ultrasound-rawdata-exchange 1.3.0

Ultrasound Raw data eXchange file format C++ implementation and wrapping in Python and Matlab

URX

Description

The Ultrasound Raw data eXchange file format is a structure of data to store ultrasound acquisition.

You may use it with various languages (C++, Python and MATLAB).

Get more informations in the Wiki about class diagram.

Table of Contents

• Common installation and usage in C++, MATLAB, Python.
• Build it yourself for C++, MATLAB, Python with CMake.

Use it with C++

There is no installer for C++ user. You need to build it yourself. If you don't need to read / write file, urx library is header-only.

See advanced uses for more information.

Configuration

First, you need to get Urx package with find_package. If package is not found, set Urx_DIR=INSTALL_PATH/lib/cmake/Urx-XXXYYY.

find_package(Urx REQUIRED)

You will have access to targets:

• Urx::Urx: header-only library of the urx struct.
• Urx::UrxUtils: library with helper to manipulate urx struct, including read / write in hdf5 file format.

CMake examples

find_package(HDF5 REQUIRED NAMES hdf5 COMPONENTS CXX hdf5::hdf5-static)
find_package(Urx REQUIRED)
add_executable(UrxTestIo ${SRCS_FILES})
target_link_libraries(
  UrxTestIo PRIVATE Urx::Urx Urx::UrxUtils hdf5::hdf5-static hdf5::hdf5_cpp-static)

Urx::UrxUtils is only needed if you use helpers. If you only need the urx file format, only Urx::Urx is needed.

hdf5::hdf5-static hdf5::hdf5_cpp-static is only needed if the library has been built with HDF5 support. In this case, hdf5 has been built in static mode.

You may found a complete example of CMakeLists.txt in test/urx or in test/io folders.

C++ examples

All dynamic memory allocation should be stored in a shared_ptr.

#include <memory>

#include <urx/dataset.h>
#include <urx/probe.h>
#include <urx/utils/io/reader.h>
#include <urx/utils/io/writer.h>

auto dataset = std::make_shared<urx::Dataset>();

auto probe = std::make_shared<urx::Probe>();
probe->description = "Probe 1";
dataset->acquisition.probes.push_back(probe);

urx::utils::io::writer::saveToFile("file.urx", *dataset);

auto dataset_loaded = urx::utils::io::reader::loadFromFile("file.urx");

You may found an example for all C++ classes in file urx/utils/test/dataset_gen.h in function generateFakeDataset and much more in the official wiki.

Use it with MATLAB

See advanced uses for more information.

MATLAB installer

Urx MATLAB homepage is hosted in MATLAB File Exchange. To download the toolbox, select Download > Toolbox. It compatibles for both Windows and Linux.

Requirements

MATLAB needs a C compiler to load the C library in Urx toolbox (i.e. Visual Studio or MinGW). To use MinGW, see [doc/matlab.md#install-mingw-c-compiler] paragraph.

Configuration

If you are using Urx from MATLAB toolbox, you just have to enable Unicode if you need it (feature('DefaultCharacterSet','UTF-8');).

Examples

dataset = urx.Dataset();

probe1 = urx.Probe();
probe1.description = 'Probe 1';
excitation1 = urx.Excitation();
dataset.acquisition.excitations = [excitation1];

urx.saveToFile('test.urx', dataset);

dataset2 = urx.loadFromFile('test.urx');

You may found a complete example in file test/matlab/+urx/+UnitTests/FileFromScratch.m and much more in the official wiki.

Important note

Some field are optional or can be empty (see C++ UML diagram). If you want to unassign a value, don't use [] but use empty method of the class (i.e. urx.ElementGeometry.empty).

Use it with Python

See advanced uses for more information.

Python wheel

Urx Python is hosted in Pypi.

From your Python's virtual environment, run pip install ultrasound_rawdata_exchange.

Examples

import ultrasound_rawdata_exchange as urx;

dataset = urx.Dataset()

probe1 = urx.Probe()
probe1.description = 'Probe 1'
excitation1 = urx.Excitation()
dataset.acquisition.excitations = [excitation1]

urx.saveToFile('test.urx', dataset)

dataset2 = urx.loadFromFile('test.urx')

You may found a basic example in folder test/python and much more in the official wiki.