Reading FI data from an UFF file recorded from an Alpinion scanner

In this example we show how to read channel data from a UFF (Ultrasound File Format) file recorded with an Alpinion scanner. You will need an internet connection to download data.

by Ole Marius Hoel Rindal olemarius@olemarius.net and Muyinatu Lediju Bell mledijubell@jhu.edu

$Last updated: 2017/09/15$

Contents

Checking the file is in the path

To read data from a UFF file the first we need is, you guessed it, a UFF file. We check if it is on the current path and download it from the USTB websever.

close all;

% data location
url='http://ustb.no/datasets/';      % if not found downloaded from here
filename='Alpinion_L3-8_FI_hyperechoic_scatterers.uff';

% checks if the data is in your data path, and downloads it otherwise.
% The defaults data path is under USTB's folder, but you can change this
% by setting an environment variable with setenv(DATA_PATH,'the_path_you_want_to_use');
tools.download(filename, url, data_path);

Reading data

Let's first check if we are lucky and the file allready contains beamformed_data that we can display.

display=true;
content = uff.index([data_path filesep filename],'/',display);

has_b_data = false;
for i = 1:length(content)
    if strcmp(content{i}.class,'uff.beamformed_data')
        has_b_data = true; % We found a beamformed data object!
    end
end

UFF: Contents of \\kant\ifi-ansatt-u08\omrindal\Repos\USTB_summer_student_2021\data\Alpinion_L3-8_FI_hyperechoic_scatterers.uff at /
   - /channel_data: channel_data [uff.channel_data] size(1,1)

If the file had beamformed data, let's read that and the channeldata, before we can jump straight to displaying the data since it's allready beamformed

if has_b_data
    b_data=uff.read_object([data_path filesep filename],'/b_data');
    b_data.plot([],'Stored image');
end

Beamforming data

If it doesn't have any beamformed data at least it should have some channel_data. So let's read that.

channel_data=uff.read_object([data_path filesep filename],'/channel_data');

UFF: reading channel_data [uff.channel_data]
UFF: reading sequence [uff.wave] [====================] 100%

And then do the normal routine of defining the scan,

x_axis=zeros(channel_data.N_waves,1);
for n=1:channel_data.N_waves
    x_axis(n)=channel_data.sequence(n).source.x;
end
z_axis=linspace(1e-3,55e-3,512).';
scan=uff.linear_scan('x_axis',x_axis,'z_axis',z_axis);

setting up and running the pipeline

mid=midprocess.das();
mid.dimension = dimension.both();

mid.channel_data=channel_data;
mid.scan=scan;

mid.transmit_apodization.window=uff.window.scanline;

mid.receive_apodization.window=uff.window.tukey25;
mid.receive_apodization.f_number=1.7;

b_data2=mid.go();

USTB General beamformer MEX v1.1.2 .............done!

Display image

And finally display the image.

b_data2.plot([],'Beamformed image');

Write info about channel data

Let's look at the info given about this dataset

channel_data.print_authorship()

Name: 		 FI dataset of hyperechoic cyst and points  
		 scatterers recorded on an Alpinion scanner with a  
		 L3-8 Probe from a CIRS General Purpose Ultrasound  
		 Phantom 
Reference: 	 www.ultrasoundtoolbox.com 
Author(s): 	 Ole Marius Hoel Rindal <olemarius@olemarius.net> 
		 Muyinatu Lediju Bell <mledijubell@jhu.edu> 
Version: 	 1.0.2 

Published with MATLAB® R2020b