neuralib.atlas.brainrender.core.BrainRenderCLI

class neuralib.atlas.brainrender.core.BrainRenderCLI

Bases: AbstractParser

Reconstruct a 3D brain view used brainrender module

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

parser description.

DEFAULT_REGION_COLORS = ['lightblue', 'pink', 'turquoise']

GROUP_SETTINGS = 'Basic Settings Option'

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

camera angle

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

Shader style to use

title: str | None

title added to the top of the window

source: str

atlas source name. allen_human_500um as human

root_alpha: float

root alpha

no_root: bool

render without root(brain) mesh

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

background color

coordinate_space: Literal['ccf', 'brainrender']

which coordinate space, by default ccf

GROUP_OPTIONAL = 'Optional Option'

annotation: tuple[str, ...] | None

whether draw point annotation. e.g., 1.5:1:0.4,-3.2:0.8:0.4 for two points

GROUP_REGION = 'Region Option'

regions: str | tuple[str, ...]

region(s) name

region_colors: str | tuple[str, ...] | None

region(s) color

regions_alpha: float

region alpha value

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

which hemisphere for rendering the region

print_tree: bool

print tree for the available regions for the given source

tree_init: str | None

init region for the tree print

print_name: bool

print acronym and the corresponding name

GROUP_OUTPUT = 'Output Option'

video_output: Path | None

video output path

output: Path | None

output path for the html, if None, preview

scene: Scene

logger = <RootLogger root (IO)>

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

render()

brainrender interactive

render_output()

io handling. i.e., video, html output

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

Export reconstruction as html

Parameters:

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

• output (Path | None) – output file path

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

• alpha (float) – brain region alpha

video_maker(output_file)

generate video

Parameters:

output_file (Path) – video output path

get_atlas_brain_globe(check_latest=False)

Return type:

BrainGlobeAtlas

EPILOG: str = None

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

USAGE: str = None

parser usage.

static __new__(cls, *args, **kwargs)

main(args=None, *, exit_on_error=True)

parsing the commandline input args and set the argument attributes, then call run().

Example

if overwrite with the argument default, use args

>>> AbstractParser().main((['--source=allen_mouse_25um', '--region=VISal,VISam,...'], []))

Parameters:

• args (list[str] | tuple[list[str]] | None) – commandline arguments, or a tuple of (prepend, append) arguments

• exit_on_error (bool) – exit when commandline parsed fail. Otherwise, raise a RuntimeError.

classmethod new_parser(**kwargs)

create an argparse.ArgumentParser.

class variable: USAGE, DESCRIPTION and EPILOG are used when creation.

>>> class A(AbstractParser):
...     @classmethod
...     def new_parser(cls, **kwargs) -> argparse.ArgumentParser:
...         return super().new_parser(**kwargs)

Parameters:

kwargs – keyword parameters to ArgumentParser

Returns:

an ArgumentParser.

Return type:

ArgumentParser