Clarification on GraphML files

[Dhanasrepo]

Hello,

Thank you for sharing your work! I’ve been analyzing your dataset and had problem understanding how the graphml files are created.

I am using VesselVio to process volumetric data into graphs and noticed that in the save_graph() function, coords_list is deleted before saving the GraphML file. However, in the PultreeDataset loader, coords_list is expected and used for edge processing and classification.

I checked a GraphML file used in published PTL Dataset and found that coords_list was still present, suggesting that either:

* VesselVio was modified to retain coords_list before saving, or

* A different post processing step was performed to restore coords_list.

Questions for Clarification

1) Did you modify VesselVio to retain coords_list in the GraphML files?

2) Could you please describe the post-processing steps from volume to graphml and npz?

This information would help us ensure reproducibility and correct processing of the data.
Thanks,
DK

[TVayne]

I experienced the same confusion, have you solved it? @Dhanasrepo

[Dhanasrepo]

@TVayne I modified the VesselVio implementation to retain the coords_list when saving the GraphML files.

However, I'm still unclear how the original volumetric data is saved as npz format in sync with the processed graphml co-ordinate system. Any clarification from the authors would be super helpful here.

[TVayne]

Thanks for your reply.

The author's data seems to overlook the relevant information of physical coordinates and set the spacing as (1,1,1). Thus, the coordinates obtained by VesselVio can be sync with npz data.

[kangxian97]

Hello, thank you for your question and discussion.

We have indeed modified the vesselvio software such that a coord_list is presented for us to provide additional information for labeling edges in our graph construction process. Regarding the vesselvio modification, we see that's important, thus we will release the vesselvio code in the near future.

And yes, we simply set the spacing as you described, such that the coordinates are aligned in the 3D space.