shapelets.docs.example_3

Example 3 - Local Pattern Orientation

See here for files and code related to this example.

This example demonstrates the local pattern orientation method (M.P. Tino (2024)) implemented in shapelets.self_assembly.quant.orientation for a square self-assembled nanostructure image (C. Tang (2008))

Overview

Local pattern orientation is concerned with relative nanostructure orientation along grain boundaries and between grains. The details of this method can be found here.

It is also important to note that this method is only applicable to images with one dominant pattern type. Images with mixed patterns are not allowed.

Configuration File

Setup

The example config contains the following:

[general]
image_name = sqrAFM2.png
method = orientation

[orientation]
pattern_order = square

where image_name and method are required parameters that specify the image filename and method used for analysis, respectively.

The orientation method requires one parameter.

pattern_order str (required)

The pattern order (symmetry) observed in the image.
Example values: stripe, square, hexagonal

Run Example

Ensure shapelets is installed before proceeding. See here for installation instructions.

This example assumes the working directory has a sub-directory analysis containing the necessary files: analysis/config and analysis/images/sqrAFM2.png.

To run the example, execute shapelets-run ./analysis/config in the command line. Depending on your computer hardware, the iterative convergence scheme may take a couple of minutes.

The output (shown below) will then be available in ./analysis/output containing the mask (top left), dilated feature orientation (top right), smoothed orientation result, and the smoothed orientation result superimposed onto the original pattern (shown below, respectively).

Additional Notes

For users who do not wish to use configuration files and would prefer to interact with shapelets via standard python programming, please see the example_3.py script here. You can use this script as a template to conduct your own analyses.

View Source

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18r"""
19
20.. include:: ../../examples/example_3/example_3.md
21
22"""