Clarification on Calibration Section

open-ephys / gui-docs

Documentation for the Open Ephys GUI

https://open-ephys.github.io/gui-docs/

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Clarification on Calibration Section #17

Closed OptogeneticsandNeuralEngineeringCore closed 1 year ago

OptogeneticsandNeuralEngineeringCore commented 1 year ago

Slight clarification on folder structure of Calibration Section for readability. Additionally:

I show that calibration files should exist in Program Files not Program Data
I don't fully understand rst, but I think that the slashes are missing on the site because of escape with reStructuredText. Per https://docutils.sourceforge.io/docs/user/rst/quickref.html#escaping you may need two slashes. Unclear because preview in git shows slashes without escape.

jsiegle commented 1 year ago

Thanks for catching this! There was recently an update to Sphinx that caused the single backslashes to not get rendered. I fixed this and also made some of the recommended changes to the "Calibrating probes" section in the latest version: https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Neuropixels-PXI.html

However, I kept the recommend calibration files location as C:\ProgramData\Open Ephys\CalibrationInfo, as this directory won't be removed if the GUI is uninstalled. Did you have calibration files there that were not getting detected?

OptogeneticsandNeuralEngineeringCore commented 1 year ago

I think that we installed via the installer and did not see "ProgramData" created. Is the user to create this folder? Additionally, we somehow got the calibration files from IMEC without the "" folder structure (all probes were in one folder) which caused confusion.

Is there a way to output from OpenEphys exactly where it is looking for these?

jsiegle commented 1 year ago

All of the config files and installed plugins should be stored in C:\ProgramData\Open Ephys, so these persist when the core applications is upgraded. This folder should be created the first time the GUI is launched. Do you still not see it?

In case the calibration files are not found, we can update the popup window to list all of the search paths that are being used.

If IMEC has updated their calibration file format to include everything in one flat directory, I think we should support that as well. This is different to what they've done previously.

anjaldoshi commented 1 year ago

FYI, ProgramData is a hidden Windows folder used by applications to store data for all users. If you're not able to find the folder, make sure "show hidden items" is enabled in the File Explorer settings as mentioned here.

Alternatively, you can just copy paste the C:\ProgramData\Open Ephys path in the File Explorer address bar. This should take you to the Open Ephys folder inside ProgramData.

OptogeneticsandNeuralEngineeringCore commented 1 year ago

Slaps forehead, feels silly, walks away Oi, yoi yoi, yup, sorry, sorry.

Also, we received the calibration files post hoc, via email, so maybe that was how the file structure changed, and may be a one off, separate (read: our own) issue.

Also also, both "ProgramData\Open Ephys" and "Program Files\Open Ephys" exist, and may serve different rolls, but may be part of my confusion. A pop up window would be great...

jsiegle commented 1 year ago

I'm going to close this pull request, but I created an issue in the neuropixels-pxi repo about making the calibration files popup message more informative: https://github.com/open-ephys-plugins/neuropixels-pxi/issues/27

We will update that in the next plugin release.