stimpyp.stimpy_core.Stimlog#

final class stimpyp.stimpy_core.Stimlog#

Bases: AbstractStimlog

class for handle the stimlog file for stimpy bitbucket 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

P = number of acquisition sample pulse (Visual parameters)

M = number of statemachine pulse

__init__(riglog, file_path, reset_mapping=None, diode_offset=True, sequential_offset=True)#

Parameters:

riglog (RiglogData) – RiglogData
file_path (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader) – stimlog filepath
diode_offset (bool) – If do the diode offset to sync the time to riglog
sequential_offset (bool) – do the sequential offset to sync time with RiglogData
reset_mapping (dict[int, list[str]] | None)

Methods

`__init__`(riglog, file_path[, reset_mapping, ...])
`get_log_dict_dataframe`()	Log dict dataframe.
`get_photo_indicator_dataframe`()	Photo Indicator dataframe.
`get_state_machine_dataframe`()	State Machine dataframe.
`get_stim_pattern`([with_dur])	Get stimulus pattern container
`get_visual_stim_dataframe`([stim_only])	Get the stimlog visual stimulation logging as dataframe.
`session_trials`()	get the session:SessionInfo dictionary (experimental and user-specific)
`stim_square_pulse_event`([sampling_rate])	Get the stimulation on-off square pulse 0,1 consecutive event

Attributes

`config`	i.e., name, commit hash, missed_frames, ...
`exp_end_time`	experimental end time (in sec, synced to riglog time with diode offset)
`exp_start_time`	experimental start time (in sec, synced to riglog time with diode offset)
`log_header`	i.e., {10: ['code','presentTime','iStim', ...], 20: ['code', 'elapsed', 'cycle', ...]}
`log_info`	i.e., {10: 'vstim', 20: 'stateMachine'}
`n_cycles`	Number of cycle for each trial
`profile_dataframe`	Dataframe with columns:
`stim_end_time`	the last stimulation end time (in sec, synced to riglog time with diode offset)
`stim_start_time`	the first stimulation start time (in sec, synced to riglog time with diode offset)
`stimulus_segment`	stimulation time segment (on-off) in sec (N, 2)
`time_offset`	time (in sec) to sync stimlog time to riglog
`time_offset_statemachine`	time offset approach using statemachine
`photo_state`	photo diode on-off.
`indicator_flag`	accumulated and zero foreach stim.
`s_on_v`	statemachine sync time on v, use for time sync if diode signal not reliable.
`state_time`	Array[float, M]
`state_cycle`	Array[float, M]
`state_new_state`	Array[float, M]
`state_old_state`	Array[float, M]
`state_elapsed`	Array[float, M]
`state_trial_type`	Array[float, M]
`time`	acquisition time in sec.
`stim_index`	stimulation index.
`trial_index`	trial index.
`contrast`	stimulus contrast.
`frame_index`	stimulation frame index, recount every N.
`ori`	direction in deg.
`sf`	spatial frequency in cyc/deg.
`tf`	temporal frequency in hz.
`phase`	stimulus phase for each N.
`pos_x`	object center position X.
`pos_y`	object center position Y.
`size_x`	object size width.
`size_y`	object size height.
`flick`	TODO.
`interpolate`	whether do the interpolate, Array[bool, P]
`mask`	TODO.
`pattern`	object pattern.

config: dict[str, Any] = {}#: i.e., name, commit hash, missed_frames, …

log_info: dict[int, str] = {}#: i.e., {10: ‘vstim’, 20: ‘stateMachine’}

log_header: dict[int, list[str]] = {}#: i.e., {10: [‘code’,’presentTime’,’iStim’, …], 20: [‘code’, ‘elapsed’, ‘cycle’, …]}

photo_state: ndarray#: photo diode on-off. Array[int, P]. value domain in (0,1)

indicator_flag: ndarray#: accumulated and zero foreach stim. Array[int, P]. value domain in (1, …)

s_on_v: ndarray#: statemachine sync time on v, use for time sync if diode signal not reliable. Array[float, M]

state_time: ndarray#: Array[float, M]

state_cycle: ndarray#: Array[float, M]

state_new_state: ndarray#: Array[float, M]

state_old_state: ndarray#: Array[float, M]

state_elapsed: ndarray#: Array[float, M]

state_trial_type: ndarray#: Array[float, M]

__init__(riglog, file_path, reset_mapping=None, diode_offset=True, sequential_offset=True)#

Parameters:

riglog (RiglogData) – RiglogData
file_path (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader) – stimlog filepath
diode_offset (bool) – If do the diode offset to sync the time to riglog
sequential_offset (bool) – do the sequential offset to sync time with RiglogData
reset_mapping (dict[int, list[str]] | None)

get_visual_stim_dataframe(stim_only=True)#

Get the stimlog visual stimulation logging as dataframe:

┌─────────────┬───────┬────────┬───────┬───┬───────┬──────┬───────────┬──────────┐
│ presentTime ┆ iStim ┆ iTrial ┆ photo ┆ … ┆ ori   ┆ sf   ┆ phase     ┆ stim_idx │
│ ---         ┆ ---   ┆ ---    ┆ ---   ┆   ┆ ---   ┆ ---  ┆ ---       ┆ ---      │
│ f64         ┆ f64   ┆ f64    ┆ f64   ┆   ┆ f64   ┆ f64  ┆ f64       ┆ f64      │
╞═════════════╪═══════╪════════╪═══════╪═══╪═══════╪══════╪═══════════╪══════════╡
│ 904.048038  ┆ 69.0  ┆ 0.0    ┆ 0.0   ┆ … ┆ 270.0 ┆ 0.16 ┆ 0.066667  ┆ 1.0      │
│ …           ┆ …     ┆ …      ┆ …     ┆ … ┆ …     ┆ …    ┆ …         ┆ …        │
│ 2710.807378 ┆ 45.0  ┆ 4.0    ┆ 0.0   ┆ … ┆ 270.0 ┆ 0.04 ┆ 11.933333 ┆ 179.0    │
│ 2710.824102 ┆ 45.0  ┆ 4.0    ┆ 0.0   ┆ … ┆ 270.0 ┆ 0.04 ┆ 11.933333 ┆ 179.0    │
└─────────────┴───────┴────────┴───────┴───┴───────┴──────┴───────────┴──────────┘

Parameters:: stim_only (bool) – only show the stimulation epoch
Returns:: visual stimuli dataframe
Return type:: DataFrame

get_state_machine_dataframe()#

State Machine dataframe:

┌──────────┬───────┬──────────┬──────────┬──────────────┬───────────┐
│ elapsed  ┆ cycle ┆ newState ┆ oldState ┆ stateElapsed ┆ trialType │
│ ---      ┆ ---   ┆ ---      ┆ ---      ┆ ---          ┆ ---       │
│ f64      ┆ f64   ┆ f64      ┆ f64      ┆ f64          ┆ f64       │
╞══════════╪═══════╪══════════╪══════════╪══════════════╪═══════════╡
│ 902.601  ┆ 0.0   ┆ 1.0      ┆ 0.0      ┆ 902.601      ┆ 0.0       │
│ 904.614  ┆ 0.0   ┆ 2.0      ┆ 1.0      ┆ 2.012        ┆ 0.0       │
│ …        ┆ …     ┆ …        ┆ …        ┆ …            ┆ …         │
│ 2711.425 ┆ 0.0   ┆ 3.0      ┆ 2.0      ┆ 3.01         ┆ 0.0       │
│ 2711.425 ┆ 0.0   ┆ 0.0      ┆ 3.0      ┆ 0.0          ┆ 0.0       │
└──────────┴───────┴──────────┴──────────┴──────────────┴───────────┘

Returns:
Return type:: DataFrame

property exp_start_time: float#: experimental start time (in sec, synced to riglog time with diode offset)

property exp_end_time: float#: experimental end time (in sec, synced to riglog time with diode offset)

property stim_start_time: float#: the first stimulation start time (in sec, synced to riglog time with diode offset)

property stim_end_time: float#: the last stimulation end time (in sec, synced to riglog time with diode offset)

property stimulus_segment: ndarray#: stimulation time segment (on-off) in sec (N, 2)

property time_offset: float | ndarray#: time (in sec) to sync stimlog time to riglog

property time_offset_statemachine: ndarray#: time offset approach using statemachine

session_trials()#

get the session:SessionInfo dictionary (experimental and user-specific)

Return type:: dict[str, SessionInfo]

get_stim_pattern(with_dur=False)#

Get stimulus pattern container

Parameters:: with_dur (bool) – if extract theoretical duration value from protocol file
Returns:: AbstractStimulusPattern based on stim type
Return type:: AbstractStimulusPattern

property profile_dataframe: DataFrame#

Dataframe with columns:

stim type index: i_stims
trial index: i_trials

get_log_dict_dataframe()#

Log dict dataframe. Github version only

Return type:: DataFrame

get_photo_indicator_dataframe()#

Photo Indicator dataframe. Github version only

Return type:: DataFrame

property n_cycles: list[int]#: Number of cycle for each trial

stim_square_pulse_event(sampling_rate=30.0)#

Get the stimulation on-off square pulse 0,1 consecutive event

Parameters:: sampling_rate (float) – sampling rate for the time domain interpolation
Returns:: Stimulus rig event
Return type:: RigEvent

time: ndarray#: acquisition time in sec. Array[float, P]

stim_index: ndarray#: stimulation index. Array[int, P]

trial_index: ndarray#: trial index. Array[int, P]

contrast: ndarray#: stimulus contrast. Array[int, P]. value domain in (0,1)

frame_index: ndarray#: stimulation frame index, recount every N. Array[int, P]

ori: ndarray#: direction in deg. Array[float, P]

sf: ndarray#: spatial frequency in cyc/deg. Array[float, P]

tf: ndarray#: temporal frequency in hz. Array[float, P]

phase: ndarray#: stimulus phase for each N. Array[float, P]

pos_x: ndarray#: object center position X. Array[float, P]

pos_y: ndarray#: object center position Y. Array[float, P]

size_x: ndarray#: object size width. Array[int, P]

size_y: ndarray#: object size height. Array[int, P]

flick: ndarray#: TODO. Array[int, P]

interpolate: ndarray#: whether do the interpolate, Array[bool, P]

mask: ndarray#: TODO. Array[bool|None, P]

pattern: ndarray#: object pattern. Array[str, P]

stimpyp.stimpy_core.Stimlog#

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