webknossos.cli._utils

Utilities to work with the CLI of webknossos.

class VoxelSizeTuple(builtins.tuple):

VoxelSizeTuple(x, y, z)

Create new instance of VoxelSizeTuple(x, y, z)

x

Alias for field number 0

y

Alias for field number 1

z

Alias for field number 2

Inherited Members

builtins.tuple: index; count

class Vec2Int(builtins.tuple):

Vec2Int(x, y)

Create new instance of Vec2Int(x, y)

x

Alias for field number 0

y

Alias for field number 1

Inherited Members

builtins.tuple: index; count

class DistributionStrategy(builtins.str, enum.Enum):

Enum of available distribution strategies.

TODO

As soon as supported by typer this enum should be replaced with typing.Literal in type hint. https://github.com/tiangolo/typer/pull/669

SLURM = <DistributionStrategy.SLURM: 'slurm'>

KUBERNETES = <DistributionStrategy.KUBERNETES: 'kubernetes'>

MULTIPROCESSING = <DistributionStrategy.MULTIPROCESSING: 'multiprocessing'>

DEBUG_SEQUENTIAL = <DistributionStrategy.DEBUG_SEQUENTIAL: 'debug_sequential'>

Inherited Members

enum.Enum: name; value
builtins.str: encode; replace; split; rsplit; join; capitalize; casefold; title; center; count; expandtabs; find; partition; index; ljust; lower; lstrip; rfind; rindex; rjust; rstrip; rpartition; splitlines; strip; swapcase; translate; upper; startswith; endswith; isascii; islower; isupper; istitle; isspace; isdecimal; isdigit; isnumeric; isalpha; isalnum; isidentifier; isprintable; zfill; format; format_map; maketrans

class LayerCategory(builtins.str, enum.Enum):

Enum of available layer categories.

TODO

As soon as supported by typer this enum should be replaced with typing.Literal in type hint. https://github.com/tiangolo/typer/pull/669

COLOR = <LayerCategory.COLOR: 'color'>

SEGMENTATION = <LayerCategory.SEGMENTATION: 'segmentation'>

Inherited Members

enum.Enum: name; value
builtins.str: encode; replace; split; rsplit; join; capitalize; casefold; title; center; count; expandtabs; find; partition; index; ljust; lower; lstrip; rfind; rindex; rjust; rstrip; rpartition; splitlines; strip; swapcase; translate; upper; startswith; endswith; isascii; islower; isupper; istitle; isspace; isdecimal; isdigit; isnumeric; isalpha; isalnum; isidentifier; isprintable; zfill; format; format_map; maketrans

class SamplingMode(builtins.str, enum.Enum):

Enum of available sampling modes.

ANISOTROPIC = <SamplingMode.ANISOTROPIC: 'anisotropic'>

ISOTROPIC = <SamplingMode.ISOTROPIC: 'isotropic'>

CONSTANT_Z = <SamplingMode.CONSTANT_Z: 'constant_z'>

Inherited Members

enum.Enum: name; value
builtins.str: encode; replace; split; rsplit; join; capitalize; casefold; title; center; count; expandtabs; find; partition; index; ljust; lower; lstrip; rfind; rindex; rjust; rstrip; rpartition; splitlines; strip; swapcase; translate; upper; startswith; endswith; isascii; islower; isupper; istitle; isspace; isdecimal; isdigit; isnumeric; isalpha; isalnum; isidentifier; isprintable; zfill; format; format_map; maketrans

class Order(builtins.str, enum.Enum):

Enum of available orders.

C = <Order.C: 'C'>

F = <Order.F: 'F'>

Inherited Members

enum.Enum: name; value
builtins.str: encode; replace; split; rsplit; join; capitalize; casefold; title; center; count; expandtabs; find; partition; index; ljust; lower; lstrip; rfind; rindex; rjust; rstrip; rpartition; splitlines; strip; swapcase; translate; upper; startswith; endswith; isascii; islower; isupper; istitle; isspace; isdecimal; isdigit; isnumeric; isalpha; isalnum; isidentifier; isprintable; zfill; format; format_map; maketrans

def parse_mag(mag_str: str) -> webknossos.geometry.mag.Mag:

Parses str input to Mag

def parse_voxel_size(voxel_size_str: str) -> Tuple[float, float, float]:

Parses str input to tuple of three floats.

def parse_vec3int( vec3int_like: Union[str, webknossos.geometry.vec3_int.Vec3Int]) -> webknossos.geometry.vec3_int.Vec3Int:

Parses str input to tuple of three integers.

def parse_vec2int(vec2int_str: str) -> webknossos.cli._utils.Vec2Int:

Parses str input to tuple of two integers.

def parse_bbox(bbox_str: str) -> webknossos.geometry.bounding_box.BoundingBox:

Parses str input to BoundingBox.

def parse_path(value: str) -> upath.core.UPath:

Parses a string value to a UPath.

def pad_or_crop_to_size_and_topleft( cube_data: numpy.ndarray, target_size: numpy.ndarray, target_topleft: numpy.ndarray) -> numpy.ndarray:

Given an numpy array and a target_size/target_topleft, the array will be padded so that it is within the bounding box described by topleft and size. If the input data is too large, the data will be cropped (evenly from opposite sides with the assumption that the most important data is in the center).