Tools for visualization of BMTK output using ParaView

cvtn A command line aplication to convert BMTK/neuron simulation data

PVCvtNeuronReader A ParaView plugin for loading data directly into ParaView

First

The dependencies need to be installed.

HDF5

Any recent version of HDF5 installed by a package manager should suffice.

Intel TBB

A recent version installed from a package manager should suffice.

VTK

If building the plugin skip this step, as the converter can get VTK from ParaView. If only building the command line converter, then VTK is required.

A typical VTK build might be acheived as follows:

wget https://www.vtk.org/files/release/9.0/VTK-9.0.0.tar.gz
tar xzfv VTK-9.0.0.tar.gz
mkdir VTK-9.0.0-build
cd VTK-9.0.0-build/
cmake \
    -DCMAKE_INSTALL_PREFIX=../VTK-9.0.0-install \
    -DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON \
    ../VTK-9.0.0
make -j
make -j install

ParaView

If you are not building the plugin skip this step. ParaView is required for the plugin and can also satisfy the VTK dependency of the command line converter.

A typical ParaView build might be acheived as follows:

git clone https://gitlab.kitware.com/paraview/paraview.git
cd paraview
./Utilities/SetupForDevelopment.sh
git checkout v5.8.1
git submodule update --recursive
cd ..
mkdir paraview-5.8.1-build
cd paraview-5.8.1-build
cmake \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX=`pwd`/../paraview-5.8.1-install  \
    -DVTK_MODULE_USE_EXTERNAL_VTK_hdf5=ON \
    -DPARAVIEW_USE_PYTHON=ON \
    -DPARAVIEW_USE_MPI=OFF \
    ../paraview
make -j
make -j install

cvtn

A command line aplication to convert BMTK/neuron simulation data

The tool can convert neruons with geometry stored in a seg_coords folder and interpolate time series data stored in a im.h5 file onto the geometry. After conversion the VTK file format is used to store data back on disk for injestion into ParaView for visualization.

In the seg_coords folder it is expected to have one file for each neuron amd the files named by the neuron number. For instance if there are 32 neurons there would be 32 files named 0.h5 ... 31.h5.

Time series data is stored in a file named im.h5 and there is a value for each coordinate in each neuron at each time point.

The converter can generate 2 types of geometry, the neurons themselves or a 3D Cartesian mesh with scalar fields interpolated onto it.

This project has a CMake build and depnds on HDF5, TBB, and VTK >= 9.0.0.

Installing the converter

Once VTK, HDF5, and Intel TBB are installed one can install the converter.

git clone [email protected]:burlen/cvtn.git
mkdir cvtn-build
cmake -DVTK_DIR=../VTK-9.0.0-build/  ../cvtn
make

Using the converter

cvt [input dir] [first neuron] [last neuron] [first step] [last step]
    [num cells] [output dir] [out file] [write geom] [write mesh] [n threads]

input dir : path where seg_coords and im.h live

first neuron : decimal number of the first neuron to load

last neuron : decimal number of the last neuron to load

first step : index of the first time step to load

last step : index of the last time step to load

num cells : number of cells in the longest side of the 3D Cartesian mesh.

output dir : path where to write the data as VTK files

out file : a name that's used when writeing output files

write geometry : 0/1 if 1 compute the neuron geometry

write mesh : 0/1 if 1 sample the scalar field onto a regular Cratesian mesh

n threads : number of threads to use (optional)

plugin

PVCvtNeuronReader - A reader plugin for ParaView

Building the plugin

git clone https://github.com/burlen/cvtn.git
mkdir cvtn-build
cd cvtn-build
cmake \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX=`pwd`/../paraview-5.8.1-install  \
    -DParaView_DIR=`pwd`/../paraview-5.8.1-install/lib64/cmake/paraview-5.8/
    -DENABLE_PLUGIN=ON \
    ../cvtn

make -j
make -j install

Loading the plugin in ParaView

Start ParaView open the Tools->ManagePlugins dialog box. Click Load New button, and navigate to the plugin install and loacte and select the PVCvtnNeuronReader.so file. Once back in the dialog expand the plugin's entry and check Autoload so that the plugin is loaded when ParaView starts.

Loadiing data

The plugin operates on a directory but must be given a file name due to how ParaView works. In the top directory of the dataset make an empty file with the .bmtk file extension.

touch master.bmtk

When this file is opened in ParaView by the File->Open dialog the PVCvtnReaderPlugin will be used.