hanyin88
commented
1 year ago Hey Seham - I ran into the same issues and it appears due to missing values in the lab csv... Have you find out a way to trouble shoot it? many thanks!
Update: fixed the issue after downgraded python form 3.9 to 3.6 and panda from higher version to the one specified by author.
Another update: turns still having issues with lower version of python/panda:
==> Processed 144000 patients... ==> Processed 148000 patients... Traceback (most recent call last): File "/Users/why217/opt/miniconda3/envs/TPS/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2657, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'patient'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/why217/opt/miniconda3/envs/TPS/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/Users/why217/opt/miniconda3/envs/TPS/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/why217/Desktop/UIUC/cs598/TPC-LoS-prediction/eICU_preprocessing/run_all_preprocessing.py", line 18, in
Final update: ---finally figured out it's still the python/panda version issues with the new M1 MacBook. Everything resolved after I made a new env of python 3.6 and pip installed all requirements.
SpeedRanger
I got the following error while running the pre-processing scripts by
python3 -m eICU_preprocessing.run_all_preprocessingFile "/anaconda3/envs/TPC_Proj/lib/python3.8/runpy.py", line 194, in_run_module_as_main return _run_code(code, main_globals, None, File "/anaconda3/envs/TPC_Proj/lib/python3.8/runpy.py", line 87, in_run_code exec(code, run_globals) File "/eICU/TPC-LoS-prediction/eICU_preprocessing/run_all_preprocessing.py", line 18, in
timeseries_main(eICU_path, test=False)
File "/eICU/TPC-LoS-prediction/eICU_preprocessing/timeseries.py", line 228, in timeseries_main
gen_timeseries_file(eICU_path, test)
File "/eICU/TPC-LoS-prediction/eICU_preprocessing/timeseries.py", line 166, in gen_timeseries_file
merged = timeseries_lab.loc[patient_chunk].append(timeseries_resp.loc[patien t_chunk], sort=False)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexing.py", line 967, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexing.py", line 1194, in _getitem_axis
return self._getitem_iterable(key, axis=axis)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexing.py", line 1132, in _getitem_iterable
keyarr, indexer = self._get_listlike_indexer(key, axis)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexing.py", line 1330, in _get_listlike_indexer
keyarr, indexer = ax._get_indexer_strict(key, axis_name)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexes/multi.py", line 2587, in _get_indexer_strict
self._raise_if_missing(key, indexer, axis_name)
File "/anaconda3/envs/TPC_Proj/lib/python3.8/site-packages/pandas/co re/indexes/multi.py", line 2605, in _raise_if_missing
raise KeyError(f"{keyarr[cmask]} not in index")
KeyError: '[141939 142056 142476 142521 142560 146391 147447 149039 149606 15300 6\n 160529 162431 166572 166709 167391 167417 171174 175528 177651 178069\n 1788 58 179142 179554] not in index'