Internal:PODM 3D

Documentation

1. Read PODM3D paper✔
2. Read Guaranteed Quality Tetrahedral Delaunay Meshing for Medical Images paper (Sect. 9) (TODO)
3. Write a proper README.md file✔
4. Add the CNF Example Meshes into the Appendix of the November Report✔
5. Create a User Manual for PODM 3D and Tessellate2D within the fields of Medical Image Computing and Computational Nuclear Femptography ✔

Execution Examples

1. Create meshes for the Computational Nuclear Femtography part of CRTC_I2M_Suite Documentation. CNF Example Meshes ✔
2. Create meshes for the Medical Image Computing part of CRTC_I2M_Suite Documentation. Medical Imaging Example Meshes ✔

Code Changes

1. Restructure repository of PODM3D based on Software engineering standards✔
2. Decouple Args from PODM✔
3. Create setArguments function✔
4. Create setInputImage(ImageType::Pointer)✔
5. Remove IOs from PODM✔
6. Implement a sizing function that will work as an extra rule and it will use the point indices of the tetrahedron that is tested✔
   1. Create UML diagrams to understand the code and the Meshing Procedure in general✔
   2. Create a list of functions that need to be modified to implement the extra Rule ✔
   3. Modify the created list (Extra Rule sizing Function list) of functions✔
   4. Create the following test sizing function to understand if modifications have been done correctly✔

      bool checkSizingFunction(double coordinatesOfTetrahedron**)
      {
          double volume = volume(coordinatesOfTetrahedron);
          double* baryCenter = baryCenter(coordinatesOfTetrahedron)
          
          // if x axis <= 55 and volume of tetrahedron > 10
          if (baryCenter[0] <= 55 && volume > 10)
             return true;
          else
             return false
      }
      

   5. Create the infrastructure to support Sizing Function pointer✔
   6. Incorporate Function Pointer to PODM by creating a setSizingFunction()✔
   7. Replace the test sizing function with the Adaptivity function that was created by Christos (The algorithm is described here)✔
   8. Understand that the current implementation supports negative weights✔
   9. Change the current implementation to use the minimum-maximum edge length of the element instead of its volume✔
   10. Identify an issue of checking sample points outside the image and solve it according to Christos's suggestions✔
7. Separate the interface, the IOs and the filters from PODM✔
8. Create a general PODM driver✔
9. Set a warning if delta > min-spacing * min-dimension-size / 5✔
10. Set a default delta:
    1. if sizing-function is off then default delta = min-spacing * min-dimension-size / 100✔
    2. if sizing-function is off then default delta = min-spacing * min-dimension-size / 20✔
11. Remove labels array of output mesh if tissues of interest < 2✔
12. Print a warning if a tissue is not recovered✔
13. Add Numa flag in CmakeLists.txt ✔
14. Add binary file support ✔
15. Improve Text output ✔
16. Create GetCleanMeshParallel function ✔
17. Identify places in the code where δ varies with regards to background values (TODO)
18. Test if multiple δ works using synthetically generated image data (TODO)

Adaptivity Results

1. Podm Result of Gagic Data image with volume grading on and δ=6, minimum Volume Size = 0.5, limit = 0.1✔
   1. 2D (Triangle): (Done by Christos)
   2. 3D (PODM): (Done with Christos)
2. Produce an Animated Adaptive Procedure video http://www.cs.odu.edu/crtc/videos/PODM3D.html ✔
   1. -> Input Image:
   2. -> Image Segmentation
   3. -> Meshing Procedure. This is a gif which is visible here: https://crtc.cs.odu.edu/images/8/89/AdaptiveMeshing.gif
   4. -> Adapted mesh
   5. -> Linear Interpolation