[WIP] Making better analysis pipeline

[sonyahanson]

Making better automated analysis and storage/plotting of analysis of fluorescence assay data

Starting with 16 spectra datasets: Abl, Src, AblGK, and SrcGK with Bos, Bsi, Gef, Erl.

To start: had to make small change to select_data in platereader.py so it could also select data from an already made dictionary instead of just an input xml file.

[sonyahanson]

So one advantage of the having select_data return a sorted list of values, is that it makes it immediately usable with the current pymc modeling framework (below), where Lstated = np.array([20.0e-6,9.15e-6,4.18e-6,1.91e-6,0.875e-6,0.4e-6,0.183e-6,0.0837e-6,0.0383e-6,0.0175e-6,0.008e-6,0.0001e-6], np.float64) # ligand concentration, M.

Obviously it would be great to have this be a dictionary with all wells and their corresponding ligand concentration, and I think this shouldn't be too hard to get the pymc modeling to take this in, but maybe that's more appropriate for a later/larger set of changes?

pymc_model = pymcmodels.make_model(Pstated, dPstated, Lstated, dLstated, 
               top_complex_fluorescence=CK2_BOS_480,
               top_ligand_fluorescence=CK2_BOS_480_lig,
               use_primary_inner_filter_correction=True, 
               use_secondary_inner_filter_correction=True, 
               assay_volume=assay_volume, DG_prior='uniform')

[jchodera]

Obviously it would be great to have this be a dictionary with all wells and their corresponding ligand concentration, and I think this shouldn't be too hard to get the pymc modeling to take this in, but maybe that's more appropriate for a later/larger set of changes?

This is essentially what #41 implements: Each Well has attached data on concentrations and measurements. See the README.md, which will go into the user guide once this gets cleaned up and merged.

[sonyahanson]

Okay. So I might punt on this until the new API is done, then. I would like to make these figures of the results for the 16 spectra relatively soon, but I've got other things I can do in the meantime...

Maybe I'll change this pull request to be about updating xml2png.py so it uses platereader.py and is only one script instead of 6 or whatever.

[jchodera]

The xml2png.py improvements sound great!

Any comments on the README.md? You can even comment line-by-line if needed.

[sonyahanson]

Since I would like to have some data to present at lab meeting next week, I might stick with my original plan for this PR and do some ad hoc analysis without the new API.

[sonyahanson]

That was not what I expected would happen. Can I reopen this?

[sonyahanson]

Maybe I can't... Will just make a new PR.