neurocarto.views.atlas

class neurocarto.views.atlas.AtlasBrainView

Atlas mouse brain displaying view component.

Used command-line arguments: * ‘–atlas’ : brain name. * ‘–atlas-root’ : data saving directory.

Event Call chain

(boundary UI components)
    -/-> (event callback)
        -> update_boundary_transform()
            -> on_boundary_transform()

(atlas UI components)
    (slice_select) -/-> (event callback)
        -> update_brain_view()
            -> update_brain_slice(update_image=False)
            -> update_boundary_transform()
                -> on_boundary_transform()
                    -> update_image()
                        -> update_region_image()
    (region_choose) -/-> (event callback)
        -> update_region_image()
    (other) -/-> (event callback)
        -> update_brain_slice()
            -> update_image()
                -> update_region_image()

__init__(config, *, logger='neurocarto.view.atlas')

Parameters:

config (CartoConfig)
logger (str)

property name: str: view name

property width: float: Width of image

property height: float: Height of image

setup(f, **kwargs)

Setup controls and plotting.

Parameters:

f (figure) – figure in middle panel
kwargs – control or plotting related parameters.

Returns:

row list.

Return type:

list[UIElement]

save_state()

Save current state into S.

Returns:: json-serializable instance.
Return type:: AtlasBrainViewState | None

restore_state(state)

Restore state from state.

Parameters:: state (AtlasBrainViewState) – json-deserializable instance.

start(): Invoked when figure is ready.

clear_labels(): Clear all labels

len_label()

number of the labels

Return type:: int

get_label(i)

Get the label text at index i.

Parameters:: i (int) – index
Returns:: label text
Raises:: IndexError – index i out of bound
Return type:: Label

find_label(pos)

Find a label around the given position.

Parameters:: pos (tuple[float, float]) – (x, y) um
Returns:: found label
Return type:: Label | None

index_label(text)

Find index of a label which its content equals to text.

Parameters:: text (str) – label text
Returns:: label index. None if not found.
Return type:: int | None

focus_label(label)

Move slice to the label’s position.

Note

Only label which its origin refer on bregma works. Otherwise, nothing will happen.

Parameters:: label (int | str | Label) – label index, content or a {Label}.

add_label(text, pos, *, origin='bregma', color='cyan', replace=True)

Add a label.

Parameters:

text (str) – label text
pos (tuple[float, float] | tuple[float, float, float]) – label position
origin (str) – origin reference point
color (str) – label color
replace – replace label which has same text content

Return type:

Label

del_label(index)

Remove labels.

Parameters:: index (int | str | Label | list[int | str | Label]) – index, list of index.

on_boundary_transform(state)

Image transforming updating callback.

Parameters:: state (BoundaryState) – updated boundary parameters.

class neurocarto.views.atlas.AtlasBrainViewState

class neurocarto.views.atlas.Label

Label(text, pos, ref, color)

text: str: Alias for field number 0

pos: tuple[float, float, float]: position, either (x, y, 1) or (ap, dv, ml) depends on origin

ref: int: Alias for field number 2

color: str: Alias for field number 3

static __new__(_cls, text, pos, ref, color)

Create new instance of Label(text, pos, ref, color)

Parameters:

text (str)
pos (tuple[float, float, float])
ref (int)
color (str)