scarlet.bbox¶

class scarlet.bbox.Box(shape, origin=None)[source]¶

Bases: object

Bounding Box for an object

A Bounding box describes the location of a data unit in the global/model coordinate system. It is used to identify spatial and channel overlap and to map from model to observed frames and back.

The BBox code is agnostic about the meaning of the dimensions. We generally use this convention:

2D shapes denote (Height, Width)
3D shapes denote (Channels, Height, Width)

Parameters

shape: tuple: Size of the box
origin: tuple: Minimum corner coordinate of the box

Attributes

D: Dimensionality of this BBox
bounds: Bounds of the box
center: Tuple of center coordinates
slices: Bounds of the box as slices
start: Tuple of start coordinates
stop: Tuple of stop coordinates

Methods

`contains`(p)	Whether the box contains a given coordinate p
`copy`()	Copy of the box
`extract_from`(image[, sub])	Extract sub-image described by this bbox from image
`from_bounds`(*bounds)	Initialize a box from its bounds
`from_data`(X[, min_value])	Define range of X above min_value
`insert_into`(image, sub)	Insert sub into image according to this bbox

property D¶: Dimensionality of this BBox

property bounds¶: Bounds of the box

property center¶: Tuple of center coordinates

contains(p)[source]¶: Whether the box contains a given coordinate p

copy()[source]¶: Copy of the box

extract_from(image, sub=None)[source]¶

Extract sub-image described by this bbox from image

Parameters

image: array: Full image
sub: array: Extracted image

Returns

sub: array

static from_bounds(*bounds)[source]¶

Initialize a box from its bounds

Parameters

bounds: tuple of (min,max) pairs: Min/Max coordinate for every dimension

Returns

bbox: scarlet.bbox.Box: A new box bounded by the input bounds.

static from_data(X, min_value=0)[source]¶

Define range of X above min_value

Parameters

X: array-like: Data to threshold
min_value: float: Minimum value of the result.

Returns

bbox: scarlet.bbox.Box: Bounding box for the thresholded X

insert_into(image, sub)[source]¶

Insert sub into image according to this bbox

Inverse operation to extract_from().

Parameters

image: array: Full image
sub: array: Extracted sub-image

Returns

image: array

property slices¶: Bounds of the box as slices

property start¶: Tuple of start coordinates

property stop¶: Tuple of stop coordinates

scarlet.bbox.overlapped_slices(bbox1, bbox2)[source]¶

Slices of bbox1 and bbox2 that overlap

Parameters

bbox1: `~scarlet.bbox.Box`
bbox2: `~scarlet.bbox.Box`

Returns

slices: tuple of slices: The slice of an array bounded by bbox1 and the slice of an array bounded by bbox in the overlapping region.