Hello,
I was experimenting with the methods of the BIDSLayout class using the test examples given in the tutorial and the bids-examples repository.
I initialized my layout:
layout2 = BIDSLayout(join(get_test_data_path(), 'synthetic'), validate=False, derivatives=True)
When I try to run:
layout2.get_collections(level='subject', merge=True).to_df(), it collects all the tsv files under the subject directory for all the subjects and stores them in a dataframe.
However when I try to run:
layout2.get_collections(level='session', merge=True).to_df()
it gives me a KeyError: "['extension'] not found in axis".
I tried to dig into the source code and found that it adds an extension column to the table.
E:\Anaconda\lib\site-packages\bids\variables\io.py in _load_tsv_variables(layout, suffix, dataset, columns, prepend_type, scope, **selectors) 432 dupes = list(set(ent_cols.columns) & set(_data.columns)) --> 433 to_drop = ['extension'] + dupes 434 ent_cols.drop(columns=to_drop, inplace=True) 435 436 _data = pd.concat([_data, ent_cols], axis=1, sort=True)
The session folders also have their own *scans.tsv files.
Since this was from the bids-examples dataset, I figured out it might be easier for you guys to test this out as well. Any solutions or suggestions?