Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -10,7 +10,7 @@ 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 .dataset_utils import vocab, concat_data, generate_deep, generate_ml, generate_text
 from .task_cohort import create_cohort
 
 
@@ -532,61 +532,13 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         items= pd.read_csv(self.mimic_path+'/icu/d_items.csv.gz',compression='gzip', header=0)
         with open(filepath, 'rb') as fp:
             dico = pickle.load(fp)
-        for key, data in dico.items():
-            
-            #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']
-                if 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=''
             
-            
-            #meds
-            if self.feat_meds:  
-                meds = data['Med']
-                if meds:
-                    meds=meds['val']
-                    feat=meds['signal'].keys()
-                    meds_val=[meds[key] for key in feat]
-                    meds_mean = [round(np.mean(c),3) for c in meds_val]
-                    feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
-                    template='{} of {}'
-                    meds_text = []
-                    for mean_val, feat_label in zip(meds_mean, feat_text):
-                        text = template.format(mean_val,feat_label)
-                        meds_text.append(text)
-                    meds_text='The medications administered are :{}.' + ';'.join(meds_text)
-            else:
-                meds_text=''
+        for key, data in dico.items():
+            cond_text,chart_text,meds_text,proc_text,out_text = self.generate_text(data,icd,items, self.feat_cond, self.feat_chart, self.feat_meds, self.feat_proc, self.feat_out)
                 
             yield int(key),{
                 'label' : data['label'],
-                'text': cond_text+chart_text+meds_text
+                'text': cond_text+chart_text+meds_text+proc_text+out_text
             }
 
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