ibllib.plots.snapshot

Classes

ReportSnapshot

ReportSnapshotProbe

Snapshot

A class to register images in form of Notes, linked to an object on Alyx.

class ReportSnapshot(session_path, object_id, content_type='session', **kwargs)[source]

Bases: ibllib.pipes.tasks.Task

register_images(widths=None, function=None, extra_dict=None)[source]

Registers images to alyx database :return:

class ReportSnapshotProbe(pid, session_path=None, one=None, brain_regions=None, brain_atlas=None, **kwargs)[source]

Bases: ibllib.plots.snapshot.ReportSnapshot

signature = {'input_files': [], 'output_files': []}
property pid_label

‘SWC_054_2020-10-05_001_probe01’

Type

returns a probe insertion stub to label titles, for example

abstract get_probe_signature()[source]
get_histology_status()[source]

Finds at which point in histology pipeline the probe insertion is :return:

get_channels(alf_object, collection)[source]
register_images(widths=None, function=None)[source]

Registers images to alyx database :return:

class Snapshot(object_id, content_type='session', one=None)[source]

Bases: object

A class to register images in form of Notes, linked to an object on Alyx.

Parameters
  • object_id – The id of the object the image should be linked to

  • content_type – Which type of object to link to, e.g. ‘session’, ‘probeinsertion’, ‘subject’,

default is ‘session’ :param one: An ONE instance, if None is given it will be instantiated.

plot()[source]

Placeholder method to be overriden by child object :return:

generate_image(plt_func, plt_kwargs)[source]

Takes a plotting function and adds the output to the Snapshot.images list for registration

Parameters
  • plt_func – A plotting function that returns the path to an image.

  • plt_kwargs – Dictionary with keyword arguments for the plotting function

register_image(image_file, text='', json_field=None, width=None)[source]

Registers an image as a Note, attached to the object specified by Snapshot.object_id

Parameters
  • image_file – Path to the image to to registered

  • text – str, text to describe the image, defaults ot empty string

  • json_field – dict, to be added to the json field of the Note

  • width – width to scale the image to, defaults to None (scale to UPLOADED_IMAGE_WIDTH in alyx.settings.py),

other options are ‘orig’ (don’t change size) or any integer (scale to width=int, aspect ratios won’t be changed)

Returns

dict, note as registered in database

register_images(image_list=None, texts=None, widths=None, jsons=None)[source]

Registers a list of images as Notes, attached to the object specified by Snapshot.object_id. The images can be passed as image_list. If None are passed, will try to register the images in Snapshot.images.

Parameters
  • image_list – List of paths to the images to to registered. If None, will try to register any images in Snapshot.images

  • texts – List of text to describe the images. If len(texts)==1, the same text will be used for all images

  • widths – List of width to scale the figure to (see Snapshot.register_image). If len(widths)==1, the same width will be used for all images

  • jsons – List of dictionaries to populate the json field of the note in Alyx. If len(jsons)==1, the same dict will be used for all images

Returns

list of dicts, notes as registered in database