ibllib.pipes.widefield_tasks

The widefield data extraction pipeline.

The widefield pipeline requires task data extraction using the FPGA (ephys_preprocessing), optogenetics, camera extraction and widefield image data compression, SVD and correction.

Pipeline:

  1. Data renamed to be ALF-compliant and symlinks created with old names for use by wfield

  2. Raw image data is compressed

  3. Renamed and compressed files are registered to Alyx, imaging snapshots attached as Alyx notes

  4. Preprocessing run to produce

Classes

WidefieldCompress

WidefieldFOV

WidefieldPreprocess

WidefieldRegisterRaw

WidefieldSync

class WidefieldRegisterRaw(session_path, **kwargs)[source]

Bases: WidefieldTask, RegisterRawDataTask

priority = 100
job_size = 'small'
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)

class WidefieldCompress(session_path, **kwargs)[source]

Bases: WidefieldTask

priority = 90
job_size = 'large'
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)

class WidefieldPreprocess(session_path, **kwargs)[source]

Bases: WidefieldTask

priority = 80
job_size = 'large'
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)

tearDown()[source]

Function after runs() Does not run if a lock is encountered by the task (status -2)

class WidefieldSync(session_path, **kwargs)[source]

Bases: WidefieldTask

priority = 40
job_size = 'small'
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)

class WidefieldFOV(session_path, **kwargs)[source]

Bases: WidefieldTask

priority = 40
job_size = 'small'
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)