Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -9,6 +9,7 @@ from urllib.request import urlretrieve
 from sklearn.model_selection import train_test_split
 from sklearn.preprocessing import LabelEncoder
 import yaml
+import numpy as np
 from .dataset_utils import vocab, concat_data, generate_deep, generate_ml
 from .task_cohort import create_cohort
 
@@ -517,6 +518,7 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             {
                 "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
                 "COND" : datasets.Value(dtype='string', id=None),
+                "CHART/LAB" : datasets.Value(dtype='string', id=None),
             }
         )
         return datasets.DatasetInfo(
@@ -531,18 +533,42 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         with open(filepath, 'rb') as fp:
             dico = pickle.load(fp)
         for key, data in dico.items():
-            conds = data['Cond']['fids']
-            text=[]
-            for code in conds:
-                desc = icd[icd['code']==code]
-                if not desc.empty:
-                    text.append(desc['description'].to_string(index=False))
-            template = 'The patient is diagnosed with {}.'
-            text = template.format('; '.join(text))
+            
+            #Diagnosis
+            if self.feat_cond:
+                conds = data['Cond']['fids']
+                cond_text=[]
+                for code in conds:
+                    desc = icd[icd['code']==code]
+                    if not desc.empty:
+                        cond_text.append(desc['description'].to_string(index=False))
+                template = 'The patient is diagnosed with {}.'
+                cond_text = template.format('; '.join(cond_text))
+            else :
+                cond_text=''
+                
+            #chart
+            if self.feat_chart:  
+                chart = data['Chart']
+                charts=chart['val']
+                feat=charts.keys()
+                chart_val=[charts[key] for key in feat]
+                chart_mean = [round(np.mean(c),3) for c in chart_val]
+                feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
+                template='{} for {}'
+                chart_text = []
+                for mean_val, feat_label in zip(chart_mean, feat_text):
+                    text = template.format(mean_val,feat_label)
+                    chart_text.append(text)
+                chart_text='The chart events mesured are : ' + '; '.join(chart_text)
+            else:
+                chart_text=''
+            
             yield int(key),{
                 'label' : data['label'],
-                'COND': text,
-                }
+                'COND': cond_text,
+                'CHART/LAB': chart_text,
+            }
 
 #############################################################################################################################
     def _info(self):