, return a pandas Series object. If false, return a numpy array.
Returns:

result – The padded input vector. All strings are created as unicode literals.
Return type:

Series or ndarray

Notes

If length is less than the length of one of the elements, these elements will be converted to strings only and returned. They will obviously not be zero-padded, but they will also not be truncated.

pphelper.utils.get_max_from_list(x)

Return the maximum value from a list or a list of lists.

Parameters:x (list) – A list or a list of lists.
Returns:The maximum value.
Return type:float