Regions of Interest

class pumpia.image_handling.roi_structures.BaseROI(image: ArrayImage, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Base class for Region of Interest (ROI) in an image.

Parameters:

image (ArrayImage) – The image associated with the ROI.
slice_num (int, optional) – The slice number of the ROI (default is 0).
name (str, optional) – The name of the ROI (default is None).
replace (bool, optional) – Whether to replace an existing ROI with the same name (default is True).
cache_values (bool, optional) – Whether to cache pixel values and calculated values (default is True).
colour (str, optional) – The colour of the ROI.
active_colour (str, optional) – The colour of the ROI when it is selected.

image

The image associated with the ROI.

Type:: ArrayImage

slice_num

The slice number of the ROI.

Type:: int

cache_values

Whether to cache pixel values and calculated values.

Type:: bool

colour

The colour of the ROI.

Type:: str

active_colour

The colour of the ROI when it is selected.

Type:: str

active

Whether the ROI is active.

Type:: bool

hidden

Whether the ROI is hidden.

Type:: bool

id_string

Type:: str

storage_string

Type:: str

tag

Type:: str

pixel_values

Type:: list[int | float | list[float]]

pixel_array

Type:: np.ndarray

mask

Type:: np.ndarray

area

Type:: float

perimeter

Type:: float

mean

Type:: PixelStatsType

std

Type:: PixelStatsType

xmin

Type:: int

xmax

Type:: int

ymin

Type:: int

ymax

Type:: int

xcent

Type:: float

ycent

Type:: float

values_str

Type:: str

menu_options

Type:: list[tuple[str, Callable[[], None]]]

delete_cache(): Deletes the cached values of the ROI.

point_is_in(x: float, y: float) → bool: Checks if a pixel is inside the ROI.

point_is_on(x: float, y: float, dist: float = 0) → bool: Checks if a pixel is on the boundary of the ROI.

move(x: int = 0, y: int = 0): Moves the ROI by the specified amount.

enlarge(x: float = 1, y: float = 1): Enlarges the ROI by the specified amount.

resize_bbox(x: int = 0, y: int = 0): Resizes the bounding box of the ROI.

rotate(angle: float = 0): Rotates the ROI by the specified angle.

copy_to_image(image: ArrayImage, slice_num: int, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = ROI_COLOUR, active_colour: str = ACTIVE_ROI_COLOUR) → 'BaseROI': Copies the ROI to another image.

move_to_image(image: ArrayImage, slice_num: int, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = ROI_COLOUR, active_colour: str = ACTIVE_ROI_COLOUR) → 'BaseROI': Moves the ROI to another image.

class pumpia.image_handling.roi_structures.Angle(image: ArrayImage, x: int, y: int, x1: int, y1: int, x2: int, y2: int, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Represents an angle ROI. Has the same attributes and methods as BaseROI unless stated below.

Parameters:

x (int) – The x-coordinate of the vertex.
y (int) – The y-coordinate of the vertex.
x1 (int) – The x-coordinate of the first point.
y1 (int) – The y-coordinate of the first point.
x2 (int) – The x-coordinate of the second point.
y2 (int) – The y-coordinate of the second point.

x

The x-coordinate of the vertex.

Type:: int

y

The y-coordinate of the vertex.

Type:: int

x1

The x-coordinate of the first point.

Type:: int

y1

The y-coordinate of the first point.

Type:: int

x2

The x-coordinate of the second point.

Type:: int

y2

The y-coordinate of the second point.

Type:: int

angle

Type:: float

angle_degrees

Type:: float

class pumpia.image_handling.roi_structures.PointROI(image: ArrayImage, x: int, y: int, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Represents a point ROI. Has the same attributes and methods as BaseROI unless stated below.

Parameters:

x (int) – The x-coordinate of the point.
y (int) – The y-coordinate of the point.

x

The x-coordinate of the point.

Type:: int

y

The y-coordinate of the point.

Type:: int

class pumpia.image_handling.roi_structures.EllipseROI(image: ArrayImage, x: int, y: int, a: int, b: int, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Represents an ellipse ROI. Has the same attributes and methods as BaseROI unless stated below.

Parameters:

x (int) – The x-coordinate of the center of the ellipse.
y (int) – The y-coordinate of the center of the ellipse.
a (int) – The length of the horizontal axis of the ellipse.
b (int) – The length of the vertical axis of the ellipse.

x

The x-coordinate of the center of the ellipse.

Type:: int

y

The y-coordinate of the center of the ellipse.

Type:: int

a

The length of the horizontal axis of the ellipse.

Type:: int

b

The length of the vertical axis of the ellipse.

Type:: int

class pumpia.image_handling.roi_structures.RectangleROI(image: ArrayImage, xmin: int, ymin: int, width: int, height: int, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Represents a rectangle ROI. Has the same attributes and methods as BaseROI unless stated below.

Parameters:

xmin (int) – The minimum x-coordinate of the rectangle.
ymin (int) – The minimum y-coordinate of the rectangle.
width (int) – The width of the rectangle.
height (int) – The height of the rectangle.

x

The minimum x-coordinate of the rectangle.

Type:: int

y

The minimum y-coordinate of the rectangle.

Type:: int

width

The width of the rectangle.

Type:: int

height

The height of the rectangle.

Type:: int

h_profile

Type:: np.ndarray

v_profile

Type:: np.ndarray

plot_h_profile(): Plots the horizontal profile of the ROI in a new window.

plot_v_profile(): Plots the vertical profile of the ROI in a new window.

class pumpia.image_handling.roi_structures.LineROI(image: ArrayImage, x1: int, y1: int, x2: int, y2: int, *, slice_num: int = 0, name: str | None = None, replace: bool = True, cache_values: bool = True, colour: str = 'yellow', active_colour: str = 'red')

Represents a line ROI. Has the same attributes and methods as BaseROI unless stated below.

Parameters:

x1 (int) – The x-coordinate of the first point.
y1 (int) – The y-coordinate of the first point.
x2 (int) – The x-coordinate of the second point.
y2 (int) – The y-coordinate of the second point.

x1

The x-coordinate of the first point.

Type:: int

y1

The y-coordinate of the first point.

Type:: int

x2

The x-coordinate of the second point.

Type:: int

y2

The y-coordinate of the second point.

Type:: int

length

Type:: float

profile

Type:: np.ndarray

x_len

Type:: int

y_len

Type:: int

plot_profile(): Plots the profile of the ROI in a new window.