TypeError: unsupported operand type(s) for +: 'float' and 'str'

[DenisSch]

(base) [as773@compute-e-16-229 e3bab0f316d22adf95d950b86ebb60]$ cat .command.log
{'masks': ['cellMask.tif'], 'image': 'unmicst-31.tif', 'channel_names': 'markers.csv', 'output': '.'}
Extracting single-cell data for unmicst-31.tif...
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Traceback (most recent call last):
  File "/n/groups/lsp/mcmicro/2020-07-27/quantification/CommandSingleCellExtraction.py", line 11, in <module>
    SingleCellDataExtraction.MultiExtractSingleCells(**args)
  File "/n/groups/lsp/mcmicro/2020-07-27/quantification/SingleCellDataExtraction.py", line 260, in MultiExtractSingleCells
    ExtractSingleCells(masks,image,channel_names,output)
  File "/n/groups/lsp/mcmicro/2020-07-27/quantification/SingleCellDataExtraction.py", line 245, in ExtractSingleCells
    scdata_z = MaskZstack(masks_loaded,image,channel_names_loaded_checked)
  File "/n/groups/lsp/mcmicro/2020-07-27/quantification/SingleCellDataExtraction.py", line 154, in MaskZstack
    new_names = [channel_names_loaded[i]+"_"+str(nm) for i in range(len(channel_names_loaded))]
  File "/n/groups/lsp/mcmicro/2020-07-27/quantification/SingleCellDataExtraction.py", line 154, in <listcomp>
    new_names = [channel_names_loaded[i]+"_"+str(nm) for i in range(len(channel_names_loaded))]
TypeError: unsupported operand type(s) for +: 'float' and 'str'

[DenisSch]

There seems to be a "space" in the marker.csv that causes this issue!

[DenisSch]

It seems to also convert NA to nan

>>> channel_names_loaded
       DNA0
0    Rabbit
1       Rat
2       NaN
3      DNA1
...