ibllib.pipes.base_tasks
Abstract base classes for dynamic pipeline tasks.
Classes
dict of list: custom sign off keys corresponding to specific devices |
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Base register raw task. To rename files 1. input and output must have the same length 2. output files must have full filename. |
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- class BehaviourTask(session_path, **kwargs)[source]
Bases:
DynamicTask
- class VideoTask(session_path, cameras, **kwargs)[source]
Bases:
DynamicTask
- class AudioTask(session_path, **kwargs)[source]
Bases:
DynamicTask
- class EphysTask(session_path, **kwargs)[source]
Bases:
DynamicTask
- class WidefieldTask(session_path, **kwargs)[source]
Bases:
DynamicTask
- class MesoscopeTask(session_path, **kwargs)[source]
Bases:
DynamicTask
- get_signatures(**kwargs)[source]
From the template signature of the task, create the exact list of inputs and outputs to expect based on the available device collection folders
Necessary because we don’t know in advance how many device collection folders (“imaging bouts”) to expect
- load_sync()[source]
Load the sync and channel map.
This method may be expanded to support other raw DAQ data formats.
- Returns:
one.alf.io.AlfBunch – A dictionary with keys (‘times’, ‘polarities’, ‘channels’), containing the sync pulses and the corresponding channel numbers.
dict – A map of channel names and their corresponding indices.
- class RegisterRawDataTask(session_path, **kwargs)[source]
Bases:
DynamicTask
Base register raw task. To rename files
input and output must have the same length
output files must have full filename
- priority = 100
- job_size = 'small'
- register_snapshots(unlink=False, collection=None)[source]
Register any photos in the snapshots folder to the session. Typically imaging users will take numerous photos for reference. Supported extensions: .jpg, .jpeg, .png, .tif, .tiff
If a .txt file with the same name exists in the same location, the contents will be added to the note text.
- Parameters:
unlink (bool) – If true, files are deleted after upload.
collection (str, list, optional) – Location of ‘snapshots’ folder relative to the session path. If None, uses ‘device_collection’ attribute (if exists) or root session path.
- Returns:
The newly registered Alyx notes.
- Return type:
list of dict
- class ExperimentDescriptionRegisterRaw(session_path, **kwargs)[source]
Bases:
RegisterRawDataTask
dict of list: custom sign off keys corresponding to specific devices
- sign_off_categories = {'neuropixel': ['raw', 'spike_sorting', 'alignment']}
- property signature
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s
(key, value) pairs
- dict(iterable) -> new dictionary initialized as if via:
d = {} for k, v in iterable:
d[k] = v
- dict(**kwargs) -> new dictionary initialized with the name=value pairs
in the keyword argument list. For example: dict(one=1, two=2)