Mimic4Dataset.py

import csv
import json
import os
import pandas as pd
import datasets
import sys
import pickle
import subprocess
import shutil
from urllib.request import urlretrieve
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder
import numpy as np
from tqdm import tqdm
import yaml


_DESCRIPTION = """\
Dataset for mimic4 data, by default for the Mortality task.
Available tasks are: Mortality, Length of Stay, Readmission, Phenotype, Mortality Custom, Length of Stay Custom, Readmission Custom, Phenotype Custom.
The data is extracted from the mimic4 database using this pipeline: 'https://github.com/healthylaife/MIMIC-IV-Data-Pipeline/tree/main'
mimic path should have this form : "path/to/mimic4data/from/username/mimiciv/2.2"
If you choose a Custom task provide a configuration file for the Time series.
"""

_HOMEPAGE = "https://huggingface.co/datasets/thbndi/Mimic4Dataset"
_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',
                'readmission' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/config/readmission.config'
        }

  

def onehot(data,task,feat_cond=False,feat_proc=False,feat_out=False,feat_chart=False,feat_meds=False):
    meds=data['Med']
    proc = data['Proc']
    out = data['Out']
    chart = data['Chart']
    cond= data['Cond']['fids']

    cond_df=pd.DataFrame()
    proc_df=pd.DataFrame()
    out_df=pd.DataFrame()
    chart_df=pd.DataFrame()
    meds_df=pd.DataFrame()

    #demographic
    demo=pd.DataFrame(columns=['Age','gender','ethnicity','label','insurance'])
    new_row = {'Age': data['age'], 'gender': data['gender'], 'ethnicity': data['ethnicity'], 'label': data['label'], 'insurance': data['insurance']}
    demo = demo.append(new_row, ignore_index=True)

    ##########COND#########
    if (feat_cond):
        #get all conds
        with open("./data/dict/"+task+"/condVocab", 'rb') as fp:
            conDict = pickle.load(fp)
        conds=pd.DataFrame(conDict,columns=['COND'])
        features=pd.DataFrame(np.zeros([1,len(conds)]),columns=conds['COND'])

        #onehot encode
        if(cond ==[]):
            cond_df=pd.DataFrame(np.zeros([1,len(features)]),columns=features['COND'])
            cond_df=cond_df.fillna(0)
        else:
            cond_df=pd.DataFrame(cond,columns=['COND'])
            cond_df['val']=1
            cond_df=(cond_df.drop_duplicates()).pivot(columns='COND',values='val').reset_index(drop=True)
            cond_df=cond_df.fillna(0)
            oneh = cond_df.sum().to_frame().T
            combined_df = pd.concat([features,oneh],ignore_index=True).fillna(0)
            combined_oneh=combined_df.sum().to_frame().T
            cond_df=combined_oneh

    ##########PROC#########
    if (feat_proc):
        with open("./data/dict/"+task+"/procVocab", 'rb') as fp:
            procDic = pickle.load(fp)

        if proc :
            feat=proc.keys()
            proc_val=[proc[key] for key in feat]
            procedures=pd.DataFrame(procDic,columns=['PROC'])
            features=pd.DataFrame(np.zeros([1,len(procedures)]),columns=procedures['PROC'])
            features.columns=pd.MultiIndex.from_product([["PROC"], features.columns])
            procs=pd.DataFrame(columns=feat)
            for p,v in zip(feat,proc_val):
                procs[p]=v
            procs.columns=pd.MultiIndex.from_product([["PROC"], procs.columns])
            proc_df = pd.concat([features,procs],ignore_index=True).fillna(0)
        else:
            procedures=pd.DataFrame(procDic,columns=['PROC'])
            features=pd.DataFrame(np.zeros([1,len(procedures)]),columns=procedures['PROC'])
            features.columns=pd.MultiIndex.from_product([["PROC"], features.columns])
            proc_df=features.fillna(0)

    ##########OUT#########
    if (feat_out):
        with open("./data/dict/"+task+"/outVocab", 'rb') as fp:
            outDic = pickle.load(fp)

        if out :
            feat=out.keys()
            out_val=[out[key] for key in feat]
            outputs=pd.DataFrame(outDic,columns=['OUT'])
            features=pd.DataFrame(np.zeros([1,len(outputs)]),columns=outputs['OUT'])
            features.columns=pd.MultiIndex.from_product([["OUT"], features.columns])
            outs=pd.DataFrame(columns=feat)
            for o,v in zip(feat,out_val):
                outs[o]=v
            outs.columns=pd.MultiIndex.from_product([["OUT"], outs.columns])
            out_df = pd.concat([features,outs],ignore_index=True).fillna(0)
        else:
            outputs=pd.DataFrame(outDic,columns=['OUT'])
            features=pd.DataFrame(np.zeros([1,len(outputs)]),columns=outputs['OUT'])
            features.columns=pd.MultiIndex.from_product([["OUT"], features.columns])
            out_df=features.fillna(0)

    ##########CHART#########
    if (feat_chart):
        with open("./data/dict/"+task+"/chartVocab", 'rb') as fp:
            chartDic = pickle.load(fp)

        if chart:
            charts=chart['val']
            feat=charts.keys()
            chart_val=[charts[key] for key in feat]
            charts=pd.DataFrame(chartDic,columns=['CHART'])
            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['CHART'])
            features.columns=pd.MultiIndex.from_product([["CHART"], features.columns])
            
            chart=pd.DataFrame(columns=feat)
            for c,v in zip(feat,chart_val):
                chart[c]=v
            chart.columns=pd.MultiIndex.from_product([["CHART"], chart.columns])
            chart_df = pd.concat([features,chart],ignore_index=True).fillna(0)
        else:
            charts=pd.DataFrame(chartDic,columns=['CHART'])
            features=pd.DataFrame(np.zeros([1,len(charts)]),columns=charts['CHART'])
            features.columns=pd.MultiIndex.from_product([["CHART"], features.columns])
            chart_df=features.fillna(0)
    
    ###MEDS
    if (feat_meds):
        with open("./data/dict/"+task+"/medVocab", 'rb') as fp:
                medDic = pickle.load(fp)

        if meds:
            feat=meds['signal'].keys()
            med_val=[meds['amount'][key] for key in feat]
            meds=pd.DataFrame(medDic,columns=['MEDS'])
            features=pd.DataFrame(np.zeros([1,len(meds)]),columns=meds['MEDS'])
            features.columns=pd.MultiIndex.from_product([["MEDS"], features.columns])
            
            med=pd.DataFrame(columns=feat)
            for m,v in zip(feat,med_val):
                med[m]=v
            med.columns=pd.MultiIndex.from_product([["MEDS"], med.columns])
            meds_df = pd.concat([features,med],ignore_index=True).fillna(0)
        else:
            meds=pd.DataFrame(medDic,columns=['MEDS'])
            features=pd.DataFrame(np.zeros([1,len(meds)]),columns=meds['MEDS'])
            features.columns=pd.MultiIndex.from_product([["MEDS"], features.columns])
            meds_df=features.fillna(0)

    dyn_df = pd.concat([meds_df,proc_df,out_df,chart_df], axis=1)
    return dyn_df,cond_df,demo

def getXY(dyn,stat,demo,concat_cols,concat):
    X_df=pd.DataFrame()
    if concat:
        dyna=dyn.copy()
        dyna.columns=dyna.columns.droplevel(0)
        dyna=dyna.to_numpy()
        dyna=dyna.reshape(1,-1)
        dyn_df=pd.DataFrame(data=dyna,columns=concat_cols)
    else:
        dyn_df=pd.DataFrame()
        for key in dyn.columns.levels[0]:     
            dyn_temp=dyn[key]
            if ((key=="CHART") or (key=="MEDS")):
                agg=dyn_temp.aggregate("mean")
                agg=agg.reset_index()
            else:
                agg=dyn_temp.aggregate("max")
                agg=agg.reset_index()

            if dyn_df.empty:
                dyn_df=agg
            else:
                dyn_df=pd.concat([dyn_df,agg],axis=0)
        dyn_df=dyn_df.T
        dyn_df.columns = dyn_df.iloc[0]
        dyn_df=dyn_df.iloc[1:,:]
        
    X_df=pd.concat([dyn_df,stat],axis=1)
    X_df=pd.concat([X_df,demo],axis=1)
    return X_df    

def encoding(X_data):
    gen_encoder = LabelEncoder()
    eth_encoder = LabelEncoder()
    ins_encoder = LabelEncoder()
    gen_encoder.fit(X_data['gender'])
    eth_encoder.fit(X_data['ethnicity'])
    ins_encoder.fit(X_data['insurance'])
    X_data['gender']=gen_encoder.transform(X_data['gender'])
    X_data['ethnicity']=eth_encoder.transform(X_data['ethnicity'])
    X_data['insurance']=ins_encoder.transform(X_data['insurance'])
    return X_data

def generate_split(path,task,concat,feat_cond=True,feat_chart=True,feat_proc=True, feat_meds=True, feat_out=False):
    with open(path, 'rb') as fp:
        dico = pickle.load(fp)
    df = pd.DataFrame.from_dict(dico, orient='index')
    X_df=pd.DataFrame()   
    #y_df=pd.DataFrame(df['label'],columns=['label'])
    taskf=task.replace(" ","_")
    for _, data in tqdm(df.iterrows(),desc='Encoding Data for '+task+' task'):
        concat_cols=[]
        sample=data
        dyn_df,cond_df,demo=onehot(sample,taskf,feat_cond,feat_chart,feat_proc, feat_meds, feat_out)
        dyn=dyn_df.copy()
        dyn.columns=dyn.columns.droplevel(0)
        cols=dyn.columns
        time=dyn.shape[0]
        for t in range(time):
            cols_t = [str(x) + "_"+str(t) for x in cols]
            concat_cols.extend(cols_t)
        
        X= getXY(dyn_df,cond_df,demo,concat_cols,concat)
        if X_df.empty:
             X_df=pd.concat([X_df,X],axis=1)
        else:
            X_df = pd.concat([X_df, X], axis=0)
    X_df=X_df.fillna(0) 
    X_df = encoding(X_df)
    #X_df=X_df.drop(['label'], axis=1)
    return X_df


class Mimic4DatasetConfig(datasets.BuilderConfig):
    """BuilderConfig for Mimic4Dataset."""

    def __init__(
        self,
        **kwargs,
    ):
        super().__init__(**kwargs)
        
class Mimic4Dataset(datasets.GeneratorBasedBuilder):
    VERSION = datasets.Version("1.0.0")

    def __init__(self, **kwargs):
        self.mimic_path = kwargs.pop("mimic_path", None)
        self.encoding = kwargs.pop("encoding",True)
        self.config_path = kwargs.pop("config_path",None)
        self.test_size = kwargs.pop("test_size",0.2)
        self.val_size = kwargs.pop("val_size",0.1)

        super().__init__(**kwargs)
        
        
    BUILDER_CONFIGS = [
        Mimic4DatasetConfig(
            name="Phenotype",
            version=VERSION,
            description="Dataset for mimic4 Phenotype task"
        ),
        Mimic4DatasetConfig(
            name="Readmission",
            version=VERSION,
            description="Dataset for mimic4 Readmission task"
        ),
        Mimic4DatasetConfig(
            name="Length of Stay",
            version=VERSION,
            description="Dataset for mimic4 Length of Stay task"
        ),
        Mimic4DatasetConfig(
            name="Mortality",
            version=VERSION,
            description="Dataset for mimic4 Mortality task"
        ),
        Mimic4DatasetConfig(
            name="Phenotype Custom",
            version=VERSION,
            description="Dataset for mimic4 Custom Phenotype task"
        ),
        Mimic4DatasetConfig(
            name="Readmission Custom",
            version=VERSION,
            description="Dataset for mimic4 Custom Readmission task"
        ),
        Mimic4DatasetConfig(
            name="Length of Stay Custom",
            version=VERSION,
            description="Dataset for mimic4 Custom Length of Stay task"
        ),
        Mimic4DatasetConfig(
            name="Mortality Custom",
            version=VERSION,
            description="Dataset for mimic4 Custom Mortality task"
        ),
    ]

    DEFAULT_CONFIG_NAME = "Mortality"

    def map_dtype(self,dtype):
        if pd.api.types.is_integer_dtype(dtype):
            return datasets.Value('int64')
        elif pd.api.types.is_float_dtype(dtype):
            return datasets.Value('float64')
        elif pd.api.types.is_string_dtype(dtype):
            return datasets.Value('string')
        else:
            raise ValueError(f"Unsupported dtype: {dtype}")
        
    def create_cohort(self):
        if self.config.name == 'Phenotype' : self.config_path = _CONFIG_URLS['phenotype'] 
        if self.config.name == 'Readmission' : self.config_path = _CONFIG_URLS['readmission'] 
        if self.config.name == 'Length of Stay' : self.config_path = _CONFIG_URLS['los'] 
        if self.config.name == 'Mortality' : self.config_path = _CONFIG_URLS['mortality']
        if self.config.name in ['Phenotype Custom','Readmission Custom','Length of Stay Custom','Mortality Custom'] and self.config.name==None:
            raise ValueError('Please provide a config file')
        
        version = self.mimic_path.split('/')[-1]
        m = self.mimic_path.split('/')[-2]
        s='/'+m+'/'+version
        
        current_directory = os.getcwd()
        if os.path.exists(os.path.dirname(current_directory)+'/MIMIC-IV-Data-Pipeline-main'):
            dir =os.path.dirname(current_directory) 
            os.chdir(dir)
        else:
            #move to parent directory of mimic data
            dir = self.mimic_path.replace(s,'')
            if dir[-1]!='/':
                dir=dir+'/'
            elif dir=='':
                dir="./"
            parent_dir = os.path.dirname(self.mimic_path)
            os.chdir(parent_dir)

        #clone git repo if doesnt exists
        repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
        if os.path.exists('MIMIC-IV-Data-Pipeline-main'):
            path_bench = './MIMIC-IV-Data-Pipeline-main'
        else:
            path_bench ='./MIMIC-IV-Data-Pipeline-main'
            subprocess.run(["git", "clone", repo_url, path_bench])
            os.makedirs(path_bench+'/mimic-iv')
            shutil.move(version,path_bench+'/mimic-iv')

        os.chdir(path_bench)
        self.mimic_path = './mimic-iv/'+version

        #download config file if not custom
        if self.config_path[0:4] == 'http':
            c = self.config_path.split('/')[-1]
            file_path, head = urlretrieve(self.config_path,c)
        else :
            file_path = self.config_path

        #create config folder
        if not os.path.exists('./config'):
            os.makedirs('config')
        #save config file in config folder
        conf='./config/'+file_path.split('/')[-1]

        if not os.path.exists(conf):
            shutil.move(file_path,'./config')

        #downloads modules from hub
        if not os.path.exists('./model/data_generation_icu_modify.py'):
            file_path, head = urlretrieve(_DATA_GEN, "data_generation_icu_modify.py")
            shutil.move(file_path, './model')

        if not os.path.exists('./preprocessing/day_intervals_preproc/day_intervals_cohort_v22.py'):
            file_path, head = urlretrieve(_DAY_INT, "day_intervals_cohort_v22.py")
            shutil.move(file_path, './preprocessing/day_intervals_preproc')
            
        file_path, head = urlretrieve(_COHORT, "cohort.py")
        if not os.path.exists('cohort.py'):
            shutil.move(file_path, './')
            
        data_dir = "./data/dict/"+self.config.name.replace(" ","_")+"/dataDic"
        sys.path.append(path_bench)
        config = self.config_path.split('/')[-1]

        script = 'python cohort.py '+ self.config.name.replace(" ","_") +" "+ self.mimic_path+ " "+path_bench+ " "+config
        
        #####################################CHANGE##########
        if not os.path.exists(data_dir) :
            os.system(script)       
        #####################################CHANGE##########
        config_path='./config/'+config
        with open(config_path) as f:
            config = yaml.safe_load(f)
        feat_cond, feat_chart, feat_proc, feat_meds, feat_out = config['diagnosis'], config['chart'], config['proc'],  config['meds'], config['output']

        with open(data_dir, 'rb') as fp:
            dataDic = pickle.load(fp)
        data = pd.DataFrame.from_dict(dataDic)
       
        data=data.T
        train_data, test_data = train_test_split(data, test_size=self.test_size, random_state=42)
        train_data, val_data = train_test_split(test_data, test_size=self.val_size, random_state=42)
        
        dict_dir = "./data/dict/"+self.config.name.replace(" ","_")
        train_dic = train_data.to_dict('index')
        test_dic = test_data.to_dict('index')
        val_dic = val_data.to_dict('index')

        train_path = dict_dir+'/train_data.pkl'
        test_path = dict_dir+'/test_data.pkl'
        val_path = dict_dir+'/val_data.pkl'
        
        with open(train_path, 'wb') as f:
            pickle.dump(train_dic, f)
        with open(val_path, 'wb') as f:
            pickle.dump(val_dic, f)
        with open(test_path, 'wb') as f:
            pickle.dump(test_dic, f)

        
        return feat_cond, feat_chart, feat_proc, feat_meds, feat_out, dict_dir
  
###########################################################RAW##################################################################

    def _info_raw(self):
        features = datasets.Features(
            {
                "label": datasets.ClassLabel(num_classes=2,names=["0", "1"]),
                "gender": datasets.Value("string"),
                "ethnicity": datasets.Value("string"),
                "insurance": datasets.Value("string"),
                "age": datasets.Value("int32"),
                "COND": datasets.Sequence(datasets.Value("string")),
                "MEDS": {
                            "signal": 
                                {
                                    "id": datasets.Sequence(datasets.Value("int32")),
                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                }
                            ,
                            "rate": 
                                {
                                    "id": datasets.Sequence(datasets.Value("int32")),
                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                }
                            ,
                            "amount": 
                                {
                                    "id": datasets.Sequence(datasets.Value("int32")),
                                    "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                }
                            
                        },
                "PROC":  {
                            "id": datasets.Sequence(datasets.Value("int32")),
                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                },
                "CHART":
                    {
                        "signal" : {
                            "id": datasets.Sequence(datasets.Value("int32")),
                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                },
                        "val" : {
                            "id": datasets.Sequence(datasets.Value("int32")),
                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                },
                    },
                "OUT":  {
                            "id": datasets.Sequence(datasets.Value("int32")),
                            "value": datasets.Sequence(datasets.Sequence(datasets.Value("float32")))
                                },
                
            }
        )
        return datasets.DatasetInfo(
            description=_DESCRIPTION,
            features=features,
            homepage=_HOMEPAGE,
            citation=_CITATION,
        )

    def __split_generators_raw(self):
        
        csv_dir = "./data/dict/"+self.config.name.replace(" ","_")

        return [
            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": csv_dir+'/train_data.pkl'}),
            datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": csv_dir+'/val_data.pkl'}),
            datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": csv_dir+'/test_data.pkl'}),
        ]

    def _generate_examples_raw(self, filepath):
        with open(filepath, 'rb') as fp:
            dataDic = pickle.load(fp)
        for hid, data in dataDic.items():
            proc_features = data['Proc']
            chart_features = data['Chart']
            meds_features = data['Med']
            out_features = data['Out']
            cond_features = data['Cond']['fids']
            eth= data['ethnicity']
            age = data['age']
            gender = data['gender']
            label = data['label']
            insurance=data['insurance']
            
            items = list(proc_features.keys())
            values =[proc_features[i] for i in items ]
            procs = {"id" : items,
                  "value": values}
            
            items_outs = list(out_features.keys())
            values_outs =[out_features[i] for i in items_outs ]
            outs = {"id" : items_outs,
                  "value": values_outs}

            #chart signal
            if ('signal' in chart_features):
                items_chart_sig = list(chart_features['signal'].keys())
                values_chart_sig =[chart_features['signal'][i] for i in items_chart_sig ]
                chart_sig = {"id" : items_chart_sig,
                        "value": values_chart_sig}
            else:
                chart_sig = {"id" : [],
                        "value": []}
            #chart val
            if ('val' in chart_features):
                items_chart_val = list(chart_features['val'].keys())
                values_chart_val =[chart_features['val'][i] for i in items_chart_val ]
                chart_val = {"id" : items_chart_val,
                        "value": values_chart_val}
            else:
                chart_val = {"id" : [],
                        "value": []}
                
            charts = {"signal" : chart_sig,
                    "val" : chart_val}

            #meds signal
            if ('signal' in meds_features):
                items_meds_sig = list(meds_features['signal'].keys())
                values_meds_sig =[meds_features['signal'][i] for i in items_meds_sig ]
                meds_sig = {"id" : items_meds_sig,
                    "value": values_meds_sig}
            else:
                meds_sig = {"id" : [],
                    "value": []}
            #meds rate
            if ('rate' in meds_features):
                items_meds_rate = list(meds_features['rate'].keys())
                values_meds_rate =[meds_features['rate'][i] for i in items_meds_rate ]
                meds_rate = {"id" : items_meds_rate,
                        "value": values_meds_rate}
            else:
                meds_rate = {"id" : [],
                        "value": []}
            #meds amount
            if ('amount' in meds_features):
                items_meds_amount = list(meds_features['amount'].keys())
                values_meds_amount =[meds_features['amount'][i] for i in items_meds_amount ]
                meds_amount = {"id" : items_meds_amount,
                        "value": values_meds_amount}
            else:
                meds_amount = {"id" : [],
                        "value": []}
            
            meds = {"signal" : meds_sig,
                    "rate" : meds_rate,
                    "amount" : meds_amount}
            
            yield int(hid), {
                "label" : label,
                "gender" : gender,
                "ethnicity" : eth,
                "insurance" : insurance,
                "age" : age,
                "COND" : cond_features,
                "PROC" : procs,
                "CHART" : charts,
                "OUT" : outs,
                "MEDS" : meds
            }


###########################################################ENCODED##################################################################
       
    def _info_encoded(self,X_encoded):
        columns = {col: self.map_dtype(X_encoded[col].dtype) for col in X_encoded.columns}
        features = datasets.Features(columns)
        return datasets.DatasetInfo(
            description=_DESCRIPTION,
            features=features,
            homepage=_HOMEPAGE,
            citation=_CITATION,
        )
    
    def __split_generators_encoded(self):
        data_dir = "./data/dict/"+self.config.name.replace(" ","_")

        return [
            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir+'/X_train_encoded.csv'}),
            datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_dir+'/X_val_encoded.csv'}),
            datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_dir+'/X_test_encoded.csv'}),
            ]

    def _generate_examples_encoded(self, filepath):
        df = pd.read_csv(filepath, header=0)
        for i, row in df.iterrows():
            yield i, row.to_dict()
        

#############################################################################################################################
    def _info(self):
        self.feat_cond, self.feat_chart, self.feat_proc, self.feat_meds, self.feat_out,self.path = self.create_cohort()

        if self.encoding :
            X_train_encoded=generate_split(self.path+'/train_data.pkl',self.config.name,True,self.feat_cond, self.feat_chart, self.feat_proc, self.feat_meds, self.feat_out)
            X_test_encoded=generate_split(self.path+'/test_data.pkl',self.config.name,True,self.feat_cond, self.feat_chart, self.feat_proc, self.feat_meds, self.feat_out)
            X_val_encoded=generate_split(self.path+'/val_data.pkl',self.config.name,True,self.feat_cond, self.feat_chart, self.feat_proc, self.feat_meds, self.feat_out)
            
            X_train_encoded.to_csv(self.path+"/X_train_encoded.csv", index=False)
            X_test_encoded.to_csv(self.path+"/X_test_encoded.csv", index=False)
            X_val_encoded.to_csv(self.path+"/X_val_encoded.csv", index=False)
            return self._info_encoded(X_train_encoded)
        else:
            return self._info_raw()

    def _split_generators(self, dl_manager):
        if self.encoding :
            return self.__split_generators_encoded()
        else:
            return self.__split_generators_raw()

    def _generate_examples(self, filepath):
        if not self.encoding :
            yield from self._generate_examples_raw(filepath)
        else:
            yield from self._generate_examples_encoded(filepath)