This repo is created for MM project - Reconstruction and Visualization of 3D Anatomical Structures Using a Sequence of 2D Ultrasound Images. Please create your branch to write codes for this project.

Accredit

Some of the scripts are written based on course lectures.

Installation

All commands listed here are sample commands and written based on Windows OS. To run the scripts on other OS, please change the commands accordingly.

Prerequisites

• Python 3.8
• vtk == 9.1.0

Setup Python environment and install vtk

• setup python virtual environment: python3.8 -m venv env
• activate virtual environment: env/Scripts/activate
• install vtk: pip install -r requirements.txt (Conflicts between packages may occur when using this command to install packages. Please solve the conflicts manually according to the exact errors)
• run a specific script with this command: python python/filename.py
• run stand_alone.py followed by .mat file path to directly get the result

python stand_alone.py -p "your_mat_path"

About folders and files

• python folder has the following python scripts;

  • import_data.py: import data from .mat file；
  • filters.py: remove noise and artifacts, and augment surface；
  • realignment.py: realignment US image frames；
  • vol_pixel_filter.py: smooth 3D volume surface；
  • import_and_filt.py: import data and perform filtering；
  • import_and_preprocess.py: import data and perform surface augmentation, realignment, and surface smoothing all at once (recommended)；
  • mat2mhd_sitk_singlefile.py: convert a single .mat file to .mhd file using SimpleITK (recommended);
  • mat2mhd_sitk_batchfiles.py: convert .mat files in one folder to .mhd files using SimpeITK (recommended);
  • rendering_vtk_1win.py: display visualization results with VTK using volume and surface rendering in one viewport (recommended);
  • rendering_vtk_3win.py: display volume rendering, surface rendering and volume and surface combined rendering results with VTK with three viewports (recommended);
  • render_vista.py: perform reconstruction and volume rendering from .mat file/files using PyVista (recommended);
  • render_vtknp.py: perform volume rendering from .mat file/files using Numpy and VTK (need to be improved and not recommended);
  • mat2mhd_vtk.py: convert a single .mat file to .mhd file using VTK (need to be improved and not recommended);
  • matscanner.py: Print the keys of a .mat file and get the dimension of arrays.

• output has sample results of volume rendering.