Visual debug Gadgetron in Ubuntu using Eclipse - jackyko1991/gadgetron GitHub Wiki

Gadgetron components are often developed in linux environment. This wiki page describes a set up to allow visual debug gadgetron process/gadgets/toolboxes in linux usingthe Eclipse (http://www.eclipse.org/downloads/download.php?file=/technology/epp/downloads/release/oxygen/R/eclipse-cpp-oxygen-R-linux-gtk-x86_64.tar.gz).

Install Eclipse

sudo apt-get install eclipse eclipse-cdt

Compile Gadgetron and related packages

This section will describe how to set up gadgetron on your local folder(~). Instead of installing Gadgetron to system folder (/usr/local), the Gadgetron and related packages will be installed to ~/local.

Install Gadgetron dependencies

If the dependencies of Gadgetron has not been installed, system admin should conduct the installation:

sudo apt-get install wget build-essential emacs python-pip libhdf5-serial-dev cmake git-core libboost-all-dev libfftw3-dev h5utils jq libzmq-dev hdf5-tools liblapack-dev libxml2-dev libfreetype6-dev pkg-config libxslt-dev libarmadillo-dev libace-dev gcc-multilib libgtest-dev python-dev liblapack-dev liblapacke-dev libatlas-base-dev libatlas-dev libplplot-dev libdcmtk-dev supervisor 

sudo pip install --upgrade pip
sudo pip install setuptools
sudo pip install Cython
sudo pip install numpy 
sudo pip install pyxb psutil lxml pydicom
sudo pip install 'h5py==2.5.0'

Compile ISMRMRD (https://github.com/ismrmrd/ismrmrd) and Gadgetron (https://github.com/gadgetron/gadgetron)

echo "This script will set up Gadgetron and related libraries in the home folder ~/local. The old installed gadgetron will be deleted!!!"

# set up the working directory to be the home folder
GT_WORKING_DIR=~
GT_INSTALL_DIR=${GT_WORKING_DIR}/local

# the branch to pull, can be changed
BRANCHNAME=master

# Build type
BUILD_TYPE=Release
# for debug, BUILD_TYPE=Debug

# Generator
GENERATOR="Eclipse CDT4 - Unix Makefiles"

# --------------------------------------------------------------------------------------------
# pull source from git hub

[email protected]:ismrmrd/ismrmrd.git
ISMRMRD_BRANCH=${BRANCHNAME}

[email protected]:gadgetron/gadgetron.git
GT_BRANCH=${BRANCHNAME}

[email protected]:ismrmrd/siemens_to_ismrmrd.git
GT_CONVERTER_BRANCH=${BRANCHNAME}

[email protected]:ismrmrd/ismrmrd-python.git
ISMRMRD_PYTHON_API_BRANCH=${BRANCHNAME}

[email protected]:ismrmrd/ismrmrd-python-tools.git
ISMRMRD_PYTHON_TOOLS_BRANCH=${BRANCHNAME}

# ----------------------------------------------------------------------------------------------------------
# clean the old installation
# ----------------------------------------------------------------------------------------------------------
rm -R -f ${GT_WORKING_DIR}/local
mkdir -k ${GT_WORKING_DIR}/local
mkdir -k ${GT_WORKING_DIR}/mrprogs

GADGETRON_HOME=${GT_WORKING_DIR}/local
ISMRMRD_HOME=${GT_WORKING_DIR}/local
CMAKE_PREFIX_PATH=${GT_WORKING_DIR}/local/lib/cmake/ISMRMRD

# ----------------------------------------------------------------------------------------------------------
#ISMRMRD PYTHON API, require sudo to install
# ----------------------------------------------------------------------------------------------------------
cd ${GT_WORKING_DIR}/mrprogs
git clone ${ISMRMRD_PYTHON_API_REPO}
cd ismrmrd-python
# sudo python setup.py install

# ----------------------------------------------------------------------------------------------------------
#ISMRMRD PYTHON TOOLS, require sudo to install
# ----------------------------------------------------------------------------------------------------------
cd ${GT_WORKING_DIR}/mrprogs
git clone ${ISMRMRD_PYTHON_TOOLS_REPO}
cd ismrmrd-python-tools
# sudo python setup.py install

# ----------------------------------------------------------------------------------------------------------
# ismrmrd
# ----------------------------------------------------------------------------------------------------------

rm -R -f ${GT_WORKING_DIR}/mrprogs/ismrmrd
cd ${GT_WORKING_DIR}/mrprogs
git clone ${ISMRMRD_REPO} ${GT_WORKING_DIR}/mrprogs/ismrmrd
cd ${GT_WORKING_DIR}/mrprogs/ismrmrd
git checkout -b ${ISMRMRD_BRANCH} origin/${ISMRMRD_BRANCH}

rm -R -f ${GT_WORKING_DIR}/mrprogs/build_ismrmrd_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs
mkdir build_ismrmrd_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs/build_ismrmrd_${BUILD_TYPE}

cmake -G "${GENERATOR}" -DCMAKE_INSTALL_PREFIX=${GT_INSTALL_DIR} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DJava_JAVAC_EXECUTABLE= -DJava_JAVA_EXECUTABLE= -DJAVA_INCLUDE_PATH=  ../ismrmrd

make -j $(nproc)
make install

# ----------------------------------------------------------------------------------------------------------
# gadgetron
# ----------------------------------------------------------------------------------------------------------

rm -R -f ${GT_WORKING_DIR}/mrprogs/gadgetron
cd ${GT_WORKING_DIR}/mrprogs
git clone  ${GT_REPO} ${GT_WORKING_DIR}/mrprogs/gadgetron
cd ${GT_WORKING_DIR}/mrprogs/gadgetron
git checkout -b ${GT_BRANCH} origin/${GT_BRANCH}

rm -R -f ${GT_WORKING_DIR}/mrprogs/build_gadgetron_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs
mkdir build_gadgetron_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs/build_gadgetron_${BUILD_TYPE}

cmake -G "${GENERATOR}" -DCMAKE_INSTALL_PREFIX=${GT_INSTALL_DIR} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DCMAKE_PREFIX_PATH=${GT_WORKING_DIR}/local/lib/cmake/ISMRMRD ../gadgetron

make -j $(nproc)
make install
    
# ----------------------------------------------------------------------------------------------------------
# siemens_to_ismrmrd
# ----------------------------------------------------------------------------------------------------------

rm -R -f ${GT_WORKING_DIR}/mrprogs/siemens_to_ismrmrd
cd ${GT_WORKING_DIR}/mrprogs
git clone  ${GT_CONVERTER_REPO}  ${GT_WORKING_DIR}/mrprogs/siemens_to_ismrmrd
cd ${GT_WORKING_DIR}/mrprogs/siemens_to_ismrmrd
git checkout -b ${GT_CONVERTER_BRANCH} origin/${GT_CONVERTER_BRANCH}

rm -R -f ${GT_WORKING_DIR}/mrprogs/build_siemens_to_ismrmrd_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs
mkdir build_siemens_to_ismrmrd_${BUILD_TYPE}
cd ${GT_WORKING_DIR}/mrprogs/build_siemens_to_ismrmrd_${BUILD_TYPE}

cmake -DCMAKE_INSTALL_PREFIX=${GT_INSTALL_DIR} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DCMAKE_PREFIX_PATH=${GT_WORKING_DIR}/local/lib/cmake/ISMRMRD ../siemens_to_ismrmrd

make -j $(nproc)
make install

# ----------------------------------------------------------------------------------------------------------
# make gadgetron ready
# ----------------------------------------------------------------------------------------------------------
cp -f ${GT_INSTALL_DIR}/share/gadgetron/config/gadgetron.xml.example ${GT_INSTALL_DIR}/share/gadgetron/config/gadgetron.xml

Set up shell environment to run gadgetron

The shell $PATH and $LD_LIBRARY_PATH environmental variables have to be extended to reflect the installed gadgetron and ismrmrd:

# setup gadgetron
export ISMRMRD_HOME=~/local
export GADGETRON_HOME=~/local
export GADGETRON_DEBUG_FOLDER=~/Debug

export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:/opt/intel/compiler/lib/intel64:/opt/intel/lib/intel64:${ISMRMRD_HOME}/lib:${GADGETRON_HOME}/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/lib:${LD_LIBRARY_PATH}
export PATH=~/local/bin:~/local/usr/bin:${ISMRMRD_HOME}/bin:${GADGETRON_HOME}/bin:~/local/bin:${PATH}