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jjhelmus / nmrglue

A module for working with NMR data in Python
BSD 3-Clause "New" or "Revised" License
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Read and write files so that Topspin can read them #85

Closed kaustubhmote closed 5 years ago

kaustubhmote commented 5 years ago

Currently, the functionality to write files in Bruker's formats is pretty good, but the files are not written out in a way that will make them accessible from Topspin. 2 things need to be done to make this happen: (i) Write acquN files in addition to acquNs files and (ii) write out the procN and procNs files in the correct subfolders. These commits give options to the user to do these things via write and read functions in bruker.py. The following changes are made:

  1. bruker.write will now write acquN files in addition to acquNs files to the given directory. These will be identical files. Another option was to read and write out the acquN, but that adds unnecessary keys to the dictionary. This is a change in default behaviour, but it seems harmless to me even if the purpose of writing out the file was is not to read back the data in Topspin (one additional file is written out).
  2. If read_procs is set to True in the bruker.read function, any pdata folders inside the given directory will also be searched and by default the procNs files in folder number 1 will be read. If folder number 1 in not present, one of the other folders is read in.
  3. write has 3 new arguments (procs_files, write_procs, and pdata_folder). The first two arguments are similar to their acqus counterparts. pdata_folder will allow the user to define a (integer) subfolder where these are stored. By default, all the options are disabled, so the behaviour of the function should not be altered otherwise.

At some point in the (hopefully) near future, I plan to put in functionality to write out processed data that can be read in Topspin. The additions in this PR will be required to be able to read these data back in Topspin. In any case, these additions already help out in pre-processing the data (for example, splitting and sorting interleaved datasets) that can be then processed in Topspin.

jjhelmus commented 5 years ago

Thanks for putting this together. Merging.

kaustubhmote commented 5 years ago

Thanks,

A slightly tangential question: Do you prefer opening a Issue and then making a PR? Or something like this one is acceptable?

jjhelmus commented 5 years ago

However you feel like contributing is fine by me, either with or without an accompanying issue.