Introduction and licensing

This is a collection of different tools I had to develop. Everything in this repository is licensed under the Attribution-NonCommercial-ShareAlike 4.0 International License.

To do

Add tests
Split CommonTools into vtk only and itk/vtk parts
Doxygen documentation is outdated. Also need to correct the cmake files for the doxygen

Contents of subfolders

BasicMeshoperations

A collection of random tools to use with meshes: mesh converters, mesh smoothers, distance transforms, etc.

DistTransform

Calculates a distance transform on a mesh from a collection of seeds (uses fast marching) The distance is calculated from blobs stored in vtkShortArray associated with the vertices. The distance of the point point_id to the blob blob_id is returned in array "DT" and can be accessed by

array = polydata.GetPointData().GetArray('DT')
tuple = array.GetTuple(point_id)
distance = tuple[blob_id]

Example image (left - DT, right - red blob):

FillSurfaceHoles

Implementation similar to ReMesh. Detects and fills holes on the surface. Implements P. Liepa "Filling Holes in Meshes". Has 3 smoothing modes: none, inverse edge lengths and cotangent weights. Here's a sample result.

LVMeshFromMRI

Creates a smoother mesh using splines longitudinally from short axis contours in MRI and a reference point. This was ported from VTK 5.x and needs testing. There's also a python script in Python/mri_mesh_from_contours. The input shape are the landmarks in 3D. One of them is the reference point (which is either the first or the last or has a special ID). Also it is possible that the IDs are used to differentiate between endocardiumn and epicardium. Check the code. Example reconstruction:

Example from the MRI corrector (only python)

Todo:

The code needs a better documentation
Python script was failing with the new VTK/mayavi
Compilation fails with vmtk from Ubuntu 16.04 distribution. Need a replacement. For now uniform remeshing is disabled.

LaplaceBasedVolMesh

Generates a volumetric mesh of any structure with two boundaries. The elements are wedges aligned radially. This was ported from VTK 5.x and needs testing. Examples can be seen in the following figures.

Please cite B. Paun, B. Bijnens, T. Iles, P. A. Iaizzo, C. Butakoff, "Patient Independent Representation of the Detailed Cardiac Ventricular Anatomy", Medical Image Analysis, Accepted 2016.

Todo:

Test

Teichmuller Mapping (T-Map)

Based on the paper "Teichmuller Mapping (T-Map) and Its Applications to Landmark Matching Registration", SIAM Journal on Imaging Sciences, Volume 7, Issue 1

Only dirichlet boundary conditions supported
Only fixed boundary for now

Todo

Cleanup the code

Zerike Decomposition

2D Zernike Decomposition/Reconstruction of an image using multi-precision arithmetics. Optimized for running on a cluster. Programmed together with Arnau Vallve: https://www.linkedin.com/in/arnauvallve

Matlab

A landmarking tool for 2D images (Matlab).
ASM Fusion script (Matlab). Please cite my paper.