understanding how T.csv is composed

[briancohn]

Hi @davidcsterratt

Is this the way that T.CSV is generated?

generating a final result of:

[briancohn]

in particular the last tear goes over the last index; is that right?

[davidcsterratt]

The meaning of V0, VB, and VF is:

• V0 - point index of apex of tear
• VB - point index of vertex of tear in backward direction (gb pointers show this direction)
• VF - point index of vertex of tear in forward direction (gf pointers show this direction) The function labelTearPoints() labels a set of three unlabelled points appropriately.

[briancohn]

thanks!

Functions

permute_tear_vertices <- function(list_of_tear_triplets){
    lapply(list_of_tear_triplets, function(x){
            retistruct::labelTearPoints(annotated_outline_with_tears,x)
            })
}

compose_tear_triplets_dataframe <- function(list_of_tear_triplets) {
         do.call('rbind',permute_tear_vertices(list_of_tear_triplets))
}

Usage Example

list_of_tear_triplets <- list(

            c(23,18,28),
            c(35,31,37),
            c(48,45,51),
            c(64,58,69),
            c(87,78,93),
            c(100,96,105),
            c(109,115,122),
            c(135,131,1)
            )
compose_tear_triplets_dataframe(list_of_tear_triplets)

[briancohn]

retistructgui is not reliable (not your fault I know) so I'm implementing a pipeline for retina markup that does not require it. It will be manual but it's not so bad.

People will just assemble files by writing down the vertex numbers:

[briancohn]

we are investigating a possible approach with D3/javascript in the future as well

[davidcsterratt]

Interesting. The interface is definitely a weak point. I'd been thinking that some sort of integration with ImageJ/Fiji might be a way forward, but I'm not expert in that package, so I don't know how easy it would be to create an equivalent interface for marking up tears. Also, I think R is going to be better for producing plots, so I don't see the whole system moving to ImageJ.