diff --git a/image_processing/build_dataset.py b/image_processing/build_dataset.py index 4c7456910c6a0253a6fbf6154dadd46e378d0e80..c618576cebdc857d38a2836eab4d342615adc789 100644 --- a/image_processing/build_dataset.py +++ b/image_processing/build_dataset.py @@ -124,6 +124,7 @@ def create_antibio_dataset(path='data/label_raw/230804_strain_peptides_antibiogr df[test] = df[test].map(lambda x :float(str(x).replace('>','').replace('<',''))) #categorise each antibioresistance according to AST breakpoints table df[test+' cat']= 'NA' + df=df.copy() if 'mic' in test or 'vitek' in test : try : df.loc[df[test] <= antibiotic_enterrobacter_breakpoints[test]['S'], test+ ' cat'] = 'S' @@ -156,6 +157,8 @@ def create_antibio_dataset(path='data/label_raw/230804_strain_peptides_antibiogr df['path_ana'] = df['sample_name'].map(lambda x: create_fname(x,analyse='ANA')) df['path_aer'] = df['sample_name'].map(lambda x: create_fname(x, analyse='AER')) + print('Reference dataset extracted') + return df