Scanning Transmission Electron Microscopy

This module contains functions for Scanning Transmission Electron Microscopy (STEM) data. There are two main functions in this module. non4dstem is designed to handle STEM files that are not 4D scans. It supports 2D and 3D .dm4, .ser, and .emd files. This function uses the Hyperspy package. Any files that can be processed by Hyperspy should also be compatible with this function. stemarray4d is designed to break down a 4D STEM .raw image into 2D images. This function uses the py4DSTEM package. Any files that can be processed by py4DSTEM should also work with this function.

4D STEM

stemarray4d takes a 4D STEM .raw scan as input and converts it into a series of 2D .png image slices. There are three types of output: a folder containing the 2D image slices, a maximum projection image, and a mean projection image. Here is an example of how the function stemarray4d can be used:

from project_chameleon.stemarray4d import stemarray4d
stemarray4d('example_file.raw', 'new_file')

In this example, ‘example_file.raw’ is the STEM scan file containing the data. ‘new_file’ is the base name used for all generated output files. The mean and max images will be labeled accordingly (e.g., ‘new_file_max.png’). The individual image slices will include the slice number (e.g., ‘new_file13.png’). No metadata is collected or displayed by this function.

Non-4D STEM

non4dstem takes a non-4D .dm4, .ser, or .emd file as input and converts it into a plot saved as a .png file. This function supports both single file and folder inputs. Here is an example of how the function non4dstem can be used:

from project_chameleon.non4dstem import non4dstem
non4dstem(data_file='test_file.ser', output_file='new_file.png')

In this example, ‘test_file.ser’ is the non-4D STEM file containing the data, and ‘new_file.png’ is the output image file for the resulting plot. To use the function with folders, replace data_file with data_folder, and output_file with output_folder. These parameters should be folder paths.

When processing folders, all compatible files in the specified input folder will be processed, and their plots will be saved as .png files in the output folder. No metadata is extracted or displayed by this function.

Below is more information on the main functions:

non4dstem.non4dstem(data_folder=None, outputs_folder=None, data_file=None, output_file=None)

non4dstem is a function that takes an input folder or file containing 2D and 3D STEM images and converts those files into plots that are saved either in output folder or as a single output file. This function was tested on .dm4 files, .ser files, and .emd files, but can handle any filetypes that can be parserd by the hyperspy ‘load’ function. This file can only take inputs in specific pairings. data_file can be paired with output_file and outputs_folder. data_folder may only be paired with outputs_folder. There may only be one data input and one output type input.

Args:

data_folder should be a folder holding all non 4D files that are being processed. data_file should be a string or path to a single file non 4D stem file. outputs_folder is a string which will be the name out the folder that holds all the processed images. output_file is a string which will be the name of the single file output. All inputs are optional. Some are conditionally required.

Returns:

this function does not return anything. It saves converted files as .png images in the folder labeled output_folder, or as single .png images.

Exceptions:

data_folder must be a folder. data_folder must contain files. output_folder must not contain a file extension. Will throw exceptions if there are any mismatches in input pairings.

stemarray4d.stemarray4d(file_name, output_name)

stemarray4d() is a function designed to take raw 4D STEM files and process them into 2D image slices. This function also generates mean and max images from the 4D scan. Any 4D .raw scans that can be processed by py4DSTEM should be able to be processed by this function.

Args:

file_name should be a 4D STEM .raw file ending in ‘.raw’. output_name should be a string which will be the name of all outputs combined with the designator of the specific output.

Returns:

does not return anything. There are three primary outputs: a mean image, a max image, and a folder containing the decomposed 2D images of the 4D .raw image.

Exceptions:

file_name must be a file. file_name must end with ‘.raw’. output_name must not contain a file extension.