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 26.05.2017

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.

clear all; close all;
% data location
url='http://ustb.no/datasets/';      % if not found downloaded from here
local_path = [ustb_path(),'/data/']; % location of example data
addpath(local_path);

% We have two different Alpinion CPWC datasets, comment out the one to use
filename='Alpinion_L3-8_FI_hyperechoic_scatterers.uff';
%filename='Alpinion_L3-8_FI_hypoechoic.uff';

% check if the file is available in the local path or downloads otherwise
tools.download(filename, url, local_path);

Reading data

Now that the file is on the path let us create a UFF object to interact with the file. We open it in "append" mode.

uff_file=uff(filename)

uff_file = 

  uff with properties:

    filename: 'Alpinion_L3-8_FI_hyperechoic_scatterers.uff'
     version: 'v1.0.1'
        mode: 'append'
     verbose: 1

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

display=true;
content = uff_file.index('/',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 Alpinion_L3-8_FI_hyperechoic_scatterers.uff at /
   - /b_data: b_data [uff.beamformed_data] size(1,1)
   - /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_file.read('/b_data');
    channel_data=uff_file.read('/channel_data');
else

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

    channel_data=uff_file.read('/channel_data');

And then do the normal routine of defining the scan,

    z_axis=linspace(1e-3,55e-3,512).';
    sca=uff.linear_scan();
    idx = 1;
    for n=1:numel(channel_data.sequence)
        sca(n)=uff.linear_scan(channel_data.sequence(n).source.x,z_axis);
    end

setting up and running the beamforming

    bmf=beamformer();
    bmf.channel_data=channel_data;
    bmf.scan=sca;

    bmf.receive_apodization.window=uff.window.tukey25;
    bmf.receive_apodization.f_number=1.7;
    bmf.receive_apodization.apex.distance=Inf;

    b_data=bmf.go({process.das_mex process.stack});

Now we can save this beamformed image to that file, so that we don't have to wait for the beamforming next time.

    uff_file.write(b_data,'b_data');

end

UFF: reading b_data [uff.beamformed_data]
UFF: reading sequence [uff.wave]
Processed 256/256
UFF: reading channel_data [uff.channel_data]
UFF: reading sequence [uff.wave]
Processed 256/256

Display image

And finally display the image.

b_data.plot([],strrep(filename,'_',' '));

Write info about channel data

Let's look at the info given about this dataset

channel_data.print_info()

Name: 		 FI dataset of hyperechoic cyst and points  
		 scatterers recorded on an Alpinion scanner with a  
		 L3-8 Probe from a CIRC General Purpose Ultrasound  
		 Phantom 
Reference: 	 www.ultrasoundtoolbox.com 
Author(s): 	 Ole Marius Hoel Rindal <olemarius@olemarius.no> 
		 Muyinatu Lediju Bell <mledijubell@jhu.edu> 
Version: 	 1.0.1 

Published with MATLAB® R2015a