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data

This module contains the ImageCapture and ImageSeries classes, which are the base datatypes used to store and manipulate images and image series in the FPM framework. The ImageCapture class represents a single image capture, while the ImageSeries class represents a series of images captured with the same optical magnification and pixel size. The ImageSeries class also contains methods for saving and loading image series data to and from disk.

Function: get_device​

fpm_py.data.get_device():
    ...

Class: ImageCapture​

fpm_py.data.ImageCapture:
    ...

A single image capture with associated k-vector.

Args:​

  • image (torch.Tensor): The image data
  • k_vector (torch.Tensor): The k-vector associated with the image

Raises:​

  • ValueError: If the image is not 2D or the k_vector is not 1x2

Instance method: post_init​

fpm_py.data.ImageCapture().__post_init__(self)

Class: ImageSeries​

fpm_py.data.ImageSeries:
    ...

A series of images captured with the same optical magnification and pixel size.

Args:​

  • image_stack (list[ImageCapture]): A list of ImageCapture objects
  • optical_magnification (float): The optical magnification of the images
  • pixel_size (float): The physical size of a pixel in the image, in micrometers
  • effective_magnification (float): The effective magnification of the images. If not provided, it will be calculated as optical_magnification / pixel_size

Raises:​

  • ValueError: If the images in the stack do not have the same shape
  • ValueError: If effective_magnification is not provided and both optical_magnification and pixel_size are not provided

Instance method: post_init​

fpm_py.data.ImageSeries().__post_init__(self)

Class method: from_dict​

fpm_py.data.ImageSeries.from_dict(data: dict)

Load an ImageSeries object saved as a dictionary.

Args:​

  • path (str): The path to load the object from

Returns:​

  • ImageSeries: The loaded ImageSeries object

Class method: load​

fpm_py.data.ImageSeries.load(path: str)

Instance method: to_dict​

fpm_py.data.ImageSeries().to_dict(self)

Convert the ImageSeries object to a dictionary.

Instance method: save​

fpm_py.data.ImageSeries().save(
    self,
    path
)