neuralib.atlas.brainrender.core

neuralib.atlas.brainrender.core.RoiType

RoiType for rendering points

class neuralib.atlas.brainrender.core.BrainReconstructor

Wrapper for brainrender 3D reconstruction

DESCRIPTION: str = 'reconstruct a 3D brain view used brainrender module'

parser description.

EPILOG: str = '\n        Data shape of points.\n        (N, 3) floating matrix with row (x, y, z), or (N, 4) with row (x, y, z, r),\n        where r indicate the index (start from 1, 0 means non-region) in --regions.\n        Correspond points and region will use the same color.\n        '

parser epilog. Could be override as a method if its content is dynamic-generated.

title: str

source: str

atlas source name. allen_human_500um as human

no_root: bool

render without root(brain) mesh

with_source: bool

whether draw the location for source (experiment dependent)

csv_file: Path | None

csv file

points_file: list[Path]

radius: float

each roi radius

output: Path

output path for the html, if None, preview

regions: str

region_colors: str

regions_alpha: float

region alpha

hemisphere: Literal['right', 'left', 'both']

which hemisphere

video_output: Path | None

video output

background: Literal['white', 'black']

background color

camera_angle: Literal['sagittal', 'sagittal2', 'frontal', 'top', 'top_side', 'three_quarters']

shader_style: Literal['metallic', 'cartoon', 'plastic', 'shiny', 'glossy']

scene: Scene

__init__()

post_parsing()

called when all argument attributes are set but before run().

It is used for a common operation for a common option class, for example, checking arguments before doing things.

run()

called when all argument attributes are set

property n_files: int

add_points(rois_list)

Parameters:

rois_list (list[list[ndarray] | ndarray])

add_points_from_file()

load()

Overwrite by children

reconstruct()

classmethod export(reconstructor, output=None, areas=None, alpha=0.15)

export reconstruction as html TODO check export / view were different hemispheres, seems opposite in export..

Parameters:

• reconstructor (BrainReconstructor | None) – BrainRenderReconstructor if use the current scene, and –output cli. Otherwise, general func usage

• output (Path | None)

• areas (list[str] | None) – list of area(s)

• alpha (float)

Returns:

video_maker(output_file)

Parameters:

output_file (Path)

get_atlas_brain_globe(check_latest=False)

Return type:

BrainGlobeAtlas