core
gait_analysis package:
EventBout
EventBout (event_type:str, event_id:int, start_idx:int, end_idx:int, fps:int)
Analysis of the gait_analysis package is mainly composed of identifying different types of events and their combined analysis thereafter. This class represents the core interface for these analyses, as it bundles all relevant information of such events.
Attributes: self.event_type(str): type of event (e.g. “freezing” or “gait”) self.event_id(int): index of the occurance of this event type in a recording in chronological order self.start_idx(int): frame index in which this event bout starts self.end_idx(int): frame index at which this event bout ends self.fps(int): frames-per-second of the recording self.duration(float): duration of the event bout in s
| Type | Details | |
|---|---|---|
| event_type | str | type of event (e.g. “immobility” or “gait”) |
| event_id | int | evnt index (e.g. 0 for the first occurance of this event type in a recording) |
| start_idx | int | index of the frame at which this event bout starts |
| end_idx | int | index of the frame at which this event bout ends |
| fps | int | frames-per-second value of the corresponding video recording |
| Returns | None |
TrackedRecording
TrackedRecording (filepath:pathlib.Path, week_id:int)
While the analysis depends mainly on the identification of EventBouts and their integrated analyses, TrackedRecordings are the data objects on which these events are identified. They are implemented here as an abstract base class, as they will require slightly different functionalities depending on whether a 2D or 3D tracking needs to be handled.
| Type | Details | |
|---|---|---|
| filepath | Path | the filepath to the output of DLC (.h5 or .csv file) |
| week_id | int | the experimental week post injection in which the recording was performed. Has to be an element of the self.valid_week_ids list |
| Returns | None |
Bodypart
Bodypart (bodypart_id:str, df:pandas.core.frame.DataFrame, fps:int)
Bundles all information and functions needed to process the data of a single bodypart (i.e. marker id). Requires that the coordinates have already been normalized (translated & rotated) and converted to cm.
| Type | Details | |
|---|---|---|
| bodypart_id | str | The ID of the bodypart, i.e. the marker_id |
| df | DataFrame | The normalized (rotated & translated) & converted (in cm) DataFrame that holds the DLC tracking information about this marker |
| fps | int | frames-per-second at which this recording was acquired |
| Returns | None |