Welcome to Atherosclerotic Plaque G&R in AceFEM’s documentation!

Introduction

Overall of the atherosclerotic plaque G&R project.

Description of the GIF

Project Structure

Warning

To access the project directories and files you need the VPN credentials. The project is hosted on a private server.

To clone the repository, use the following command:

git clone <gituser>@192.168.1.100:/home/alessandro/Drive/GitRepos/acePlaque-tesi.git

Note

The project is based on both Python and AceFEM/AceGEN tools.

The main operative sub-packages are:

AceFEM/AceGEN tools:

Python packages:

Directories and files:

The proejct structure is as follows:

project/
│
├── T00_Common/                # Contains general documentation and common scripts
│    │
│    ├── py/
│    │    ├── myPatientsModulesV2/     # Contains modules related to patient data processing
│    │    │   ├── patientMain.py       # Main script for patient data handling
│    │    │   └── nrrdAux.py           # Auxiliary functions for NRRD file processing
│    │    │
│    │    ├── mesh-importer_v2/        # Contains mesh conversion tools
│    │    │   └── meshConversion.py    # Main script for mesh conversion
│    │    │
│    │    ├── myModulesV2/             # General utility modules
│    │    │   ├── postResults.py       # Functions to post-process results
│    │    │   └── importMeshFromTXT.py # Functions to import meshes from TXT files
│    │    │
│    │    └── myAceplaque/             # Contains core meshing tools
│    │        └── mesher.py            # Main meshing script
│    ├── Elements/
│    │   ├── Elements.nb
│    │   ├── BoundaryPressureP2
│    │   └── O2P1YG
│    │
│    ├── auxFncs/
│    │   ├── myExpRoutines.m
│    │   ├── myFileName.m
│    │   ├── myLoading.m
│    │   ├── myPostAuxialiars.m
│    │   └── Kernel/
│    │
│    ├── createMPHmesh.m
│    └── generate-interpolation-materials.wls
│
├── T01_Patient0/              # Contains patient-specific data
│     ├── mesh/               # Patient-specific data
│     │   ├── ...
│     │
│     └── growth.nb/
│
└── TXY_PatientABC

Installation

Install Anaconda and create an enviroment with all dependencies list in conda environment.

conda env create -f environment.yml

Usage

The package allows for three main operations:

  • Convert mesh into AceFEM suitable FEM meshes

  • Run hyperelastic FEM simulations including G&R based on the homogenous stress hypothesis

  • Export and post-process the results in a user-friendly and very efficient manner

The following sections describe the main steps to perform each of the operations.

Convert mesh

See Structural mesh generator for details.

Using the myAceplaque.py package, it is possible to convert (headless) the patient meshes (wall, lipid, fibrotic, calcification) into the format required by the FEM model, including the materials description.

The script automatically exports all the files in the assigned file_dir/mesh/ folder, where file_dir is a user-specified folder.

import myAceplaque.mesher as plq
# paths = ...
myMesh = plq.myMesh(paths)
myMesh.assign_material_map(spacing=0.0001)
myMesh.write_material_map()
myMesh.create_volumetric_wall_mesh(block_height_multiplier=0.8,
            hmax='5E-4',
            hmin='3.5E-4')

In the end, the algorithm allows to write:

  • mesh.h5, containing all the mesh information

  • interpMatx.m, representing the MATX type of material

  • interpFibr.m, representing the FIBR type of material

  • interpCalc.m, representing the CALC type of material

  • interpLrnc.m, representing the LRNC type of material

  • surfaces.json, containing the association between the integer tag of each surface and its structural type (used to assign boundary conditions):

    • internal, the lumen

    • external

    • top and bottom

Run simulation

Post-processing

AceFEM

Python auxiliary modules

References