Internal:PODM 3D

Documentation

Fall 2019

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 CNF Adaptivity Report

Spring 2020

1. Create a User Manual for PODM 3D and Tessellate2D within the fields of Medical Image Computing and Computational Nuclear Femptography ✔

Execution Examples

Fall 2019

1. Create meshes for the Computational Nuclear Femtography part of CRTC_I2M_Suite Documentation. CNF Example Meshes ✔

Spring 2020

1. Create meshes for the Medical Image Computing part of CRTC_I2M_Suite Documentation. Medical Imaging Example Meshes ✔

Summer 2020

1. Create meshes for the Bioinformatics part of CRTC_I2M_Suite Documentation. Bioinformatics Example Meshes ✔

Code

Fall 2019

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 points 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)✔
      1. Understand that the current implementation supports negative weights✔
      2. Change the current implementation to use the minimum-maximum edge length of the element instead of its volume✔
      3. 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✔

Spring 2020

1. Create a general PODM driver✔
2. Set a warning if delta > min-spacing * min-dimension-size / 5✔
3. Set a default delta: ✔
   1. if sizing-function is off then default delta = min-spacing * min-dimension-size / 100 ✔
   2. if sizing-function is on then default delta = min-spacing * min-dimension-size / 20 ✔
4. Remove labels array if there is only 1 label of interest ✔
5. Print a warning if a label is not recovered✔
6. Add Numa flag in CmakeLists.txt ✔
7. Add binary file support ✔
8. Improve Text output ✔
9. Create label-filter for images ✔
   1. Preserve a set of labels of an image ✔
   2. Exclude a set of labels of an image ✔
10. Remove redundant volume threshold checks that don't contribute anything to the meshing procedure ✔

Summer 2020

1. Libraries:
   1. Update ITK to v5.1.0 ✔
   2. Update VTK to v9.0.1 ✔
   3. Remove Boost from PODM (preserve it only for CGAL) ✔
2. Save the label of a cell after its creation and Remove the expensive label recalculation in GetCleanMesh/GetCleanMeshParallel✔
3. Compute Mesh Results in Parallel (TODO)
   1. Implement Parallel version of GetCleanMesh function ✔
   2. Testing ✔
   3. Speed-Up ✔
   4. Assigned as default ✔
4. Upgrade the define NO_IO_WRITING
   1. Rename it to IO_WRITING ✔
   2. Create functions for loading and writing of auxiliary files ✔
   3. Create a compile flag for it, which will also enable the creation of the auxiliary files folder ✔
   4. Fix truncation error when loading box ✔
5. Compute Box, Resized image and surface in Parallel ✔
   1. Implement Parallel version of ComputeBoxAndSurface function ✔
   2. Testing ✔
   3. Speed-Up ✔
   4. Assigned as default ✔
6. Sizing function:
   1. Control min edge and max edge using a percentage of the diagonal ✔
   2. Find values of samples points using linear interpolation ✔

Fall 2020

1. Fix shift of origin if delta not multiple of the spacing ✔
2. Handle CNF images with spacing different than 1, and origin different than {0, 0, 0} ✔
   1. Upgrade Image Segmentation ✔
   2. Upgrade Sizing function ✔
   3. Upgrade Linear Interpolation ✔
3. Change ImageSegmentation to create an image inside the requested grid domain ✔

Spring 2021

1. [Christos] Addition of Extra points at the beginning of meshing ✔
2. [Polykarpos] Loading and saving the state of PODM mesher ✔
3. Load Dynamically Sizing Functions and their initialization as a shared Library using function pointers ✔
4. Detect special cases of Christos and Polykarpos additions ✔
5. Accept double instead of float type precision images ✔
6. Fix PODM not working on Wahab (TODO)
7. Remeshing by using a mesh instead of an image as input and background mesh (TODO)
8. Create upscale-image-filter (TODO)
9. Replace CGAL Predicates with: (TODO)
   1. Predicates Construction Kit:
      1. Paper
      2. Code
      3. Benchmark: PCK vs CGAL Predicates Benchmark
      4. Note: see Geogram branch
   2. Adaptive Precision Floating-Point Arithmetic and Fast Robust Predicates for Computational Geometry:
      1. Paper
      2. Code
10. Smoothing (TODO)
    1. Feature preserving Delaunay mesh generation from 3D multi-material images
    2. CGAL Sources:
       1. https://doc.cgal.org/latest/Mesh_3/index.html
       2. https://doc.cgal.org/latest/Mesh_3/index.html#fig__mesh3protectionimage3D
       3. https://doc.cgal.org/latest/Mesh_3/index.html#fig__mesh3HybridDomainExample
    3. PODM3D citations:
       1. Volume conserving smoothing for piecewise linear curves, surfaces, and triple lines
       2. An anisotropic scale-invariant unstructured mesh generator suitable for volumetric imaging data
       3. Variational generation of prismatic boundary-layer meshes for biomedical computing, International Journal for Numerical Methods
    4. Prof, Andrey Suggestions:
       1. Isosurface Stuffing: Fast Tetrahedral Meshes with Good Dihedral Angles
       2. CERTIFIED FUNCTIONS FOR MESH GENERATION
       3. GENERALIZED INSERTION REGION GUIDES FOR DELAUNAY MESH REFINEMENT
11. Μultiple δ (TODO)
    1. Implement multiple δ (TODO)
    2. Use different δ values (possibly uniform based) according to the surface of each label of a segmented image (TODO)
12. Produce the Voronoi Mesh out of the Delaunay (TODO)
    1. Check what TetGen does (TODO)
    2. Research conversion methods (TODO)