organoid_tracker.image_loading.array_image_loader module

class organoid_tracker.image_loading.array_image_loader.SingleImageLoader(array: ndarray, file_name: str = '')

Bases: ImageLoader

An image loader that just displays a single 3D array. Useful if you’re writing a quick script.

copy() → ImageLoader

Copies the image loader, so that you can use it on another thread.

first_time_point_number() → Optional[int]

Gets the first time point for which images are available.

get_2d_image_array(time_point: TimePoint, image_channel: ImageChannel, image_z: int) → Optional[ndarray]

Loads one single 2d slice of an image. Returns None if there is no image for this z, time point or channel. Note: the image z always goes from 0 to image_size_z - 1.

get_3d_image_array(time_point: TimePoint, image_channel: ImageChannel) → Optional[ndarray]

Loads an image, usually from disk. Returns None if there is no image for this time point or channel.

get_channel_count() → int

Gets the number of available channels.

get_image_size_zyx() → Optional[Tuple[int, int, int]]

Gets the image size. Returns None if there are no images.

last_time_point_number() → Optional[int]

Gets the last time point (inclusive) for which images are available.

serialize_to_config() → Tuple[str, str]

Serializes this image loader into a path and a file/series name. This can be stored in configuration files.

Note: not every image loader can be serialized fully using just two strings. There is also a newer method, self.serialize_to_dictionary(), which does contain all information.