Update day_intervals_cohort_v22.py

day_intervals_cohort_v22.py

@@ -249,7 +249,7 @@ def get_case_ctrls(df:pd.DataFrame, gap:int, group_col:str, visit_col:str, admit
     # print(f"[ {gap.days} DAYS ] {invalid.shape[0]} hadm_ids are invalid")
 
 
-def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir, disease_label, cohort_output=None, summary_output=None):
+def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir,mimic_path, disease_label, cohort_output=None, summary_output=None):
     """Extracts cohort data and summary from MIMIC-IV data based on provided parameters.
 
     Parameters:
@@ -257,7 +257,7 @@ def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir, disea
     summary_output: name of summary output file
     use_ICU: state whether to use ICU patient data or not
     label: Can either be '{day} day Readmission' or 'Mortality', decides what binary data label signifies"""
-    print("===========MIMIC-IV v2.0============")
+    print("===========MIMIC-IV v2============")
     if not cohort_output:
         cohort_output="cohort_" + use_ICU.lower() + "_" + label.lower().replace(" ", "_") + "_" + str(time) + "_" + disease_label
     if not summary_output:
@@ -307,7 +307,7 @@ def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir, disea
         death_col='dod'
 
     pts = get_visit_pts(
-        mimic4_path=root_dir+'/',
+        mimic4_path=mimic_path,
         group_col=group_col,
         visit_col=visit_col,
         admit_col=admit_col,
@@ -340,7 +340,7 @@ def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir, disea
     #print(cohort.head())
     
     if use_disease:
-        hids=disease_cohort.extract_diag_cohort(cohort['hadm_id'],icd_code,root_dir+"/mimiciv/2.0/")
+        hids=disease_cohort.extract_diag_cohort(cohort['hadm_id'],icd_code,mimic_path)
         #print(hids.shape)
         #print(cohort.shape)
         #print(len(list(set(hids['hadm_id'].unique()).intersection(set(cohort['hadm_id'].unique())))))
@@ -350,7 +350,7 @@ def extract_data(use_ICU:str, label:str, time:int, icd_code:str, root_dir, disea
     #print(cohort[cols].head())
     # save output
     cohort=cohort.rename(columns={"race":"ethnicity"})
-    cohort[cols].to_csv(root_dir+"/data/cohort/"+cohort_output+".csv.gz", index=False, compression='gzip')
+    cohort[cols].to_csv("./data/cohort/"+cohort_output+".csv.gz", index=False, compression='gzip')
     print("[ COHORT SUCCESSFULLY SAVED ]")
 
     summary = "\n".join([