Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -1,5 +1,3 @@
-import csv
-import json
 import os
 import pandas as pd
 import datasets
@@ -13,10 +11,7 @@ from sklearn.preprocessing import LabelEncoder
 import numpy as np
 from tqdm import tqdm
 import yaml
-import torch
 import time
-from pathlib import Path
-import importlib
 
 
 _DESCRIPTION = """\
@@ -32,7 +27,6 @@ _CITATION = "https://proceedings.mlr.press/v193/gupta22a.html"
 _URL = "https://github.com/healthylaife/MIMIC-IV-Data-Pipeline"
 _DATA_GEN = 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/data_generation_icu_modify.py'
 _DAY_INT= 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/day_intervals_cohort_v22.py'
-#_COHORT = 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/cohort.py'
 _CONFIG_URLS = {'los' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/config/los.config',
                 'mortality' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/config/mortality.config',
                 'phenotype' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/config/phenotype.config',
@@ -989,26 +983,22 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
     def _generate_examples_deep(self, filepath):
         with open(filepath, 'rb') as fp:
             dico = pickle.load(fp)
-            for key, data in dico.items():
-                proc_features = data['proc']
-                chart_features = data['chart']
-                meds_features = data['meds']
-                out_features = data['out']
-                cond_features = data['stat']
-                demo= data['demo']
-                label = data['label']
-                lab=data['lab']
-
-                yield int(key), {
-                    'label': label,
-                    'DEMO': demo,
-                    'COND': cond_features,
-                    'MEDS': meds_features,
-                    'PROC': proc_features,
-                    'CHART': chart_features,
-                    'OUT': out_features,
-                    'LAB': lab,
-                    }
+        
+        task=self.config.name.replace(" ","_")
+        if 'Custom' in task:
+            task = task.rsplit('_', 1)[0]
+        for key, data in tqdm(dico.items(),desc='Encoding Splits Data for '+task+' task'):
+            stat, demo, meds, chart, out, proc, lab, y = getXY_deep(data, task, self.feat_cond,  self.feat_proc,  self.feat_out,  self.feat_chart, self.feat_meds)
+            yield int(key), {
+                'label': y,
+                'DEMO': demo,
+                'COND': stat,
+                'MEDS': meds,
+                'PROC': proc,
+                'CHART': chart,
+                'OUT': out,
+                'LAB': lab,
+                }
     
 #############################################################################################################################
     def _info(self):
@@ -1027,7 +1017,7 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             return self.__split_generators_encoded()
 
         elif self.encoding == 'deep' :
-            return self.__split_generators_deep()
+            return self.__split_generators_raw()
         else:
             return self.__split_generators_raw()