Update task_cohort.py

task_cohort.py

@@ -4,9 +4,6 @@ import yaml
 import time
 import yaml
 import sys
-from .day_intervals_cohort_v22 import extract_data
-from .data_generation_icu_modify import Generator_icu
-from .data_generation_modify import Generator
 
 def check_config_file(task,config_file):
     with open(config_file) as f:
@@ -135,6 +132,9 @@ def create_cohort(task, mimic_path, config_path):
     import day_intervals_cohort
     import feature_selection_icu
     import feature_selection_hosp
+    import day_instervals_cohort_v22
+    import data_generation_icu_modify
+    import data_generation_modify
 
     
     root_dir = os.path.dirname(os.path.abspath('UserInterface.ipynb'))
@@ -199,7 +199,7 @@ def create_cohort(task, mimic_path, config_path):
 
     #-----------------------------------------------EXTRACT MIMIC-----------------------------------------------------
     if version == '2':
-        cohort_output = extract_data(icu_no_icu,label,tim,icd_code, root_dir,version_path,disease_label)
+        cohort_output = day_instervals_cohort_v22.extract_data(icu_no_icu,label,tim,icd_code, root_dir,version_path,disease_label)
 
     elif version == '1':
         cohort_output = day_intervals_cohort.extract_data(icu_no_icu,label,tim,icd_code, root_dir,version_path,disease_label)
@@ -275,7 +275,7 @@ def create_cohort(task, mimic_path, config_path):
             thresh=config['outlier']
             left_thresh=config['left_outlier']
         feature_selection_hosp.preprocess_features_hosp(cohort_output, False,False, False,lab_flag,False,False,False,clean_chart,impute_outlier_chart,thresh,left_thresh)
-    # ---------------------------------------tim-Series Representation--------------------------------------------
+    # ---------------------------------------time-Series Representation--------------------------------------------
     if radimp == 'forward fill and mean' :
         impute='Mean'
     elif radimp =='forward fill and median':
@@ -284,9 +284,9 @@ def create_cohort(task, mimic_path, config_path):
         impute = False
     
     if data_icu:
-        gen=Generator(task,cohort_output,data_mort,data_admn,data_los,diag_flag,proc_flag,out_flag,chart_flag,med_flag,impute,include,bucket,predW)
+        gen=data_generation_icu_modify.Generator_icu(task,cohort_output,data_mort,data_admn,data_los,diag_flag,proc_flag,out_flag,chart_flag,med_flag,impute,include,bucket,predW)
     else:
-        gen=Generator(cohort_output,data_mort,data_admn,data_los,diag_flag,lab_flag,proc_flag,med_flag,impute,include,bucket,predW)
+        gen=data_generation_modify.Generator(cohort_output,data_mort,data_admn,data_los,diag_flag,lab_flag,proc_flag,med_flag,impute,include,bucket,predW)
     
     end = time.time()
     print("Time elapsed : ", round((end - start)/60,2),"mins")