tshape_analysis

This script contains code for several shape analysis metrics designed to be used on contours taken from ultrasound images of the tongue.

The analysis metrics are:

• Procrustes analysis
• Modified Curvature Index
• Fourier analysis of the tongue profile

The code is written in Python.

Data type and output file

• The data this script is designed to run on consists of .csv files containing x and y coordinate points for a series of tongue shape contours. The filename/s of the .csv files should be structured as: identifier_symbolforsegmenttype.csv (e.g. ‘01FC_ara’ where 01FC is the participant, and ‘ara’ is the stimulus item or segment type).

• The script assumes the first column of data in the .csv is the x coordinates for the first shape, and the second column is the y coordinates for the first shape. Subsequent columns in the same .csv file are for additional shapes.

• If your .csv files have header lines, the n_header_lines parameter (by default set to 0) can be used to ignore the header data in your files.

• To run the Procrustes analysis, there must be a file in the directory containing the resting, or baseline comparison shape. The name of this file must be structured as: identifier_rest.csv. If this file is not available, no Procrustes analysis will be performed.

• The default output filename is: shape_analysis_data_out.csv. The output file contains a row for every contour, and includes the following data:

  • ID (taken from filename)
  • symbol (taken from filename)
  • repetition (based on location in .csv file)
  • MCI - Modified Curvature Index value
  • procrustes - Procrustes Analysis value
  • real_1 - real part of 1st Fourier coefficient
  • imag_1 - imaginary part of 1st Fourier coefficient
  • mod_1 - modulus (magnitude) of 1st Fourier coefficient
  • real_2 - real part of 2nd Fourier coefficient
  • imag_2 - imaginary part of 2nd Fourier coefficient
  • mod_2 - modulus (magnitude) of 2nd Fourier coefficient
  • real_3 - real part of 3rd Fourier coefficient
  • imag_3 - imaginary part of 3rd Fourier coefficient
  • mod_3 - modulus (magnitude) of 3rd Fourier coefficient

Instructions for use

• The script expects the .csv files containing the data to be in the current working directory.
• The script can be run in Python or in a terminal window
• If you use the terminal window, type in the file path (including the filename) for ‘shape_analysis.py’. Press Enter to execute the script.
• If you are in Python, type: import shape_analysis then shape_analysis.doIt()

Test data

Contained in the ‘test data’ folder of this repository are a number of .csv files with tongue contours for various shapes. The filenames are constructed as required by the script - i.e. ’01FC’ is the participant ID, and ‘ara’ etc. is the utterance. For all of these files, the tongue contours represent the midpoint of the middle segment of the utterance, i.e. /r/, /l/, /g/ etc. There are 6 repetitions of each segment type. The data is in the mid-sagittal plane, collected from a typical, female speaker of American English.

The authors make no promise of continued support or development of the code contained in this repository.