stimpyp.stimpy_core.StimpyProtocol

class stimpyp.stimpy_core.StimpyProtocol

Bases: AbstractStimProtocol

class for handle the protocol file for stimpy bitbucket/github version (mainly tested in the commits derived from master branch)

Dimension parameters:

N = numbers of visual stimulation (on-off pairs) = (T * S)

T = number of trials

S = number of Stim Type

C = number of Cycle

__init__(name, options, visual_stimuli, version)

Parameters:

• name (str)

• options (dict[str, Any])

• visual_stimuli (DataFrame)

• version (Literal['pyvstim', 'stimpy-bit', 'stimpy-git', 'debug'])

Methods

__init__(name, options, visual_stimuli, version)
evolve_param_headers()	Get parameter header which set in the 'evolveParams, i.g., 'phase'
load(file)	Load *.prot file
loads(content[, name])	load string

Attributes

background	background for non-stimulation epoch.
blank_duration	blank duration between each visual stimulus (in sec)
controller	protocol controller name
end_blank_duration	blank duration after the visual stimulation epoch
evolve_params	Get value from 'evolveParams'.
is_shuffle	if shuffle stimulation
mask	todo check in stimpy
n_stimuli	number of stimuli (S)
n_trials	(T,)
reward_duration	reward zone duration use in the vr branch
start_blank_duration	blank duration before starting the visual stimulation epoch (in sec)
stim_params
stimulus_type	stimulus type
texture	stimulus texture, {circle, sqr.
tf
total_duration	total protocol duration
trial_blank_duration	blank duration between trials (in sec) TODO check stimpy source code
trial_duration	trial duration
visual_duration	total visual duration
name	protocol name.
options	protocol options
visual_stimuli_dataframe	visual stimuli dataframe.
version	date of major changes

classmethod load(file)

Load *.prot file

Parameters:

file (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader) – file path

Return type:

Self

classmethod loads(content, name='<string>')

load string

Parameters:

• content (str)

• name (str)

Return type:

Self

property controller: str

protocol controller name

property is_shuffle: bool

if shuffle stimulation

property background: float

background for non-stimulation epoch. Note the default value need to check in user-specific stimpy version

property start_blank_duration: int

blank duration before starting the visual stimulation epoch (in sec)

property blank_duration: int

blank duration between each visual stimulus (in sec)

property trial_blank_duration: int

blank duration between trials (in sec) TODO check stimpy source code

property end_blank_duration: int

blank duration after the visual stimulation epoch

property reward_duration: float

reward zone duration use in the vr branch

property trial_duration: int

trial duration

property visual_duration: int

total visual duration

property total_duration: int

total protocol duration

property texture: str

stimulus texture, {circle, sqr… todo check in stimpy}

__init__(name, options, visual_stimuli, version)

Parameters:

• name (str)

• options (dict[str, Any])

• visual_stimuli (DataFrame)

• version (Literal['pyvstim', 'stimpy-bit', 'stimpy-git', 'debug'])

property mask: str

todo check in stimpy

property n_stimuli: int

number of stimuli (S)

property n_trials: int

(T,)

property stim_params: tuple[str, ...]

property stimulus_type: str

stimulus type

name: str

protocol name. related to filename

options: dict[str, Any]

protocol options

visual_stimuli_dataframe: pl.DataFrame

visual stimuli dataframe. row number: S

version: STIMPY_SOURCE_VERSION

date of major changes

class EvoledParameter

Bases: dict[str, Any]

handle the evolveParams header in the protocol file only available in stimpy-bit version

__new__(**kwargs)

clear() → None.  Remove all items from D.

copy() → a shallow copy of D

fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /)

Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D's items

pop(k[, d]) → v, remove specified key and return the corresponding value.

If the key is not found, return the default if given; otherwise, raise a KeyError.

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D's values

__init__(keys, data)

Parameters:

• keys (list[str])

• data (ndarray)

keys() → a set-like object providing a view on D's keys

evolve_param_headers()

Get parameter header which set in the ‘evolveParams, i.g., ‘phase’

Returns:

header list.

Return type:

list[str]

property evolve_params: EvoledParameter

Get value from ‘evolveParams’.

Examples:

>>> log: StimpyProtocol

How many parameters in evolveParams

>>> len(log.evolve_params)

List parameter in ‘evolveParams’

>>> log.evolve_params.keys()

Dose parameter ‘phase’ in ‘evolveParams’?

>>> 'phase' in log.evolve_params

Get phase value from ‘evolveParams’.

>>> log.evolve_params['phase']

Returns:

property tf: ndarray