App is expecting key.txt to be CSV #3
Description
Jasleen is running into this error (on parc-stats-v1.1 branch)
Traceback (most recent call last):
File "/export/prod/5f984bdc82260651b50a20aa/5fb2c3345079858265dace12/createColorLUT.py", line 46, in <module>
main()
File "/export/prod/5f984bdc82260651b50a20aa/5fb2c3345079858265dace12/createColorLUT.py", line 43, in main
createColorLUT(keyfile,outfile)
File "/export/prod/5f984bdc82260651b50a20aa/5fb2c3345079858265dace12/createColorLUT.py", line 13, in createColorLUT
df = df[[2,3]]
File "/usr/local/lib/python3.6/dist-packages/pandas/core/frame.py", line 2806, in __getitem__
indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1]
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1553, in _get_listlike_indexer
keyarr, indexer, o._get_axis_number(axis), raise_missing=raise_missing
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1640, in _validate_read_indexer
raise KeyError(f"None of [{key}] are in the [{axis_name}]")
KeyError: "None of [Int64Index([2, 3], dtype='int64')] are in the [columns]"
The input key.txt is not CSV, but stored in this format (generated by app-roiGenerator)
lh.hv4 -> 1
lh.lO1 -> 2
lh.lO2 -> 3
lh.tO1 -> 4
lh.tO2 -> 5
lh.v1 -> 6
lh.v2 -> 7
lh.v3 -> 8
lh.v3a -> 9
lh.v3b -> 10
lh.vO1 -> 11
lh.vO2 -> 12
rh.hv4 -> 13
rh.lO1 -> 14
rh.lO2 -> 15
rh.tO1 -> 16
rh.tO2 -> 17
rh.v1 -> 18
rh.v2 -> 19
rh.v3 -> 20
rh.v3a -> 21
rh.v3b -> 22
rh.vO1 -> 23
rh.vO2 -> 24
key.txt is really supposed to look like this
0 -> 0 == Unknown
1 -> 1 == Left-Cerebral-Exterior
2 -> 2 == Left-Cerebral-White-Matter
3 -> 3 == Left-Cerebral-Cortex
4 -> 4 == Left-Lateral-Ventricle
5 -> 5 == Left-Inf-Lat-Vent
As I reported in brainlife/app-roiGenerator#3 , key.txt should be deprecated by label.json. It would be ideal if app-roiGenerator outputs label.json, and have app-freesurfer-stats reads label.json - and maybe fall back to reading key.txt if it doesn't exist?