Image

An image is a 2D dataset (two spatial dimensions), assumed to by a grayscale image. Colourmaps may be applied when plotting.

Syntax

Image(Img, calibration=0)

Input

Required:

• Img: a 2D numpy array

Optional:

• calibration: calibration of the spatial dimensions (in meter/pixel). Used for plotting the image with a scalebar. Default is 0; a calibration value of 0 means no calibration is set and no scalebar can be displayed.

Methods

PadImg

A function to pad the sides of the image with NaN, for certain image processing functions.

Syntax

PadImg(pad)

Input

Required

• pad: the number of pixels to pad around each edge, (2x2 numpy array or 2x2 tuple) in the format: ((axis0_before, axis0_after), (axis1_before, axis1_after))

SaveImageAsPNG

A function to save the image to a png file with pixel values from 0 to 255 (grayscale). Can also handle colourmaps (eg matplotlib colourmaps) applied to grayscale images through indexing the images. Can handle alpha values in the applied colourmap.

Input

Required:

• filename: the filename to which the image should be saved. Can include the filepath to a folder
• clim: the colour limits of the image to be written; this argument allows changing of the contrast limits of the image before saving, otherwise the user can input the Imglim attribute of the Image object.

Optional:

• cmap: the colourmap to be applied, should be a matplotlib colormap object. Default is None, in which case the image will be saved in grayscale.

Example Usage

Import Image class, set scalebar to 10nm per pixel, initialize Image class. import Image
scale = 1e-8
Im = Image.Image(data, calibration=scale)