neuralib.atlas.brainrender.core.BrainRenderCLI

class neuralib.atlas.brainrender.core.BrainRenderCLI[source]

Bases: AbstractParser

Reconstruct a 3D brain view used brainrender module

__init__()

Methods

`__init__`()
`export`(reconstructor[, output, areas, alpha])	Export reconstruction as html
`get_atlas_brain_globe`([check_latest])
`main`([args, exit_on_error])	parsing the commandline input args and set the argument attributes, then call `run()`.
`new_parser`(**kwargs)	create an `argparse.ArgumentParser`.
`post_parsing`()	called when all argument attributes are set but before `run()`.
`render`()	brainrender interactive
`render_output`()	io handling.
`run`()	called when all argument attributes are set
`video_maker`(output_file)	generate video

Attributes

`DEFAULT_REGION_COLORS`
`DESCRIPTION`	parser description.
`EPILOG`	parser epilog.
`GROUP_OPTIONAL`
`GROUP_OUTPUT`
`GROUP_REGION`
`GROUP_SETTINGS`
`USAGE`	parser usage.
`annotation`	whether draw point annotation.
`background`	background color
`camera_angle`	camera angle
`coordinate_space`	which coordinate space, by default ccf
`hemisphere`	which hemisphere for rendering the region
`logger`
`no_root`	render without root(brain) mesh
`output`	output path for the html, if None, preview
`print_name`	print acronym and the corresponding name
`print_tree`	print tree for the available regions for the given source
`region_colors`	region(s) color
`regions`	region(s) name
`regions_alpha`	region alpha value
`root_alpha`	root alpha
`shader_style`	Shader style to use
`source`	atlas source name.
`title`	title added to the top of the window
`tree_init`	init region for the tree print
`video_output`	video output path
`scene`

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()[source]

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()[source]: called when all argument attributes are set

render()[source]: brainrender interactive

render_output()[source]: io handling. i.e., video, html output

classmethod export(reconstructor, output=None, areas=None, alpha=0.15)[source]

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)[source]

generate video

Parameters:: output_file (Path) – video output path

get_atlas_brain_globe(check_latest=False)[source]

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