Images

class pumpia.image_handling.image_structures.BaseImageSet

Abstract base class for images that can be shown.

Type:: str

id_string

Type:: str

menu_options

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

class pumpia.image_handling.image_structures.ArrayImage(shape: tuple[int, int, int, int], num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.ArrayImage(shape: tuple[int, int, int], num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.ArrayImage(shape: tuple[int, int], num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.ArrayImage(shape: tuple[int, ...], num_samples: int = 1, mode: str | None = None)

Represents an image based on an array. Has the same attributes and methods as BaseImageSet unless stated below.

Parameters:

shape (tuple[int, ...]) – The shape of the image.
num_samples (int) – Number of samples in the image, >1 for colour images, e.g. RGB is 3 (default is 1).
mode (str | None) – Mode of the image e.g. RGB (default is None)

x

The x location of the image on a Viewer.

Type:: float

y

The y location of the image on a Viewer.

Type:: float

zoom

The zoom level of the image on a Viewer.

Type:: float

rotation

The rotation of the image on a Viewer.

Type:: float

shape

The shape of the image.

Type:: tuple[int, …]

num_samples

Number of samples in the image, >1 for colour images (e.g. RGB is 3)

Type:: int

mode

Mode of the image for viewing e.g. RGB (see Pillow modes for more)

Type:: str | None

is_multisample

Type:: bool

is_rgb

Type:: bool

current_slice

Type:: int

location

Type:: tuple[float, float]

num_slices

Type:: int

array

Type:: np.ndarray

current_slice_array

Type:: np.ndarray

vmax

Type:: float | None

vmin

Type:: float | None

window

Type:: float | None

level

Type:: float | None

rois

Type:: set[‘BaseROI’]

roi_names

Type:: list[str]

user_window

Type:: float | None

user_level

Type:: float | None

pixel_size

Type:: tuple[float, float, float]

aspect

Type:: float

z_profile

Type:: np.ndarray

get_rois(slice_num: int | Literal['All'] | None = None) → set['BaseROI']: Returns the set of ROIs in the image.

add_roi(roi: 'BaseROI', replace: bool = True): Adds an ROI to the image.

remove_roi(roi: 'BaseROI'): Removes an ROI from the image.

change_slice(amount: int = 1) → None: Changes the current slice by the given amount.

reset(): Resets the image properties to their default values.

class pumpia.image_handling.image_structures.FileImageSet(shape: tuple[int, int, int, int], filepath: Path, num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.FileImageSet(shape: tuple[int, int, int], filepath: Path, num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.FileImageSet(shape: tuple[int, int], filepath: Path, num_samples: int = 1, mode: str | None = None)

Represents an ArrayImage built from a file. Has the same attributes and methods as ArrayImage unless stated below.

Parameters:

shape (tuple[int, ...]) – The shape of the image.
filepath (Path) – The file path of the image.
num_samples (int) – Number of samples in the image (default is 1).
mode (str | None) – Mode of the image e.g. RGB (default is None)

filepath

The file path of the image.

Type:: Path

class pumpia.image_handling.image_structures.ImageCollection(shape: tuple[int, int, int, int], num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.ImageCollection(shape: tuple[int, int, int], num_samples: int = 1, mode: str | None = None)

class pumpia.image_handling.image_structures.ImageCollection(shape: tuple[int, int], num_samples: int = 1, mode: str | None = None)

Represents a collection of ArrayImage objects. Has the same attributes and methods as ArrayImage unless stated below.

Parameters:

shape (tuple[int, ...]) – The shape of the image.
num_samples (int) – Number of samples in the image (default is 1).
mode (str | None) – Mode of the image e.g. RGB (default is None)

image_set

The list of images in the collection.

Type:: list[ArrayImage]

current_image

The current image object.

Type:: ArrayImage

add_image(image: ArrayImage): Adds an image to the collection.