Julie-Fabre/bombcell

"makepretty" is nonexistent

lukebun opened this issue · 2 comments

lukebun commented

Hello,

Thank you for sharing this tool I think that it will be incredibly useful and I've already started to apply it to my own data. However, I ran into a few problems.

The first problem is that the function "makepretty" appears to be nonexistent. It's called in multiple files, but I do not believe it is declared. I was able to produce figures by commenting all "makepretty" lines out. I would appreciate it if these files could be included.

2 other minor problems: (1) the GUI at the bottom of "bc_qualityMetric_pipeline" seems to expect data for raw waveforms, but by default param.extractRaw in "bc_qualityParamValues" is set to 0 so these data don't exist. Changing the variable and rerunning solves the problem. (2) in "bc_qualityMetric_pipeline" the comment says that ephysMetaDir should have a ".meta" file but OpenEphys only outputs a ".oebin" file. Using the ".oebin" file instead works, but I had some confusion hunting for the nonexistent ".meta" file.

Julie-Fabre commented

Hi lukebun,

Thank you for your issue!

To answer your comments in order:

  1. Good catch for the makepretty function. It was in another repo of mine, and I've moved it to bombcell.
  2. Yes, you're right. I've changed the default to param.extractRaw=1, which is what it should be set to. I changed the GUI to accommodate for when param.extractRaw=0.
  3. Yes, good point. Bombcell accepts both .meta and .oebin meta files. I've updated the comment in the pipeline.

Let me know if you run into more problems,
Cheers

Julie-Fabre commented

FYI - Since this function is shared and used in several if my repos, I ending up moving the makepretty function to a different repo: prettify-matlab. It's now called prettify-plot and has extended "prettifying" capabilities.
Without this repo, bombcell will still run and will use the old makepretty function, but output a warning text.

Marking this issue as closed now. Thank you for comments! If you have more issues or comments, feel free to open it up again/ up a new one or email me.
Cheers