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

In this example we show how to read channel and beamformed 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

$Last updated: 2017/09/15$

Checking the file is in the path
Reading channel data
Beamform data
Display image
Write info about channel data

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
filename='Alpinion_L3-8_CPWC_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 channel 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

Error using h5infoc
The filename specified was either not found on the MATLAB path or it contains unsupported characters.

Error in h5info (line 108)
    hinfo = h5infoc(filename,location, useUtf8);

Error in uff/index (line 23)
    info=h5info(filename,location);

Error in CPWC_UFF_Alpinion (line 34)
content = uff.index([data_path filesep filename],'/',display);

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

Beamform 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');

And then do the normal routine of defining the scan,

scan=uff.linear_scan();
scan.x_axis = linspace(channel_data.probe.x(1),channel_data.probe.x(end),512).';
scan.z_axis = linspace(1e-3,50e-3,512).';

setting up midprocessor

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

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

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

b_data2=mid.go();

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