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Kitware / SlicerSALT

An open-source, free comprehensive software that will allow biomedical scientists to precisely locate shape changes in their imaging studies. This software called Slicer Shape AnaLysis Toolbox (SlicerSALT), will enhance the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.
https://salt.slicer.org
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S-rep hypothesis testing work #291

Open bpaniagua opened 1 year ago

bpaniagua commented 1 year ago
  1. Generate a module that does batch fits of s-reps
  2. Read the documentation sent by Mohsen incl. paper describing the method and R-codebase
  3. Generate a module for hypothesis testing in S-reps
Connor-Bowley commented 1 year ago

The new pipeline creator is a good candidate for this. The (unmerged) new pipeline creator plus the work in this commit can make a module that does initial-fit + refinement. The batch processing part of the new pipeline infrastructure has not been started however.

vicory commented 1 year ago
  1. Generate a module that does batch fits of s-reps

@allemangD @HarryDC

Going to use this issue to expand on this part. Batch fitting needs to run two modules:

1) SRepCreator: Given an input surface and some parameters generates an initial s-rep 2) SRepRefiner: Given an input surface and the initial s-rep generated by 1), improves the fit

The initial stitching of those two together should be in the commit that Connor linked above, the missing piece is just the batch processing.

HarryDC commented 1 year ago

Yea I looked at the two pipelines, i think those are good to go, I have the creator in a state too where it can potentially store multiple output paramters/nodes. And we are ready to create a pipeline from the two parts.

I can put up a SlicerSalt branch that has the connors branch in SRep and my pipelines working branch tied together, i'll set up a combined pipeline so that all the parameters are exposed in the Creator/Refiner pipeline, you should then be able to create a .csv with all the input nodes and input parameters and run that through the Creator/Refiner

HarryDC commented 1 year ago

@vicory Where should the created combined module live ? Checked into SREP as a module or as something under SlicerSALT ?

bpaniagua commented 1 year ago

Hi Harry, The new module should live under s-reps.

HarryDC commented 1 year ago

Quick update, it took a bit of hand editing (the annotations that limit the inputs and confer the defaults aren't copied by the pipeline creator) but this is the Combined Module.

image

The list of parameters is long as I exposed all the parameters of both the generation and the refinement pipelines

I'll push updates Slicer/SRep/Pipenline branches so you can test this