This part is confusing me [lines 20-24]: if masscolumn is None: metalcolumn =

Pretty sure this is an artefact remaining from either a debugging/or variable re

masscolumn and metalcolumn in ometiff2analysis.py about imctools HOT 1 CLOSED

bodenmillergroup commented on August 16, 2024

masscolumn and metalcolumn in ometiff2analysis.py

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votti commented on August 16, 2024

Pretty sure this is an artefact remaining from either a debugging/or variable renaming. This should definitely be removed.
I am not explicitly checking for it and relying on pandas of throwing an error. Definitely not good practice and should be done explicitly.
The logic of the function should be:

If pannelcsv is None:
   returns a .tiff with containing all the channels of the acquisition
   # in this case metalcolumn and massscolumn can be unspecified
else:
   load pannel with filename pannelcsv
   if the pannel has only 1 column:
           # assume the csv is just a list of metal
           return a tiff containing the channels specified in the pannel
           # in this case metalcolumn and massscolumn can be unspecified
  else:
          # asssumes the csv is a table, thus needs a specification
          # which is the  metalcolumn or masscolumn
          if masscolumn is None:
                 # requires that the metalcolumn needs to be specifiec
                return a tiff containing the channels specified in the metalcolumn
          else:
                return a tiff containing the channels specified in the masscolumn

Thus it depends on
a) if pannelcsv is None -> metalcolumn and massscolumn can be None
b) the pannel is a 1 column csv -> metalcolumn and massscolumn can be None
c) the pannel has multiple columns -> either metalcolumn and massscolum need be not None

The code readability and error checks should be definitely improved here.

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