get-progression turns 2-digits session labels to 3 digits

When I run

clinicadl tsvtools get-progression labels.tsv --time_horizon 36

and then

clinicadl tsvtools analysis merged.tsv labels.tsv analysis.tsv

I get the following error:

KeyError: ('sub-ADNI002S0685', 'ses-M048')

It comes from the fact that get-progression converts 2-digits session labels to 3-digits labels (e.g. ses-M48 to ses-M048) in labels.tsv, whereas they stay 2-digits labels in merged.tsv. To be more precise it is done by the function merged_tsv_reader called at the begining of get_progression.

clinicadl/clinicadl/utils/tsvtools_utils.py

Lines 15 to 25 in ff2f892

    
           def merged_tsv_reader(merged_tsv_path: Path): 
        
               if not merged_tsv_path.is_file(): 
        
                   raise ClinicaDLTSVError(f"{merged_tsv_path} file was not found. ") 
        
               bids_df = pd.read_csv(merged_tsv_path, sep="\t") 
        
               for i in bids_df.index: 
        
                   session = bids_df["session_id"][i] 
        
                   if len(session) == 7: 
        
                       bids_df.loc[(i), "session_id"] = session[:5] + "0" + session[5:7] 
        
               return bids_df

So my question is: what is the purpose of converting 2-digits to 3-digits labels?

And a more general remark: shouldn't we switch the whole ClinicaDL to 3-digits labels to be consistent with Clinica? (see aramis-lab/clinicadl_handbook#23)

There is no problem if the labels.tsv and merged.tsv files already contain 3-digits labels, as they are outputted now by Clinica.

	def merged_tsv_reader(merged_tsv_path: Path):
	if not merged_tsv_path.is_file():
	raise ClinicaDLTSVError(f"{merged_tsv_path} file was not found. ")
	bids_df = pd.read_csv(merged_tsv_path, sep="\t")

	for i in bids_df.index:
	session = bids_df["session_id"][i]
	if len(session) == 7:
	bids_df.loc[(i), "session_id"] = session[:5] + "0" + session[5:7]

	return bids_df