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rhlee12 / Fluoro-Package

Repo for porting PARAFAC and EEM plot generation from Matlab
MIT License
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Solid State Correction #5

Open rhlee12 opened 6 years ago

rhlee12 commented 6 years ago

Per email from M. Bowman:

We talked some about having a script that could do multiple corrections and spit them all out in a set of figures.

I was thinking it would be nice to consider the corrections of: 1) Sample - Sample holder 2) Sample - NaCO3 3) Sample - CombBlank 4) (Sample - CombBlank) - NaCO3 5) (Sample - CombBlank) - Sample Holder 6) ( (Sample - CombBlank) - NaCO3)- Sample Holder

This should all be simple, but requires setting up matrix subtraction for each combo, then plotting, then storing in a grob, then saving output.

rhlee12 commented 6 years ago

@maggiebowman6 - would it be possible to add an example file set covering the above correction combinations?

maggiebowman6 commented 6 years ago

Hi @rhlee12 have all the data collected, I can manually do the subtractions and plot them. I will add these raw data files and the data products (corrected eems) to a folder.

rhlee12 commented 6 years ago

To do:

maggiebowman6 commented 6 years ago

Hi @rhlee12 these are starting to look really cool. I would be really curious to see what the FI, HIX, and Freshness look like and compare that to extracted samples. I think I will have a bunch more samples to process through this correcting soon. Tomorrow hopefully I can get this run on my computer.

maggiebowman6 commented 6 years ago

Hi @rhlee12 When I run the code it isn't saving the PNG files for the images anywhere I can find. The code for 180316 samples does not do it either. I don't know where it is saving it to.

rhlee12 commented 6 years ago

Oh no! @maggiebowman6 could you push (or email) the script version you used? Where does getwd() say the working directory is when you run it in R?

maggiebowman6 commented 6 years ago

My working directory is: C:/Users/maggi/OneDrive/Documents/GitHub/Fluoro-Package/fluoro

I am using the files from the solid state folder: correct_plot_scrip.R (180316) correct_plot_script_mmb.R (180516 samples)

rhlee12 commented 6 years ago

well, found the issue. In the code it was set to dump the plots to tempdir() (line 59).

If you run list.files(tempdir()) I bet R says they're there.

I went ahead and changed the save.dir parameter to ../180516/corrected/ and ../180316/corrected/ in each script for you--let me know if any more issues crop up. I'll try to make this script cleaner/into a function here this week, to avoid this.

maggiebowman6 commented 6 years ago

Fixed Thank you!!!

maggiebowman6 commented 6 years ago

Hi @rhlee12 The code has started to error out the detector and I had to move to the f3. If I put F3 data up in a folder here tonight can you try and get the f3 data to process?