Author: Catalina Tobon Gomez (catactg@gmail.com)
This code generates a standardized unfold map as described in
Standardized unfold mapping: a technique to permit left atrial regional data display and analysis. Williams SE, Tobon-Gomez C, Zuluaga MA, Chubb H, Butakoff C, Karim R, Ahmed E, Camara O, Rhode KS. J Interv Card Electrophysiol. 2017 Sep 7. doi: 10.1007/s10840-017-0281-3.
Please cite this reference when using this code.
The pipeline is split in four parts.
- run_standardization: standardizes meshes from a raw mesh. Depends on VMTK, VTK and MeshLab
- run_currents: registers mesh to an atlas using currents registration. Depends on VTK, MATLAB and ./currents_build
- run_sum: computes standardized unfold map. Depends on VMTK and VTK
- run_quantification: computes regional quantification (extent or mean value). Depends on VMTK and VTK
Clone the repository and cd into it:
$ git clone https://github.com/catactg/sum
$ cd sumSet paths according to your system in constants.py
MATLAB_BIN_PATH
CURRENTS_BUILD_PATH
MESHLABSERVER_PATH
Default parameters of the algorithm can be modified in main.py inside the get_parameters() method.
main.py [-h] --meshfile MESHFILE --datatype DATATYPE
[--pvcliptype PVCLIPTYPE]
[--paired_unfold_disk PAIRED_UNFOLD_DISK]
[--mitral_clip_type MITRAL_CLIP_TYPE] [--use_seed_selector]
[--use_laa_seed] [--use_similarity] [--use_glyphs]
[--visualize] [--skip_standardization] [--skip_currents]
[--skip_sum] [--skip_quantification]
-h, --help show this help message and exit
--meshfile MESHFILE Full path to mesh file in VTK format
--datatype DATATYPE Data type to process: force | lge | lat
--pvcliptype PVCLIPTYPE How to clip the pulmonary veins: short | long
--paired_unfold_disk PAIRED_UNFOLD_DISK
Full path to a paired unfold disk. The edges of the
current unfold will be overlaid on the paired unfold
disk
--mitral_clip_type MITRAL_CLIP_TYPE
The algorithm will compute a mitral plane based on the
body and PVs centroids. If the meshfile already
contains a mitral plane clip, use the 'manual' option
to preserve it
--use_seed_selector Seed selection will always run for a new case. To
select new seeds, activate this flag
--use_laa_seed Activate seed for appendage
--use_similarity The method uses an affine transform to initialize mesh
registration. Activate this flag to use a similarity
transform
--use_glyphs Activate glyph on visualization. Recommended for spare
measurements (e.g. some lat meshes)
--visualize Activate visualization
--skip_standardization Skip run_standardization step
--skip_currents Skip run_currents step
--skip_sum Skip run_sum step
--skip_quantification Skip run_quantification step
Data was created by using a mesh from the LASC challenge and adding mock scalars onto it: force, lge, and lat.
Run the command lines below and the PNG output should be identical to the one in ./data/expected_output.
python ./main.py --meshfile ./data/force/mock_force.vtk --datatype force
python ./main.py --meshfile ./data/lge/mock_lge.vtk --datatype lge --paired_unfold_disk ./data/force/mock_force_FTI_disk_uniform.vtp
python ./main.py --meshfile ./data/lat/mock_lat.vtk --datatype lat
python ./main.py --meshfile ./data/lat/mock_lat.vtk --datatype lat --use_glyph --skip_standardization --skip_currents
The scripts in this repository were successfully run with:
The easiest way to install everything you need using the VMTK conda package. It inclues Python, NumPy, VMTK and VTK.
First, download miniconda and install it from terminal:
wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh
sh Miniconda2-latest-MacOSX-x86_64.sh
Create an environment and activate it:
conda create --name vmtk
source activate vmtk
Finally, install vmtk:
conda install -c vmtk/label/dev itk vtk vmtk
Anytime you wish to use vmtk (e.g. to run the code in this repository) you will need to activate the environment:
source activate vmtk
BSD 2-Clause