How to plot the generated volume ?

[jeremieglt]

Hi,

I want to use SIMPA to generate images with customed (and non random) tissue volumes for my master's thesis and I am still getting a first hands on right now. I had a little interrogation about volume generation : is there a simple way to visualize in 3D the tissue volumes that we generate at the very beggining of the pipeline ? I didn't see any function or example going in that way and I tried to just take the 3D array of "Tags.DATA_FIELD_SEGMENTATION" and plot it with with different methods (pyplot, plotly and blender) but nothing gave any good result. I however saw in your paper that you had some nice visualizations : did you use an external method or did I miss something in the package ?

Thank you in advance for your reading,
Jeremie

[kdreher]

Hi Jeremi,
I would say in most cases, it is not really needed to do a full 3D visualization. Usually, just plotting different viewpoints along different axes is sufficient to find out what's going on. These are for example implemented in our minimal optical example.

If you really want to have something like in the simpa paper, you can reproduce the results in the paper repository. Especially the tissue generation folder would be interesting for that. Note, that 3D voxelized visualizations might take a while because matplotlib plots each voxel in a volume as a separate vector element.

[jeremieglt]

Hi Kris,
Thanks a lot for your answer and help. With the current volume that I want to simulate, only plotting 2D slices could indeed be a good first approximation but 3D plotting could help me at some point to verify that elements are correctly placed in space.

[kdreher]

Ok, then I guess the way we visualize segmentation masks in the tissue generation folder of the paper repository should be helpful.