dataset_utils.py

import pandas as pd
import pickle
import numpy as np
import torch

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##                   MIMIC IV DATASET UTILITY FUNCTIONS                       ##
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def create_vocab(file,task):
    with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
        condVocab = pickle.load(fp)
    condVocabDict={}
    condVocabDict[0]=0
    for val in range(len(condVocab)):
        condVocabDict[condVocab[val]]= val+1    

    return condVocabDict

def gender_vocab():
    genderVocabDict={}
    genderVocabDict['<PAD>']=0
    genderVocabDict['M']=1
    genderVocabDict['F']=2

    return genderVocabDict

def vocab(task,diag_flag,proc_flag,out_flag,chart_flag,med_flag,lab_flag):
        condVocabDict={}
        procVocabDict={}
        medVocabDict={}
        outVocabDict={}
        chartVocabDict={}
        labVocabDict={}
        ethVocabDict={}
        ageVocabDict={}
        genderVocabDict={}
        insVocabDict={}
        
        ethVocabDict=create_vocab('ethVocab',task)
        with open('./data/dict/'+task+'/ethVocabDict', 'wb') as fp:
            pickle.dump(ethVocabDict, fp)
            
        ageVocabDict=create_vocab('ageVocab',task)
        with open('./data/dict/'+task+'/ageVocabDict', 'wb') as fp:
            pickle.dump(ageVocabDict, fp)
        
        genderVocabDict=gender_vocab()
        with open('./data/dict/'+task+'/genderVocabDict', 'wb') as fp:
            pickle.dump(genderVocabDict, fp)
            
        insVocabDict=create_vocab('insVocab',task)
        with open('./data/dict/'+task+'/insVocabDict', 'wb') as fp:
            pickle.dump(insVocabDict, fp)
        
        if diag_flag:
            file='condVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                condVocabDict = pickle.load(fp)
        if proc_flag:
            file='procVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                procVocabDict = pickle.load(fp)
        if med_flag:
            file='medVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                medVocabDict = pickle.load(fp)
        if out_flag:
            file='outVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                outVocabDict = pickle.load(fp)
        if chart_flag:
            file='chartVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                chartVocabDict = pickle.load(fp)
        if lab_flag:
            file='labsVocab'
            with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
                labVocabDict = pickle.load(fp)
        
        return (len(condVocabDict),len(procVocabDict),len(medVocabDict),len(outVocabDict),len(chartVocabDict),len(labVocabDict),
                ethVocabDict,genderVocabDict,ageVocabDict,insVocabDict,condVocabDict,procVocabDict,medVocabDict,outVocabDict,chartVocabDict,labVocabDict)

###################################
# CONCATENATE DATA FROM           #
# DICT TO CREATE CSV FILES        #
###################################
def concat_data(data,interval,feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict):
    meds=data['Med']
    proc = data['Proc']
    out = data['Out']
    charts = data['Chart']
    cond= data['Cond']['fids']

    proc_df=pd.DataFrame()
    out_df=pd.DataFrame()
    cond_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):
        cond_df=pd.DataFrame(np.zeros([1,len(condDict)]),columns=condDict)
        if cond:
            for c in cond : cond_df[c]=1

    ##########PROC#########
    if (feat_proc):
        if proc :
            feat=proc.keys()
            proc_val=[proc[key] for key in feat]
            proc_df=pd.DataFrame(np.zeros([interval,len(procDict)]),columns=procDict)
            for p,v in zip(feat,proc_val):
                proc_df[p]=v
            proc_df.columns=pd.MultiIndex.from_product([["PROC"], proc_df.columns])
        else:
            procedures=pd.DataFrame(procDict,columns=['PROC'])
            features=pd.DataFrame(np.zeros([interval,len(procedures)]),columns=procedures['PROC'])
            features.columns=pd.MultiIndex.from_product([["PROC"], features.columns])
            proc_df=features.fillna(0)

    ##########OUT#########
    if (feat_out):
        if out :
            feat=out.keys()
            out_val=[out[key] for key in feat]
            out_df=pd.DataFrame(np.zeros([interval,len(outDict)]),columns=outDict)
            for o,v in zip(feat,out_val):
                out_df[o]=v
            out_df.columns=pd.MultiIndex.from_product([["OUT"], out_df.columns])
        else:
            outputs=pd.DataFrame(outDict,columns=['OUT'])
            features=pd.DataFrame(np.zeros([interval,len(outputs)]),columns=outputs['OUT'])
            features.columns=pd.MultiIndex.from_product([["OUT"], features.columns])
            out_df=features.fillna(0)

    ##########CHART#########
    if (feat_chart):
        if charts:
            charts=charts['val']
            feat=charts.keys()
            chart_val=[charts[key] for key in feat]
            chart_df=pd.DataFrame(np.zeros([interval,len(chartDict)]),columns=chartDict)
            for c,v in zip(feat,chart_val):
                chart_df[c]=v
            chart_df.columns=pd.MultiIndex.from_product([["CHART"], chart_df.columns])
        else:
            charts=pd.DataFrame(chartDict,columns=['CHART'])
            features=pd.DataFrame(np.zeros([interval,len(charts)]),columns=charts['CHART'])
            features.columns=pd.MultiIndex.from_product([["CHART"], features.columns])
            chart_df=features.fillna(0)
        ##########LAB#########
    
    if (feat_lab):
        if charts:
            feat=charts.keys()
            chart_val=[charts[key] for key in feat]
            chart_df=pd.DataFrame(np.zeros([interval,len(chartDict)]),columns=chartDict)
            for c,v in zip(feat,chart_val):
                chart_df[c]=v
            chart_df.columns=pd.MultiIndex.from_product([["LAB"], chart_df.columns])
        else:
            charts=pd.DataFrame(chartDict,columns=['LAB'])
            features=pd.DataFrame(np.zeros([interval,len(charts)]),columns=charts['LAB'])
            features.columns=pd.MultiIndex.from_product([["LAB"], features.columns])
            chart_df=features.fillna(0)
    
    ###MEDS
    if (feat_meds):
        if meds:
            feat=meds['signal'].keys()
            med_val=[meds['amount'][key] for key in feat]
            meds_df=pd.DataFrame(np.zeros([interval,len(medDict)]),columns=medDict)           
            for m,v in zip(feat,med_val):
                meds_df[m]=v
            meds_df.columns=pd.MultiIndex.from_product([["MEDS"], meds_df.columns])
        else:
            meds=pd.DataFrame(medDict,columns=['MEDS'])
            features=pd.DataFrame(np.zeros([interval,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


###################################
# CALLED FOR "tensor" ENCODING    #
###################################
def generate_deep(data,interval,task,feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict, eth_vocab,gender_vocab,age_vocab,ins_vocab):
    meds = []
    charts = []
    proc = []
    out = []
    lab = []
    stat = []
    demo = []
    dyn,cond_df,demo=concat_data(data,interval,feat_cond,feat_proc,feat_out,feat_chart,feat_meds,feat_lab,condDict, procDict, outDict, chartDict, medDict)
    if feat_chart:
        charts = dyn['CHART'].fillna(0).values
    if feat_meds:
        meds = dyn['MEDS'].fillna(0).values
    if feat_proc:
        proc = dyn['PROC'].fillna(0).values
    if feat_out:
        out = dyn['OUT'].fillna(0).values
    if feat_lab:
        lab = dyn['LAB'].fillna(0).values
    if feat_cond:
        stat=cond_df.values[0]
    y = int(demo['label'])
    
    demo["gender"].replace(gender_vocab, inplace=True)
    demo["ethnicity"].replace(eth_vocab, inplace=True)
    demo["insurance"].replace(ins_vocab, inplace=True)
    demo["Age"].replace(age_vocab, inplace=True)
    demo=demo[["gender","ethnicity","insurance","Age"]]
    demo = demo.values[0]
    return stat, demo, meds, charts, out, proc, lab, y


###################################
# CALLED FOR "aggreg" OR          #
# "concat" ENCODING               #
###################################
def generate_ml(dyn, stat, demo, concat_cols, concat):
    X_df = pd.DataFrame()
    dyn.to_csv("./data/dyn.csv")
    if concat:
        dyna=dyn.copy()
        dyna.columns=dyna.columns.droplevel(0)
        dyna=dyna.to_numpy()
        dyna=np.nan_to_num(dyna, copy=False)
        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, demo], axis=1)
    return X_df 


###################################
# CALLED FOR "text" ENCODING      #
###################################
def generate_text(data,icd,items,feat_cond,feat_chart,feat_meds, feat_proc, feat_out):
    #Demographics
    age = data['age']
    gender = data['gender']
    if gender=='F':
        gender='female'
    elif gender=='M':
        gender='male'
    else:
        gender='unknown'
    ethn=data['ethnicity'].lower()
    ins=data['insurance']

    #Diagnosis
    if feat_cond:
        conds = data.get('Cond', {}).get('fids', [])
        conds=[icd[icd['icd_code'] == code]['long_title'].to_string(index=False) for code in conds if not icd[icd['icd_code'] == code].empty]
        cond_text = '; '.join(conds)
        cond_text = f"The patient ({ethn} {gender}, {age} years old, covered by {ins}) was diagnosed with {cond_text}. " if cond_text else ''
    else:
        cond_text = ''
            
    #chart
    if feat_chart:
        chart = data.get('Chart', {})
        if chart:
            charts = chart.get('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]
            chart_text = '; '.join(f"{mean_val} for {feat_label}" for mean_val, feat_label in zip(chart_mean, feat_text))
            chart_text = f"The chart events measured were: {chart_text}. "
        else:
            chart_text = 'No chart events were measured. '
    else:
        chart_text = ''
        
        
    #meds
    if feat_meds:
        meds = data.get('Med', {})
        if meds:
            feat = meds['signal'].keys()
            meds_val = [meds['amount'][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]
            meds_text = '; '.join(f"{mean_val} of {feat_label}" for mean_val, feat_label in zip(meds_mean, feat_text))
            meds_text = f"The mean amounts of medications administered during the episode were: {meds_text}. "
        else:
            meds_text = 'No medications were administered. '
    else:
        meds_text = ''

    #proc
    if feat_proc:  
        proc = data['Proc']
        if proc:
            feat=proc.keys()
            feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
            template = 'The procedures performed were: {}. '
            proc_text= template.format('; '.join(feat_text))
        else:
            proc_text='No procedures were performed. '
    else:
        proc_text=''
    
    #out
    if feat_out:  
        out = data['Out']
        if out:
            feat=out.keys()
            feat_text = [(items[items['itemid']==f]['label']).to_string(index=False) for f in feat]
            template ='The outputs collected were: {}.'
            out_text = template.format('; '.join(feat_text))
        else:
            out_text='No outputs were collected.'
    else:
        out_text=''

    return cond_text,chart_text,meds_text,proc_text,out_text