[simdecs2.git] / src / java / org / ufcspa / simdecs / util / UnBBayesUtil.java

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package org.ufcspa.simdecs.util;

import java.io.File;
import java.security.InvalidParameterException;
import java.util.*;
import javax.persistence.EntityManager;
import org.ufcspa.simdecs.entities.Nodo;
import org.ufcspa.simdecs.entities.NodoPaciente;
import org.ufcspa.simdecs.entities.Paciente;
import org.ufcspa.simdecs.entities.Rede;
import org.ufcspa.simdecs.exceptions.InvalidNodeState;
import unbbayes.io.xmlbif.version6.XMLBIFIO;
import unbbayes.prs.Node;
import unbbayes.prs.bn.JunctionTreeAlgorithm;
import unbbayes.prs.bn.ProbabilisticNetwork;
import unbbayes.prs.bn.ProbabilisticNode;
import unbbayes.prs.bn.TreeVariable;

/**
 *
 * @author maroni
 */
public class UnBBayesUtil {

    
    private ProbabilisticNetwork rede;

    public UnBBayesUtil(Rede redeEntity) throws Exception {
        abreRede(redeEntity);
    }
        
    public final void abreRede(Rede redeEntity) throws Exception {
System.out.println(redeEntity);
if (redeEntity != null)
    System.out.println("NOME DA REDE A ABRIR: " + redeEntity.getArquivo());
        // required to run unbbayes gui classes on server
        System.setProperty("java.awt.headless", "false"); 
System.out.println("PONTO 1");
//        rede = new ProbabilisticNetwork("rede"+redeEntity.getId());
        
System.out.println("PONTO 2");
        XMLBIFIO.loadXML(new File(redeEntity.getArquivo()), rede);
System.out.println("PONTO 3");
        
        compilar();
System.out.println("PONTO 4");
    }

    public void compilar() {
        JunctionTreeAlgorithm jt = new JunctionTreeAlgorithm();
	jt.setNet(rede);	    
	jt.run();
    }
    
    
    public Node getNodeByName(String nodeName) {
        for(Node node : rede.getNodes()) {
            if (node.getName().toLowerCase().equals(nodeName.toLowerCase()))
                return node;
        }
        
        return null;
    }
    
    
    public void setNodeState(ProbabilisticNode node, Object ... stateProbs) throws Exception {
        HashMap<String, Float> states = new HashMap<String, Float>();
        String state = null;
        Float  probability = null;
        
        for (Object stateProb : stateProbs) {
            if (state == null)
                if (stateProb instanceof String)
                    state = (String) stateProb;
                else
                    throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
            else if (state != null)
                if ( !(stateProb instanceof String) ) {
                    if (stateProb instanceof Integer)
                        probability =  new Float ((Integer) stateProb);
                    else if (stateProb instanceof Float)
                        probability =  (Float) stateProb;
                    else
                        throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
                        
                    states.put(state.toLowerCase(), probability);
                    probability = null;
                    state = null;
                } else
                    throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
        }
                
        float likelihood[] = new float[node.getStatesSize()]; //nr. de estados do nodo
        for(int i=0; i < node.getStatesSize(); i++) {
            Float prob = states.get(node.getStateAt(i).toLowerCase());
            states.remove(node.getStateAt(i).toLowerCase());
            if (prob != null)
                likelihood[i] = prob;
            else
                likelihood[i] = 0;                
        }

        if (states.size() > 0) {
            StringBuilder invalidStates = new StringBuilder();
            for (String key : states.keySet()) {
                invalidStates.append(key);
                invalidStates.append(" ");
            }
            throw new InvalidNodeState("Estados de nodos inválidos: " + invalidStates);
        }

        node.addLikeliHood(likelihood);
        rede.updateEvidences();            
    }
    
    public List<ProbabilisticBean> getProbabilidades(TreeVariable node) {
                
        List<ProbabilisticBean> listProbs = new ArrayList<ProbabilisticBean>();
        
        for (int i=0; i < node.getStatesSize(); i++)
            listProbs.add(new ProbabilisticBean(node.getStateAt(i), node.getMarginalAt(i)));

        return listProbs;
    }
    
    public float getProbabilidadeByState(TreeVariable node, String state) {
        for (ProbabilisticBean bean : getProbabilidades(node)) {
            if (state.toLowerCase().equals(bean.getState().toLowerCase()))
                return bean.getProbability();
        }
        
        return 0;
    }

    public List<ProbabilisticBean> getProbabilidadesAscOrder(TreeVariable node) {
        List<ProbabilisticBean> listProbs = getProbabilidades(node);
        
        Collections.sort(listProbs, new Comparator() {
            @Override
            public int compare(Object o1, Object o2) {
                ProbabilisticBean nodo1 = (ProbabilisticBean) o1;
                ProbabilisticBean nodo2 = (ProbabilisticBean) o2;
                
                if (nodo1.getProbability() > nodo2.getProbability())
                    return 1;
                else if (nodo1.getProbability() < nodo2.getProbability())
                    return -1;
                else
                    return 0;
            }
        });        
        
        return listProbs;
    }
    
    public List<ProbabilisticBean> getProbabilidadesDescOrder(TreeVariable node) {
        List<ProbabilisticBean> listProbs = getProbabilidades(node);
        
        Collections.sort(listProbs, new Comparator() {
            @Override
            public int compare(Object o1, Object o2) {
                ProbabilisticBean nodo1 = (ProbabilisticBean) o1;
                ProbabilisticBean nodo2 = (ProbabilisticBean) o2;
                
                if (nodo1.getProbability() > nodo2.getProbability())
                    return -1;
                else if (nodo1.getProbability() < nodo2.getProbability())
                    return 1;
                else
                    return 0;
            }
        });        
        
        return listProbs;
    }
    
    public static UnBBayesUtil getRedePaciente(EntityManager em, Paciente paciente) throws Exception {
        
        UnBBayesUtil unBUtil = new UnBBayesUtil(paciente.getRede());

        List<NodoPaciente> nodosPaciente = em.createQuery("From NodoPaciente np Where np.paciente.id=:pPaciente")
                                             .setParameter("pPaciente", paciente.getId())
                                             .getResultList();
        
        for(NodoPaciente nodo : nodosPaciente) {
            ProbabilisticNode pn = (ProbabilisticNode) unBUtil.getNodeByName(nodo.getNodo().getNome());
            if (pn != null)
                unBUtil.setNodeState(pn, "Yes", 1, "Not", 0);
        }
        
        return unBUtil;
    }
    
    public List<NodoBean> getProbabilidades(EntityManager em, String tipoNodo) {
        Iterator<Nodo> itNodos = em.createNamedQuery("Nodo.getByTipo")
                                   .setParameter("pTipo", tipoNodo)
                                   .getResultList().iterator();
        
        ArrayList nodos = new ArrayList<NodoBean>();

        while(itNodos.hasNext()) {
            Nodo nodo = itNodos.next();
            NodoBean nodoBean = new NodoBean(nodo, (Float) getProbabilidadeByState((TreeVariable) getNodeByName(nodo.getNome()), "Yes"));
            nodos.add(nodoBean);
        }
        
        Collections.sort(nodos, new Comparator() {
            @Override
            public int compare(Object o1, Object o2) {
                NodoBean nodo1 = (NodoBean) o1;
                NodoBean nodo2 = (NodoBean) o2;
                
                if (nodo1.getProbabilidade() > nodo2.getProbabilidade())
                    return -1;
                else if (nodo1.getProbabilidade() < nodo2.getProbabilidade())
                    return 1;
                else
                    return 0;
            }
        });
        
        return nodos;
    }

    public Nodo getPrimeiroDiagnostico(EntityManager em) {
        List<NodoBean> diagnosticos = getProbabilidades(em, Nodo.DIAGNOSTICO);
        for(NodoBean nodoBean : diagnosticos) {
            return nodoBean.getNodo();
        }
        
        return null;
    }

    public Nodo getSegundoDiagnostico(EntityManager em) {
        List<NodoBean> diagnosticos = getProbabilidades(em, Nodo.DIAGNOSTICO);
        
        int d=1;
        float probabilidadeDiag1=0;
        float probabilidadeDiag2=0;
        Nodo segundoDiagnostico=null;
        for(NodoBean nodoBean : diagnosticos) {
            if (d == 1)
                probabilidadeDiag1 = nodoBean.getPercentualProbabilidade();            
            if (d == 2) {
                probabilidadeDiag2 = nodoBean.getPercentualProbabilidade();
                segundoDiagnostico = nodoBean.getNodo();
            }

            if (d++ == 2)
                break;
        }
        
        float diferenca = probabilidadeDiag1 - probabilidadeDiag2;
        if (diferenca <= 25)
            return segundoDiagnostico;
        else
            return null;
    }
    
    public List<Nodo> getCondutas(EntityManager em) {
        List<NodoBean> condutas = getProbabilidades(em, Nodo.CONDUTA);
        List<Nodo> condutasRetornar = new ArrayList<Nodo>();
        for(NodoBean conduta : condutas) {
            if (conduta.getPercentualProbabilidade() < 50)
                continue;
            
            condutasRetornar.add(conduta.getNodo());
//System.out.println("CONDUTA*: " + conduta.getNodo().getNomeAmigavel());
        }
        
        return condutasRetornar;
        
    }
}
Commit	Line	Data
25aea581	1	/*
	2	* To change this template, choose Tools \| Templates
	3	* and open the template in the editor.
	4	*/
	5	package org.ufcspa.simdecs.util;
	6
	7	import java.io.File;
	8	import java.security.InvalidParameterException;
	9	import java.util.*;
56f36e0a	10	import javax.persistence.EntityManager;
	11	import org.ufcspa.simdecs.entities.Nodo;
	12	import org.ufcspa.simdecs.entities.NodoPaciente;
	13	import org.ufcspa.simdecs.entities.Paciente;
25aea581	14	import org.ufcspa.simdecs.entities.Rede;
	15	import org.ufcspa.simdecs.exceptions.InvalidNodeState;
	16	import unbbayes.io.xmlbif.version6.XMLBIFIO;
	17	import unbbayes.prs.Node;
	18	import unbbayes.prs.bn.JunctionTreeAlgorithm;
	19	import unbbayes.prs.bn.ProbabilisticNetwork;
	20	import unbbayes.prs.bn.ProbabilisticNode;
	21	import unbbayes.prs.bn.TreeVariable;
	22
	23	/**
	24	*
	25	* @author maroni
	26	*/
	27	public class UnBBayesUtil {
	28
	29
	30	private ProbabilisticNetwork rede;
	31
	32	public UnBBayesUtil(Rede redeEntity) throws Exception {
	33	abreRede(redeEntity);
	34	}
	35
	36	public final void abreRede(Rede redeEntity) throws Exception {
77e00f06	37	System.out.println(redeEntity);
	38	if (redeEntity != null)
	39	System.out.println("NOME DA REDE A ABRIR: " + redeEntity.getArquivo());
25aea581	40	// required to run unbbayes gui classes on server
25aea581	41	System.setProperty("java.awt.headless", "false");
dfca7926	42	System.out.println("PONTO 1");
050a5e2a	43	// rede = new ProbabilisticNetwork("rede"+redeEntity.getId());
7870db59	44
dfca7926	45	System.out.println("PONTO 2");
25aea581	46	XMLBIFIO.loadXML(new File(redeEntity.getArquivo()), rede);
dfca7926	47	System.out.println("PONTO 3");
25aea581	48
25aea581	49	compilar();
dfca7926	50	System.out.println("PONTO 4");
25aea581	51	}
	52
	53	public void compilar() {
	54	JunctionTreeAlgorithm jt = new JunctionTreeAlgorithm();
	55	jt.setNet(rede);
	56	jt.run();
	57	}
	58
	59
	60	public Node getNodeByName(String nodeName) {
	61	for(Node node : rede.getNodes()) {
	62	if (node.getName().toLowerCase().equals(nodeName.toLowerCase()))
	63	return node;
	64	}
	65
	66	return null;
	67	}
	68
	69
	70	public void setNodeState(ProbabilisticNode node, Object ... stateProbs) throws Exception {
	71	HashMap<String, Float> states = new HashMap<String, Float>();
	72	String state = null;
	73	Float probability = null;
	74
	75	for (Object stateProb : stateProbs) {
	76	if (state == null)
	77	if (stateProb instanceof String)
	78	state = (String) stateProb;
	79	else
	80	throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
	81	else if (state != null)
	82	if ( !(stateProb instanceof String) ) {
	83	if (stateProb instanceof Integer)
	84	probability = new Float ((Integer) stateProb);
	85	else if (stateProb instanceof Float)
	86	probability = (Float) stateProb;
	87	else
	88	throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
	89
	90	states.put(state.toLowerCase(), probability);
	91	probability = null;
	92	state = null;
	93	} else
	94	throw new InvalidParameterException("Os parametros devem ser informados no formato: state(string), prob(float), ..., ...");
	95	}
	96
	97	float likelihood[] = new float[node.getStatesSize()]; //nr. de estados do nodo
	98	for(int i=0; i < node.getStatesSize(); i++) {
	99	Float prob = states.get(node.getStateAt(i).toLowerCase());
	100	states.remove(node.getStateAt(i).toLowerCase());
	101	if (prob != null)
	102	likelihood[i] = prob;
	103	else
	104	likelihood[i] = 0;
	105	}
	106
	107	if (states.size() > 0) {
	108	StringBuilder invalidStates = new StringBuilder();
	109	for (String key : states.keySet()) {
	110	invalidStates.append(key);
	111	invalidStates.append(" ");
	112	}
	113	throw new InvalidNodeState("Estados de nodos inválidos: " + invalidStates);
	114	}
115
116	node.addLikeliHood(likelihood);
117	rede.updateEvidences();
118	}
119
120	public List<ProbabilisticBean> getProbabilidades(TreeVariable node) {
121
122	List<ProbabilisticBean> listProbs = new ArrayList<ProbabilisticBean>();
123
124	for (int i=0; i < node.getStatesSize(); i++)
125	listProbs.add(new ProbabilisticBean(node.getStateAt(i), node.getMarginalAt(i)));
126
127	return listProbs;
128	}
129
130	public float getProbabilidadeByState(TreeVariable node, String state) {
131	for (ProbabilisticBean bean : getProbabilidades(node)) {
132	if (state.toLowerCase().equals(bean.getState().toLowerCase()))
133	return bean.getProbability();
134	}
135
136	return 0;
137	}
138
139	public List<ProbabilisticBean> getProbabilidadesAscOrder(TreeVariable node) {
140	List<ProbabilisticBean> listProbs = getProbabilidades(node);
141
142	Collections.sort(listProbs, new Comparator() {
143	@Override
144	public int compare(Object o1, Object o2) {
145	ProbabilisticBean nodo1 = (ProbabilisticBean) o1;
146	ProbabilisticBean nodo2 = (ProbabilisticBean) o2;
147
148	if (nodo1.getProbability() > nodo2.getProbability())
149	return 1;
150	else if (nodo1.getProbability() < nodo2.getProbability())
151	return -1;
152	else
153	return 0;
154	}
155	});
156
157	return listProbs;
158	}
159
160	public List<ProbabilisticBean> getProbabilidadesDescOrder(TreeVariable node) {
161	List<ProbabilisticBean> listProbs = getProbabilidades(node);
162
163	Collections.sort(listProbs, new Comparator() {
164	@Override
165	public int compare(Object o1, Object o2) {
166	ProbabilisticBean nodo1 = (ProbabilisticBean) o1;
167	ProbabilisticBean nodo2 = (ProbabilisticBean) o2;
168
169	if (nodo1.getProbability() > nodo2.getProbability())
170	return -1;
171	else if (nodo1.getProbability() < nodo2.getProbability())
172	return 1;
173	else
174	return 0;
175	}
176	});
177
178	return listProbs;
179	}
180
56f36e0a	181	public static UnBBayesUtil getRedePaciente(EntityManager em, Paciente paciente) throws Exception {
	182
	183	UnBBayesUtil unBUtil = new UnBBayesUtil(paciente.getRede());
	184
	185	List<NodoPaciente> nodosPaciente = em.createQuery("From NodoPaciente np Where np.paciente.id=:pPaciente")
	186	.setParameter("pPaciente", paciente.getId())
	187	.getResultList();
	188
	189	for(NodoPaciente nodo : nodosPaciente) {
	190	ProbabilisticNode pn = (ProbabilisticNode) unBUtil.getNodeByName(nodo.getNodo().getNome());
	191	if (pn != null)
	192	unBUtil.setNodeState(pn, "Yes", 1, "Not", 0);
	193	}
	194
	195	return unBUtil;
	196	}
25aea581	197
56f36e0a	198	public List<NodoBean> getProbabilidades(EntityManager em, String tipoNodo) {
	199	Iterator<Nodo> itNodos = em.createNamedQuery("Nodo.getByTipo")
	200	.setParameter("pTipo", tipoNodo)
	201	.getResultList().iterator();
	202
	203	ArrayList nodos = new ArrayList<NodoBean>();
	204
	205	while(itNodos.hasNext()) {
	206	Nodo nodo = itNodos.next();
	207	NodoBean nodoBean = new NodoBean(nodo, (Float) getProbabilidadeByState((TreeVariable) getNodeByName(nodo.getNome()), "Yes"));
	208	nodos.add(nodoBean);
	209	}
	210
	211	Collections.sort(nodos, new Comparator() {
	212	@Override
	213	public int compare(Object o1, Object o2) {
	214	NodoBean nodo1 = (NodoBean) o1;
	215	NodoBean nodo2 = (NodoBean) o2;
	216
	217	if (nodo1.getProbabilidade() > nodo2.getProbabilidade())
	218	return -1;
	219	else if (nodo1.getProbabilidade() < nodo2.getProbabilidade())
	220	return 1;
	221	else
	222	return 0;
	223	}
	224	});
	225
	226	return nodos;
	227	}
	228
	229	public Nodo getPrimeiroDiagnostico(EntityManager em) {
	230	List<NodoBean> diagnosticos = getProbabilidades(em, Nodo.DIAGNOSTICO);
	231	for(NodoBean nodoBean : diagnosticos) {
	232	return nodoBean.getNodo();
	233	}
	234
	235	return null;
	236	}
	237
	238	public Nodo getSegundoDiagnostico(EntityManager em) {
	239	List<NodoBean> diagnosticos = getProbabilidades(em, Nodo.DIAGNOSTICO);
	240
	241	int d=1;
	242	float probabilidadeDiag1=0;
	243	float probabilidadeDiag2=0;
	244	Nodo segundoDiagnostico=null;
	245	for(NodoBean nodoBean : diagnosticos) {
	246	if (d == 1)
	247	probabilidadeDiag1 = nodoBean.getPercentualProbabilidade();
	248	if (d == 2) {
	249	probabilidadeDiag2 = nodoBean.getPercentualProbabilidade();
	250	segundoDiagnostico = nodoBean.getNodo();
	251	}
	252
	253	if (d++ == 2)
	254	break;
	255	}
	256
	257	float diferenca = probabilidadeDiag1 - probabilidadeDiag2;
	258	if (diferenca <= 25)
	259	return segundoDiagnostico;
	260	else
	261	return null;
262	}
263
264	public List<Nodo> getCondutas(EntityManager em) {
265	List<NodoBean> condutas = getProbabilidades(em, Nodo.CONDUTA);
266	List<Nodo> condutasRetornar = new ArrayList<Nodo>();
267	for(NodoBean conduta : condutas) {
268	if (conduta.getPercentualProbabilidade() < 50)
269	continue;
270
271	condutasRetornar.add(conduta.getNodo());
272	//System.out.println("CONDUTA*: " + conduta.getNodo().getNomeAmigavel());
273	}
274
275	return condutasRetornar;
276
277	}
25aea581	278	}