Posts by Tania Castillo
Week 12 : Experimenting with ODFs implementation
- 24 August 2023
There were different issues I needed to address for the ODF implementation. Even though I could not solve any of them completely, I did check each of the issues and made some progress. All the work in progress is being recorded in the following branch SH-for-ODF-impl, which when ready will be associated with a well-structured PR.
Week 11 : Adjusting ODF implementation and looking for solutions on issues found
- 16 August 2023
I continued to experiment with the ODF glyph implementation. Thanks to one of my mentors I figured out how to get the missing data corresponding to the SH coefficients \(a^l_m\) part of the function \(f(\theta, \phi)\) described here. I also was told to make sure to implement the correct SH basis since there are different definitions from the literature, I have to focus now in the one proposed by Descoteaux, described in this paper, which is labeled in dipy as descoteaux07. To do this I had to make a small adjustment to the base implementation that I took as a reference, from which I obtained a first result using SH of order 4.
Week 10 : Start of SH implementation experiments
- 08 August 2023
I started formally working on SH implementation. I was told to start first doing a simple program where I can modify in real-time the order \(l\) and degree \(m\), parameters corresponding to the Spherical Harmonics function \(Y^m_l(\theta,\phi)=\), based on previous work. That is just one part of the final ODF calculation, but here is what a first experimental script looks like.
Week 9: Tutorial done and polishing DTI uncertainty
- 31 July 2023
I addressed the comments from the tutorial of PR #818 related to how to display specific visualizations I wanted to make. I was suggested to use ShowManager to handle the zoom of the scene and also to use GridUI to display several actors at the same time for a visual quality comparison of the tensors. Below are some images generated for the tutorial that is almost done.
Week 8: Working on Ellipsoid Tutorial and exploring SH
- 25 July 2023
I mainly worked on the ellipsoid actor tutorial, as PR #791 is finally merged, so I was able to complete the tutorial by adding my implementation. In addition, during the weekly meeting, I received a good overview of the next issue I will be working on, which is using raymarching SDFs to display spherical harmonics (SH) for visualizing ODF glyphs for DTI. I got several ideas and resources which I can start experimenting with, such as Shadertoy and some base implementations from other FURY contributors. The main drawback when creating these objects is the amount of data required to create them, because depending on the SH order, the number of parameters that the function receives may vary, also unlike the tensors, which are represented only with a 3x3 matrix, here we could have more than 9 values associated with a single glyph, so passing the information from python to the shaders is not so trivial, besides requiring more resources as there is more information that needs to be processed. Some ideas I received were using matrixes instead of vectors, using templating, or even using texture to pass the data. I started to explore these options further, as well as to review in more detail the existing implementations of SH with raymarching, in order to understand them better.
Week 7: Adjustments on the Uncertainty Cones visualization
- 17 July 2023
I was told to refactor some parts of the uncertainty PR, since I was relying too much on dipy functions which is not good because it makes maintenance more difficult as dipy requires FURY for some functionalities. So I did some adjustments on the uncertainty function parameters and the corresponding tests, hopefully I managed to get with the most appropriate definition but I need to receive a first feedback to see how much I have to adjust the implementation. As I had to delete some relevant code lines inside the uncertainty calculation which consisted of preprocessing the data in order to define the necessary variables for the uncertainty formula, I was also suggested to make a tutorial of this new feature, so I can explain in detail how to obtain and adjust the necessary information, before passing it to the actor, and in general how and what is the purpose of this new function.
Week 6: First draft of the Ellipsoid tutorial
- 10 July 2023
#PR 818: Tutorial on using ellipsoid actor to visualize tensor ellipsoids for DTI
Week 5: Preparing the data for the Ellipsoid tutorial
- 03 July 2023
During the weekly meeting with my mentors, there was a small discussion over the naming of the actor and its usage. On the one hand, although the purpose of the actor is to visualize diffusion tensor ellipsoids, the idea is that it can also be used for any other type of visualization that requires the use of ellipsoids, so in the end, we decided to keep the name ellipsoid as it is more generic. On the other hand, as there is already an actor made for the purpose of tensor visualization, namely tensor_slicer, it might not be obvious how and why one would use this new ellipsoid actor for this purpose, thus it was proposed to make a tutorial that can clarify this. The main difference between both actors relies on the quality and the amount of data that can be displayed, so the idea is to show the difference between both alternatives so the user can choose which one to use depending on their needs. To prepare the tutorial the first step was to add the data I will use on fury-data so I can then fetch and load the datasets I need to work on the tutorial.
Week 4: First draft of the DTI uncertainty visualization
- 27 June 2023
#PR 810: DTI uncertainty visualization
Week 3: Working on uncertainty and details of the first PR
- 19 June 2023
I made some adjustments to the ellipsoid actor definition, now called tensor. This was something discussed in the weekly meeting as the coming changes are related to this actor, the idea now is to have a tensor actor that allows choosing between displaying the tensor ellipsoids or the uncertainty cones (later on). I also worked on the uncertainty calculation, and the cone SDF for the visualization, so I plan to do a WIP PR next to start getting feedback on this new addition.
Week 2: Making adjustments to the Ellipsoid Actor
- 12 June 2023
I made some minor adjustments to the last PR I submitted. Last time it was a draft since I was waiting for the weekly meeting to know how to proceed, but now it is ready. I am waiting for the review so I can make the necessary corrections and adjustments to merge this first PR soon.
Week 1: Ellipsoid actor implemented with SDF
- 05 June 2023
PR #791: Ellipsoid actor implemented with SDF
Week 0: Community Bounding Period
- 02 June 2023
Hello everyone, my name is Tania Castillo, I am close to finishing my degree in Computer Science and I think this is a great opportunity to put my learning and skills into practice. I will be working with FURY on improving the visualization of DTI tensors and HARDI ODFs glyphs by using well-known techniques in computer graphics.