neuralib.atlas.view.AbstractSliceView

class neuralib.atlas.view.AbstractSliceView

Bases: object

SliceView ABC for different plane type

Dimension parameters:

AP = anterior-posterior

DV = dorsal-ventral

ML = medial-lateral

W = view width

H = view height

__init__(view_type, plane, resolution, reference)

Parameters:

• view_type (Literal['annotation', 'reference']) – DATA_SOURCE_TYPE. {‘ccf_annotation’, ‘ccf_template’, ‘allensdk_annotation’}

• plane (Literal['coronal', 'sagittal', 'transverse']) – PLANE_TYPE`. {‘coronal’, ‘sagittal’, ‘transverse’}

• resolution (int) – um/pixel

• reference (ndarray) – Array[uint16, [AP, DV, ML]]

Methods

__init__(view_type, plane, resolution, reference)
coor_on(plane, o)	map slice point (x, y) at plane plane back to volume point (ap, dv, ml)
offset(h, v)
plane(offset)	Get image plane.
plane_at(slice_index)
plot_max_projection(ax, *[, ...])	Plot max projection for the given plane_type

Attributes

REFERENCE_FROM	reference from which axis
bregma
height	height (pixel) in a specific plane view
height_mm	height (um) in a specific plane view
max_projection_axis
n_ap	number of slices along AP axis
n_dv	number of slices along DV axis
n_ml	number of slices along ML axis
n_planes	number of planes in a specific plane view
project_index	plane(p), x, y of index order in (AP, DV, ML)
reference_point	reference point in a specific plane view.
width	width (pixel) in a specific plane view
width_mm	width (um) in a specific plane view
view_type	VIEW_TYPE.
plane_type	PLANE_TYPE`.
resolution	um/pixel
reference	Array[float, [AP, DV, ML]]
grid_x	Array[int, [W, H]]
grid_y	Array[int, [W, H]]

REFERENCE_FROM: ClassVar[str] = ''

reference from which axis

static __new__(cls, view_type, plane, resolution, reference)

Parameters:

• view_type (Literal['annotation', 'reference'])

• plane (Literal['coronal', 'sagittal', 'transverse'])

• resolution (int)

• reference (ndarray)

__init__(view_type, plane, resolution, reference)

Parameters:

• view_type (Literal['annotation', 'reference']) – DATA_SOURCE_TYPE. {‘ccf_annotation’, ‘ccf_template’, ‘allensdk_annotation’}

• plane (Literal['coronal', 'sagittal', 'transverse']) – PLANE_TYPE`. {‘coronal’, ‘sagittal’, ‘transverse’}

• resolution (int) – um/pixel

• reference (ndarray) – Array[uint16, [AP, DV, ML]]

view_type: Final[Literal['annotation', 'reference']]

VIEW_TYPE. {‘annotation’, ‘reference’}

plane_type: Final[Literal['coronal', 'sagittal', 'transverse']]

PLANE_TYPE`. {‘coronal’, ‘sagittal’, ‘transverse’}

resolution: Final[int]

um/pixel

reference: Final[ndarray]

Array[float, [AP, DV, ML]]

grid_y: Final[ndarray]

Array[int, [W, H]]

grid_x: Final[ndarray]

Array[int, [W, H]]

property bregma: ndarray

property n_ap: int

number of slices along AP axis

property n_dv: int

number of slices along DV axis

property n_ml: int

number of slices along ML axis

abstract property n_planes: int

number of planes in a specific plane view

abstract property width: int

width (pixel) in a specific plane view

abstract property height: int

height (pixel) in a specific plane view

property width_mm: float

width (um) in a specific plane view

property height_mm: float

height (um) in a specific plane view

abstract property reference_point: int

reference point in a specific plane view. aka, bregma plane index

abstract property project_index: tuple[int, int, int]

plane(p), x, y of index order in (AP, DV, ML)

Returns:

(p, x, y)

abstract property max_projection_axis: int

plot_max_projection(ax, *, annotation_regions=None, annotation_cmap='hsv')

Plot max projection for the given plane_type

Parameters:

• ax (Axes) – Axes

• annotation_regions (str | list[str] | None) – annotation_regions

• annotation_cmap (str) – camp for the annotation regions, defaults to ‘hsv’

plane_at(slice_index)

Parameters:

slice_index (int)

Return type:

SlicePlane

offset(h, v)

Parameters:

• h (int) – horizontal plane diff to the center. right side positive.

• v (int) – vertical plane diff to the center. bottom side positive.

Returns:

(H, W) array

Return type:

ndarray

plane(offset)

Get image plane.

Parameters:

offset (int | tuple[int, int, int] | ndarray) – Array[int, height, width] or tuple (plane, dh, dv)

Returns:

Return type:

ndarray

coor_on(plane, o)

map slice point (x, y) at plane plane back to volume point (ap, dv, ml)

Parameters:

• plane (ndarray) – plane number of array

• o (tuple[ndarray, ndarray]) – tuple of (x, y)

Returns:

(ap, dv, ml)

Return type:

tuple[int | ndarray, …]