yanhaozhang / embedded-deformation-graph-for-winter-school

Aortic 3D Deformation Reconstruction

This project is a learning material for 2021 Winter school on SLAM in deformable environments. Here, we provide a Matlab implementation of embedded deformation graph [1]. This implementation is used for the tutorial class. We also provide some functions of a Matlab implementation of our ICRA 2020 paper related to aortic deformation reconstruction [2]. This is used for the project assignment.

I will release the whole code of AortaDef. So even if you miss to attend this project, you will still be able to have access to the whole project after this winter school.

EDGraph

The implementation of EDGraph is in EDGraph. You can run ./EDGraph/main_edgraph3D.m using Matlab, and see how the ear of a bunny is deformed according to the given control points.

You can run ./EDGraph/main_edgraph3D_aorta.m to practice the ED Graph using a segmented mesh presenting part of the aorta.

Don't forget to switch the grid_size in EDGraph3D.m. It controls the grid size when down sampling for the ED nodes. You can do this by uncomment the following line in EDGraph/@EDGraph3D/EDGraph3D.m.

properties
        num_nearestpts = 6;          % for weights of ednode connection    
        grid_size      = 10/1;       % Downsampling grid size for EDnodes  
        % grid_size      = 0.02;       % this is for the bunny data.
end

Here, the computer vision toolbox is used for down-sampling the vertices.

Aortic 3D Reconstruction

The Matlab functions for aortic 3D deformation reconstruction is in AortaDef. A brief introduction of this project assignment is ./document/WinterSchool_Project_AorticDef_intro.pdf. You can refer to ./document/WinterSchool_Project_AorticDef_doc.pdf for more details on how to finish this assignment.

Please finish the following functions for the todo part.

• camera_projection_model.m
• calculate_projectionContour.m
• calculate_correspondence_observation2ModelContour.m (This might not be easy)
• camera_projection_model_Jacobian.m
• calculate_Error.m
• calculate_Jacobian.m
• update_pts_position.m
• Gauss_Newton_Optimization.m (optional)

Contacts:

Yanhao Zhang: [email protected]. Any discussions or concerns are welcomed :)

Citation

Embedded deformation graph:

@incollection{sumner2007embedded,
  title={Embedded deformation for shape manipulation},
  author={Sumner, Robert W and Schmid, Johannes and Pauly, Mark},
  booktitle={ACM SIGGRAPH 2007 papers},
  pages={80--es},
  year={2007}
}

Aortic 3D deformation reconstruction:

@inproceedings{zhang2020aortic,
  title={Aortic 3D deformation reconstruction using 2D x-ray fluoroscopy and 3D pre-operative data for endovascular interventions},
  author={Zhang, Yanhao and Zhao, Liang and Huang, Shoudong},
  booktitle={2020 IEEE International Conference on Robotics and Automation (ICRA)},
  pages={2393--2399},
  year={2020},
  organization={IEEE}
}