PerovStats

An program to process AFM scans of perovskite and generate usable data and statistics.

Installation

To install PerovStats directly from GitHub via ssh:

pip install git@github.com:AFM-SPM/PerovStats.git

To install PerovStats by cloning from the GitHub repository:

git clone https://github.com/AFM-SPM/PerovStats.git
cd PerovStats
pip install -r requirements.txt

Documentation

Basic usage

Run the command perovstats in the terminal.

• Uses src/perovstats/default_config.yaml for configuration options, below details custom arguments avaliable.

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Command-line interface

usage: perovstats [-h] [-c CONFIG_FILE] [-d BASE_DIR] [-e FILE_EXT] [-n CHANNEL] [-o OUTPUT_DIR] [-w EDGE_WIDTH]

Command-line interface for PerovStats workflow.

options:
  -h, --help            show this help message and exit
  -c CONFIG_FILE, --config_file CONFIG_FILE
                        Path to configuration file
  -d BASE_DIR, --base_dir BASE_DIR
                        Directory in which to search for data files
  -e FILE_EXT, --file_ext FILE_EXT
                        File extension of the data files
  -n CHANNEL, --channel CHANNEL
                        Name of data channel to use
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                        Directory to which to output results
  -w EDGE_WIDTH, --edge_width EDGE_WIDTH
                        Edge width as proportion of Nyquist frequency

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Accepted file types

Currently PerovStats only handles .spm files generated from an AFM scan.

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Features

• Image frequency splitting to isolate perovskite topology (optional)
• Automatic segmentation and grain finding of an image
• Statistics and .csv generation about processed image, including:
  • Image-wide statistics
    • Number of grains found
    • Grains per nm^2
    • Pixel to nm scaling
    • Mean, median, and mode grain sizes
  • Per-grain statistics
    • Grain area
    • Grain circularity rating (0-1)
  • Metadata about values determined during processing such as the cutoff frequency (if frequency splitting was used) and the threshold used for grain finding

License

This software is licensed under the GPLv3.