[ae9c43]: / prescreen / evaluation / fetch_radio.py

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"""
fetches radiology reports from validation cohort
"""
import pandas as pd
def get_frames():
base_path = 'data/cohorte_validation'
# regular expression to find radiology reports
pattern = "recist"
## DITEP OK
path = base_path + '/ditep_inclus.csv'
ditep_inclus = pd.read_csv(path, sep=';', encoding='utf-8')\
.drop('Unnamed: 0', axis=1)
mask_scanner = ditep_inclus['CR'].str.contains(pattern, case=False)
ditep_inclus = ditep_inclus[mask_scanner]
ditep_inclus = ditep_inclus.groupby('nip', as_index=False).agg('first')
## DITEP screenfail
path = base_path + '/ditep_sf.csv'
ditep_sf = pd.read_csv(path, sep=';', encoding='utf-8')\
.drop('Unnamed: 0', axis=1)
mask_scanner = ditep_sf['CR'].str.contains(pattern, case=False)
ditep_sf = ditep_sf[mask_scanner]
ditep_sf = ditep_sf.groupby('nip', as_index=False).agg('first')
## poumons inclus
path = base_path + '/poumons_inclusion.csv'
poumons = pd.read_csv(path, sep=';', encoding='utf-8')\
.drop('Unnamed: 0', axis=1)
mask_scanner = poumons['CR'].str.contains(pattern, case=False)
poumons = poumons[mask_scanner]
poumons = poumons.groupby('nip', as_index=False).agg('first')
# poumons SF
path = base_path + '/poumons_sf.csv'
poumons_sf = pd.read_csv(path, sep=';', encoding='utf-8')\
.drop('Unnamed: 0', axis=1)
mask_scanner = poumons_sf['CR'].str.contains(pattern, case=False)
poumons_sf = poumons_sf[mask_scanner]
poumons_sf = poumons_sf.groupby('nip', as_index=False).agg('first')
return ditep_inclus, ditep_sf, poumons, poumons_sf