How to save and interpret pupil data

[mckennabrown]

Hi!
This is somewhat similar to #64, although I'm asking about different aspects of the pupil data.

Is there a way to save just pupil area without computing the fullSVD? I'm particularly interested in steps using the python GUI.

Additionally, it might be helpful to specify in the documentation that the "save ROIs" button just saves information about the drawn ellipse and settings, not the actual pupil within the pupil ROI.

[mckennabrown]

I've looked and it seems the saved roi data doesn't change based on how I modify the ROIs (specifically I increased saturation for a pupil ROI and saved the ROI and checked the .npy data and the saved saturation remained the same). Am I interpreting the saved ROIs incorrectly?

[maxseppo]

I'm also curious if there is a way to compute only pupil diameter.

[ZiTao956]

I also want only to compute pupil ROI. And I would like to have the output of the pupil ROI after increase saturation.

[maxyccc]

The code ensures that motSVD and movSVD cannot both be unchecked:

facemap/facemap/gui/gui.py

Line 1289 in 97ea2aa

if self.motSVD_checkbox.isChecked() or self.movSVD_checkbox.isChecked():

However, if no other ROI types (motion SVD type) are selected, the loop will only perform pupil extraction, even if motSVD and movSVD are selected.

see this:

facemap/facemap/process.py

Line 638 in 97ea2aa

def run(

and this:

facemap/facemap/process.py

Line 302 in 97ea2aa

def process_ROIs(

This can be confirmed by comparing the total time consumed during execution.
Just remember to uncheck the multivideo (FullSVD == false) and no other ROI types (nroi == 0).

[maxyccc]

The "Save ROIs" button is designed for the following workflow:

Load video 1 → Set the pupil ROI and saturation for video 1 → Save ROIs (this adds the video 1 to the batch list).
Load video 2 → Set the pupil ROI and saturation for video 2 → Save ROIs (this adds the video 2 to the batch list).
Repeat for all videos.

see this:

facemap/facemap/gui/gui.py

Line 1231 in 97ea2aa

self.batchlist.append(savename)

Once all videos are loaded and their ROIs saved, press "Process Batch,"

By the time you wake up next morning, the videos will be fully analyzed.