Merge branch 'master' of /cygdrive/z/vitor/Yap/yap-6.3

C/absmi.c

@@ -2081,8 +2081,13 @@ Yap_absmi(int inp)
 	      goto failloop;
 	    } else
 #endif /* FROZEN_STACKS */
-	      if (IN_BETWEEN(H0,pt1,H) && IsAttVar(pt1))
+	      if (IN_BETWEEN(H0,pt1,H)) {
-		goto failloop;		       	    
+		if (IsAttVar(pt1)) {
+		  goto failloop;	
+		} else if (*pt1 == (CELL)FunctorBigInt) {
+		  Yap_CleanOpaqueVariable(pt1);
+		}	       	  
+	      }  
 #ifdef FROZEN_STACKS  /* TRAIL */
 	    /* don't reset frozen variables */
 	    if (pt0 < TR_FZ)

C/amasm.c

@@ -252,7 +252,7 @@ STATIC_PROTO(yamop *a_if, (op_numbers, union clause_obj *, int, yamop *, int, st
 STATIC_PROTO(yamop *a_cut, (clause_info *,yamop *, int, struct intermediates *));
 #ifdef YAPOR
 STATIC_PROTO(yamop *a_try, (op_numbers, CELL, CELL, int, int, yamop *, int, struct intermediates *));
-STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, int, int, yamop *, int, struct intermediates *));
+STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, int, yamop *, int, struct intermediates *));
 #else
 STATIC_PROTO(yamop *a_try, (op_numbers, CELL, CELL, yamop *, int, struct intermediates *));
 STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, yamop *,  int, struct intermediates *));
@@ -2155,7 +2155,7 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
 #endif
 #ifdef YAPOR
     INIT_YAMOP_LTT(code_p, nofalts);
-    if (hascut)
+    if (cip->clause_has_cut)
       PUT_YAMOP_CUT(code_p);
     if (ap->PredFlags & SequentialPredFlag)
       PUT_YAMOP_SEQ(code_p);
@@ -2167,7 +2167,7 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
 
 static yamop *
 #ifdef YAPOR
-a_either(op_numbers opcode, CELL opr, CELL lab, int nofalts, int hascut, yamop *code_p, int pass_no, struct intermediates *cip)
+a_either(op_numbers opcode, CELL opr, CELL lab, int nofalts, yamop *code_p, int pass_no, struct intermediates *cip)
 #else
 a_either(op_numbers opcode, CELL opr, CELL lab, yamop *code_p, int pass_no, struct intermediates *cip)
 #endif /* YAPOR */
@@ -2179,7 +2179,7 @@ a_either(op_numbers opcode, CELL opr, CELL lab, yamop *code_p, int pass_no, stru
     code_p->u.Osblp.p0 =  cip->CurrentPred;
 #ifdef YAPOR
     INIT_YAMOP_LTT(code_p, nofalts);
-    if (hascut)
+    if (cip->clause_has_cut)
       PUT_YAMOP_CUT(code_p);
     if (cip->CurrentPred->PredFlags & SequentialPredFlag)
       PUT_YAMOP_SEQ(code_p);
@@ -3583,7 +3583,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
       }
       code_p = a_either(_either,
 	       -Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
-	       Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, 0, code_p, pass_no, cip);
+	       Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, code_p, pass_no, cip);
 #else
       code_p = a_either(_either,
 	       -Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
@@ -3596,7 +3596,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
 	either_inst[either_cont++] = code_p;
       code_p = a_either(_or_else,
 	       -Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
-	       Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, 0, code_p, pass_no, cip);
+	       Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, code_p, pass_no, cip);
 #else
       code_p = a_either(_or_else,
 	       -Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
@@ -3608,7 +3608,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
 #ifdef YAPOR
       if (pass_no)
 	either_inst[either_cont++] = code_p;
-      code_p = a_either(_or_last, 0, 0, 0, 0, code_p, pass_no, cip);
+      code_p = a_either(_or_last, 0, 0, 0, code_p, pass_no, cip);
       if (pass_no) {
 	int cont = 1;
 	do {

C/bignum.c

@@ -25,9 +25,10 @@ static char     SccsId[] = "%W% %G%";
 #include <string.h>
 #endif
 
+#include "YapHeap.h"
+
 #ifdef USE_GMP
 
-#include "YapHeap.h"
 #include "eval.h"
 #include "alloc.h"
 
@@ -59,6 +60,7 @@ Yap_MkBigIntTerm(MP_INT *big)
   return AbsAppl(ret);
 }
 
+
 MP_INT *
 Yap_BigIntOfTerm(Term t)
 {
@@ -127,9 +129,60 @@ Yap_RatTermToApplTerm(Term t)
   return Yap_MkApplTerm(FunctorRDiv,2,ts);
 }
 
-
 #endif
 
+Term
+Yap_AllocExternalDataInStack(CELL tag, size_t bytes)
+{
+  CACHE_REGS
+  Int nlimbs;
+  MP_INT *dst = (MP_INT *)(H+2);
+  CELL *ret = H;
+
+  nlimbs = ALIGN_YAPTYPE(bytes,CELL)/CellSize;
+  if (nlimbs > (ASP-ret)-1024) {
+    return TermNil;
+  }
+  H[0] = (CELL)FunctorBigInt;
+  H[1] = tag;
+  dst->_mp_size = 0;
+  dst->_mp_alloc = nlimbs;
+  H = (CELL *)(dst+1)+nlimbs;
+  H[0] = EndSpecials;
+  H++;
+  if (tag != EXTERNAL_BLOB) {
+    TrailTerm(TR) = AbsPair(ret);
+    TR++;
+  }
+  return AbsAppl(ret);
+}
+
+int Yap_CleanOpaqueVariable(CELL *pt)
+{
+  CELL blob_info, blob_tag;
+  MP_INT *blobp;
+#ifdef DEBUG
+  /* sanity checking */
+  if (pt[0] != (CELL)FunctorBigInt) {
+    Yap_Error(SYSTEM_ERROR, TermNil, "CleanOpaqueVariable bad call");
+    return FALSE;
+  }
+#endif
+  blob_tag = pt[1];
+  if (blob_tag < USER_BLOB_START ||
+      blob_tag >= USER_BLOB_END) {
+    Yap_Error(SYSTEM_ERROR, AbsAppl(pt), "clean opaque: bad blob with tag " UInt_FORMAT ,blob_tag);
+    return FALSE;
+  }
+  blob_info = blob_tag - USER_BLOB_START;
+  if (!GLOBAL_OpaqueHandlers)
+    return FALSE;
+  blobp = (MP_INT *)(pt+2);
+  if (!GLOBAL_OpaqueHandlers[blob_info].fail_handler)
+    return TRUE;
+  return (GLOBAL_OpaqueHandlers[blob_info].fail_handler)((void *)(blobp+1));
+}
+
 Term
 Yap_MkULLIntTerm(YAP_ULONG_LONG n)
 {

C/c_interface.c

@@ -390,6 +390,8 @@ X_API Bool    STD_PROTO(YAP_IsDbRefTerm,(Term));
 X_API Bool    STD_PROTO(YAP_IsAtomTerm,(Term));
 X_API Bool    STD_PROTO(YAP_IsPairTerm,(Term));
 X_API Bool    STD_PROTO(YAP_IsApplTerm,(Term));
+X_API Bool    STD_PROTO(YAP_IsExternalDataInStackTerm,(Term));
+X_API Bool    STD_PROTO(YAP_IsOpaqueObjectTerm,(Term, int));
 X_API Term    STD_PROTO(YAP_MkIntTerm,(Int));
 X_API Term    STD_PROTO(YAP_MkBigNumTerm,(void *));
 X_API Term    STD_PROTO(YAP_MkRationalTerm,(void *));
@@ -463,7 +465,7 @@ X_API IOSTREAM   *STD_PROTO(YAP_TermToStream,(Term));
 X_API IOSTREAM   *STD_PROTO(YAP_InitConsult,(int, char *));
 X_API void    STD_PROTO(YAP_EndConsult,(IOSTREAM *));
 X_API Term    STD_PROTO(YAP_Read, (IOSTREAM *));
-X_API void    STD_PROTO(YAP_Write, (Term, int (*)(wchar_t), int));
+X_API void    STD_PROTO(YAP_Write, (Term, IOSTREAM *, int));
 X_API Term    STD_PROTO(YAP_CopyTerm, (Term));
 X_API Term    STD_PROTO(YAP_WriteBuffer, (Term, char *, unsigned int, int));
 X_API char   *STD_PROTO(YAP_CompileClause, (Term));
@@ -536,13 +538,11 @@ X_API Term     STD_PROTO(YAP_ModuleUser,(void));
 X_API Int      STD_PROTO(YAP_NumberOfClausesForPredicate,(PredEntry *));
 X_API int      STD_PROTO(YAP_MaxOpPriority,(Atom, Term));
 X_API int      STD_PROTO(YAP_OpInfo,(Atom, Term, int, int *, int *));
-
+X_API Term     STD_PROTO(YAP_AllocExternalDataInStack,(size_t));
-static int (*do_putcf)(wchar_t);
+X_API void    *STD_PROTO(YAP_ExternalDataInStackFromTerm,(Term));
-
+X_API int      STD_PROTO(YAP_NewOpaqueType,(void *));
-static int do_yap_putc(int streamno,wchar_t ch) {
+X_API Term     STD_PROTO(YAP_NewOpaqueObject,(int, size_t));
-  do_putcf(ch);
+X_API void    *STD_PROTO(YAP_OpaqueObjectFromTerm,(Term));
-  return(ch);
-}
 
 static int
 dogc(void)
@@ -1677,7 +1677,6 @@ YAP_ExecuteOnCut(PredEntry *pe, CPredicate exec_code, struct cut_c_str *top)
     if (pe->PredFlags & CArgsPredFlag) {
       val = execute_cargs_back(pe, exec_code, ctx PASS_REGS);
     } else {
-      fprintf(stderr,"ctx=%p\n",ctx);
       val = ((codev)(args-LCL0,0,ctx));
     }
     /* make sure we clean up the frames left by the user */
@@ -2314,6 +2313,65 @@ YAP_RunGoal(Term t)
   return(out);
 }
 
+X_API Term
+YAP_AllocExternalDataInStack(size_t bytes)
+{
+  Term t = Yap_AllocExternalDataInStack(EXTERNAL_BLOB, bytes);
+  if (t == TermNil)
+    return 0L;
+  return t;
+}
+
+X_API Bool
+YAP_IsExternalDataInStackTerm(Term t)
+{
+  return IsExternalBlobTerm(t, EXTERNAL_BLOB);
+}
+
+X_API void *
+YAP_ExternalDataInStackFromTerm(Term t)
+{
+  return ExternalBlobFromTerm (t);
+}
+
+int YAP_NewOpaqueType(void *f)
+{
+  int i;
+  if (!GLOBAL_OpaqueHandlers) {
+    GLOBAL_OpaqueHandlers = malloc(sizeof(opaque_handler_t)*(USER_BLOB_END-USER_BLOB_START));
+    if (!GLOBAL_OpaqueHandlers) {
+      /* no room */
+      return -1;
+    }
+  } else if (GLOBAL_OpaqueHandlersCount == USER_BLOB_END-USER_BLOB_START) {
+    /* all types used */
+    return -1;
+  }
+  i = GLOBAL_OpaqueHandlersCount++;
+  memcpy(GLOBAL_OpaqueHandlers+i,f,sizeof(opaque_handler_t));
+  return i+USER_BLOB_START;
+}
+
+Term YAP_NewOpaqueObject(int tag, size_t bytes)
+{
+  Term t = Yap_AllocExternalDataInStack((CELL)tag, bytes);
+  if (t == TermNil)
+    return 0L;
+  return t;
+}
+
+X_API Bool
+YAP_IsOpaqueObjectTerm(Term t, int tag)
+{
+  return IsExternalBlobTerm(t, (CELL)tag);
+}
+
+X_API void *
+YAP_OpaqueObjectFromTerm(Term t)
+{
+  return ExternalBlobFromTerm (t);
+}
+
 X_API Term
 YAP_RunGoalOnce(Term t)
 {
@@ -2369,7 +2427,6 @@ YAP_RestartGoal(void)
   BACKUP_MACHINE_REGS();
   if (LOCAL_AllowRestart) {
     P = (yamop *)FAILCODE;
-    do_putcf = myputc;
     LOCAL_PrologMode = UserMode;
     out = Yap_exec_absmi(TRUE);
     LOCAL_PrologMode = UserCCallMode;
@@ -2589,12 +2646,11 @@ YAP_Read(IOSTREAM *inp)
 }
 
 X_API void
-YAP_Write(Term t, int (*myputc)(wchar_t), int flags)
+YAP_Write(Term t, IOSTREAM *stream, int flags)
 {
   BACKUP_MACHINE_REGS();
 
-  do_putcf = myputc;		/*  */
+  Yap_dowrite (t, stream, flags, 1200);
-  Yap_plwrite (t, do_yap_putc, flags, 1200);
 
   RECOVER_MACHINE_REGS();
 }
@@ -2774,6 +2830,7 @@ YAP_Init(YAP_init_args *yap_init)
   Yap_init_yapor_global_local_memory();
   LOCAL = REMOTE(0);
 #endif /* YAPOR_COPY || YAPOR_COW || YAPOR_SBA */
+  GLOBAL_PrologShouldHandleInterrupts = yap_init->PrologShouldHandleInterrupts;
   Yap_InitSysbits();  /* init signal handling and time, required by later functions */
   GLOBAL_argv = yap_init->Argv;
   GLOBAL_argc = yap_init->Argc;
@@ -2821,7 +2878,6 @@ YAP_Init(YAP_init_args *yap_init)
   } else {
     Heap = yap_init->HeapSize;
   }
-  GLOBAL_PrologShouldHandleInterrupts = yap_init->PrologShouldHandleInterrupts;
   Yap_InitWorkspace(Heap, Stack, Trail, Atts,
 	      yap_init->MaxTableSpaceSize,
 	      yap_init->NumberWorkers,

C/compiler.c

@@ -735,7 +735,7 @@ c_arg(Int argno, Term t, unsigned int arity, unsigned int level, compiler_struct
   } else if (IsPairTerm(t)) {
     cglobs->space_used += 2;
     if (optimizer_on && level < 6) {
-#if !defined(THREADS)
+#if !defined(THREADS) && !defined(YAPOR)
       /* discard code sharing because we cannot write on shared stuff */
       if (!(cglobs->cint.CurrentPred->PredFlags & (DynamicPredFlag|LogUpdatePredFlag))) {
 	if (try_store_as_dbterm(t, argno, arity, level, cglobs))

C/exec.c

@@ -961,7 +961,7 @@ exec_absmi(int top USES_REGS)
 	restore_H();
 	/* set stack */
 	ASP = (CELL *)PROTECT_FROZEN_B(B);
-	Yap_StartSlots( PASS_REGS1 );
+	Yap_PopSlots();
 	LOCK(LOCAL_SignalLock);
 	/* forget any signals active, we're reborne */
 	LOCAL_ActiveSignals = 0;
@@ -991,9 +991,9 @@ exec_absmi(int top USES_REGS)
       LOCAL_PrologMode = UserMode;
     }
   } else {
+    Yap_CloseSlots( PASS_REGS1 );
     LOCAL_PrologMode = UserMode;
   }
-  Yap_CloseSlots( PASS_REGS1 );
   YENV = ASP;
   YENV[E_CB] = Unsigned (B);
   out = Yap_absmi(0);

C/grow.c

@@ -399,7 +399,7 @@ AdjustTrail(int adjusting_heap, int thread_copying USES_REGS)
 #if defined(YAPOR_THREADS)
   }
 #endif
-  /* moving the trail is simple */
+  /* moving the trail is simple, yeaahhh! */
   while (ptt != tr_base) {
     register CELL reg = TrailTerm(ptt-1);
 #ifdef FROZEN_STACKS
@@ -420,8 +420,6 @@ AdjustTrail(int adjusting_heap, int thread_copying USES_REGS)
     } else if (IsPairTerm(reg)) {
       TrailTerm(ptt) = AdjustPair(reg PASS_REGS);
 #ifdef MULTI_ASSIGNMENT_VARIABLES /* does not work with new structures */
-    /* check it whether we are protecting a
-       multi-assignment */
     } else if (IsApplTerm(reg)) {
       TrailTerm(ptt) = AdjustAppl(reg PASS_REGS);
 #endif

C/heapgc.c

@@ -1325,7 +1325,7 @@ mark_variable(CELL_PTR current USES_REGS)
 	  sz++;
 #if DEBUG
 	  if (next[sz] != EndSpecials)  {
-	    fprintf(stderr,"[ Error: could not find EndSpecials at blob %p type %lx ]\n", next, next[1]);
+	    fprintf(stderr,"[ Error: could not find EndSpecials at blob %p type " UInt_FORMAT " ]\n", next, next[1]);
 	}
 #endif
 	  MARK(next+sz);
@@ -1658,14 +1658,23 @@ mark_trail(tr_fr_ptr trail_ptr, tr_fr_ptr trail_base, CELL *gc_H, choiceptr gc_B
 #endif
       }
     } else if (IsPairTerm(trail_cell)) {
-      /* can safely ignore this */
+      /* cannot safely ignore this */
       CELL *cptr = RepPair(trail_cell);
-      if (IN_BETWEEN(LOCAL_GlobalBase,cptr,H) &&
+      if (IN_BETWEEN(LOCAL_GlobalBase,cptr,H)) {
-	  GlobalIsAttVar(cptr)) {
+	if (GlobalIsAttVar(cptr)) {
-	TrailTerm(trail_base) = (CELL)cptr;
+	  TrailTerm(trail_base) = (CELL)cptr;
-	mark_external_reference(&TrailTerm(trail_base) PASS_REGS);
+	  mark_external_reference(&TrailTerm(trail_base) PASS_REGS);
-	TrailTerm(trail_base) = trail_cell;
+	  TrailTerm(trail_base) = trail_cell;
-      } 
+	} else if (*cptr == (CELL)FunctorBigInt) {
+	  TrailTerm(trail_base) = AbsAppl(cptr);
+	  mark_external_reference(&TrailTerm(trail_base) PASS_REGS);
+	  TrailTerm(trail_base) = trail_cell;	  
+	} 
+#ifdef DEBUG
+	else
+	  fprintf(GLOBAL_stderr,"OOPS in GC: weird trail entry at %p:" UInt_FORMAT "\n", &TrailTerm(trail_base), (CELL)cptr);
+#endif
+      }
     }
 #if  MULTI_ASSIGNMENT_VARIABLES
     else {
@@ -1904,11 +1913,11 @@ mark_choicepoints(register choiceptr gc_B, tr_fr_ptr saved_TR, int very_verbose
       PredEntry *pe = Yap_PredForChoicePt(gc_B);
 #if defined(ANALYST) || defined(DEBUG)
       if (pe == NULL) {
-	fprintf(GLOBAL_stderr,"%%       marked %ld (%s)\n", LOCAL_total_marked, Yap_op_names[opnum]);
+	fprintf(GLOBAL_stderr,"%%       marked  " UInt_FORMAT " (%s)\n", LOCAL_total_marked, Yap_op_names[opnum]);
       } else if (pe->ArityOfPE) {
-	fprintf(GLOBAL_stderr,"%%       %s/%d marked %ld (%s)\n", RepAtom(NameOfFunctor(pe->FunctorOfPred))->StrOfAE, pe->ArityOfPE, LOCAL_total_marked, Yap_op_names[opnum]);
+	fprintf(GLOBAL_stderr,"%%       %s/%d marked  " UInt_FORMAT " (%s)\n", RepAtom(NameOfFunctor(pe->FunctorOfPred))->StrOfAE, pe->ArityOfPE, LOCAL_total_marked, Yap_op_names[opnum]);
       } else {
-	fprintf(GLOBAL_stderr,"%%       %s marked %ld (%s)\n", RepAtom((Atom)(pe->FunctorOfPred))->StrOfAE, LOCAL_total_marked, Yap_op_names[opnum]);
+	fprintf(GLOBAL_stderr,"%%       %s marked  " UInt_FORMAT " (%s)\n", RepAtom((Atom)(pe->FunctorOfPred))->StrOfAE, LOCAL_total_marked, Yap_op_names[opnum]);
       }
 #else
       if (pe == NULL) {
@@ -2450,11 +2459,19 @@ sweep_trail(choiceptr gc_B, tr_fr_ptr old_TR USES_REGS)
 	CELL *pt0 = RepPair(trail_cell);
 	CELL flags;
 
-	if (IN_BETWEEN(LOCAL_GlobalBase, pt0, H) && GlobalIsAttVar(pt0)) {
+	if (IN_BETWEEN(LOCAL_GlobalBase, pt0, H)) {
-	  TrailTerm(dest) = trail_cell;
+	  if (GlobalIsAttVar(pt0)) {
-	  /* be careful with partial gc */
+	    TrailTerm(dest) = trail_cell;
-	  if (HEAP_PTR(TrailTerm(dest))) {
+	    /* be careful with partial gc */
-	    into_relocation_chain(&TrailTerm(dest), GET_NEXT(trail_cell) PASS_REGS);
+	    if (HEAP_PTR(TrailTerm(dest))) {
+	      into_relocation_chain(&TrailTerm(dest), GET_NEXT(trail_cell) PASS_REGS);
+	    }
+	  } else if (*pt0 == (CELL)FunctorBigInt) {
+	    TrailTerm(dest) = trail_cell;
+	    /* be careful with partial gc */
+	    if (HEAP_PTR(TrailTerm(dest))) {
+	      into_relocation_chain(&TrailTerm(dest), GET_NEXT(trail_cell) PASS_REGS);
+	    }
 	  }
 	  dest++;
 	  trail_ptr++;

H/TermExt.h

@@ -86,7 +86,9 @@ typedef enum
     CLAUSE_LIST =  0x40,
     BLOB_STRING =  0x80, /* SWI style strings */
     BLOB_WIDE_STRING =  0x81, /* SWI style strings */
-    EXTERNAL_BLOB =  0x100 /* for SWI emulation */
+    EXTERNAL_BLOB =  0x100, /* generic data */
+    USER_BLOB_START =  0x1000, /* user defined blob */
+    USER_BLOB_END =  0x1100 /* end of user defined blob */
   } 
 big_blob_type;
 
@@ -438,6 +440,25 @@ IsLargeNumTerm (Term t)
 		    && (FunctorOfTerm (t) >= FunctorLongInt)));
 }
 
+inline EXTERN int IsExternalBlobTerm (Term, CELL);
+
+inline EXTERN int
+IsExternalBlobTerm (Term t, CELL tag)
+{
+  return (int) (IsApplTerm (t) &&
+		FunctorOfTerm (t) == FunctorBigInt &&
+		RepAppl(t)[1] == tag);
+}
+
+inline EXTERN void *ExternalBlobFromTerm (Term);
+
+inline EXTERN void *
+ExternalBlobFromTerm (Term t)
+{
+  MP_INT *base = (MP_INT *)(RepAppl(t)+2);
+  return (void *) (base+1);
+}
+
 
 
 

H/YapHeap.h

@@ -33,6 +33,12 @@ typedef int (*SWI_PLGetStreamPositionFunction)(void *);
 
 #include "../include/dswiatoms.h"
 
+typedef int (*Opaque_CallOnFail)(void *);
+
+typedef struct opaque_handler_struct {
+  Opaque_CallOnFail fail_handler;
+} opaque_handler_t;
+
 #ifndef INT_KEYS_DEFAULT_SIZE
 #define INT_KEYS_DEFAULT_SIZE 256
 #endif

H/Yapproto.h

@@ -120,6 +120,8 @@ int    STD_PROTO(Yap_IsStringTerm, (Term));
 int    STD_PROTO(Yap_IsWideStringTerm, (Term));
 Term   STD_PROTO(Yap_RatTermToApplTerm, (Term));
 void   STD_PROTO(Yap_InitBigNums, (void));
+Term   STD_PROTO(Yap_AllocExternalDataInStack, (CELL, size_t));
+int    STD_PROTO(Yap_CleanOpaqueVariable, (CELL *));
 
 /* c_interface.c */
 Int    STD_PROTO(YAP_Execute,(struct pred_entry *, CPredicate));

H/dglobals.h

@@ -102,6 +102,8 @@
 
 #define GLOBAL_Executable Yap_global->Executable_
 #endif
+#define GLOBAL_OpaqueHandlersCount Yap_global->OpaqueHandlersCount_
+#define GLOBAL_OpaqueHandlers Yap_global->OpaqueHandlers_
 #if  __simplescalar__
 #define GLOBAL_pwd Yap_global->pwd_
 #endif

H/hglobals.h

@@ -102,6 +102,8 @@ typedef struct global_data {
 
   char  Executable_[YAP_FILENAME_MAX];
 #endif
+  int  OpaqueHandlersCount_;
+  struct opaque_handler_struct*  OpaqueHandlers_;
 #if  __simplescalar__
   char  pwd_[YAP_FILENAME_MAX];
 #endif

H/iglobals.h

@@ -102,6 +102,8 @@ static void InitGlobal(void) {
 
 
 #endif
+  GLOBAL_OpaqueHandlersCount = 0;
+  GLOBAL_OpaqueHandlers = NULL;
 #if  __simplescalar__
 
 #endif

H/rglobals.h

@@ -102,6 +102,8 @@ static void RestoreGlobal(void) {
 
 
 #endif
+
+
 #if  __simplescalar__
 
 #endif

H/yapio.h

@@ -67,6 +67,7 @@
 #define YP_FILE		FILE
 
 int     STD_PROTO(YP_putc,(int, int));
+void    STD_PROTO(Yap_dowrite, (Term, IOSTREAM *, int, int));
 
 #else
 
@@ -96,8 +97,6 @@ int     STD_PROTO(YP_putc,(int, int));
 #define fclose	ERR_fclose
 #define fflush	ERR_fflush
 
-
-
 /* flags for files in IOSTREAM struct */
 #define _YP_IO_WRITE	1
 #define _YP_IO_READ	2

MYDDAS/myddas_odbc.c

@@ -154,18 +154,6 @@ static int SQLBINDCOL(SQLHSTMT       sthandle,
   return TRUE;
 }
 
-static int SQLFREESTMT(SQLHSTMT       sthandle,
-		       SQLUSMALLINT   opt,
-		       char *         print)
-{                                                                 
-  SQLRETURN retcode;                                              
-  retcode = SQLFreeStmt(sthandle,opt);
-
-  if (retcode != SQL_SUCCESS && retcode != SQL_SUCCESS_WITH_INFO) 
-    return odbc_error(SQL_HANDLE_STMT, sthandle, "SQLFreeStmt", print);
-  return TRUE;
-}
-
 static int SQLNUMRESULTCOLS(SQLHSTMT        sthandle,
 			    SQLSMALLINT *   ncols,
 			    char *          print)
@@ -421,8 +409,9 @@ c_db_odbc_query( USES_REGS1 ) {
 	/* +1 because of '\0' */
 	bind_space = malloc(sizeof(char)*(ColumnSizePtr+1));
 	data_info = malloc(sizeof(SQLINTEGER));
-	if (!SQLBINDCOL(hstmt,i,SQL_C_CHAR,bind_space,(ColumnSizePtr+1),data_info,"db_query"))
+	if (!SQLBINDCOL(hstmt,i,SQL_C_CHAR,bind_space,(ColumnSizePtr+1),data_info,"db_query")) {
 	  return FALSE;
+	}
 	
 	properties[0] = MkIntegerTerm((Int)bind_space);
 	properties[2] = MkIntegerTerm((Int)data_info);
@@ -444,7 +433,7 @@ c_db_odbc_query( USES_REGS1 ) {
     {
       if (!SQLCLOSECURSOR(hstmt,"db_query"))
 	return FALSE;
-      if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_query"))
+      if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_query"))
 	return FALSE;
       return FALSE;
     }
@@ -466,7 +455,7 @@ c_db_odbc_number_of_fields( USES_REGS1 ) {
   char sql[256];
   SQLSMALLINT number_fields;
 
-  sprintf(sql,"DESCRIBE %s",relation);
+  sprintf(sql,"SELECT column_name from INFORMATION_SCHEMA.COLUMNS where table_name = \'%s\'",relation);
   
   if (!SQLALLOCHANDLE(SQL_HANDLE_STMT, hdbc, &hstmt, "db_number_of_fields"))
     return FALSE;
@@ -482,7 +471,7 @@ c_db_odbc_number_of_fields( USES_REGS1 ) {
   
   if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields"))
     return FALSE;
-  if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_number_of_fields"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields"))
     return FALSE;
   
   if (!Yap_unify(arg_fields, MkIntegerTerm(number_fields)))
@@ -506,7 +495,7 @@ c_db_odbc_get_attributes_types( USES_REGS1 ) {
   Term head, list;
   list = arg_types_list;
 
-  sprintf(sql,"DESCRIBE %s",relation);
+  sprintf(sql,"SELECT column_name,data_type FROM INFORMATION_SCHEMA.COLUMNS where table_name = \'%s\'",relation);
 
   if (!SQLALLOCHANDLE(SQL_HANDLE_STMT, hdbc, &hstmt, "db_get_attributes_types"))
     return FALSE;
@@ -547,7 +536,7 @@ c_db_odbc_get_attributes_types( USES_REGS1 ) {
   
   if (!SQLCLOSECURSOR(hstmt,"db_get_attributes_types"))
     return FALSE;
-  if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_get_attributes_types"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_get_attributes_types"))
     return FALSE;
   return TRUE;
 }
@@ -585,12 +574,31 @@ c_db_odbc_row_cut( USES_REGS1 ) {
   
   if (!SQLCLOSECURSOR(hstmt,"db_row_cut"))
     return FALSE; 
-  if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_row_cut"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_row_cut"))
     return FALSE; 
    
   return TRUE;
 }
 
+static int
+release_list_args(Term arg_list_args, Term arg_bind_list, const char *error_msg)
+{
+  Term list = arg_list_args;
+  Term list_bind = arg_bind_list;
+  
+  while (IsPairTerm(list_bind))
+    {
+      Term head_bind = HeadOfTerm(list_bind);
+
+      list = TailOfTerm(list);
+      list_bind = TailOfTerm(list_bind);
+      
+      free((char *)IntegerOfTerm(ArgOfTerm(1,head_bind)));
+      free((SQLINTEGER *)IntegerOfTerm(ArgOfTerm(3,head_bind)));
+    }
+  return TRUE;
+}
+
 /* db_row: ResultSet x BindList x ListOfArgs -> */
 static Int
 c_db_odbc_row( USES_REGS1 ) {
@@ -611,9 +619,12 @@ c_db_odbc_row( USES_REGS1 ) {
     {
       if (!SQLCLOSECURSOR(hstmt,"db_row"))
 	return FALSE; 
-      if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_row"))
+      if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_row"))
 	return FALSE; 
-  
+      if (!release_list_args(arg_list_args, arg_bind_list, "db_row")) {
+	return FALSE;
+      }
+ 
       cut_fail(); 
       return FALSE;
     }
@@ -699,7 +710,7 @@ c_db_odbc_number_of_fields_in_query( USES_REGS1 ) {
   if (!Yap_unify(arg_fields, MkIntegerTerm(number_cols))){
     if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields_in_query"))
       return FALSE;
-    if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_number_of_fields_in_query"))
+    if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields_in_query"))
       return FALSE;
  
     return FALSE;
@@ -707,7 +718,7 @@ c_db_odbc_number_of_fields_in_query( USES_REGS1 ) {
   
   if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields_in_query"))
     return FALSE;
-  if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_number_of_fields_in_query"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields_in_query"))
     return FALSE;
  
   return TRUE;
@@ -775,7 +786,7 @@ c_db_odbc_get_fields_properties( USES_REGS1 ) {
 
   if (!SQLCLOSECURSOR(hstmt2,"db_get_fields_properties"))
     return FALSE;
-  if (!SQLFREESTMT(hstmt2,SQL_CLOSE,"db_get_fields_properties"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt2, "db_get_fields_properties"))
     return FALSE;
   
   for (i=1;i<=num_fields;i++)
@@ -816,9 +827,8 @@ c_db_odbc_get_fields_properties( USES_REGS1 ) {
   
   if (!SQLCLOSECURSOR(hstmt,"db_get_fields_properties"))
     return FALSE;
-  if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_get_fields_properties"))
+  if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt2, "db_get_fields_properties"))
     return FALSE;
-    
   return TRUE;
 }
 

configure

@@ -9927,6 +9927,9 @@ mkdir -p  packages/clib/maildrop
 mkdir -p  packages/clib/maildrop/rfc822
 mkdir -p  packages/clib/maildrop/rfc2045
 mkdir -p  packages/CLPBN
+mkdir -p  packages/CLPBN/clpbn
+mkdir -p  packages/CLPBN/clpbn/bp
+mkdir -p  packages/CLPBN/clpbn/bp/xmlParser
 mkdir -p  packages/clpqr
 mkdir -p  packages/cplint
 mkdir -p  packages/cplint/approx
@@ -10619,8 +10622,8 @@ esac
 
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 # Files that config.status was made for.
-config_files="`echo $ac_config_files`"
+config_files="$ac_config_files"
-config_headers="`echo $ac_config_headers`"
+config_headers="$ac_config_headers"
 
 _ACEOF
 

configure.in

@@ -2103,6 +2103,9 @@ mkdir -p  packages/clib/maildrop
 mkdir -p  packages/clib/maildrop/rfc822
 mkdir -p  packages/clib/maildrop/rfc2045
 mkdir -p  packages/CLPBN
+mkdir -p  packages/CLPBN/clpbn
+mkdir -p  packages/CLPBN/clpbn/bp
+mkdir -p  packages/CLPBN/clpbn/bp/xmlParser
 mkdir -p  packages/clpqr
 mkdir -p  packages/cplint
 mkdir -p  packages/cplint/approx

docs/yap.tex

@@ -16811,13 +16811,29 @@ only two boolean flags are accepted: @code{YAPC_ENABLE_GC} and
 @code{YAPC_ENABLE_AGC}.  The first enables/disables the standard garbage
 collector, the second does the same for the atom garbage collector.`
 
+@item  @code{YAP_TERM} YAP_AllocExternalDataInStack(@code{size_t bytes})
+@item  @code{void *} YAP_ExternalDataInStackFromTerm(@code{YAP_Term t})
+@item  @code{YAP_Bool} YAP_IsExternalDataInStackTerm(@code{YAP_Term t})
+@findex YAP_AllocExternalDataInStack (C-Interface function)
+
+The next routines allow one to store external data in the Prolog
+execution stack. The first routine reserves space for @var{sz} bytes
+and returns an opaque handle. The second routines receives the handle
+and returns a pointer to the data.  The last routine checks if a term
+is an opaque handle.
+
+Data will be automatically reclaimed during
+backtracking. Also, this storage is opaque to the Prolog garbage compiler,
+so it should not be used to store Prolog terms. On the other hand, it
+may be useful to store arrays in a compact way, or pointers to external objects.
+
 @item  @code{int} YAP_HaltRegisterHook(@code{YAP_halt_hook f, void *closure})
 @findex YAP_HaltRegisterHook (C-Interface function)
 
 Register the function @var{f} to be called if YAP is halted. The
-function is called with two arguments: the exit code of the process (@code{0}
+function is called with two arguments: the exit code of the process
-if this cannot be determined on your operating system) and the closure
+(@code{0} if this cannot be determined on your operating system) and
-argument @var{closure}. 
+the closure argument @var{closure}.
 @c See also @code{at_halt/1}.
 
 @end table
@@ -16850,6 +16866,7 @@ implementing the predicate and @var{arity} is its arity.
 @findex YAP_UserBackCutCPredicate (C-Interface function)
 @findex YAP_PRESERVE_DATA (C-Interface function)
 @findex YAP_PRESERVED_DATA (C-Interface function)
+@findex YAP_PRESERVED_DATA_CUT (C-Interface function)
 @findex YAP_cutsucceed (C-Interface function)
 @findex YAP_cutfail (C-Interface function)
 For the second kind of predicates we need three C functions. The first one
@@ -16915,11 +16932,15 @@ static int start_n100(void)
 @end example
 
 The routine starts by getting the dereference value of the argument.
-The call to @code{YAP_PRESERVE_DATA} is used to initialize the memory which will
+The call to @code{YAP_PRESERVE_DATA} is used to initialize the memory
-hold the information to be preserved across backtracking. The first
+which will hold the information to be preserved across
-argument is the variable we shall use, and the second its type. Note
+backtracking. The first argument is the variable we shall use, and the
-that we can only use @code{YAP_PRESERVE_DATA} once, so often we will
+second its type. Note that we can only use @code{YAP_PRESERVE_DATA}
-want the variable to be a structure.
+once, so often we will want the variable to be a structure. This data
+is visible to the garbage collector, so it should consist of Prolog
+terms, as in the example. It is also correct to store pointers to
+objects external to YAP stacks, as the garbage collector will ignore
+such references.
 
 If the argument of the predicate is a variable, the routine initializes the 
 structure to be preserved across backtracking with the information
@@ -16988,6 +17009,34 @@ when pruning the execution of the predicate, @var{arity} is the
 predicate arity, and @var{sizeof} is the size of the data to be
 preserved in the stack. In this example, we would have something like
 
+@example
+void
+init_n100(void)
+@{
+  YAP_UserBackCutCPredicate("n100", start_n100, continue_n100, cut_n100, 1, 1);
+@}
+@end example
+The argument before last is the predicate's arity. Notice again the
+last argument to the call. function argument gives the extra space we
+want to use for @code{PRESERVED_DATA}. Space is given in cells, where
+a cell is the same size as a pointer. The garbage collector has access
+to this space, hence users should use it either to store terms or to
+store pointers to objects outside the stacks.
+
+The code for @code{cut_n100} could be:
+@example
+static int cut_n100(void)
+@{
+  YAP_PRESERVED_DATA_CUT(n100_data,n100_data_type*);
+
+  fprintf("n100 cut with counter %ld\n", YAP_IntOfTerm(n100_data->next_solution));
+  return TRUE;
+@}
+@end example
+Notice that we have to use @code{YAP_PRESERVED_DATA_CUT}: this is
+because the Prolog engine is at a different state during cut.
+
+If no work is required at cut, we can use:
 @example
 void
 init_n100(void)
@@ -16995,8 +17044,7 @@ init_n100(void)
   YAP_UserBackCutCPredicate("n100", start_n100, continue_n100, NULL, 1, 1);
 @}
 @end example
-Notice that we do not actually need to do anything on receiving a cut in
+in this case no code is executed at cut time.
-this case.
 
 @node Loading Objects, Save&Rest, Writing C, C-Interface
 @section Loading Object Files
@@ -17272,9 +17320,9 @@ Associate the term @var{value} with the atom @var{at}. The term
 @var{value} must be a constant. This functionality is used by YAP as a
 simple way for controlling and communicating with the Prolog run-time.
 
-@item  @code{YAP_Term} YAP_Read(@code{int (*)(void)} @var{GetC})
+@item  @code{YAP_Term} YAP_Read(@code{IOSTREAM *Stream})
 @findex  YAP_Read/1
-Parse a Term  using the function @var{GetC} to input characters.
+Parse a @var{Term} from the stream @var{Stream}.
 
 @item  @code{YAP_Term} YAP_Write(@code{YAP_Term} @var{t})
 @findex  YAP_CopyTerm/1
@@ -17282,13 +17330,13 @@ Copy a Term @var{t} and all associated constraints. May call the garbage
 collector and returns @code{0L} on error (such as no space being
 available).
 
-@item  @code{void} YAP_Write(@code{YAP_Term} @var{t}, @code{void (*)(int)}
+@item  @code{void} YAP_Write(@code{YAP_Term} @var{t}, @code{IOSTREAM}
-@var{PutC}, @code{int} @var{flags})
+@var{stream}, @code{int} @var{flags})
 @findex  YAP_Write/3
-Write a Term @var{t} using the function @var{PutC} to output
+Write a Term @var{t} using the stream @var{stream} to output
 characters. The term is written according to a mask of the following
 flags in the @code{flag} argument: @code{YAP_WRITE_QUOTED},
-@code{YAP_WRITE_HANDLE_VARS},  and @code{YAP_WRITE_IGNORE_OPS}.
+@code{YAP_WRITE_HANDLE_VARS}, @code{YAP_WRITE_USE_PORTRAY},  and @code{YAP_WRITE_IGNORE_OPS}.
 
 @item  @code{void} YAP_WriteBuffer(@code{YAP_Term} @var{t}, @code{char *}
 @var{buff}, @code{unsigned int}

include/YapInterface.h

@@ -237,7 +237,7 @@ extern X_API void PROTO(YAP_UserBackCPredicate,(CONST char *, YAP_Bool (*)(void)
 
 /*  void UserBackCPredicate(char *name, int *init(), int *cont(), int *cut(), int
     arity, int extra) */
-extern X_API void PROTO(YAP_UserBackCutCPredicate,(char *, YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Arity, unsigned int));
+extern X_API void PROTO(YAP_UserBackCutCPredicate,(CONST char *, YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Arity, unsigned int));
 
 /*  void CallProlog(YAP_Term t) */
 extern X_API YAP_Bool PROTO(YAP_CallProlog,(YAP_Term t));
@@ -245,9 +245,9 @@ extern X_API YAP_Bool PROTO(YAP_CallProlog,(YAP_Term t));
 /*  void cut_fail(void) */
 extern X_API void PROTO(YAP_cut_up,(void));
 
-#define YAP_cut_succeed() { YAP_cut_up(); return TRUE; }
+#define YAP_cut_succeed() do { YAP_cut_up(); return TRUE; } while(0)
 
-#define YAP_cut_fail() { YAP_cut_up(); return FALSE; }
+#define YAP_cut_fail() do { YAP_cut_up(); return FALSE; } while(0)
 
 /*  void *AllocSpaceFromYAP_(int) */
 extern X_API void *PROTO(YAP_AllocSpaceFromYap,(unsigned int));
@@ -555,6 +555,17 @@ extern X_API int PROTO(YAP_MaxOpPriority,(YAP_Atom, YAP_Term));
 /*    int  YAP_OpInfo(Atom, Term, int, int *, int *)  */
 extern X_API int  PROTO(YAP_OpInfo,(YAP_Atom, YAP_Term, int, int *, int *));
 
+/*    YAP_Bool  YAP_IsExternalDataInStackTerm(YAP_Term)  */
+extern X_API YAP_Bool PROTO(YAP_IsExternalDataInStackTerm,(YAP_Term));
+
+extern X_API YAP_opaque_tag_t PROTO(YAP_NewOpaqueType,(struct YAP_opaque_handler_struct *));
+
+extern X_API YAP_Bool PROTO(YAP_IsOpaqueObjectTerm,(YAP_Term, YAP_opaque_tag_t));
+
+extern X_API YAP_Term PROTO(YAP_NewOpaqueObject,(YAP_opaque_tag_t, size_t));
+
+extern X_API void *PROTO(YAP_OpaqueObjectFromTerm,(YAP_Term));
+
 #define YAP_InitCPred(N,A,F)  YAP_UserCPredicate(N,F,A)
 
 __END_DECLS

include/yap_structs.h

@@ -101,9 +101,10 @@ typedef double YAP_Float;
 #define YAP_FULL_BOOT_FROM_PROLOG  4
 #define YAP_BOOT_ERROR            -1
 
-#define YAP_WRITE_QUOTED		0
+#define YAP_WRITE_QUOTED		1
-#define YAP_WRITE_HANDLE_VARS		1
 #define YAP_WRITE_IGNORE_OPS		2
+#define YAP_WRITE_HANDLE_VARS		2
+#define YAP_WRITE_USE_PORTRAY		8
 
 #define YAP_CONSULT_MODE           0
 #define YAP_RECONSULT_MODE         1
@@ -204,6 +205,14 @@ typedef int  (*YAP_agc_hook)(void *_Atom);
 
 typedef void  (*YAP_halt_hook)(int exit_code, void *closure);
 
+typedef int YAP_opaque_tag_t;
+
+typedef int (*YAP_Opaque_CallOnFail)(void *);
+
+typedef struct YAP_opaque_handler_struct {
+  YAP_Opaque_CallOnFail fail_handler;
+} YAP_opaque_handler_t;
+
 /********* execution mode ***********************/
 
 typedef enum

library/MYDDAS/myddas_prolog2sql.ypp

@@ -241,6 +241,8 @@ tokenize_arguments([FirstArg|RestArgs],[TokFirstArg|TokRestArgs]):-
 %
 % --------------------------------------------------------------------------------------
 
+:- dynamic attribute/4.
+
 query_generation([],_,[]).
 
 query_generation([Conjunction|Conjunctions],ProjectionTerm,[Query|Queries]):-
@@ -1157,9 +1159,9 @@ column_atom(att(RangeVar,Attribute),QueryList,Diff):-
    column_atom(Attribute,X2,Diff).
 
 column_atom(rel(Relation,RangeVar),QueryList,Diff):-
-	column_atom('`',QueryList,X0),
+	column_atom('',QueryList,X0),
 	column_atom(Relation,X0,X1),
-	column_atom('` ',X1,X2),
+	column_atom(' ',X1,X2),
 	column_atom(RangeVar,X2,Diff).
 
 column_atom('$const$'(String),QueryList,Diff):-

library/lammpi/prologterms2c.c

@@ -142,12 +142,6 @@ p2c_putc(const int c) {
 /*
  * Function used by YAP to read a char from a string
  */                                                                                               
-static int
-p2c_getc(void) {
-  if( BUFFER_POS < BUFFER_LEN ) 
-    return BUFFER_PTR[BUFFER_POS++];
-  return -1;
-}
 /*
  * Writes a term to a stream.
  */
@@ -177,7 +171,7 @@ read_term_from_stream(const int fd) {
   if ( size> BUFFER_SIZE)
     expand_buffer(size-BUFFER_SIZE);
   read(fd,BUFFER_PTR,size);            // read term from stream
-  return YAP_Read( p2c_getc );
+  return YAP_ReadBuffer( BUFFER_PTR , NULL);
 }
 /*********************************************************************************************
  * Conversion: Prolog Term->char[] and char[]->Prolog Term
@@ -229,7 +223,7 @@ string2term(char *const ptr,const size_t *size) {
   }
   BUFFER_POS=0;
   LOCAL_ErrorMessage=NULL;
-  t = YAP_Read(p2c_getc);
+  t = YAP_ReadBuffer( BUFFER_PTR , NULL );
   if ( t==FALSE ) {
     write_msg(__FUNCTION__,__FILE__,__LINE__,"FAILED string2term>>>>size:%d %d %s\n",BUFFER_SIZE,strlen(BUFFER_PTR),LOCAL_ErrorMessage);
     exit(1);

library/mpi/mpi.c

@@ -30,7 +30,6 @@ static char *rcsid = "$Header: /Users/vitor/Yap/yap-cvsbackup/library/mpi/mpi.c,
 #include <string.h>
 #include <mpi.h>
 
-Term    STD_PROTO(YAP_Read, (int (*)(void)));
 void    STD_PROTO(YAP_Write, (Term, void (*)(int), int));
 
 STATIC_PROTO (Int p_mpi_open, (void));
@@ -105,15 +104,6 @@ mpi_putc(Int ch)
   }
 }
 
-static Int
-mpi_getc(void)
-{
-  if( bufptr < bufsize ) return buf[bufptr++];
-  else return -1;
-}
-
-
-
 
 /*
  * C Predicates
@@ -301,7 +291,7 @@ p_mpi_receive()          /* mpi_receive(-data, ?orig, ?tag) */
   /* parse received string into a Prolog term */
 
   bufptr = 0;
-  t = YAP_Read( mpi_getc );
+  t = YAP_ReadBuffer( buf, NULL );
 
   if( t == TermNil ) {
     retv = FALSE;
@@ -384,7 +374,7 @@ p_mpi_bcast3()           /* mpi_bcast( ?data, +root, +max_size ) */
     bufptr = 0;
 
     /* parse received string into a Prolog term */
-    return Yap_unify( YAP_Read(mpi_getc), ARG1 );
+    return Yap_unify( YAP_ReadBuffer( buf, NULL ), ARG1 );
   }    
 }
 
@@ -464,7 +454,7 @@ p_mpi_bcast2()           /* mpi_bcast( ?data, +root ) */
     bufstrlen = strlen(buf);
     bufptr = 0;
 
-    return Yap_unify(YAP_Read( mpi_getc ), ARG1);
+    return Yap_unify(YAP_ReadBuffer( buf, NULL ), ARG1);
   }
 }
 

misc/GLOBALS

@@ -120,6 +120,8 @@ char*				DIRNAME					=NULL
 char 				Executable[YAP_FILENAME_MAX]		void
 #endif
 
+int				OpaqueHandlersCount			=0
+struct opaque_handler_struct* 	OpaqueHandlers				=NULL
 
 #if  __simplescalar__
 char				pwd[YAP_FILENAME_MAX]			void

packages/CLPBN/clpbn/bp/BPNodeInfo.cpp

@@ -0,0 +1,149 @@
+#include <cassert>
+#include <cmath>
+
+#include <iostream>
+
+#include "BPNodeInfo.h"
+#include "BPSolver.h"
+
+BPNodeInfo::BPNodeInfo (BayesNode* node)
+{
+  node_ = node;
+  ds_   = node->getDomainSize();
+  piValsCalc_ = false;
+  ldValsCalc_ = false;
+  nPiMsgsRcv_ = 0;
+  nLdMsgsRcv_ = 0;
+  piVals_.resize (ds_, 1);
+  ldVals_.resize (ds_, 1);
+  const BnNodeSet& childs  = node->getChilds();
+  for (unsigned i = 0; i < childs.size(); i++) {
+    cmsgs_.insert (make_pair (childs[i], false));
+  }
+  const BnNodeSet& parents = node->getParents();
+  for (unsigned i = 0; i < parents.size(); i++) {
+    pmsgs_.insert (make_pair (parents[i], false));
+  }
+}
+
+
+
+ParamSet
+BPNodeInfo::getBeliefs (void) const
+{
+  double sum = 0.0;
+  ParamSet beliefs (ds_);
+  for (unsigned xi = 0; xi < ds_; xi++) {
+    double prod = piVals_[xi] * ldVals_[xi];
+    beliefs[xi] = prod;
+    sum += prod;
+  }
+  assert (sum);
+  //normalize the beliefs
+  for (unsigned xi = 0; xi < ds_; xi++) {
+    beliefs[xi] /= sum;
+  }
+  return beliefs;
+}
+
+
+
+bool
+BPNodeInfo::readyToSendPiMsgTo (const BayesNode* child) const
+{
+  for (unsigned i = 0; i < inChildLinks_.size(); i++) {
+    if (inChildLinks_[i]->getSource() != child
+        && !inChildLinks_[i]->messageWasSended())  {
+      return false;
+    }
+  }
+  return true;
+}
+
+
+
+bool
+BPNodeInfo::readyToSendLambdaMsgTo (const BayesNode* parent) const
+{
+  for (unsigned i = 0; i < inParentLinks_.size(); i++) {
+    if (inParentLinks_[i]->getSource() != parent
+        && !inParentLinks_[i]->messageWasSended())  {
+      return false;
+    }
+  }
+  return true;
+}
+
+
+
+double
+BPNodeInfo::getPiValue (unsigned idx) const
+{
+  assert (idx >=0 && idx < ds_);
+  return piVals_[idx];
+}
+
+
+
+void
+BPNodeInfo::setPiValue (unsigned idx, Param value)
+{
+  assert (idx >=0 && idx < ds_);
+  piVals_[idx] = value;
+}
+
+
+
+double 
+BPNodeInfo::getLambdaValue (unsigned idx) const
+{
+  assert (idx >=0 && idx < ds_);
+  return ldVals_[idx];
+}
+
+
+
+void 
+BPNodeInfo::setLambdaValue (unsigned idx, Param value)
+{
+  assert (idx >=0 && idx < ds_);
+  ldVals_[idx] = value;
+}
+
+
+
+double
+BPNodeInfo::getBeliefChange (void)
+{
+  double change = 0.0;
+  if (oldBeliefs_.size() == 0) {
+    oldBeliefs_ = getBeliefs();
+    change = 9999999999.0;
+  } else {
+    ParamSet currentBeliefs = getBeliefs();
+    for (unsigned xi = 0; xi < ds_; xi++) {
+      change += abs (currentBeliefs[xi] - oldBeliefs_[xi]);
+    }
+    oldBeliefs_ = currentBeliefs;
+  }
+  return change;
+}
+
+
+
+bool
+BPNodeInfo::receivedBottomInfluence (void) const
+{
+  // if all lambda values are equal, then neither
+  // this node neither its descendents have evidence,
+  // we can use this to don't send lambda messages his parents
+  bool childInfluenced = false;
+  for (unsigned xi = 1; xi < ds_; xi++) {
+    if (ldVals_[xi] != ldVals_[0]) {
+      childInfluenced = true;
+      break;
+    }
+  }
+  return childInfluenced;
+}
+

packages/CLPBN/clpbn/bp/BPNodeInfo.h

@@ -0,0 +1,82 @@
+#ifndef BP_BP_NODE_H
+#define BP_BP_NODE_H
+
+#include <vector>
+#include <map>
+
+#include "BPSolver.h"
+#include "BayesNode.h"
+#include "Shared.h"
+
+//class Edge;
+
+using namespace std;
+
+class BPNodeInfo
+{
+  public:
+    BPNodeInfo (int);
+    BPNodeInfo (BayesNode*);
+
+    ParamSet               getBeliefs (void) const;
+    double                 getPiValue (unsigned) const;
+    void                   setPiValue (unsigned, Param);
+    double                 getLambdaValue (unsigned) const;
+    void                   setLambdaValue (unsigned, Param);
+    double                 getBeliefChange (void);
+    bool                   receivedBottomInfluence (void) const;
+
+    ParamSet& getPiValues (void)              { return piVals_; }
+    ParamSet& getLambdaValues (void)          { return ldVals_; }
+    bool arePiValuesCalculated (void)         { return piValsCalc_; }
+    bool areLambdaValuesCalculated (void)     { return ldValsCalc_; }
+    void markPiValuesAsCalculated (void)      { piValsCalc_ = true; }
+    void markLambdaValuesAsCalculated (void)  { ldValsCalc_ = true; }
+    void incNumPiMsgsRcv (void)               { nPiMsgsRcv_ ++;     }
+    void incNumLambdaMsgsRcv (void)           { nLdMsgsRcv_ ++;     }
+
+    bool receivedAllPiMessages (void)
+    {
+      return node_->getParents().size() == nPiMsgsRcv_;
+    }
+
+    bool receivedAllLambdaMessages (void)
+    {
+      return node_->getChilds().size() == nLdMsgsRcv_;
+    }
+
+    bool readyToSendPiMsgTo (const BayesNode*) const ;
+    bool readyToSendLambdaMsgTo (const BayesNode*) const;
+
+    CEdgeSet getIncomingParentLinks (void)  { return inParentLinks_;  }
+    CEdgeSet getIncomingChildLinks (void)   { return inChildLinks_;   }
+    CEdgeSet getOutcomingParentLinks (void) { return outParentLinks_; }
+    CEdgeSet getOutcomingChildLinks (void)  { return outChildLinks_;  }
+   
+    void addIncomingParentLink  (Edge* l)   { inParentLinks_.push_back (l);  }
+    void addIncomingChildLink   (Edge* l)   { inChildLinks_.push_back (l);   }
+    void addOutcomingParentLink (Edge* l)   { outParentLinks_.push_back (l); }
+    void addOutcomingChildLink  (Edge* l)   { outChildLinks_.push_back (l);  }
+   
+  private:
+    DISALLOW_COPY_AND_ASSIGN (BPNodeInfo);
+
+    ParamSet               piVals_;     // pi values
+    ParamSet               ldVals_;     // lambda values
+    ParamSet               oldBeliefs_;
+    unsigned               nPiMsgsRcv_;
+    unsigned               nLdMsgsRcv_;
+    bool                   piValsCalc_;
+    bool                   ldValsCalc_;
+    EdgeSet                inParentLinks_;
+    EdgeSet                inChildLinks_;
+    EdgeSet                outParentLinks_;
+    EdgeSet                outChildLinks_;
+    unsigned               ds_;
+    const BayesNode*       node_;
+    map<const BayesNode*, bool> pmsgs_;
+    map<const BayesNode*, bool> cmsgs_;
+};
+
+#endif //BP_BP_NODE_H
+

packages/CLPBN/clpbn/bp/BPSolver.h

@@ -1,259 +1,106 @@
-#ifndef BP_BPSOLVER_H
+#ifndef BP_BP_SOLVER_H
-#define BP_BPSOLVER_H
+#define BP_BP_SOLVER_H
 
 #include <vector>
-#include <string>
 #include <set>
 
 #include "Solver.h"
 #include "BayesNet.h"
-#include "BpNode.h"
+#include "BPNodeInfo.h"
 #include "Shared.h"
 
 using namespace std;
 
-class BPSolver;
+class BPNodeInfo;
 
 static const string PI = "pi" ;
 static const string LD = "ld" ;
 
+
 enum MessageType {PI_MSG, LAMBDA_MSG};
+enum JointCalcType {CHAIN_RULE, JUNCTION_NODE};
 
-class BPSolver;
+class Edge
-struct Edge
 {
-  Edge (BayesNode* s, BayesNode* d, MessageType t)
+  public:
-  { 
+    Edge (BayesNode* s, BayesNode* d, MessageType t)
-    source       = s;
+    { 
-    destination  = d;
+      source_ = s;
-    type         = t;
+      destin_ = d;
-  }
+      type_   = t;
-  string getId (void) const 
+      if (type_ == PI_MSG) {
-  {
+        currMsg_.resize (s->getDomainSize(), 1);
-    stringstream ss;
+        nextMsg_.resize (s->getDomainSize(), 1);
-    type == PI_MSG ? ss << PI : ss << LD;
+      } else {
-    ss << source->getVarId() << "." << destination->getVarId();
+        currMsg_.resize (d->getDomainSize(), 1);
-    return ss.str();
+        nextMsg_.resize (d->getDomainSize(), 1);
-  }
-  string toString (void) const
-  {
-    stringstream ss;
-    type == PI_MSG ? ss << PI << "(" : ss << LD << "(" ;
-    ss << source->getLabel() << " --> " ;
-    ss << destination->getLabel();
-    ss << ")" ;
-    return ss.str();
-  }
-  BayesNode*        source;
-  BayesNode*        destination;
-  MessageType       type;
-  static BPSolver*  klass;
-};
-
-
-
-/*
-class BPMessage
-{
-  BPMessage (BayesNode* parent, BayesNode* child) 
-  {
-    parent_ = parent;
-    child_  = child;
-    currPiMsg_.resize (child->getDomainSize(),  1);
-    currLdMsg_.resize (parent->getDomainSize(), 1);
-    nextLdMsg_.resize (parent->getDomainSize(), 1);
-    nextPiMsg_.resize (child->getDomainSize(),  1);
-    piResidual_ = 1.0;
-    ldResidual_ = 1.0;
-  }
-
-  Param getPiMessageValue (int idx) const
-  {
-    assert (idx >=0 && idx < child->getDomainSize());
-    return currPiMsg_[idx];
-  }
-
-  Param getLambdaMessageValue (int idx) const
-  {
-    assert (idx >=0 && idx < parent->getDomainSize());
-    return currLdMsg_[idx];
-  }
-
-  const ParamSet& getPiMessage (void) const
-  {
-    return currPiMsg_;
-  }
-
-  const ParamSet& getLambdaMessage (void) const
-  {
-    return currLdMsg_;
-  }
-
-  ParamSet& piNextMessageReference (void)
-  {
-    return nextPiMsg_;
-  }
-
-  ParamSet& lambdaNextMessageReference (const BayesNode* source)
-  {
-    return nextLdMsg_;
-  }
-
-  void updatePiMessage (void)
-  {
-    currPiMsg_ = nextPiMsg_;
-    Util::normalize (currPiMsg_);
-  }
-
-  void updateLambdaMessage (void)
-  {
-    currLdMsg_ = nextLdMsg_;
-    Util::normalize (currLdMsg_);
-  }
-
-  double getPiResidual (void)
-  {
-    return piResidual_;
-  }
-
-  double getLambdaResidual (void)
-  {
-    return ldResidual_;
-  }
-
-  void updatePiResidual (void)
-  {
-    piResidual_ = Util::getL1dist (currPiMsg_, nextPiMsg_);
-  }
-
-  void updateLambdaResidual (void)
-  {
-    ldResidual_ = Util::getL1dist (currLdMsg_, nextLdMsg_);
-  }
-
-  void clearPiResidual (void)
-  {
-    piResidual_ = 0.0;
-  }
-
-  void clearLambdaResidual (void)
-  {
-    ldResidual_ = 0.0;
-  }
-
-  BayesNode*        parent_;
-  BayesNode*        child_;
-  ParamSet          currPiMsg_; // current pi messages
-  ParamSet          currLdMsg_; // current lambda messages
-  ParamSet          nextPiMsg_;
-  ParamSet          nextLdMsg_;
-  Param             piResidual_;
-  Param             ldResidual_;
-};
-
-
-
-class NodeInfo
-{
-  NodeInfo (BayesNode* node)
-  {
-    node_ = node;
-    piVals_.resize (node->getDomainSize(), 1);
-    ldVals_.resize (node->getDomainSize(), 1);
-  }
-
-  ParamSet getBeliefs (void) const
-  {
-    double sum = 0.0;
-    ParamSet beliefs (node_->getDomainSize());
-    for (int xi = 0; xi < node_->getDomainSize(); xi++) {
-      double prod = piVals_[xi] * ldVals_[xi];
-      beliefs[xi] = prod;
-      sum += prod;
-    }
-    assert (sum);
-    //normalize the beliefs
-    for (int xi = 0; xi < node_->getDomainSize(); xi++) {
-      beliefs[xi] /= sum;
-    }
-    return beliefs;
-  }
-
-  double getPiValue (int idx) const
-  {
-    assert (idx >=0 && idx < node_->getDomainSize());
-    return piVals_[idx];
-  }
-
-  void setPiValue (int idx, double value)
-  {
-    assert (idx >=0 && idx < node_->getDomainSize());
-    piVals_[idx] = value;
-  }
-
-  double getLambdaValue (int idx) const
-  {
-    assert (idx >=0 && idx < node_->getDomainSize());
-    return ldVals_[idx];
-  }
-
-  void setLambdaValue (int idx, double value)
-  {
-    assert (idx >=0 && idx < node_->getDomainSize());
-    ldVals_[idx] = value;
-  }
-
-  ParamSet& getPiValues (void)
-  {
-    return piVals_;
-  }
-
-  ParamSet& getLambdaValues (void)
-  {
-    return ldVals_;
-  }
-
-  double getBeliefChange (void)
-  {
-    double change = 0.0;
-    if (oldBeliefs_.size() == 0) {
-      oldBeliefs_ = getBeliefs();
-      change = MAX_CHANGE_;
-    } else {
-      ParamSet currentBeliefs = getBeliefs();
-      for (int xi = 0; xi < node_->getDomainSize(); xi++) {
-        change += abs (currentBeliefs[xi] - oldBeliefs_[xi]);
       }
-      oldBeliefs_ = currentBeliefs;
+      msgSended_ = false;
+      residual_ = 0.0;
     }
-    return change;
+  
-  }
+    //void setMessage (ParamSet msg)
+    //{
+    //  Util::normalize (msg);
+    //  residual_ = Util::getMaxNorm (currMsg_, msg);
+    //  currMsg_ = msg;
+    //}
 
-  bool hasReceivedChildInfluence (void) const
+    void setNextMessage (CParamSet msg)
-  {
+    {
-    // if all lambda values are equal, then neither
+      nextMsg_ = msg;
-    // this node neither its descendents have evidence,
+      Util::normalize (nextMsg_);
-    // we can use this to don't send lambda messages his parents
+      residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
-    bool childInfluenced = false;
+    }
-    for (int xi = 1; xi < node_->getDomainSize(); xi++) {
+
-      if (ldVals_[xi] != ldVals_[0]) {
+    void updateMessage (void)
-        childInfluenced = true;
+    {
-        break;
+      currMsg_ = nextMsg_;
+      if (DL >= 3) {
+        cout << "updating " << toString() << endl;
       }
+      msgSended_ = true;
+    }
+   
+    void updateResidual (void)
+    {
+      residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
     }
-    return childInfluenced;
-  }
 
-  BayesNode*             node_;
+    string toString (void) const
-  ParamSet               piVals_;     // pi values
+    {
-  ParamSet               ldVals_;     // lambda values
+      stringstream ss;
-  ParamSet               oldBeliefs_;
+      if (type_ == PI_MSG) {
+        ss << PI;
+      } else if (type_ == LAMBDA_MSG) {
+        ss << LD;
+      } else {
+        abort();
+      }
+      ss << "(" << source_->getLabel();
+      ss << " --> " << destin_->getLabel() << ")" ;
+      return ss.str();
+    }
+
+    BayesNode*   getSource (void) const        { return source_; }
+    BayesNode*   getDestination (void) const   { return destin_; }
+    MessageType  getMessageType (void) const   { return type_; }
+    CParamSet    getMessage (void) const       { return currMsg_; }
+    bool         messageWasSended (void) const { return msgSended_; }
+    double       getResidual (void) const      { return residual_; }
+    void         clearResidual (void)          { residual_ = 0.0; }
+ 
+  private:
+    BayesNode*   source_;
+    BayesNode*   destin_;
+    MessageType  type_;
+    ParamSet     currMsg_;
+    ParamSet     nextMsg_;
+    bool         msgSended_;
+    double       residual_;
 };
-*/
 
 
-bool compareResidual (const Edge&, const Edge&);
-
 class BPSolver : public Solver
 {
   public:
@@ -261,190 +108,85 @@ class BPSolver : public Solver
    ~BPSolver (void);
 
     void                runSolver (void);
-    ParamSet            getPosterioriOf (const Variable* var) const;
+    ParamSet            getPosterioriOf (Vid) const;
-    ParamSet            getJointDistribution (const NodeSet&) const;
+    ParamSet            getJointDistributionOf (const VidSet&);
+  
 
   private:
     DISALLOW_COPY_AND_ASSIGN (BPSolver);
 
     void                initializeSolver (void);
-    void                incorporateEvidence (BayesNode*);
     void                runPolyTreeSolver (void);
-    void                polyTreePiMessage (BayesNode*, BayesNode*);
+    void                runLoopySolver (void);
-    void                polyTreeLambdaMessage (BayesNode*, BayesNode*);
-    void                runGenericSolver (void);
     void                maxResidualSchedule (void);
     bool                converged (void) const;
     void                updatePiValues (BayesNode*);
     void                updateLambdaValues (BayesNode*);
-    void                calculateNextPiMessage (BayesNode*, BayesNode*);
+    ParamSet            calculateNextLambdaMessage (Edge* edge);
-    void                calculateNextLambdaMessage (BayesNode*, BayesNode*);
+    ParamSet            calculateNextPiMessage (Edge* edge);
+    ParamSet            getJointByJunctionNode (const VidSet&) const;
+    ParamSet            getJointByChainRule (const VidSet&) const;
     void                printMessageStatusOf (const BayesNode*) const;
     void                printAllMessageStatus (void) const;
-    // inlines
+
-    void                updatePiMessage (BayesNode*, BayesNode*);
+    ParamSet getMessage (Edge* edge)
-    void                updateLambdaMessage (BayesNode*, BayesNode*);
+    {
-    void                calculateNextMessage (const Edge&);
+      if (DL >= 3) {
-    void                updateMessage (const Edge&);
+        cout << "    calculating " << edge->toString() << endl;
-    void                updateValues (const Edge&);
+      }
-    double              getResidual (const Edge&) const;
+      if (edge->getMessageType() == PI_MSG) {
-    void                updateResidual (const Edge&);
+        return calculateNextPiMessage (edge);
-    void                clearResidual (const Edge&);
+      } else if (edge->getMessageType() == LAMBDA_MSG) {
-    BpNode*             M (const BayesNode*) const;
+        return calculateNextLambdaMessage (edge);
-    friend bool         compareResidual (const Edge&, const Edge&);
+      } else {
+        abort();
+      }
+      return ParamSet();
+    }
+
+    void updateValues (Edge* edge)
+    {
+      if (!edge->getDestination()->hasEvidence()) {
+        if (edge->getMessageType() == PI_MSG) {
+          updatePiValues (edge->getDestination());
+        } else if (edge->getMessageType() == LAMBDA_MSG) {
+          updateLambdaValues (edge->getDestination());
+        } else {
+          abort();
+        }
+      }
+    }
+
+    BPNodeInfo* M (const BayesNode* node) const
+    {
+      assert (node);
+      assert (node == bn_->getBayesNode (node->getVarId()));
+      assert (node->getIndex() < nodesI_.size());
+      return nodesI_[node->getIndex()];
+    }
 
     const BayesNet*     bn_;
-    vector<BpNode*>     msgs_;
+    vector<BPNodeInfo*> nodesI_;
-    Schedule            schedule_;
+    unsigned            nIter_;
-    int                 nIter_;
+    vector<Edge*>       links_;
-    int                 maxIter_;
+    bool                useAlwaysLoopySolver_;
-    double              accuracy_;
+    JointCalcType       jointCalcType_;
-    vector<Edge>        updateOrder_;
-    bool                forceGenericSolver_;
 
     struct compare
     {
-      inline bool operator() (const Edge& e1, const Edge& e2)
+      inline bool operator() (const Edge* e1, const Edge* e2)
       {
-        return compareResidual (e1, e2);
+        return e1->getResidual() > e2->getResidual();
       }
     };
 
-    typedef multiset<Edge, compare> SortedOrder;
+    typedef multiset<Edge*, compare> SortedOrder;
     SortedOrder sortedOrder_;
 
-    typedef unordered_map<string, SortedOrder::iterator> EdgeMap;
+    typedef map<Edge*, SortedOrder::iterator> EdgeMap;
     EdgeMap edgeMap_;
 
 };
 
-
+#endif //BP_BP_SOLVER_H
-
-inline void
-BPSolver::updatePiMessage (BayesNode* source, BayesNode* destination)
-{
-  M(source)->updatePiMessage(destination);
-}
-
-
-
-inline void
-BPSolver::updateLambdaMessage (BayesNode* source, BayesNode* destination)
-{
-  M(destination)->updateLambdaMessage(source);
-}
-
-
-
-inline void
-BPSolver::calculateNextMessage (const Edge& e)
-{
-  if (DL >= 1) {
-    cout << "calculating " << e.toString() << endl;
-  }
-  if (e.type == PI_MSG) {
-    calculateNextPiMessage (e.source, e.destination);
-  } else {
-    calculateNextLambdaMessage (e.source, e.destination);
-  }
-}
-
-
-
-inline void
-BPSolver::updateMessage (const Edge& e)
-{
-  if (DL >= 1) {
-      cout << "updating " << e.toString() << endl;
-    }
-  if (e.type == PI_MSG) {
-    M(e.source)->updatePiMessage(e.destination);
-  } else {
-    M(e.destination)->updateLambdaMessage(e.source);
-  }
-}
-
-
-
-inline void
-BPSolver::updateValues (const Edge& e)
-{
-  if (!e.destination->hasEvidence()) {
-    if (e.type == PI_MSG) {
-      updatePiValues (e.destination);
-    } else {
-      updateLambdaValues (e.destination);
-    }
-  }
-}
-
-
-
-inline double
-BPSolver::getResidual (const Edge& e) const
-{
-  if (e.type == PI_MSG) {
-    return M(e.source)->getPiResidual(e.destination);
-  } else {
-    return M(e.destination)->getLambdaResidual(e.source);
-  }
-}
-
-
-
-inline void
-BPSolver::updateResidual (const Edge& e)
-{
-  if (e.type == PI_MSG) {
-    M(e.source)->updatePiResidual(e.destination);
-  } else {
-    M(e.destination)->updateLambdaResidual(e.source);
-  }
-}
-
-
-
-inline void
-BPSolver::clearResidual (const Edge& e)
-{
-  if (e.type == PI_MSG) {
-    M(e.source)->clearPiResidual(e.destination);
-  } else {
-    M(e.destination)->clearLambdaResidual(e.source);
-  }
-}
-
-
-
-inline bool
-compareResidual (const Edge& e1, const Edge& e2)
-{
-  double residual1;
-  double residual2;
-  if (e1.type == PI_MSG) {
-    residual1 = Edge::klass->M(e1.source)->getPiResidual(e1.destination);
-  } else {
-    residual1 = Edge::klass->M(e1.destination)->getLambdaResidual(e1.source);
-  }
-  if (e2.type == PI_MSG) {
-    residual2 = Edge::klass->M(e2.source)->getPiResidual(e2.destination);
-  } else {
-    residual2 = Edge::klass->M(e2.destination)->getLambdaResidual(e2.source);
-  }
-  return residual1 > residual2;
-}
-
-
-
-inline BpNode*
-BPSolver::M (const BayesNode* node) const
-{
-  assert (node);
-  assert (node == bn_->getNode (node->getVarId()));
-  assert (node->getIndex() < msgs_.size());
-  return msgs_[node->getIndex()];
-}
-
-
-#endif
 

packages/CLPBN/clpbn/bp/BayesNet.cpp

@@ -1,30 +1,24 @@
+#include <cstdlib>
+#include <cassert>
+
 #include <iostream>
 #include <fstream>
 #include <sstream>
 #include <iomanip>
-#include <cassert>
-#include <cstdlib>
-#include <map>
 
 #include "xmlParser/xmlParser.h"
 
 #include "BayesNet.h"
 
 
-BayesNet::BayesNet (void)
-{
-}
-
-
-
 BayesNet::BayesNet (const char* fileName)
 {
   map<string, Domain> domains;
   XMLNode xMainNode = XMLNode::openFileHelper (fileName, "BIF");
   // only the first network is parsed, others are ignored
   XMLNode xNode = xMainNode.getChildNode ("NETWORK");
-  int nVars = xNode.nChildNode ("VARIABLE");
+  unsigned nVars = xNode.nChildNode ("VARIABLE");
-  for (int i = 0; i < nVars; i++) {
+  for (unsigned i = 0; i < nVars; i++) {
     XMLNode var = xNode.getChildNode ("VARIABLE", i);
     string type = var.getAttribute ("TYPE");
     if (type != "nature") {
@@ -32,9 +26,9 @@ BayesNet::BayesNet (const char* fileName)
       abort();
     }
     Domain domain;
-    string label = var.getChildNode("NAME").getText();
+    string varLabel = var.getChildNode("NAME").getText();
-    int domainSize = var.nChildNode ("OUTCOME");
+    unsigned dsize = var.nChildNode ("OUTCOME");
-    for (int j = 0; j < domainSize; j++) {
+    for (unsigned j = 0; j < dsize; j++) {
       if (var.getChildNode("OUTCOME", j).getText() == 0) {
         stringstream ss;
         ss << j + 1;
@@ -43,37 +37,37 @@ BayesNet::BayesNet (const char* fileName)
         domain.push_back (var.getChildNode("OUTCOME", j).getText());
       }
     }
-    domains.insert (make_pair (label, domain));
+    domains.insert (make_pair (varLabel, domain));
   }
 
-  int nDefs = xNode.nChildNode ("DEFINITION");
+  unsigned nDefs = xNode.nChildNode ("DEFINITION");
   if (nVars != nDefs) {
-    cerr << "error: different number of variables and definitions";
+    cerr << "error: different number of variables and definitions" << endl;
-    cerr << endl;
+    abort();
   }
 
-  queue<int> indexes;
+  queue<unsigned> indexes;
-  for (int i = 0; i < nDefs; i++) {
+  for (unsigned i = 0; i < nDefs; i++) {
     indexes.push (i);
   }
 
   while (!indexes.empty()) {
-    int index = indexes.front();
+    unsigned index = indexes.front();
     indexes.pop();
     XMLNode def = xNode.getChildNode ("DEFINITION", index);
-    string label = def.getChildNode("FOR").getText();
+    string varLabel = def.getChildNode("FOR").getText();
     map<string, Domain>::const_iterator iter;
-    iter = domains.find (label);
+    iter = domains.find (varLabel);
     if (iter == domains.end()) {
-      cerr << "error: unknow variable `" << label << "'" << endl;
+      cerr << "error: unknow variable `" << varLabel << "'" << endl;
       abort();
     }
     bool processItLatter = false;
-    NodeSet parents;
+    BnNodeSet parents;
-    int nParams = iter->second.size();
+    unsigned nParams = iter->second.size();
     for (int j = 0; j < def.nChildNode ("GIVEN"); j++) {
       string parentLabel = def.getChildNode("GIVEN", j).getText();
-      BayesNode* parentNode = getNode (parentLabel);
+      BayesNode* parentNode = getBayesNode (parentLabel);
       if (parentNode) {
         nParams *= parentNode->getDomainSize();
         parents.push_back (parentNode);
@@ -95,7 +89,7 @@ BayesNet::BayesNet (const char* fileName)
     }
 
     if (!processItLatter) {
-      int count = 0;
+      unsigned count = 0;
       ParamSet params (nParams);
       stringstream s (def.getChildNode("TABLE").getText());
       while (!s.eof() && count < nParams) {
@@ -104,11 +98,11 @@ BayesNet::BayesNet (const char* fileName)
       }
        if (count != nParams) {
         cerr << "error: invalid number of parameters " ;
-        cerr << "for variable `" << label << "'" << endl;
+        cerr << "for variable `" << varLabel << "'" << endl;
         abort();
       } 
       params = reorderParameters (params, iter->second.size());
-      addNode (label, iter->second, parents, params);
+      addNode (varLabel, iter->second, parents, params);
     }
   }
   setIndexes();
@@ -118,7 +112,6 @@ BayesNet::BayesNet (const char* fileName)
 
 BayesNet::~BayesNet (void)
 {
-  Statistics::writeStats();
   for (unsigned i = 0; i < nodes_.size(); i++) {
     delete nodes_[i];
   }
@@ -127,25 +120,25 @@ BayesNet::~BayesNet (void)
 
 
 BayesNode*
-BayesNet::addNode (unsigned varId)
+BayesNet::addNode (Vid vid)
 {
-  indexMap_.insert (make_pair (varId, nodes_.size()));
+  indexMap_.insert (make_pair (vid, nodes_.size()));
-  nodes_.push_back (new BayesNode (varId));
+  nodes_.push_back (new BayesNode (vid));
   return nodes_.back();
 }
 
 
 
 BayesNode*
-BayesNet::addNode (unsigned varId,
+BayesNet::addNode (Vid vid,
                    unsigned dsize,
                    int evidence,
-                   NodeSet& parents,
+                   BnNodeSet& parents,
                    Distribution* dist)
 {
-  indexMap_.insert (make_pair (varId, nodes_.size()));
+  indexMap_.insert (make_pair (vid, nodes_.size()));
   nodes_.push_back (new BayesNode (
-      varId, dsize, evidence, parents, dist));
+      vid, dsize, evidence, parents, dist));
   return nodes_.back();
 }
 
@@ -154,7 +147,7 @@ BayesNet::addNode (unsigned varId,
 BayesNode*
 BayesNet::addNode (string label,
                    Domain domain,
-                   NodeSet& parents, 
+                   BnNodeSet& parents, 
                    ParamSet& params)
 {
   indexMap_.insert (make_pair (nodes_.size(), nodes_.size()));
@@ -169,9 +162,9 @@ BayesNet::addNode (string label,
 
 
 BayesNode*
-BayesNet::getNode (unsigned varId) const
+BayesNet::getBayesNode (Vid vid) const
 {
-  IndexMap::const_iterator it = indexMap_.find(varId);
+  IndexMap::const_iterator it = indexMap_.find (vid);
   if (it == indexMap_.end()) {
     return 0;
   } else {
@@ -182,7 +175,7 @@ BayesNet::getNode (unsigned varId) const
 
 
 BayesNode*
-BayesNet::getNode (string label) const
+BayesNet::getBayesNode (string label) const
 {
   BayesNode* node = 0;
   for (unsigned i = 0; i < nodes_.size(); i++) {
@@ -196,6 +189,15 @@ BayesNet::getNode (string label) const
 
 
 
+
+Variable*
+BayesNet::getVariable (Vid vid) const
+{
+  return getBayesNode (vid);
+}
+
+
+
 void
 BayesNet::addDistribution (Distribution* dist)
 {
@@ -219,15 +221,15 @@ BayesNet::getDistribution (unsigned distId) const
 
 
 
-const NodeSet&
+const BnNodeSet&
-BayesNet::getNodes (void) const
+BayesNet::getBayesNodes (void) const
 {
   return nodes_;
 }
 
 
 
-int
+unsigned
 BayesNet::getNumberOfNodes (void) const
 {
   return nodes_.size();
@@ -235,10 +237,10 @@ BayesNet::getNumberOfNodes (void) const
 
 
 
-NodeSet
+BnNodeSet
 BayesNet::getRootNodes (void) const
 {
-  NodeSet roots;
+  BnNodeSet roots;
   for (unsigned i = 0; i < nodes_.size(); i++) {
     if (nodes_[i]->isRoot()) {
       roots.push_back (nodes_[i]);
@@ -249,10 +251,10 @@ BayesNet::getRootNodes (void) const
 
 
 
-NodeSet
+BnNodeSet
 BayesNet::getLeafNodes (void) const
 {
-  NodeSet leafs;
+  BnNodeSet leafs;
   for (unsigned i = 0; i < nodes_.size(); i++) {
     if (nodes_[i]->isLeaf()) {
       leafs.push_back (nodes_[i]);
@@ -276,30 +278,32 @@ BayesNet::getVariables (void) const
 
 
 BayesNet*
-BayesNet::pruneNetwork (BayesNode* queryNode) const
+BayesNet::getMinimalRequesiteNetwork (Vid vid) const
 {
-  NodeSet queryNodes;
+  return getMinimalRequesiteNetwork (VidSet() = {vid});
-  queryNodes.push_back (queryNode);
-  return pruneNetwork (queryNodes);
 }
 
 
 
 BayesNet*
-BayesNet::pruneNetwork (const NodeSet& interestedVars) const
+BayesNet::getMinimalRequesiteNetwork (const VidSet& queryVids) const
 {
-  /*
+  BnNodeSet queryVars;
-  cout << "interested vars: " ;
+  for (unsigned i = 0; i < queryVids.size(); i++) {
-  for (unsigned i = 0; i < interestedVars.size(); i++) {
+    assert (getBayesNode (queryVids[i]));
-    cout << interestedVars[i]->getLabel() << " " ;
+    queryVars.push_back (getBayesNode (queryVids[i]));
   }
-  cout << endl;
+  // cout << "query vars: " ;
-  */
+  // for (unsigned i = 0; i < queryVars.size(); i++) {
+  //   cout << queryVars[i]->getLabel() << " " ;
+  // }
+  // cout << endl;
+
   vector<StateInfo*> states (nodes_.size(), 0);
 
   Scheduling scheduling;
-  for (NodeSet::const_iterator it = interestedVars.begin();
+  for (BnNodeSet::const_iterator it = queryVars.begin();
-      it != interestedVars.end(); it++) {
+      it != queryVars.end(); it++) {
     scheduling.push (ScheduleInfo (*it, false, true));
   }
 
@@ -378,18 +382,18 @@ BayesNet::constructGraph (BayesNet* bn,
                    states[i]->markedOnTop;
     }
     if (isRequired) {
-      NodeSet parents;
+      BnNodeSet parents;
       if (states[i]->markedOnTop) {
-        const NodeSet& ps = nodes_[i]->getParents();
+        const BnNodeSet& ps = nodes_[i]->getParents();
         for (unsigned j = 0; j < ps.size(); j++) {
-          BayesNode* parent = bn->getNode (ps[j]->getVarId());
+          BayesNode* parent = bn->getBayesNode (ps[j]->getVarId());
           if (!parent) {
             parent = bn->addNode (ps[j]->getVarId());
           }
           parents.push_back (parent);
         }
       }
-      BayesNode* node = bn->getNode (nodes_[i]->getVarId());
+      BayesNode* node = bn->getBayesNode (nodes_[i]->getVarId());
       if (node) {
         node->setData      (nodes_[i]->getDomainSize(),
                             nodes_[i]->getEvidence(), parents,
@@ -411,65 +415,6 @@ BayesNet::constructGraph (BayesNet* bn,
   bn->setIndexes();
 }
 
-/*
-void
-BayesNet::constructGraph (BayesNet* bn,
-                          const vector<StateInfo*>& states) const
-{
-  for (unsigned i = 0; i < nodes_.size(); i++) {
-    if (states[i]) {
-      if (nodes_[i]->hasEvidence() && states[i]->visited) {
-        NodeSet parents;
-        if (states[i]->markedOnTop) {
-          const NodeSet& ps = nodes_[i]->getParents();
-          for (unsigned j = 0; j < ps.size(); j++) {
-            BayesNode* parent = bn->getNode (ps[j]->getVarId());
-            if (parent == 0) {
-              parent = bn->addNode (ps[j]->getVarId());
-            }
-            parents.push_back (parent);
-          }
-        }
-
-        BayesNode* n = bn->getNode (nodes_[i]->getVarId());
-        if (n) {
-          n->setData  (nodes_[i]->getDomainSize(),
-                       nodes_[i]->getEvidence(), parents,
-                       nodes_[i]->getDistribution());
-        } else {
-          bn->addNode (nodes_[i]->getVarId(),
-                       nodes_[i]->getDomainSize(),
-                       nodes_[i]->getEvidence(), parents, 
-                       nodes_[i]->getDistribution());
-        }
-        
-      } else if (states[i]->markedOnTop) {
-        NodeSet parents;
-        const NodeSet& ps = nodes_[i]->getParents();
-        for (unsigned j = 0; j < ps.size(); j++) {
-          BayesNode* parent = bn->getNode (ps[j]->getVarId());
-          if (parent == 0) {
-            parent = bn->addNode (ps[j]->getVarId());
-          }
-          parents.push_back (parent);
-        }
-
-        BayesNode* n = bn->getNode (nodes_[i]->getVarId());
-        if (n) {
-          n->setData  (nodes_[i]->getDomainSize(),
-                       nodes_[i]->getEvidence(), parents,
-                       nodes_[i]->getDistribution());
-        } else {
-          bn->addNode (nodes_[i]->getVarId(),
-                       nodes_[i]->getDomainSize(),
-                       nodes_[i]->getEvidence(), parents,
-                       nodes_[i]->getDistribution());
-        }
-      }
-    }
-  }
-}*/
-
 
 
 bool
@@ -480,70 +425,6 @@ BayesNet::isSingleConnected (void) const
 
 
 
-vector<DomainConf>
-BayesNet::getDomainConfigurationsOf (const NodeSet& nodes)
-{
-  int nConfs = 1;
-  for (unsigned i = 0; i < nodes.size(); i++) {
-    nConfs *= nodes[i]->getDomainSize();
-  }
-
-  vector<DomainConf> confs (nConfs);
-  for (int i = 0; i < nConfs; i++) {
-    confs[i].resize (nodes.size());
-  }
-
-  int nReps = 1;
-  for (int i = nodes.size() - 1; i >= 0; i--) {
-    int index = 0;
-    while (index < nConfs) {
-      for (int j = 0; j < nodes[i]->getDomainSize(); j++) {
-        for (int r = 0; r < nReps; r++) {
-          confs[index][i] = j; 
-          index++;
-        }
-      }
-    }
-    nReps *= nodes[i]->getDomainSize();
-  }
-
-  return confs;
-}
-
-
-
-vector<string>
-BayesNet::getInstantiations (const NodeSet& parents_)
-{
-  int nParents = parents_.size();
-  int rowSize = 1;
-  for (unsigned i = 0; i < parents_.size(); i++) {
-    rowSize *= parents_[i]->getDomainSize();
-  }
-  int nReps     = 1;
-  vector<string> headers (rowSize);
-  for (int i = nParents - 1; i >= 0; i--) {
-    Domain domain = parents_[i]->getDomain();
-    int index = 0;
-    while (index < rowSize) {
-      for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
-        for (int r = 0; r < nReps; r++) {
-          if (headers[index] != "") {
-            headers[index] = domain[j] + "," + headers[index];
-          } else {
-            headers[index] = domain[j];
-          }
-          index++;
-        }
-      }
-    }
-    nReps *= parents_[i]->getDomainSize();
-  }
-  return headers;
-}
-
-
-
 void
 BayesNet::setIndexes (void)
 {
@@ -565,7 +446,7 @@ BayesNet::freeDistributions (void)
 
 
 void
-BayesNet::printNetwork (void) const
+BayesNet::printGraphicalModel (void) const
 {
   for (unsigned i = 0; i < nodes_.size(); i++) {
     cout << *nodes_[i];
@@ -575,32 +456,11 @@ BayesNet::printNetwork (void) const
 
 
 void
-BayesNet::printNetworkToFile (const char* fileName) const
+BayesNet::exportToDotFormat (const char* fileName,
+                             bool showNeighborless,
+                             CVidSet& highlightVids) const
 {
-  string s = "../../" ;
+  ofstream out (fileName);
-  s += fileName;
-  ofstream out (s.c_str());
-  if (!out.is_open()) {
-    cerr << "error: cannot open file to write at " ;
-    cerr << "BayesNet::printToFile()" << endl;
-    abort();
-  }
-  for (unsigned i = 0; i < nodes_.size(); i++) {
-    out << *nodes_[i];
-  }
-  out.close();
-}
- 
-
-
-void
-BayesNet::exportToDotFile (const char* fileName,
-                           bool showNeighborless,
-                           const NodeSet& highlightNodes) const
-{
-  string s = "../../" ;
-  s+= fileName;
-  ofstream out (s.c_str());
   if (!out.is_open()) {
     cerr << "error: cannot open file to write at " ;
     cerr << "BayesNet::exportToDotFile()" << endl;
@@ -608,13 +468,6 @@ BayesNet::exportToDotFile (const char* fileName,
   }
 
   out << "digraph \"" << fileName << "\" {" << endl;
-  for (unsigned i = 0; i < nodes_.size(); i++) {
-    const NodeSet& childs = nodes_[i]->getChilds();
-    for (unsigned j = 0; j < childs.size(); j++) {
-      out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
-      out << '"' << childs[j]->getLabel() << '"' << endl;
-    }
-  }
 
   for (unsigned i = 0; i < nodes_.size(); i++) {
     if (showNeighborless || nodes_[i]->hasNeighbors()) {
@@ -627,9 +480,24 @@ BayesNet::exportToDotFile (const char* fileName,
     }
   }
 
-  for (unsigned i = 0; i < highlightNodes.size(); i++) {
+  for (unsigned i = 0; i < highlightVids.size(); i++) {
-    out << '"' << highlightNodes[i]->getLabel() << '"' ;
+    BayesNode* node = getBayesNode (highlightVids[i]);
-    out << " [shape=box]" << endl;
+    if (node) {
+      out << '"' << node->getLabel() << '"' ;
+     // out << " [shape=polygon, sides=6]" << endl;
+      out << " [shape=box3d]" << endl;
+    } else {
+      cout << "error: invalid variable id: " << highlightVids[i] << endl;
+      abort();
+    }
+  }
+
+  for (unsigned i = 0; i < nodes_.size(); i++) {
+    const BnNodeSet& childs = nodes_[i]->getChilds();
+    for (unsigned j = 0; j < childs.size(); j++) {
+      out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
+      out << '"' << childs[j]->getLabel() << '"' << endl;
+    }
   }
 
   out << "}" << endl;
@@ -639,11 +507,9 @@ BayesNet::exportToDotFile (const char* fileName,
 
 
 void
-BayesNet::exportToBifFile (const char* fileName) const
+BayesNet::exportToBifFormat (const char* fileName) const
 {
-  string s = "../../" ;
+  ofstream out (fileName);
-  s += fileName;
-  ofstream out (s.c_str());
   if(!out.is_open()) {
     cerr << "error: cannot open file to write at " ;
     cerr << "BayesNet::exportToBifFile()" << endl;
@@ -666,7 +532,7 @@ BayesNet::exportToBifFile (const char* fileName) const
   for (unsigned i = 0; i < nodes_.size(); i++) {
     out << "<DEFINITION>" << endl;
     out << "\t<FOR>" << nodes_[i]->getLabel() << "</FOR>" << endl;
-    const NodeSet& parents = nodes_[i]->getParents();
+    const BnNodeSet& parents = nodes_[i]->getParents();
     for (unsigned j = 0; j < parents.size(); j++) {
       out << "\t<GIVEN>" << parents[j]->getLabel();
       out << "</GIVEN>" << endl;
@@ -682,7 +548,7 @@ BayesNet::exportToBifFile (const char* fileName) const
   }
   out << "</NETWORK>" << endl;
   out << "</BIF>" << endl << endl;
-  out.close();  
+  out.close();
 }
 
 
@@ -731,8 +597,8 @@ vector<int>
 BayesNet::getAdjacentNodes (int v) const
 {
   vector<int> adjacencies;
-  const NodeSet& parents = nodes_[v]->getParents();
+  const BnNodeSet& parents = nodes_[v]->getParents();
-  const NodeSet& childs  = nodes_[v]->getChilds();
+  const BnNodeSet& childs  = nodes_[v]->getChilds();
   for (unsigned i = 0; i < parents.size(); i++) {
     adjacencies.push_back (parents[i]->getIndex());
   }
@@ -745,8 +611,8 @@ BayesNet::getAdjacentNodes (int v) const
 
 
 ParamSet
-BayesNet::reorderParameters (const ParamSet& params,
+BayesNet::reorderParameters (CParamSet params,
-                             int domainSize) const
+                             unsigned domainSize) const
 {
   // the interchange format for bayesian networks keeps the probabilities 
   // in the following order:
@@ -773,15 +639,15 @@ BayesNet::reorderParameters (const ParamSet& params,
 
 
 ParamSet
-BayesNet::revertParameterReorder (const ParamSet& params,
+BayesNet::revertParameterReorder (CParamSet params,
-                                  int domainSize) const
+                                  unsigned domainSize) const
 {
   unsigned count    = 0;
   unsigned rowSize  = params.size() / domainSize;
   ParamSet reordered;
   while (reordered.size() < params.size()) {
     unsigned idx = count;
-    for (int i = 0; i < domainSize; i++) {
+    for (unsigned i = 0; i < domainSize; i++) {
       reordered.push_back (params[idx]);
       idx += rowSize;
     }

packages/CLPBN/clpbn/bp/BayesNet.h

@@ -4,8 +4,6 @@
 #include <vector>
 #include <queue>
 #include <list>
-#include <string>
-#include <unordered_map>
 #include <map>
 
 #include "GraphicalModel.h"
@@ -46,42 +44,42 @@ struct StateInfo
 
 typedef vector<Distribution*>  DistSet;
 typedef queue<ScheduleInfo, list<ScheduleInfo> > Scheduling;
-typedef unordered_map<unsigned, unsigned> Histogram;
+typedef map<unsigned, unsigned> Histogram;
-typedef unordered_map<unsigned, double>   Times;
+typedef map<unsigned, double>   Times;
 
 
 class BayesNet : public GraphicalModel
 {
   public:
-    BayesNet (void);
+    BayesNet (void) {};
     BayesNet (const char*);
    ~BayesNet (void);
 
     BayesNode*           addNode (unsigned);
-    BayesNode*           addNode (unsigned, unsigned, int, NodeSet&, Distribution*);
+    BayesNode*           addNode (unsigned, unsigned, int, BnNodeSet&,
-    BayesNode*           addNode (string, Domain, NodeSet&, ParamSet&);
+                             Distribution*);
-    BayesNode*           getNode (unsigned) const;
+    BayesNode*           addNode (string, Domain, BnNodeSet&, ParamSet&);
-    BayesNode*           getNode (string) const;
+    BayesNode*           getBayesNode (Vid) const;
+    BayesNode*           getBayesNode (string) const;
+    Variable*            getVariable (Vid) const;
     void                 addDistribution (Distribution*);
     Distribution*        getDistribution (unsigned) const;
-    const NodeSet&       getNodes (void) const;
+    const BnNodeSet&     getBayesNodes (void) const;
-    int                  getNumberOfNodes (void) const;
+    unsigned             getNumberOfNodes (void) const;
-    NodeSet              getRootNodes (void) const;
+    BnNodeSet            getRootNodes (void) const;
-    NodeSet              getLeafNodes (void) const;
+    BnNodeSet            getLeafNodes (void) const;
     VarSet               getVariables (void) const;
-    BayesNet*            pruneNetwork (BayesNode*) const;
+    BayesNet*            getMinimalRequesiteNetwork (Vid) const;
-    BayesNet*            pruneNetwork (const NodeSet& queryNodes) const;
+    BayesNet*            getMinimalRequesiteNetwork (const VidSet&) const;
-    void                 constructGraph (BayesNet*, const vector<StateInfo*>&) const;
+    void                 constructGraph (BayesNet*, 
+                             const vector<StateInfo*>&) const;
     bool                 isSingleConnected (void) const;
-    static vector<DomainConf> getDomainConfigurationsOf (const NodeSet&);
-    static vector<string>     getInstantiations (const NodeSet& nodes);
     void                 setIndexes (void);
     void                 freeDistributions (void);
-    void                 printNetwork (void) const;
+    void                 printGraphicalModel (void) const;
-    void                 printNetworkToFile (const char*) const;
+    void                 exportToDotFormat (const char*, bool = true,
-    void                 exportToDotFile (const char*, bool = true,
+                             CVidSet = VidSet()) const;
-                                          const NodeSet& = NodeSet()) const;
+    void                 exportToBifFormat (const char*) const;
-    void                 exportToBifFile (const char*) const;
 
     static Histogram     histogram_;
     static Times         times_;
@@ -93,12 +91,12 @@ class BayesNet : public GraphicalModel
     bool                 containsUndirectedCycle (int, int,
                                                   vector<bool>&)const;
     vector<int>          getAdjacentNodes (int) const ;
-    ParamSet             reorderParameters (const ParamSet&, int) const;
+    ParamSet             reorderParameters (CParamSet, unsigned) const;
-    ParamSet             revertParameterReorder (const ParamSet&, int) const;
+    ParamSet             revertParameterReorder (CParamSet, unsigned) const;
     void                 scheduleParents (const BayesNode*, Scheduling&) const;
     void                 scheduleChilds (const BayesNode*, Scheduling&) const;
 
-    NodeSet              nodes_;
+    BnNodeSet            nodes_;
     DistSet              dists_;
     IndexMap             indexMap_;
 };
@@ -108,8 +106,8 @@ class BayesNet : public GraphicalModel
 inline void
 BayesNet::scheduleParents (const BayesNode* n, Scheduling& sch) const
 {
-  const NodeSet& ps = n->getParents();
+  const BnNodeSet& ps = n->getParents();
-  for (NodeSet::const_iterator it = ps.begin(); it != ps.end(); it++) {
+  for (BnNodeSet::const_iterator it = ps.begin(); it != ps.end(); it++) {
     sch.push (ScheduleInfo (*it, false, true));
   }
 }
@@ -119,11 +117,11 @@ BayesNet::scheduleParents (const BayesNode* n, Scheduling& sch) const
 inline void
 BayesNet::scheduleChilds (const BayesNode* n, Scheduling& sch) const
 {
-  const NodeSet& cs = n->getChilds();
+  const BnNodeSet& cs = n->getChilds();
-  for (NodeSet::const_iterator it = cs.begin(); it != cs.end(); it++) {
+  for (BnNodeSet::const_iterator it = cs.begin(); it != cs.end(); it++) {
     sch.push (ScheduleInfo (*it, true, false));
   }
 }
 
-#endif
+#endif //BP_BAYES_NET_H
 

packages/CLPBN/clpbn/bp/BayesNode.cpp

@@ -1,26 +1,21 @@
+#include <cstdlib>
+#include <cassert>
+
 #include <iostream>
 #include <sstream>
 #include <iomanip>
-#include <cassert>
-#include <cstdlib>
 
 #include "BayesNode.h"
 
 
-BayesNode::BayesNode (unsigned varId) : Variable (varId)
+BayesNode::BayesNode (Vid vid,
-{
-}
-
-
-
-BayesNode::BayesNode (unsigned varId,
                       unsigned dsize,
                       int evidence,
-                      const NodeSet& parents,
+                      const BnNodeSet& parents,
-                      Distribution* dist) : Variable(varId, dsize, evidence)
+                      Distribution* dist) : Variable (vid, dsize, evidence)
 {
-  parents_   = parents;
+  parents_  = parents;
-  dist_      = dist;
+  dist_     = dist;
   for (unsigned int i = 0; i < parents.size(); i++) {
     parents[i]->addChild (this);
   }
@@ -28,15 +23,15 @@ BayesNode::BayesNode (unsigned varId,
 
 
 
-BayesNode::BayesNode (unsigned varId,
+BayesNode::BayesNode (Vid vid,
                       string label,
                       const Domain& domain,
-                      const NodeSet& parents,
+                      const BnNodeSet& parents,
-                      Distribution* dist) : Variable(varId, domain)
+                      Distribution* dist) : Variable (vid, domain,
+                                                      NO_EVIDENCE, label)
 {
-  label_     = new string (label);
+  parents_  = parents;
-  parents_   = parents;
+  dist_     = dist;
-  dist_      = dist;
   for (unsigned int i = 0; i < parents.size(); i++) {
     parents[i]->addChild (this);
   }
@@ -47,11 +42,11 @@ BayesNode::BayesNode (unsigned varId,
 void
 BayesNode::setData (unsigned dsize,
                     int evidence,
-                    const NodeSet& parents,
+                    const BnNodeSet& parents,
                     Distribution* dist)
 {
   setDomainSize (dsize);
-  evidence_  = evidence;
+  setEvidence (evidence);
   parents_   = parents;
   dist_      = dist;
   for (unsigned int i = 0; i < parents.size(); i++) {
@@ -135,19 +130,18 @@ BayesNode::getCptEntries (void)
 {
   if (dist_->entries.size() == 0) {
     unsigned rowSize  = getRowSize();
-    unsigned nParents = parents_.size();
+    vector<DConf> confs (rowSize);
-    vector<DomainConf> confs (rowSize);
 
     for (unsigned i = 0; i < rowSize; i++) {  
-      confs[i].resize (nParents);
+      confs[i].resize (parents_.size());
     }
 
-    int nReps = 1;
+    unsigned nReps = 1;
-    for (int i = nParents - 1; i >= 0; i--) {
+    for (int i = parents_.size() - 1; i >= 0; i--) {
       unsigned index = 0;
       while (index < rowSize) {
-        for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
+        for (unsigned j = 0; j < parents_[i]->getDomainSize(); j++) {
-          for (int r = 0; r < nReps; r++) {
+          for (unsigned r = 0; r < nReps; r++) {
             confs[index][i] = j;
             index++;
           }
@@ -184,7 +178,7 @@ BayesNode::cptEntryToString (const CptEntry& entry) const
 {
   stringstream ss;
   ss << "p(" ;
-  const DomainConf& conf = entry.getParentConfigurations();
+  const DConf& conf = entry.getDomainConfiguration();
   int row = entry.getParameterIndex() / getRowSize();
   ss << getDomain()[row]; 
   if (parents_.size() > 0) {
@@ -207,7 +201,7 @@ BayesNode::cptEntryToString (int row, const CptEntry& entry) const
 {
   stringstream ss;
   ss << "p(" ;
-  const DomainConf& conf = entry.getParentConfigurations();
+  const DConf& conf = entry.getDomainConfiguration();
   ss << getDomain()[row]; 
   if (parents_.size() > 0) {
     ss << "|" ;
@@ -227,16 +221,16 @@ BayesNode::cptEntryToString (int row, const CptEntry& entry) const
 vector<string> 
 BayesNode::getDomainHeaders (void) const
 {
-  int nParents = parents_.size();
+  unsigned nParents = parents_.size();
-  int rowSize  = getRowSize(); 
+  unsigned rowSize  = getRowSize(); 
-  int nReps     = 1;
+  unsigned nReps     = 1;
   vector<string> headers (rowSize);
   for (int i = nParents - 1; i >= 0; i--) {
     Domain domain = parents_[i]->getDomain();
-    int index = 0;
+    unsigned index = 0;
     while (index < rowSize) {
-      for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
+      for (unsigned j = 0; j < parents_[i]->getDomainSize(); j++) {
-        for (int r = 0; r < nReps; r++) {
+        for (unsigned r = 0; r < nReps; r++) {
           if (headers[index] != "") {
             headers[index] = domain[j] + "," + headers[index];
           } else {
@@ -270,7 +264,7 @@ operator << (ostream& o, const BayesNode& node)
   o << endl;
 
   o << "Parents:  " ;
-  const NodeSet& parents = node.getParents();
+  const BnNodeSet& parents = node.getParents();
   if (parents.size() != 0) {
     for (unsigned int i = 0; i < parents.size() - 1; i++) {
       o << parents[i]->getLabel() << ", " ;
@@ -280,7 +274,7 @@ operator << (ostream& o, const BayesNode& node)
   o << endl;
   
   o << "Childs:   " ;
-  const NodeSet& childs = node.getChilds();
+  const BnNodeSet& childs = node.getChilds();
   if (childs.size() != 0) {
     for (unsigned int i = 0; i < childs.size() - 1; i++) {
       o << childs[i]->getLabel() << ", " ;

packages/CLPBN/clpbn/bp/BayesNode.h

@@ -1,9 +1,7 @@
-#ifndef BP_BAYESNODE_H
+#ifndef BP_BAYES_NODE_H
-#define BP_BAYESNODE_H
+#define BP_BAYES_NODE_H
 
 #include <vector>
-#include <string>
-#include <sstream>
 
 #include "Variable.h"
 #include "CptEntry.h"
@@ -16,11 +14,12 @@ using namespace std;
 class BayesNode : public Variable
 {
   public:
-    BayesNode (unsigned);
+    BayesNode (Vid vid) : Variable (vid) {}
-    BayesNode (unsigned, unsigned, int, const NodeSet&, Distribution*);
+    BayesNode (Vid, unsigned, int, const BnNodeSet&, Distribution*);
-    BayesNode (unsigned, string, const Domain&, const NodeSet&, Distribution*);
+    BayesNode (Vid, string, const Domain&, const BnNodeSet&, Distribution*);
 
-    void                     setData (unsigned, int, const NodeSet&, Distribution*);
+    void                     setData (unsigned, int, const BnNodeSet&,
+                                      Distribution*);
     void                     addChild (BayesNode*);
     Distribution*            getDistribution (void);
     const ParamSet&          getParameters (void);
@@ -34,11 +33,21 @@ class BayesNode : public Variable
     int                      getIndexOfParent (const BayesNode*) const;
     string                   cptEntryToString (const CptEntry&) const;
     string                   cptEntryToString (int, const CptEntry&) const;
-    // inlines
+
-    const NodeSet&           getParents (void) const;
+    const BnNodeSet& getParents (void) const { return parents_; }
-    const NodeSet&           getChilds (void) const;
+    const BnNodeSet& getChilds (void) const  { return childs_; }
-    double                   getProbability (int, const CptEntry& entry);
+
-    unsigned                 getRowSize (void) const;
+    unsigned getRowSize (void) const
+    { 
+      return dist_->params.size() / getDomainSize();
+    }
+
+    double getProbability (int row, const CptEntry& entry)
+    {
+      int col = entry.getParameterIndex();
+      int idx = (row * getRowSize()) + col;
+      return dist_->params[idx];
+    }
 
   private:
     DISALLOW_COPY_AND_ASSIGN (BayesNode);
@@ -46,46 +55,12 @@ class BayesNode : public Variable
     Domain                   getDomainHeaders (void) const;
     friend ostream&          operator << (ostream&, const BayesNode&);
 
-    NodeSet                  parents_;
+    BnNodeSet                parents_;
-    NodeSet                  childs_;
+    BnNodeSet                childs_;
     Distribution*            dist_;
 };
 
 ostream& operator << (ostream&, const BayesNode&);
 
-
+#endif //BP_BAYES_NODE_H
-
-inline const NodeSet&
-BayesNode::getParents (void) const
-{
-  return parents_;
-}
-
-
-
-inline const NodeSet&
-BayesNode::getChilds (void) const
-{
-  return childs_;
-}
-
-
-
-inline double
-BayesNode::getProbability (int row, const CptEntry& entry)
-{
-  int col = entry.getParameterIndex();
-  int idx = (row * getRowSize()) + col;
-  return dist_->params[idx];
-}
-
-
-
-inline unsigned 
-BayesNode::getRowSize (void) const
-{ 
-  return dist_->params.size() / getDomainSize();
-}
-
-#endif
 

packages/CLPBN/clpbn/bp/CountingBP.cpp

@@ -0,0 +1,198 @@
+#include "CountingBP.h"
+
+
+CountingBP::~CountingBP (void)
+{
+  delete lfg_;
+  delete fg_;
+  for (unsigned i = 0; i < links_.size(); i++) {
+    delete links_[i];
+  }
+  links_.clear();
+}
+
+
+
+ParamSet
+CountingBP::getPosterioriOf (Vid vid) const
+{
+  FgVarNode* var = lfg_->getEquivalentVariable (vid);
+  ParamSet probs;
+
+  if (var->hasEvidence()) {
+    probs.resize (var->getDomainSize(), 0.0);
+    probs[var->getEvidence()] = 1.0;
+  } else {
+    probs.resize (var->getDomainSize(), 1.0);
+    CLinkSet links = varsI_[var->getIndex()]->getLinks();
+    for (unsigned i = 0; i < links.size(); i++) {
+      ParamSet msg = links[i]->getMessage();
+      CountingBPLink* l = static_cast<CountingBPLink*> (links[i]);
+      Util::pow (msg, l->getNumberOfEdges());
+      for (unsigned j = 0; j < msg.size(); j++) {
+        probs[j] *= msg[j];
+      }
+    }
+    Util::normalize (probs);
+  }
+  return probs;
+}
+
+
+
+void
+CountingBP::initializeSolver (void)
+{
+  lfg_ = new LiftedFG (*fg_);
+  unsigned nUncVars    = fg_->getFgVarNodes().size();
+  unsigned nUncFactors = fg_->getFactors().size();
+  CFgVarSet vars = fg_->getFgVarNodes();
+  unsigned nNeighborLessVars = 0;
+  for (unsigned i = 0; i < vars.size(); i++) {
+    CFactorSet factors = vars[i]->getFactors();
+    if (factors.size() == 1 && factors[0]->getFgVarNodes().size() == 1) {
+      nNeighborLessVars ++;
+    }
+  }
+  // cout << "UNCOMPRESSED FACTOR GRAPH" << endl;
+  // fg_->printGraphicalModel();
+  fg_->exportToDotFormat ("uncompress.dot");
+
+  FactorGraph *temp; 
+  temp = fg_;
+  fg_  = lfg_->getCompressedFactorGraph();
+  unsigned nCompVars    = fg_->getFgVarNodes().size();
+  unsigned nCompFactors = fg_->getFactors().size();
+  
+  Statistics::updateCompressingStats (nUncVars,
+                                      nUncFactors,
+                                      nCompVars,
+                                      nCompFactors,
+                                      nNeighborLessVars);
+
+  cout << "COMPRESSED FACTOR GRAPH" << endl;
+  fg_->printGraphicalModel();
+  //fg_->exportToDotFormat ("compress.dot");
+
+  SPSolver::initializeSolver();
+}
+
+
+
+void
+CountingBP::createLinks (void)
+{
+  const FactorClusterSet fcs = lfg_->getFactorClusters();
+  for (unsigned i = 0; i < fcs.size(); i++) {
+    const VarClusterSet vcs = fcs[i]->getVarClusters();
+    for (unsigned j = 0; j < vcs.size(); j++) {
+      unsigned c = lfg_->getGroundEdgeCount (fcs[i], vcs[j]);
+      links_.push_back (
+        new CountingBPLink (fcs[i]->getRepresentativeFactor(),
+                            vcs[j]->getRepresentativeVariable(), c));
+      //cout << (links_.back())->toString() << " edge count =" << c << endl;
+    }
+  }
+  return;
+}
+
+
+
+void 
+CountingBP::deleteJunction (Factor* f, FgVarNode*)
+{
+  f->freeDistribution();
+}
+
+
+
+void
+CountingBP::maxResidualSchedule (void)
+{
+  if (nIter_ == 1) {
+    for (unsigned i = 0; i < links_.size(); i++) {
+      links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
+      SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
+      linkMap_.insert (make_pair (links_[i], it));
+      if (DL >= 2 && DL < 5) {
+        cout << "calculating " << links_[i]->toString() << endl;
+      }
+    }
+    return;
+  }
+
+  for (unsigned c = 0; c < links_.size(); c++) {
+    if (DL >= 2) {
+      cout << endl << "current residuals:" << endl;
+      for (SortedOrder::iterator it = sortedOrder_.begin();
+          it != sortedOrder_.end(); it ++) {
+        cout << "    " << setw (30) << left << (*it)->toString();
+        cout << "residual = " << (*it)->getResidual() << endl;
+      }
+    }
+
+    SortedOrder::iterator it = sortedOrder_.begin();
+    Link* link = *it;
+    if (DL >= 2) {
+      cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
+    }
+    if (link->getResidual() < SolverOptions::accuracy) {
+      return;
+    }
+    link->updateMessage();
+    link->clearResidual();
+    sortedOrder_.erase (it);
+    linkMap_.find (link)->second = sortedOrder_.insert (link);
+
+    // update the messages that depend on message source --> destin
+    CFactorSet factorNeighbors = link->getVariable()->getFactors();
+    for (unsigned i = 0; i < factorNeighbors.size(); i++) {
+      CLinkSet links = factorsI_[factorNeighbors[i]->getIndex()]->getLinks();
+      for (unsigned j = 0; j < links.size(); j++) {
+        if (links[j]->getVariable() != link->getVariable()) { //FIXMEFIXME
+          if (DL >= 2 && DL < 5) {
+            cout << "    calculating " << links[j]->toString() << endl;
+          }
+          links[j]->setNextMessage (getFactor2VarMsg (links[j]));
+          LinkMap::iterator iter = linkMap_.find (links[j]);
+          sortedOrder_.erase (iter->second);
+          iter->second = sortedOrder_.insert (links[j]);
+        }
+      }
+    }
+  }
+}
+
+
+
+ParamSet
+CountingBP::getVar2FactorMsg (const Link* link) const
+{
+  const FgVarNode* src = link->getVariable();
+  const Factor* dest   = link->getFactor();
+  ParamSet msg;
+  if (src->hasEvidence()) {
+    cout << "has evidence" << endl;
+    msg.resize (src->getDomainSize(), 0.0);
+    msg[src->getEvidence()] = link->getMessage()[src->getEvidence()];
+    cout << "-> " << link->getVariable()->getLabel()	 << " " << link->getFactor()->getLabel() << endl;
+    cout << "-> p2s " << Util::parametersToString (msg) << endl;
+  } else {
+    msg = link->getMessage();
+  }
+  const CountingBPLink* l = static_cast<const CountingBPLink*> (link);
+  Util::pow (msg, l->getNumberOfEdges() - 1);
+  CLinkSet links = varsI_[src->getIndex()]->getLinks();
+  for (unsigned i = 0; i < links.size(); i++) {
+    if (links[i]->getFactor() != dest) {
+      ParamSet msgFromFactor = links[i]->getMessage();
+      CountingBPLink* l = static_cast<CountingBPLink*> (links[i]);
+      Util::pow (msgFromFactor, l->getNumberOfEdges());
+      for (unsigned j = 0; j < msgFromFactor.size(); j++) {
+        msg[j] *= msgFromFactor[j];
+      }
+    }
+  }
+  return msg;
+}
+

packages/CLPBN/clpbn/bp/CountingBP.h

@@ -0,0 +1,45 @@
+#ifndef BP_COUNTING_BP_H
+#define BP_COUNTING_BP_H
+
+#include "SPSolver.h"
+#include "LiftedFG.h"
+
+class Factor;
+class FgVarNode;
+
+class CountingBPLink : public Link
+{
+  public:
+    CountingBPLink (Factor* f, FgVarNode* v, unsigned c) : Link (f, v)
+    {
+      edgeCount_ = c;
+    }
+  
+    unsigned getNumberOfEdges (void) const { return edgeCount_; }
+
+  private:
+    unsigned edgeCount_;
+};
+
+
+class CountingBP : public SPSolver
+{
+  public:
+    CountingBP (FactorGraph& fg) : SPSolver (fg) { }
+   ~CountingBP (void);
+
+    ParamSet        getPosterioriOf (Vid) const;
+
+   private:
+     void           initializeSolver (void);
+     void           createLinks (void);
+     void           deleteJunction (Factor*, FgVarNode*);
+
+     void           maxResidualSchedule (void);
+     ParamSet       getVar2FactorMsg (const Link*) const;
+
+     LiftedFG*      lfg_;
+};
+
+#endif // BP_COUNTING_BP_H
+

packages/CLPBN/clpbn/bp/CptEntry.h

@@ -1,5 +1,5 @@
-#ifndef BP_CPTENTRY_H
+#ifndef BP_CPT_ENTRY_H
-#define BP_CPTENTRY_H
+#define BP_CPT_ENTRY_H
 
 #include <vector>
 
@@ -10,62 +10,34 @@ using namespace std;
 class CptEntry
 {
   public:
-    CptEntry (unsigned, const vector<unsigned>&);
+    CptEntry (unsigned index, const DConf& conf)
+    {
+      index_ = index;
+      conf_  = conf;
+    }
 
-    unsigned                getParameterIndex (void) const;
+    unsigned getParameterIndex (void) const          { return index_; }
-    const vector<unsigned>& getParentConfigurations (void) const;
+    const DConf& getDomainConfiguration (void) const { return conf_;  }
-    bool                    matchConstraints (const DomainConstr&) const;
+
-    bool                    matchConstraints (const vector<DomainConstr>&) const;
+    bool matchConstraints (const DConstraint& constr) const
+    {
+      return conf_[constr.first] == constr.second;
+    }
+
+    bool matchConstraints (const vector<DConstraint>& constrs) const
+    {
+      for (unsigned j = 0; j < constrs.size(); j++) {
+        if (conf_[constrs[j].first] != constrs[j].second) {
+          return false;
+        }
+      }
+      return true;
+    }
 
   private:
-    unsigned                index_;
+    unsigned   index_;
-    vector<unsigned>        confs_;
+    DConf      conf_;
 };
 
+#endif //BP_CPT_ENTRY_H
 
-
-inline
-CptEntry::CptEntry (unsigned index, const vector<unsigned>& confs)
-{
-  index_ = index;
-  confs_ = confs;
-}
-
-
-
-inline unsigned
-CptEntry::getParameterIndex (void) const
-{
-  return index_;
-}
-
-
-
-inline const vector<unsigned>&
-CptEntry::getParentConfigurations (void) const
-{
-  return confs_;
-}
-
-
-
-inline bool
-CptEntry::matchConstraints (const DomainConstr& constr) const
-{
-  return confs_[constr.first] == constr.second;
-}
-
-
-
-inline bool
-CptEntry::matchConstraints (const vector<DomainConstr>& constrs) const
-{
-  for (unsigned j = 0; j < constrs.size(); j++) {
-    if (confs_[constrs[j].first] != constrs[j].second) {
-      return false;
-    }
-  }
-  return true;
-}
-
-#endif

packages/CLPBN/clpbn/bp/Distribution.h

@@ -2,8 +2,8 @@
 #define BP_DISTRIBUTION_H
 
 #include <vector>
-#include <string>
 
+#include "CptEntry.h"
 #include "Shared.h"
 
 using namespace std;
@@ -11,16 +11,18 @@ using namespace std;
 struct Distribution
 {
   public:
-    Distribution (unsigned id)
+    Distribution (unsigned id, bool shared = false)
     {
       this->id     = id;
       this->params = params;
+      this->shared = shared;
     }
 
-    Distribution (const ParamSet& params)
+    Distribution (const ParamSet& params, bool shared = false)
     {
       this->id     = -1;
       this->params = params;
+      this->shared = shared;
     }
 
     void updateParameters (const ParamSet& params)
@@ -31,10 +33,11 @@ struct Distribution
     unsigned          id;
     ParamSet          params;
     vector<CptEntry>  entries;
+    bool              shared;
 
   private:
     DISALLOW_COPY_AND_ASSIGN (Distribution);
 };
 
-#endif
+#endif //BP_DISTRIBUTION_H
 

packages/CLPBN/clpbn/bp/Factor.cpp

@@ -1,37 +1,37 @@
-#include <iostream>
-#include <sstream>
 #include <cstdlib>
 #include <cassert>
 
+#include <iostream>
+#include <sstream>
+
 #include "Factor.h"
 #include "FgVarNode.h"
 
 
-int Factor::indexCount_ = 0;
+Factor::Factor (const Factor& g)
-
+{
-Factor::Factor (FgVarNode* var) {
+  copyFactor (g);
-  vs_.push_back (var);
-  int nParams = var->getDomainSize();
-  // create a uniform distribution
-  double val = 1.0 / nParams;
-  ps_ = ParamSet (nParams, val);
-  id_ = indexCount_;
-  indexCount_ ++;
 }
 
 
 
-Factor::Factor (const FgVarSet& vars) {
+Factor::Factor (FgVarNode* var)
-  vs_ = vars;
+{
+  Factor (FgVarSet() = {var});
+}
+
+
+
+Factor::Factor (const FgVarSet& vars)
+{
+  vars_ = vars;
   int nParams = 1;
-  for (unsigned i = 0; i < vs_.size(); i++) {
+  for (unsigned i = 0; i < vars_.size(); i++) {
-    nParams *= vs_[i]->getDomainSize();
+    nParams *= vars_[i]->getDomainSize();
   }
   // create a uniform distribution
   double val = 1.0 / nParams;
-  ps_ = ParamSet (nParams, val);
+  dist_ = new Distribution (ParamSet (nParams, val));
-  id_ = indexCount_;
-  indexCount_ ++;
 }
 
 
@@ -39,10 +39,17 @@ Factor::Factor (const FgVarSet& vars) {
 Factor::Factor (FgVarNode* var,
                 const ParamSet& params)
 {
-  vs_.push_back (var);
+  vars_.push_back (var);
-  ps_ = params;
+  dist_ = new Distribution (params);
-  id_ = indexCount_;
+}
-  indexCount_ ++;
+
+
+
+Factor::Factor (FgVarSet& vars,
+                Distribution* dist)
+{
+  vars_ = vars;
+  dist_ = dist;
 }
 
 
@@ -50,42 +57,8 @@ Factor::Factor (FgVarNode* var,
 Factor::Factor (const FgVarSet& vars,
                 const ParamSet& params)
 {
-  vs_ = vars;
+  vars_ = vars;
-  ps_ = params;
+  dist_ = new Distribution (params);
-  id_ = indexCount_;
-  indexCount_ ++;
-}
-
-
-
-const FgVarSet&
-Factor::getFgVarNodes (void) const
-{
-  return vs_;
-}
-
-
-
-FgVarSet&
-Factor::getFgVarNodes (void)
-{
-  return vs_;
-}
-
-
-
-const ParamSet&
-Factor::getParameters (void) const
-{
-  return ps_;
-}
-
-
-
-ParamSet&
-Factor::getParameters (void)
-{
-  return ps_;
 }
 
 
@@ -93,75 +66,95 @@ Factor::getParameters (void)
 void
 Factor::setParameters (const ParamSet& params)
 {
-  //cout << "ps size:     " << ps_.size() << endl;
+  assert (dist_->params.size() == params.size());
-  //cout << "params size: " << params.size() << endl;
+  dist_->updateParameters (params);
-  assert (ps_.size() == params.size());
-  ps_ = params;
 }
 
 
 
-Factor&
+void
-Factor::operator= (const Factor& g)
+Factor::copyFactor (const Factor& g)
 {
-  FgVarSet vars = g.getFgVarNodes();
+  vars_ = g.getFgVarNodes();
-  ParamSet params = g.getParameters();
+  dist_ = new Distribution (g.getDistribution()->params);
-  return *this;
 }
 
 
 
-Factor&
+void
-Factor::operator*= (const Factor& g)
+Factor::multiplyByFactor (const Factor& g, const vector<CptEntry>* entries)
 {
-  FgVarSet gVs        = g.getFgVarNodes();
+  if (vars_.size() == 0) {
+    copyFactor (g);
+    return;
+  }
+
+  const FgVarSet& gVs = g.getFgVarNodes();
   const ParamSet& gPs = g.getParameters();
 
-  bool hasCommonVars = false;
+  bool factorsAreEqual = true;
-  vector<int> varIndexes;
+  if (gVs.size() == vars_.size()) {
-  for (unsigned i = 0; i < gVs.size(); i++) {
+    for (unsigned i = 0; i < vars_.size(); i++) {
-    int idx = getIndexOf (gVs[i]);
+      if (gVs[i] != vars_[i]) {
-    if (idx == -1) {
+        factorsAreEqual = false;
-      insertVariable (gVs[i]);
+        break;
-      varIndexes.push_back (vs_.size() - 1);
-    } else {
-      hasCommonVars = true;
-      varIndexes.push_back (idx);
-    }
-  }
- 
-  if (hasCommonVars) {
-   vector<int> offsets (gVs.size());
-    offsets[gVs.size() - 1] = 1;
-    for (int i = gVs.size() - 2; i >= 0; i--) {
-      offsets[i] = offsets[i + 1] * gVs[i + 1]->getDomainSize();
-    }
-    vector<CptEntry> entries = getCptEntries();
-    for (unsigned i = 0; i < entries.size(); i++) {
-      int idx = 0;
-      const DomainConf conf = entries[i].getParentConfigurations();
-      for (unsigned j = 0; j < varIndexes.size(); j++) {
-        idx += offsets[j] * conf[varIndexes[j]];
       }
-      //cout << "ps_[" << i << "] = " << ps_[i] << " * " ;
-      //cout << gPs[idx] << " , idx = " << idx << endl;
-      ps_[i] = ps_[i] * gPs[idx];
     }
   } else {
-    // if the originally factors doesn't have common factors.
+    factorsAreEqual = false;
-    // we don't have to make domain comparations
+  }
-    unsigned idx = 0;
+
-    for (unsigned i = 0; i < ps_.size(); i++) {
+  if (factorsAreEqual) {
-      //cout << "ps_[" << i << "] = " << ps_[i] << " * " ;
+    // optimization: if the factors contain the same set of variables,
-      //cout << gPs[idx] << " , idx = " << idx << endl;
+    // we can do 1 to 1 operations on the parameteres
-      ps_[i] = ps_[i] * gPs[idx];
+    for (unsigned i = 0; i < dist_->params.size(); i++) {
-      idx ++;
+      dist_->params[i] *= gPs[i];
-      if (idx >= gPs.size()) {
+    }
-        idx = 0;
+  } else {
+    bool hasCommonVars = false;
+    vector<unsigned> gVsIndexes;
+    for (unsigned i = 0; i < gVs.size(); i++) {
+      int idx = getIndexOf (gVs[i]);
+      if (idx == -1) {
+        insertVariable (gVs[i]);
+        gVsIndexes.push_back (vars_.size() - 1);
+      } else {
+        hasCommonVars = true;
+        gVsIndexes.push_back (idx);
+      }
+    }
+    if (hasCommonVars) {
+      vector<unsigned> gVsOffsets (gVs.size());
+      gVsOffsets[gVs.size() - 1] = 1;
+      for (int i = gVs.size() - 2; i >= 0; i--) {
+        gVsOffsets[i] = gVsOffsets[i + 1] * gVs[i + 1]->getDomainSize();
+      }
+
+      if (entries == 0) {
+        entries = &getCptEntries();
+      }
+
+      for (unsigned i = 0; i < entries->size(); i++) {
+        unsigned idx = 0;
+        const DConf& conf = (*entries)[i].getDomainConfiguration();
+        for (unsigned j = 0; j < gVsIndexes.size(); j++) {
+          idx += gVsOffsets[j] * conf[ gVsIndexes[j] ];
+        }
+        dist_->params[i] = dist_->params[i] * gPs[idx];
+      }
+    } else {
+      // optimization: if the original factors doesn't have common variables,
+      // we don't need to marry the states of the common variables
+      unsigned count = 0;
+      for (unsigned i = 0; i < dist_->params.size(); i++) {
+        dist_->params[i] *= gPs[count];
+        count ++;
+        if (count >= gPs.size()) {
+          count = 0;
+        }
       }
     }
   }
-  return *this;
 }
 
 
@@ -169,81 +162,109 @@ Factor::operator*= (const Factor& g)
 void
 Factor::insertVariable (FgVarNode* var)
 {
-  int c = 0;
+  assert (getIndexOf (var) == -1);
-  ParamSet newPs (ps_.size() * var->getDomainSize());
+  ParamSet newPs;
-  for (unsigned i = 0; i < ps_.size(); i++) {
+  newPs.reserve (dist_->params.size() * var->getDomainSize());
-    for (int j = 0; j < var->getDomainSize(); j++) {
+  for (unsigned i = 0; i < dist_->params.size(); i++) {
-      newPs[c] = ps_[i];
+    for (unsigned j = 0; j < var->getDomainSize(); j++) {
-      c ++;
+      newPs.push_back (dist_->params[i]);
     }
   }
-  vs_.push_back (var);
+  vars_.push_back (var);
-  ps_ = newPs;
+  dist_->updateParameters (newPs);
 }
 
 
 
 void
-Factor::marginalizeVariable (const FgVarNode* var) {
+Factor::removeVariable (const FgVarNode* var)
-  int varIndex = getIndexOf (var);
-  marginalizeVariable (varIndex);
-}
-
-
-
-void
-Factor::marginalizeVariable (unsigned varIndex)
 {
-  assert (varIndex >= 0 && varIndex < vs_.size());
+  int varIndex = getIndexOf (var);
-  int distOffset    = 1;
+  assert (varIndex >= 0 && varIndex < (int)vars_.size());
-  int leftVarOffset = 1;
+
-  for (unsigned i = vs_.size() - 1; i > varIndex; i--) {
+  // number of parameters separating a different state of `var', 
-    distOffset    *= vs_[i]->getDomainSize();
+  // with the states of the remaining variables fixed
-    leftVarOffset *= vs_[i]->getDomainSize();
+  unsigned varOffset = 1;
-  }
+
-  leftVarOffset *= vs_[varIndex]->getDomainSize();
+  // number of parameters separating a different state of the variable
+  // on the left of `var', with the states of the remaining vars fixed
+  unsigned leftVarOffset = 1;
+
+  for (int i = vars_.size() - 1; i > varIndex; i--) {
+    varOffset     *= vars_[i]->getDomainSize();
+    leftVarOffset *= vars_[i]->getDomainSize();
+  }
+  leftVarOffset *= vars_[varIndex]->getDomainSize();
+
+  unsigned offset    = 0;
+  unsigned count1    = 0;
+  unsigned count2    = 0;
+  unsigned newPsSize = dist_->params.size() / vars_[varIndex]->getDomainSize();
 
-  int ds             = vs_[varIndex]->getDomainSize();
-  int count          = 0;
-  int offset         = 0;
-  int startIndex     = 0;
-  int currDomainIdx  = 0;
-  unsigned newPsSize = ps_.size() / ds;
   ParamSet newPs;
   newPs.reserve (newPsSize);
 
-  stringstream ss;
+  // stringstream ss;
-  ss << "marginalizing " << vs_[varIndex]->getLabel();
+  // ss << "marginalizing " << vars_[varIndex]->getLabel();
-  ss << " from factor " << getLabel() << endl;
+  // ss << " from factor " << getLabel() << endl;
   while (newPs.size() < newPsSize) {
-    ss << "  sum = ";
+    // ss << "  sum = ";
     double sum = 0.0;
-    for (int j = 0; j < ds; j++) {
+    for (unsigned i = 0; i < vars_[varIndex]->getDomainSize(); i++) {
-      if (j != 0) ss << " + ";
+      // if (i != 0) ss << " + ";
-      ss << ps_[offset];
+      // ss << dist_->params[offset];
-      sum    = sum    + ps_[offset];
+      sum    += dist_->params[offset];
-      offset = offset + distOffset;
+      offset += varOffset;
     }
     newPs.push_back (sum);
-    count ++;
+    count1 ++;
-    if (varIndex == vs_.size() - 1) {
+    if (varIndex == (int)vars_.size() - 1) {
-      offset = count * ds;
+      offset = count1 * vars_[varIndex]->getDomainSize();
     } else {
-      offset = offset - distOffset + 1;
+      if (((offset - varOffset + 1) % leftVarOffset) == 0) {
-      if ((offset % leftVarOffset) == 0) {
+        count1 = 0;
-        currDomainIdx ++;
+        count2 ++;
-        startIndex = leftVarOffset * currDomainIdx;
-        offset = startIndex;
-        count = 0;
-      } else {
-        offset = startIndex + count;
       }
+      offset = (leftVarOffset * count2) + count1;
     }
-    ss << " = " << sum << endl;
+    // ss << " = " << sum << endl;
   }
-  //cout << ss.str() << endl;
+  // cout << ss.str() << endl;
-  ps_ = newPs;
+  vars_.erase (vars_.begin() + varIndex);
-  vs_.erase (vs_.begin() + varIndex);
+  dist_->updateParameters (newPs);
+}
+
+
+
+const vector<CptEntry>&
+Factor::getCptEntries (void) const
+{
+  if (dist_->entries.size() == 0) {
+    vector<DConf> confs (dist_->params.size());
+    for (unsigned i = 0; i < dist_->params.size(); i++) {
+      confs[i].resize (vars_.size());
+    }
+
+    unsigned nReps = 1;
+    for (int i = vars_.size() - 1; i >= 0; i--) {
+      unsigned index = 0;
+      while (index < dist_->params.size()) {
+        for (unsigned j = 0; j < vars_[i]->getDomainSize(); j++) {
+          for (unsigned r = 0; r < nReps; r++) {
+            confs[index][i] = j; 
+            index++;
+          }
+        }
+      }
+      nReps *= vars_[i]->getDomainSize();
+    }
+    dist_->entries.clear();
+    dist_->entries.reserve (dist_->params.size());
+    for (unsigned i = 0; i < dist_->params.size(); i++) {
+      dist_->entries.push_back (CptEntry (i, confs[i]));
+    }
+  }
+  return dist_->entries;
 }
 
 
@@ -252,11 +273,10 @@ string
 Factor::getLabel (void) const
 {
   stringstream ss;
-  ss << "f(" ;
+  ss << "Φ(" ;
-  // ss << "Φ(" ;
+  for (unsigned i = 0; i < vars_.size(); i++) {
-  for (unsigned i = 0; i < vs_.size(); i++) {
+    if (i != 0) ss << "," ;
-    if (i != 0) ss << ", " ;
+    ss << vars_[i]->getLabel();
-    ss << "v" << vs_[i]->getVarId();
   }
   ss << ")" ;
   return ss.str();
@@ -264,62 +284,24 @@ Factor::getLabel (void) const
 
 
 
-string
+void
-Factor::toString (void) const
+Factor::printFactor (void)
 {
   stringstream ss;
-  ss << "vars: " ;
+  ss << getLabel() << endl;
-  for (unsigned i = 0; i < vs_.size(); i++) {
+  ss << "--------------------" << endl;
-    if (i != 0) ss << ", " ;
+  VarSet vs;
-    ss << "v" << vs_[i]->getVarId();
+  for (unsigned i = 0; i < vars_.size(); i++) {
+    vs.push_back (vars_[i]);
   }
-  ss << endl;
+  vector<string> domainConfs = Util::getInstantiations (vs);
-  vector<CptEntry> entries = getCptEntries();
+  const vector<CptEntry>& entries = getCptEntries();
   for (unsigned i = 0; i < entries.size(); i++) {
-    ss << "Φ(" ;
+    ss << "Φ(" << domainConfs[i] << ")" ;
-    char s = 'a' ;
+    unsigned idx = entries[i].getParameterIndex();
-    const DomainConf& conf = entries[i].getParentConfigurations();
+    ss << " = " << dist_->params[idx] << endl;
-    for (unsigned j = 0; j < conf.size(); j++) {
-      if (j != 0) ss << "," ;
-      ss << s << conf[j] + 1;
-      s++;
-    }
-    ss << ") = " << ps_[entries[i].getParameterIndex()] << endl;
   }
-  return ss.str();
+  cout << ss.str();
-}
-
-
-
-vector<CptEntry>
-Factor::getCptEntries (void) const
-{
-  vector<DomainConf> confs (ps_.size());
-  for (unsigned i = 0; i < ps_.size(); i++) {
-    confs[i].resize (vs_.size());
-  }
-
-  int nReps = 1;
-  for (int i = vs_.size() - 1; i >= 0; i--) {
-    unsigned index = 0;
-    while (index < ps_.size()) {
-      for (int j = 0; j < vs_[i]->getDomainSize(); j++) {
-        for (int r = 0; r < nReps; r++) {
-          confs[index][i] = j; 
-          index++;
-        }
-      }
-    }
-    nReps *= vs_[i]->getDomainSize();
-  }
-  
-  vector<CptEntry> entries;
-  for (unsigned i = 0; i < ps_.size(); i++) {
-    for (unsigned j = 0; j < vs_.size(); j++) {
-    }
-    entries.push_back (CptEntry (i, confs[i]));
-  }
-  return entries;
 }
 
 
@@ -327,20 +309,11 @@ Factor::getCptEntries (void) const
 int
 Factor::getIndexOf (const FgVarNode* var) const
 {
-  for (unsigned i = 0; i < vs_.size(); i++) {
+  for (unsigned i = 0; i < vars_.size(); i++) {
-    if (vs_[i] == var) {
+    if (vars_[i] == var) {
       return i;
     }
   }
   return -1;
 }
 
-
-
-Factor operator* (const Factor& f, const Factor& g)
-{
-  Factor r = f;
-  r *= g;
-  return r;
-}
-

packages/CLPBN/clpbn/bp/Factor.h

@@ -3,43 +3,46 @@
 
 #include <vector>
 
+#include "Distribution.h"
 #include "CptEntry.h"
 
 using namespace std;
 
 class FgVarNode;
+class Distribution;
 
 class Factor
 {
   public:
+    Factor (void) { }
+    Factor (const Factor&);
     Factor (FgVarNode*);
-    Factor (const FgVarSet&);
+    Factor (CFgVarSet);
     Factor (FgVarNode*, const ParamSet&);
-    Factor (const FgVarSet&, const ParamSet&);
+    Factor (FgVarSet&, Distribution*);
+    Factor (CFgVarSet, CParamSet);
 
-    const FgVarSet&            getFgVarNodes (void) const;
+    void      setParameters (CParamSet);
-    FgVarSet&                  getFgVarNodes (void);
+    void      copyFactor (const Factor& f);
-    const ParamSet&            getParameters (void) const;
+    void      multiplyByFactor (const Factor& f, const vector<CptEntry>* = 0);
-    ParamSet&                  getParameters (void);
+    void      insertVariable (FgVarNode* index);
-    void                       setParameters (const ParamSet&);
+    void      removeVariable (const FgVarNode* var);
-    Factor&                    operator= (const Factor& f);
+    const vector<CptEntry>& getCptEntries (void) const;
-    Factor&                    operator*= (const Factor& f);
+    string    getLabel (void) const;
-    void                       insertVariable (FgVarNode* index);
+    void      printFactor (void);
-    void                       marginalizeVariable (const FgVarNode* var);
+
-    void                       marginalizeVariable (unsigned);
+    CFgVarSet getFgVarNodes (void) const        { return vars_; }
-    string                     getLabel (void) const;
+    CParamSet getParameters (void) const        { return dist_->params; }
-    string                     toString (void) const;
+    Distribution* getDistribution (void) const  { return dist_; }
+    unsigned getIndex (void) const              { return index_; }
+    void setIndex (unsigned index)              { index_ = index; }
+    void freeDistribution (void)                { delete dist_; dist_ = 0;}
+    int                       getIndexOf (const FgVarNode*) const;
 
   private:
-    vector<CptEntry>           getCptEntries() const;
+    FgVarSet                  vars_;
-    int                        getIndexOf (const FgVarNode*) const;
+    Distribution*             dist_;
-
+    unsigned                  index_;
-    FgVarSet                   vs_;
-    ParamSet                   ps_;
-    int                        id_;
-    static int                 indexCount_;
 };
 
-Factor operator* (const Factor&, const Factor&);
+#endif //BP_FACTOR_H
-
-#endif

packages/CLPBN/clpbn/bp/FactorGraph.cpp

@@ -1,23 +1,26 @@
+#include <cstdlib>
+#include <vector>
+#include <set>
+
 #include <iostream>
 #include <fstream>
 #include <sstream>
-#include <vector>
-#include <cstdlib>
 
 #include "FactorGraph.h"
 #include "FgVarNode.h"
 #include "Factor.h"
+#include "BayesNet.h"
 
 
 FactorGraph::FactorGraph (const char* fileName)
 {
-  string line;
   ifstream is (fileName);
   if (!is.is_open()) {
     cerr << "error: cannot read from file " + std::string (fileName) << endl;
     abort();
   }
 
+  string line;
   while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
   getline (is, line);
   if (line != "MARKOV") {
@@ -39,7 +42,7 @@ FactorGraph::FactorGraph (const char* fileName)
 
   while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
   for (int i = 0; i < nVars; i++) {
-    varNodes_.push_back (new FgVarNode (i, domainSizes[i]));
+    addVariable (new FgVarNode (i, domainSizes[i]));
   }
 
   int nFactors;
@@ -50,11 +53,11 @@ FactorGraph::FactorGraph (const char* fileName)
     is >> nFactorVars;
     FgVarSet factorVars;
     for (int j = 0; j < nFactorVars; j++) {
-      int varId;
+      int vid;
-      is >> varId;
+      is >> vid;
-      FgVarNode* var = getVariableById (varId);
+      FgVarNode* var = getFgVarNode (vid);
-      if (var == 0) {
+      if (!var) {
-        cerr << "error: invalid variable identifier (" << varId << ")" << endl;
+        cerr << "error: invalid variable identifier (" << vid << ")" << endl;
         abort();
       }
       factorVars.push_back (var);
@@ -87,6 +90,33 @@ FactorGraph::FactorGraph (const char* fileName)
 
 
 
+FactorGraph::FactorGraph (const BayesNet& bn)
+{
+  const BnNodeSet& nodes = bn.getBayesNodes();
+  for (unsigned i = 0; i < nodes.size(); i++) {
+    FgVarNode* varNode = new FgVarNode (nodes[i]);
+    varNode->setIndex (i);
+    addVariable (varNode);
+  }
+
+  for (unsigned i = 0; i < nodes.size(); i++) {
+    const BnNodeSet& parents = nodes[i]->getParents();
+    if (!(nodes[i]->hasEvidence() && parents.size() == 0)) {
+      FgVarSet factorVars = { varNodes_[nodes[i]->getIndex()] };
+      for (unsigned j = 0; j < parents.size(); j++) {
+        factorVars.push_back (varNodes_[parents[j]->getIndex()]);
+      }
+      Factor* f = new Factor (factorVars, nodes[i]->getDistribution());
+      factors_.push_back (f);
+      for (unsigned j = 0; j < factorVars.size(); j++) {
+        factorVars[j]->addFactor (f);
+      }
+    }
+  }
+}
+
+
+
 FactorGraph::~FactorGraph (void)
 {
   for (unsigned i = 0; i < varNodes_.size(); i++) {
@@ -99,18 +129,67 @@ FactorGraph::~FactorGraph (void)
 
 
 
-FgVarSet
+void
-FactorGraph::getFgVarNodes (void) const
+FactorGraph::addVariable (FgVarNode* varNode)
 {
-  return varNodes_;
+  varNodes_.push_back (varNode);
+  varNode->setIndex (varNodes_.size() - 1);
+  indexMap_.insert (make_pair (varNode->getVarId(), varNodes_.size() - 1));
 }
 
 
 
-vector<Factor*>
+void
-FactorGraph::getFactors (void) const
+FactorGraph::removeVariable (const FgVarNode* var)
 {
-  return factors_;
+  if (varNodes_[varNodes_.size() - 1] == var) {
+    varNodes_.pop_back();
+  } else {
+    for (unsigned i = 0; i  < varNodes_.size(); i++) {
+      if (varNodes_[i] == var) {
+        varNodes_.erase (varNodes_.begin() + i);
+        return;
+      }
+    }
+    assert (false);
+  }
+  indexMap_.erase (indexMap_.find (var->getVarId()));
+}
+
+
+
+void
+FactorGraph::addFactor (Factor* f)
+{
+  factors_.push_back (f);
+  const FgVarSet& factorVars = f->getFgVarNodes();
+  for (unsigned i = 0; i < factorVars.size(); i++) {
+    factorVars[i]->addFactor (f);
+  }
+}
+
+
+
+void
+FactorGraph::removeFactor (const Factor* f)
+{
+  const FgVarSet& factorVars = f->getFgVarNodes();
+  for (unsigned i = 0; i < factorVars.size(); i++) {
+    if (factorVars[i]) {
+      factorVars[i]->removeFactor (f);
+    }
+  }
+  if (factors_[factors_.size() - 1] == f) {
+    factors_.pop_back();
+  } else {
+    for (unsigned i = 0; i  < factors_.size(); i++) {
+      if (factors_[i] == f) {
+        factors_.erase (factors_.begin() + i);
+        return;
+      }
+    }
+    assert (false);
+  }
 }
 
 
@@ -127,47 +206,142 @@ FactorGraph::getVariables (void) const
 
 
 
-FgVarNode*
+Variable*
-FactorGraph::getVariableById (unsigned id) const
+FactorGraph::getVariable (Vid vid) const
 {
-  for (unsigned i = 0; i < varNodes_.size(); i++) {
+  return getFgVarNode (vid);
-    if (varNodes_[i]->getVarId() == id) {
-      return varNodes_[i];
-    }
-  }
-  return 0;
-}
-
-
-
-FgVarNode*
-FactorGraph::getVariableByLabel (string label) const
-{
-  for (unsigned i = 0; i < varNodes_.size(); i++) {
-    stringstream ss;
-    ss << "v" << varNodes_[i]->getVarId();
-    if (ss.str() == label) {
-      return varNodes_[i];
-    }
-  }
-  return 0;
 }
 
 
 
 void
-FactorGraph::printFactorGraph (void) const
+FactorGraph::setIndexes (void)
+{
+  for (unsigned i = 0; i < varNodes_.size(); i++) {
+    varNodes_[i]->setIndex (i);
+  }
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    factors_[i]->setIndex (i);
+  }
+}
+
+
+
+void
+FactorGraph::freeDistributions (void)
+{
+  set<Distribution*> dists;
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    dists.insert (factors_[i]->getDistribution());
+  }
+  for (set<Distribution*>::iterator it = dists.begin();
+      it != dists.end(); it++) {
+    delete *it;
+  }
+}
+
+
+
+void
+FactorGraph::printGraphicalModel (void) const
 {
   for (unsigned i = 0; i < varNodes_.size(); i++) {
     cout << "variable number " << varNodes_[i]->getIndex() << endl;
     cout << "Id          = "   << varNodes_[i]->getVarId() << endl;
+    cout << "Label       = "   << varNodes_[i]->getLabel() << endl;
     cout << "Domain size = "   << varNodes_[i]->getDomainSize() << endl;
     cout << "Evidence    = "   << varNodes_[i]->getEvidence() << endl;
-    cout << endl;
+    cout << "Factors     = " ;
+    for (unsigned j = 0; j < varNodes_[i]->getFactors().size(); j++) {
+      cout << varNodes_[i]->getFactors()[j]->getLabel() << " " ;
+    }
+    cout << endl << endl;
   }
-  cout << endl;
   for (unsigned i = 0; i < factors_.size(); i++) {
-    cout << factors_[i]->toString() << endl;
+    factors_[i]->printFactor();
+    cout << endl;
   }
 }
 
+
+
+void
+FactorGraph::exportToDotFormat (const char* fileName) const
+{
+  ofstream out (fileName);
+  if (!out.is_open()) {
+    cerr << "error: cannot open file to write at " ;
+    cerr << "FactorGraph::exportToDotFile()" << endl;
+    abort();
+  }
+
+  out << "graph \"" << fileName << "\" {" << endl;
+
+  for (unsigned i = 0; i < varNodes_.size(); i++) {
+    if (varNodes_[i]->hasEvidence()) {
+      out << '"' << varNodes_[i]->getLabel() << '"' ;
+      out << " [style=filled, fillcolor=yellow]" << endl;
+    }
+  }
+
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    out << '"' << factors_[i]->getLabel() << '"' ;
+    out << " [label=\"" << factors_[i]->getLabel() << "\\n(";
+    out << factors_[i]->getDistribution()->id << ")" << "\"" ;
+    out << ", shape=box]" << endl;
+  }
+
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    CFgVarSet myVars = factors_[i]->getFgVarNodes();
+    for (unsigned j = 0; j < myVars.size(); j++) {
+      out << '"' << factors_[i]->getLabel() << '"' ;
+      out << " -- " ;
+      out << '"' << myVars[j]->getLabel() << '"' << endl;
+    }
+  }
+
+  out << "}" << endl;
+  out.close();
+}
+
+
+
+void
+FactorGraph::exportToUaiFormat (const char* fileName) const
+{
+  ofstream out (fileName);
+  if (!out.is_open()) {
+    cerr << "error: cannot open file to write at " ;
+    cerr << "FactorGraph::exportToUaiFormat()" << endl;
+    abort();
+  }
+
+  out << "MARKOV" << endl;
+  out << varNodes_.size() << endl;
+  for (unsigned i = 0; i < varNodes_.size(); i++) {
+    out << varNodes_[i]->getDomainSize() << " " ;
+  }
+  out << endl;
+
+  out << factors_.size() << endl;
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    CFgVarSet factorVars = factors_[i]->getFgVarNodes();
+    out << factorVars.size();
+    for (unsigned j = 0; j < factorVars.size(); j++) {
+      out << " " << factorVars[j]->getIndex();
+    }
+    out << endl;
+  }
+
+  for (unsigned i = 0; i < factors_.size(); i++) {
+    CParamSet params = factors_[i]->getParameters();
+    out << endl << params.size() << endl << " " ;
+    for (unsigned j = 0; j < params.size(); j++) {
+      out << params[j] << " " ;
+    }
+    out << endl;
+  }
+
+  out.close();
+}
+

packages/CLPBN/clpbn/bp/FactorGraph.h

@@ -1,8 +1,7 @@
-#ifndef BP_FACTORGRAPH_H
+#ifndef BP_FACTOR_GRAPH_H
-#define BP_FACTORGRAPH_H
+#define BP_FACTOR_GRAPH_H
 
 #include <vector>
-#include <string>
 
 #include "GraphicalModel.h"
 #include "Shared.h"
@@ -11,25 +10,48 @@ using namespace std;
 
 class FgVarNode;
 class Factor;
+class BayesNet;
 
 class FactorGraph : public GraphicalModel
 {
   public:
-    FactorGraph (const char* fileName);
+    FactorGraph (void) {};
+    FactorGraph (const char*);
+    FactorGraph (const BayesNet&);
    ~FactorGraph (void);
-
+   
-    FgVarSet            getFgVarNodes (void) const;
+    void                addVariable (FgVarNode*);
-    vector<Factor*>     getFactors (void) const;
+    void                removeVariable (const FgVarNode*);
+    void                addFactor (Factor*);
+    void                removeFactor (const Factor*);
     VarSet              getVariables (void) const;
-    FgVarNode*          getVariableById (unsigned) const;
+    Variable*           getVariable (unsigned) const;
-    FgVarNode*          getVariableByLabel (string) const;
+    void                setIndexes (void);
-    void                printFactorGraph (void) const;
+    void                freeDistributions (void);
+    void                printGraphicalModel (void) const;
+    void                exportToDotFormat (const char*) const;
+    void                exportToUaiFormat (const char*) const;
+  
+    const FgVarSet& getFgVarNodes (void) const { return varNodes_; }
+    const FactorSet& getFactors (void) const   { return factors_; }
+
+    FgVarNode* getFgVarNode (Vid vid) const
+    {
+      IndexMap::const_iterator it = indexMap_.find (vid);
+      if (it == indexMap_.end()) {
+        return 0;
+      } else {
+        return varNodes_[it->second];
+      }
+    }
 
   private:
     DISALLOW_COPY_AND_ASSIGN (FactorGraph);
 
-    FgVarSet varNodes_;
+    FgVarSet            varNodes_;
-    vector<Factor*>     factors_;
+    FactorSet           factors_;
+    IndexMap            indexMap_;
 };
 
-#endif
+#endif // BP_FACTOR_GRAPH_H
+

packages/CLPBN/clpbn/bp/FgVarNode.h

@@ -1,8 +1,7 @@
-#ifndef BP_VARIABLE_H
+#ifndef BP_FG_VAR_NODE_H
-#define BP_VARIABLE_H
+#define BP_FG_VAR_NODE_H
 
 #include <vector>
-#include <string>
 
 #include "Variable.h"
 #include "Shared.h"
@@ -14,15 +13,31 @@ class Factor;
 class FgVarNode : public Variable
 {
   public:
-    FgVarNode (int varId, int dsize) : Variable (varId, dsize) { }
+    FgVarNode (unsigned vid, unsigned dsize) : Variable (vid, dsize) { }
+    FgVarNode (const Variable* v) : Variable (v) { }
 
-    void                addFactor (Factor* f)      { factors_.push_back (f); }
+    void           addFactor (Factor* f)      { factors_.push_back (f); }
-    vector<Factor*>     getFactors (void) const    { return factors_; }
+    CFactorSet     getFactors (void) const    { return factors_; }
+
+    void removeFactor (const Factor* f)
+    { 
+      if (factors_[factors_.size() -1] == f) {
+        factors_.pop_back();
+      } else {
+        for (unsigned i = 0; i  < factors_.size(); i++) {
+          if (factors_[i] == f) {
+            factors_.erase (factors_.begin() + i);
+            return;
+          }
+        }
+        assert (false);
+      }
+    }
 
   private:
     DISALLOW_COPY_AND_ASSIGN (FgVarNode);
     // members
-    vector<Factor*>     factors_;
+    FactorSet           factors_;
 };
 
-#endif // BP_VARIABLE_H
+#endif // BP_FG_VAR_NODE_H

packages/CLPBN/clpbn/bp/GraphicalModel.h

@@ -1,5 +1,5 @@
-#ifndef BP_GRAPHICALMODEL_H
+#ifndef BP_GRAPHICAL_MODEL_H
-#define BP_GRAPHICALMODEL_H
+#define BP_GRAPHICAL_MODEL_H
 
 #include "Variable.h"
 #include "Shared.h"
@@ -9,9 +9,10 @@ using namespace std;
 class GraphicalModel
 {
   public:
-    virtual VarSet getVariables (void) const = 0;
+    virtual ~GraphicalModel (void) {};
-
+    virtual Variable*  getVariable          (Vid)  const = 0;
-  private:
+    virtual VarSet     getVariables         (void) const = 0;
+    virtual void       printGraphicalModel  (void) const = 0;
 };
 
-#endif
+#endif // BP_GRAPHICAL_MODEL_H

packages/CLPBN/clpbn/bp/HorusCli.cpp

@@ -1,17 +1,19 @@
-#include <iostream>
 #include <cstdlib>
+
+#include <iostream>
 #include <sstream>
 
 #include "BayesNet.h"
-#include "BPSolver.h"
-
 #include "FactorGraph.h"
 #include "SPSolver.h"
+#include "BPSolver.h"
+#include "CountingBP.h"
 
 using namespace std;
 
 void BayesianNetwork (int, const char* []);
 void markovNetwork (int, const char* []);
+void runSolver (Solver*, const VarSet&);
 
 const string USAGE = "usage: \
 ./hcli  FILE  [VARIABLE | OBSERVED_VARIABLE=EVIDENCE]..." ;
@@ -19,14 +21,40 @@ const string USAGE = "usage: \
 
 int
 main (int argc, const char* argv[])
-{
+{ 
+  /*
+  FactorGraph fg;
+  FgVarNode* varNode1 = new FgVarNode (0, 2);
+  FgVarNode* varNode2 = new FgVarNode (1, 2);
+  FgVarNode* varNode3 = new FgVarNode (2, 2);
+  fg.addVariable (varNode1);
+  fg.addVariable (varNode2);
+  fg.addVariable (varNode3);
+  Distribution* dist = new Distribution (ParamSet() = {1.2, 1.4, 2.0, 0.4});
+  fg.addFactor (new Factor (FgVarSet() = {varNode1, varNode2}, dist));
+  fg.addFactor (new Factor (FgVarSet() = {varNode3, varNode2}, dist));
+  //fg.printGraphicalModel();
+  //SPSolver sp (fg);
+  //sp.runSolver();
+  //sp.printAllPosterioris();
+  //ParamSet p = sp.getJointDistributionOf (VidSet() = {0, 1, 2});
+  //cout << Util::parametersToString (p) << endl;
+  CountingBP cbp (fg);
+  //cbp.runSolver();
+  //cbp.printAllPosterioris();
+  ParamSet p2 = cbp.getJointDistributionOf (VidSet() = {0, 1, 2});
+  cout << Util::parametersToString (p2) << endl;
+  fg.freeDistributions();
+  Statistics::printCompressingStats ("compressing.stats");
+  return 0;
+  */
   if (!argv[1]) {
     cerr << "error: no graphical model specified" << endl;
     cerr << USAGE << endl;
     exit (0);
   }
-  string fileName  = argv[1];
+  const string& fileName  = argv[1];
-  string extension = fileName.substr (fileName.find_last_of ('.') + 1);
+  const string& extension = fileName.substr (fileName.find_last_of ('.') + 1);
   if (extension == "xml") {
     BayesianNetwork (argc, argv);
   } else if (extension == "uai") {
@@ -45,13 +73,13 @@ void
 BayesianNetwork (int argc, const char* argv[])
 {
   BayesNet bn (argv[1]);
-  //bn.printNetwork();
+  //bn.printGraphicalModel();
 
-  NodeSet queryVars;
+  VarSet queryVars;
   for (int i = 2; i < argc; i++) {
-    string arg = argv[i];
+    const string& arg = argv[i];
     if (arg.find ('=') == std::string::npos) {
-      BayesNode* queryVar = bn.getNode (arg);
+      BayesNode* queryVar = bn.getBayesNode (arg);
       if (queryVar) {
         queryVars.push_back (queryVar);
       } else {
@@ -61,9 +89,9 @@ BayesianNetwork (int argc, const char* argv[])
         exit (0);
       }
     } else {
-      size_t pos   = arg.find ('=');
+      size_t pos = arg.find ('=');
-      string label = arg.substr (0, pos);
+      const string& label = arg.substr (0, pos);
-      string state = arg.substr (pos + 1);
+      const string& state = arg.substr (pos + 1);
       if (label.empty()) {
         cerr << "error: missing left argument" << endl;
         cerr << USAGE << endl;
@@ -74,7 +102,7 @@ BayesianNetwork (int argc, const char* argv[])
         cerr << USAGE << endl;
         exit (0);
       }
-      BayesNode* node = bn.getNode (label);
+      BayesNode* node = bn.getBayesNode (label);
       if (node) {
         if (node->isValidState (state)) {
           node->setEvidence (state);
@@ -94,19 +122,16 @@ BayesianNetwork (int argc, const char* argv[])
     }
   }
 
-  BPSolver solver (bn);
+  Solver* solver;
-  if (queryVars.size() == 0) {
+  if (SolverOptions::convertBn2Fg) {
-    solver.runSolver();
+    FactorGraph* fg = new FactorGraph (bn);
-    solver.printAllPosterioris();
+    fg->printGraphicalModel();
-  } else if (queryVars.size() == 1) {
+    solver = new SPSolver (*fg);
-    solver.runSolver();
+    runSolver (solver, queryVars);
-    solver.printPosterioriOf (queryVars[0]);
+    delete fg;
   } else {
-    Domain domain   = BayesNet::getInstantiations(queryVars);
+    solver = new BPSolver (bn);
-    ParamSet params = solver.getJointDistribution (queryVars);
+    runSolver (solver, queryVars);
-    for (unsigned i = 0; i < params.size(); i++) {
-      cout << domain[i] << "\t" << params[i] << endl;
-    }
   }
   bn.freeDistributions();
 }
@@ -117,11 +142,11 @@ void
 markovNetwork (int argc, const char* argv[])
 {
   FactorGraph fg (argv[1]);
-  //fg.printFactorGraph();
+  //fg.printGraphicalModel();
-
+  
   VarSet queryVars;
   for (int i = 2; i < argc; i++) {
-    string arg = argv[i];
+    const string& arg = argv[i];
     if (arg.find ('=') == std::string::npos) {
       if (!Util::isInteger (arg)) {
         cerr << "error: `" << arg << "' " ;
@@ -129,16 +154,16 @@ markovNetwork (int argc, const char* argv[])
         cerr << endl;
         exit (0);
       }
-      unsigned varId;
+      Vid vid;
       stringstream ss;
       ss << arg;
-      ss >> varId;
+      ss >> vid;
-      Variable* queryVar = fg.getVariableById (varId);
+      Variable* queryVar = fg.getFgVarNode (vid);
       if (queryVar) {
         queryVars.push_back (queryVar);
       } else {
         cerr << "error: there isn't a variable with " ;
-        cerr << "`" << varId << "' as id" ;
+        cerr << "`" << vid << "' as id" ;
         cerr << endl;
         exit (0);
       }
@@ -160,11 +185,11 @@ markovNetwork (int argc, const char* argv[])
         cerr << endl;
         exit (0);
       }
-      unsigned varId;
+      Vid vid;
       stringstream ss; 
       ss << arg.substr (0, pos);
-      ss >> varId;
+      ss >> vid;
-      Variable* var = fg.getVariableById (varId);
+      Variable* var = fg.getFgVarNode (vid);
       if (var) {
         if (!Util::isInteger (arg.substr (pos + 1))) {
           cerr << "error: `" << arg.substr (pos + 1) << "' " ;
@@ -176,7 +201,6 @@ markovNetwork (int argc, const char* argv[])
         stringstream ss; 
         ss << arg.substr (pos + 1);
         ss >> stateIndex;
-        cout << "si: " << stateIndex << endl;
         if (var->isValidStateIndex (stateIndex)) {
           var->setEvidence (stateIndex);
         } else {
@@ -188,27 +212,35 @@ markovNetwork (int argc, const char* argv[])
         }
       } else {
         cerr << "error: there isn't a variable with " ;
-        cerr << "`" << varId << "' as id" ;
+        cerr << "`" << vid << "' as id" ;
         cerr << endl;
         exit (0);
       }
     }
   }
-
+  Solver* solver = new SPSolver (fg);
-  SPSolver solver (fg);
+  runSolver (solver, queryVars);
-  if (queryVars.size() == 0) {
+  fg.freeDistributions();
-    solver.runSolver();
+}
-    solver.printAllPosterioris();
+
-  } else if (queryVars.size() == 1) {
+
-    solver.runSolver();
+
-    solver.printPosterioriOf (queryVars[0]);
+void
-  } else {
+runSolver (Solver* solver, const VarSet& queryVars)
-    assert (false); //FIXME
+{
-    //Domain domain   = BayesNet::getInstantiations(queryVars);
+  VidSet vids;
-    //ParamSet params = solver.getJointDistribution (queryVars);
+  for (unsigned i = 0; i < queryVars.size(); i++) {
-    //for (unsigned i = 0; i < params.size(); i++) {
+    vids.push_back (queryVars[i]->getVarId());
-    //  cout << domain[i] << "\t" << params[i] << endl;
+  }
-    //}
+  if (queryVars.size() == 0) {
-  }
+    solver->runSolver();
+    solver->printAllPosterioris();
+  } else if (queryVars.size() == 1) {
+    solver->runSolver();
+    solver->printPosterioriOf (vids[0]);
+  } else {
+    solver->printJointDistributionOf (vids);
+  }
+  delete solver;
 }
 

packages/CLPBN/clpbn/bp/HorusYap.cpp

@@ -1,41 +1,39 @@
 #include <cstdlib>
+#include <vector>
+
 #include <iostream>
 #include <sstream>
-#include <vector>
-#include <string>
 
 #include <YapInterface.h>
 
-#include "callgrind.h"
-
 #include "BayesNet.h"
-#include "BayesNode.h"
+#include "FactorGraph.h"
 #include "BPSolver.h"
+#include "SPSolver.h"
+#include "CountingBP.h"
 
 using namespace std;
 
+
 int
 createNetwork (void)
 {
-  Statistics::numCreatedNets ++;
+  //Statistics::numCreatedNets ++;
-  cout << "creating network number " << Statistics::numCreatedNets << endl;
+  //cout << "creating network number " << Statistics::numCreatedNets << endl;
-  if (Statistics::numCreatedNets == 1) {
-    //CALLGRIND_START_INSTRUMENTATION;
-  }
-  BayesNet* bn = new BayesNet();
 
+  BayesNet* bn = new BayesNet();
   YAP_Term varList = YAP_ARG1;
   while (varList != YAP_TermNil()) {
     YAP_Term var     = YAP_HeadOfTerm (varList);
-    unsigned varId   = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (1, var));
+    Vid vid          = (Vid) YAP_IntOfTerm (YAP_ArgOfTerm (1, var));
     unsigned dsize   = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (2, var));
-    int evidence     = (int)      YAP_IntOfTerm (YAP_ArgOfTerm (3, var));
+    int evidence     = (int) YAP_IntOfTerm (YAP_ArgOfTerm (3, var));
-    YAP_Term parentL =                           YAP_ArgOfTerm (4, var);
+    YAP_Term parentL =  YAP_ArgOfTerm (4, var);
     unsigned distId  = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (5, var));
-    NodeSet parents;
+    BnNodeSet parents;
     while (parentL != YAP_TermNil()) {
       unsigned parentId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (parentL));
-      BayesNode* parent = bn->getNode (parentId);
+      BayesNode* parent = bn->getBayesNode (parentId);
       if (!parent) {
         parent = bn->addNode (parentId);
       }
@@ -47,23 +45,20 @@ createNetwork (void)
       dist = new Distribution (distId);
       bn->addDistribution (dist);
     }
-    BayesNode* node = bn->getNode (varId);
+    BayesNode* node = bn->getBayesNode (vid);
     if (node) {
       node->setData (dsize, evidence, parents, dist);
     } else {
-      bn->addNode (varId, dsize, evidence, parents, dist);
+      bn->addNode (vid, dsize, evidence, parents, dist);
     }
     varList = YAP_TailOfTerm (varList);
   }
   bn->setIndexes();
 
-  if (Statistics::numCreatedNets == 1688) {
+  // if (Statistics::numCreatedNets == 1688) {
-    Statistics::writeStats();
+  //   Statistics::writeStats();
-    //Statistics::writeStats();
+  //   exit (0);
-    //CALLGRIND_STOP_INSTRUMENTATION;
+  // }
-    //CALLGRIND_DUMP_STATS;
-    //exit (0);
-  }
   YAP_Int p = (YAP_Int) (bn);
   return YAP_Unify (YAP_MkIntTerm (p), YAP_ARG2);
 }
@@ -73,20 +68,20 @@ createNetwork (void)
 int
 setExtraVarsInfo (void)
 {
-  BayesNet* bn     = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
+  BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
-  YAP_Term varsInfoL =                            YAP_ARG2;
+  YAP_Term varsInfoL =  YAP_ARG2;
   while (varsInfoL != YAP_TermNil()) {
     YAP_Term head    = YAP_HeadOfTerm (varsInfoL);
-    unsigned varId   = YAP_IntOfTerm  (YAP_ArgOfTerm (1, head));
+    Vid vid     = YAP_IntOfTerm  (YAP_ArgOfTerm (1, head));
     YAP_Atom label   = YAP_AtomOfTerm (YAP_ArgOfTerm (2, head));
-    YAP_Term domainL =                 YAP_ArgOfTerm (3, head);
+    YAP_Term domainL = YAP_ArgOfTerm (3, head);
     Domain domain;
     while (domainL != YAP_TermNil()) {
       YAP_Atom atom = YAP_AtomOfTerm (YAP_HeadOfTerm (domainL));
       domain.push_back ((char*) YAP_AtomName (atom));
       domainL = YAP_TailOfTerm (domainL);
     }
-    BayesNode* node = bn->getNode (varId);
+    BayesNode* node = bn->getBayesNode (vid);
     assert (node);
     node->setLabel ((char*) YAP_AtomName (label));
     node->setDomain (domain);
@@ -100,8 +95,8 @@ setExtraVarsInfo (void)
 int
 setParameters (void)
 {
-  BayesNet* bn    = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
+  BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
-  YAP_Term distList =                            YAP_ARG2;
+  YAP_Term distList = YAP_ARG2;
   while (distList != YAP_TermNil()) {
     YAP_Term dist    = YAP_HeadOfTerm (distList);
     unsigned distId  = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (1, dist));
@@ -112,6 +107,11 @@ setParameters (void)
       paramL = YAP_TailOfTerm (paramL);
     }
     bn->getDistribution(distId)->updateParameters(params);
+    if (Statistics::numCreatedNets == 4) {
+      cout << "dist " << distId << " parameters:" ;
+      cout << Util::parametersToString (params);
+      cout << endl;
+    }
     distList = YAP_TailOfTerm (distList);
   }
   return TRUE;
@@ -122,84 +122,126 @@ setParameters (void)
 int
 runSolver (void)
 {
-  BayesNet* bn      = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
+  BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
-  YAP_Term taskList =                            YAP_ARG2;
+  YAP_Term taskList = YAP_ARG2;
-
+  vector<VidSet> tasks;
-  vector<NodeSet> tasks;
+  VidSet marginalVids;
-  NodeSet marginalVars;
 
   while (taskList != YAP_TermNil()) {
     if (YAP_IsPairTerm (YAP_HeadOfTerm (taskList))) {
-      NodeSet jointVars;
+      VidSet jointVids;
       YAP_Term jointList = YAP_HeadOfTerm (taskList);      
       while (jointList != YAP_TermNil()) {
-        unsigned varId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (jointList));
+        Vid vid = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (jointList));
-        assert (bn->getNode (varId));
+        assert (bn->getBayesNode (vid));
-        jointVars.push_back (bn->getNode (varId));
+        jointVids.push_back (vid);
         jointList = YAP_TailOfTerm (jointList);
       }
-      tasks.push_back (jointVars);
+      tasks.push_back (jointVids);
     } else {
-      unsigned varId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (taskList));
+      Vid vid = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (taskList));
-      BayesNode* node = bn->getNode (varId);
+      assert (bn->getBayesNode (vid));
-      assert (node);
+      tasks.push_back (VidSet() = {vid});
-      tasks.push_back (NodeSet() = {node});
+      marginalVids.push_back (vid);
-      marginalVars.push_back (node);
     }
     taskList = YAP_TailOfTerm (taskList);
   }
-  /*
-  cout << "tasks to resolve:" << endl;
-  for (unsigned i = 0; i < tasks.size(); i++) {
-    cout << "i" << ": " ;
-    if (tasks[i].size() == 1) {
-      cout << tasks[i][0]->getVarId() << endl;
-    } else {
-      for (unsigned j = 0; j < tasks[i].size(); j++) {
-        cout << tasks[i][j]->getVarId() << " " ;
-      }
-      cout << endl;
-    }
-  }
-  */
   
-  cerr << "prunning now..." << endl;
+  // cout << "inference tasks:" << endl;
-  BayesNet* prunedNet = bn->pruneNetwork (marginalVars);
+  // for (unsigned i = 0; i < tasks.size(); i++) {
-  bn->printNetworkToFile ("net.txt");
+  //   cout << "i" << ": " ;
-  BPSolver solver (*prunedNet);
+  //   if (tasks[i].size() == 1) {
-  cerr << "solving marginals now..." << endl;
+  //     cout << tasks[i][0] << endl;
-  solver.runSolver();
+  //   } else {
-  cerr << "calculating joints now ..." << endl;
+  //     for (unsigned j = 0; j < tasks[i].size(); j++) {
+  //       cout << tasks[i][j] << " " ;
+  //     }
+  //     cout << endl;
+  //   }
+  // }
+  
+  Solver* solver     = 0;
+  GraphicalModel* gm = 0;
+  VidSet vids;
+  const BnNodeSet& nodes = bn->getBayesNodes();
+  for (unsigned i = 0; i < nodes.size(); i++) {
+    vids.push_back (nodes[i]->getVarId());
+  }
+  if (marginalVids.size() != 0) {
+    bn->exportToDotFormat ("bn unbayes.dot");
+    BayesNet* mrn = bn->getMinimalRequesiteNetwork (marginalVids);
+    mrn->exportToDotFormat ("bn bayes.dot");
+    //BayesNet* mrn = bn->getMinimalRequesiteNetwork (vids);
+    if (SolverOptions::convertBn2Fg) {
+      gm = new FactorGraph (*mrn);
+      if (SolverOptions::compressFactorGraph) {
+        solver = new CountingBP (*static_cast<FactorGraph*> (gm));
+      } else {
+        solver = new SPSolver (*static_cast<FactorGraph*> (gm));
+      }
+      if (SolverOptions::runBayesBall) {
+        delete mrn;
+      }
+    } else {
+      gm     = mrn;
+      solver = new BPSolver (*static_cast<BayesNet*> (gm));
+    }
+    solver->runSolver();
+  }
 
   vector<ParamSet> results;
   results.reserve (tasks.size());  
   for (unsigned i = 0; i < tasks.size(); i++) {
     if (tasks[i].size() == 1) {
-      BayesNode* node = prunedNet->getNode (tasks[i][0]->getVarId());
+      results.push_back (solver->getPosterioriOf (tasks[i][0]));
-      results.push_back (solver.getPosterioriOf (node));
     } else {
-      BPSolver solver2 (*bn);
+      static int count = 0;
-      cout << "calculating an join dist on: " ;
+      cout << "calculating joint... " << count ++ << endl;
-      for (unsigned j = 0; j < tasks[i].size(); j++) {
+      //if (count == 5225) {
-        cout << tasks[i][j]->getVarId() << " " ;
+      //  Statistics::printCompressingStats ("compressing.stats");
+      //}
+      Solver*      solver2  = 0;
+      GraphicalModel* gm2   = 0;
+      bn->exportToDotFormat ("joint.dot");
+      BayesNet* mrn2;
+      if (SolverOptions::runBayesBall) {
+        mrn2 = bn->getMinimalRequesiteNetwork (tasks[i]);
+      } else {
+        mrn2 = bn;
       }
-      cout << "..." << endl;
+      if (SolverOptions::convertBn2Fg) {
-      results.push_back (solver2.getJointDistribution (tasks[i]));
+        gm2 = new FactorGraph (*mrn2);
+        if (SolverOptions::compressFactorGraph) {
+          solver2 = new CountingBP (*static_cast<FactorGraph*> (gm2));
+        } else {
+          solver2 = new SPSolver (*static_cast<FactorGraph*> (gm2));
+        }
+        if (SolverOptions::runBayesBall) {
+          delete mrn2;
+        }
+      } else {
+        gm2     = mrn2;
+        solver2 = new BPSolver (*static_cast<BayesNet*> (gm2));
+      }
+      results.push_back (solver2->getJointDistributionOf (tasks[i]));
+      delete solver2;
+      delete gm2;
     }
   }
 
-  delete prunedNet;
+  delete solver;
+  delete gm;
 
   YAP_Term list = YAP_TermNil();
   for (int i = results.size() - 1; i >= 0; i--) {
     const ParamSet& beliefs = results[i];
     YAP_Term queryBeliefsL = YAP_TermNil();
     for (int j = beliefs.size() - 1; j >= 0; j--) {
-      YAP_Int sl1 = YAP_InitSlot(list);
+      YAP_Int sl1      = YAP_InitSlot (list);
-      YAP_Term belief = YAP_MkFloatTerm (beliefs[j]);
+      YAP_Term belief  = YAP_MkFloatTerm (beliefs[j]);
-      queryBeliefsL = YAP_MkPairTerm (belief, queryBeliefsL);
+      queryBeliefsL    = YAP_MkPairTerm (belief, queryBeliefsL);
-      list =  YAP_GetFromSlot(sl1);
+      list             = YAP_GetFromSlot (sl1);
-      YAP_RecoverSlots(1);
+      YAP_RecoverSlots (1);
     }
     list = YAP_MkPairTerm (queryBeliefsL, list);
   }
@@ -210,8 +252,9 @@ runSolver (void)
 
 
 int
-deleteBayesNet (void)
+freeBayesNetwork (void)
 {
+  //Statistics::printCompressingStats ("../../compressing.stats");
   BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
   bn->freeDistributions();
   delete bn;
@@ -223,10 +266,10 @@ deleteBayesNet (void)
 extern "C" void
 init_predicates (void)
 {
-  YAP_UserCPredicate ("create_network",      createNetwork,    2);
+  YAP_UserCPredicate ("create_network",        createNetwork,    2);
-  YAP_UserCPredicate ("set_extra_vars_info", setExtraVarsInfo, 2);
+  YAP_UserCPredicate ("set_extra_vars_info",   setExtraVarsInfo, 2);
-  YAP_UserCPredicate ("set_parameters",      setParameters,    2);
+  YAP_UserCPredicate ("set_parameters",        setParameters,    2);
-  YAP_UserCPredicate ("run_solver",          runSolver,        3);
+  YAP_UserCPredicate ("run_solver",            runSolver,        3);
-  YAP_UserCPredicate ("delete_bayes_net",    deleteBayesNet,   1);
+  YAP_UserCPredicate ("free_bayesian_network", freeBayesNetwork, 1);
 }
 

packages/CLPBN/clpbn/bp/LiftedFG.cpp

@@ -0,0 +1,278 @@
+
+#include "LiftedFG.h"
+#include "FgVarNode.h"
+#include "Factor.h"
+#include "Distribution.h"
+
+LiftedFG::LiftedFG (const FactorGraph& fg)
+{
+  groundFg_  = &fg;
+  freeColor_ = 0;
+
+  const FgVarSet& varNodes = fg.getFgVarNodes();
+  const FactorSet& factors = fg.getFactors();
+  varColors_.resize (varNodes.size());
+  factorColors_.resize (factors.size());
+  for (unsigned i = 0; i < factors.size(); i++) {
+    factors[i]->setIndex (i);
+  }
+
+  // create the initial variable colors
+  VarColorMap colorMap;
+  for (unsigned i = 0; i < varNodes.size(); i++) {
+    unsigned dsize = varNodes[i]->getDomainSize();
+    VarColorMap::iterator it = colorMap.find (dsize);
+    if (it == colorMap.end()) {
+      it = colorMap.insert (make_pair (
+          dsize, vector<Color> (dsize + 1,-1))).first; 
+    }
+    unsigned idx;
+    if (varNodes[i]->hasEvidence()) {
+      idx = varNodes[i]->getEvidence();
+    } else {
+      idx = dsize;
+    }
+    vector<Color>& stateColors = it->second;
+    if (stateColors[idx] == -1) {
+      stateColors[idx] = getFreeColor();
+    }
+    setColor (varNodes[i], stateColors[idx]);
+  }
+
+  // create the initial factor colors
+  DistColorMap distColors;
+  for (unsigned i = 0; i < factors.size(); i++) {
+    Distribution* dist = factors[i]->getDistribution();
+    DistColorMap::iterator it = distColors.find (dist);
+    if (it == distColors.end()) {
+      it = distColors.insert (make_pair (dist, getFreeColor())).first;
+    }
+    setColor (factors[i], it->second);
+  }
+
+  VarSignMap    varGroups;
+  FactorSignMap factorGroups;
+  bool groupsHaveChanged = true;
+  unsigned nIter = 0;
+  while (groupsHaveChanged || nIter == 1) {
+    nIter ++;
+    if (Statistics::numCreatedNets == 4) {
+      cout << "--------------------------------------------" << endl;
+      cout << "Iteration " << nIter << endl;
+      cout << "--------------------------------------------" << endl;
+    }
+
+    unsigned prevFactorGroupsSize = factorGroups.size();
+    factorGroups.clear();
+    // set a new color to the factors with the same signature
+    for (unsigned i = 0; i < factors.size(); i++) {
+      const string& signatureId = getSignatureId (factors[i]);
+      // cout << factors[i]->getLabel() << " signature: " ;
+      // cout<< signatureId << endl;
+      FactorSignMap::iterator it = factorGroups.find (signatureId);
+      if (it == factorGroups.end()) {
+        it = factorGroups.insert (make_pair (signatureId, FactorSet())).first;
+      }
+      it->second.push_back (factors[i]);
+    }
+    if (nIter > 0)
+    for (FactorSignMap::iterator it = factorGroups.begin();
+        it != factorGroups.end(); it++) {
+      Color newColor = getFreeColor();
+      FactorSet& groupMembers = it->second;
+      for (unsigned i = 0; i < groupMembers.size(); i++) {
+        setColor (groupMembers[i], newColor);
+      }
+    }
+
+    // set a new color to the variables with the same signature
+    unsigned prevVarGroupsSize = varGroups.size();
+    varGroups.clear();
+    for (unsigned i = 0; i < varNodes.size(); i++) {
+      const string& signatureId = getSignatureId (varNodes[i]);
+      VarSignMap::iterator it = varGroups.find (signatureId);
+      // cout << varNodes[i]->getLabel() << " signature: " ;
+      // cout << signatureId << endl;
+      if (it == varGroups.end()) {
+        it = varGroups.insert (make_pair (signatureId, FgVarSet())).first;
+      }
+      it->second.push_back (varNodes[i]);
+    }
+    if (nIter > 0)
+    for (VarSignMap::iterator it = varGroups.begin();
+        it != varGroups.end(); it++) {
+      Color newColor = getFreeColor();
+      FgVarSet& groupMembers = it->second;
+      for (unsigned i = 0; i < groupMembers.size(); i++) {
+        setColor (groupMembers[i], newColor);
+      }
+    }
+
+    //if (nIter >= 3) cout << "bigger than three: " << nIter << endl;
+    groupsHaveChanged = prevVarGroupsSize != varGroups.size()
+        || prevFactorGroupsSize != factorGroups.size();
+  }
+
+  printGroups (varGroups, factorGroups);
+  for (VarSignMap::iterator it = varGroups.begin();
+      it != varGroups.end(); it++) {
+    CFgVarSet vars = it->second;
+    VarCluster* vc = new VarCluster (vars);
+    for (unsigned i = 0; i < vars.size(); i++) {
+      vid2VarCluster_.insert (make_pair (vars[i]->getVarId(), vc));
+    }
+    varClusters_.push_back (vc);
+  }
+
+  for (FactorSignMap::iterator it = factorGroups.begin();
+      it != factorGroups.end(); it++) {
+    VarClusterSet varClusters;
+    Factor* groundFactor = it->second[0];
+    FgVarSet groundVars = groundFactor->getFgVarNodes();
+    for (unsigned i = 0; i < groundVars.size(); i++) {
+      Vid vid = groundVars[i]->getVarId();
+      varClusters.push_back (vid2VarCluster_.find (vid)->second);
+    }
+    factorClusters_.push_back (new FactorCluster (it->second, varClusters));
+  }
+}
+
+
+
+LiftedFG::~LiftedFG (void)
+{
+  for (unsigned i = 0; i  < varClusters_.size(); i++) {
+    delete varClusters_[i];
+  }
+  for (unsigned i = 0; i  < factorClusters_.size(); i++) {
+    delete factorClusters_[i];
+  }
+}
+
+
+
+string
+LiftedFG::getSignatureId (FgVarNode* var) const
+{
+  stringstream ss;
+  CFactorSet myFactors = var->getFactors();
+  ss << myFactors.size();
+  for (unsigned i = 0; i < myFactors.size(); i++) {
+    ss << "." << getColor (myFactors[i]);
+    ss << "." << myFactors[i]->getIndexOf(var);
+  }
+  ss << "." << getColor (var);
+  return ss.str();
+}
+
+
+
+string
+LiftedFG::getSignatureId (Factor* factor) const
+{
+  stringstream ss;
+  CFgVarSet myVars = factor->getFgVarNodes();
+  ss << myVars.size();
+  for (unsigned i = 0; i < myVars.size(); i++) {
+    ss << "." << getColor (myVars[i]);
+  }
+  ss << "." << getColor (factor);
+  return ss.str();
+}
+
+
+
+FactorGraph*
+LiftedFG::getCompressedFactorGraph (void)
+{
+  FactorGraph* fg = new FactorGraph();
+  for (unsigned i = 0; i < varClusters_.size(); i++) {
+    FgVarNode* var = varClusters_[i]->getGroundFgVarNodes()[0];
+    FgVarNode* newVar = new FgVarNode (var);
+    newVar->setIndex (i);
+    varClusters_[i]->setRepresentativeVariable (newVar);
+    fg->addVariable (newVar);
+  }
+
+  for (unsigned i = 0; i < factorClusters_.size(); i++) {
+    FgVarSet myGroundVars;
+    const VarClusterSet& myVarClusters = factorClusters_[i]->getVarClusters();
+    for (unsigned j = 0; j < myVarClusters.size(); j++) {
+      myGroundVars.push_back (myVarClusters[j]->getRepresentativeVariable());
+    }
+    Factor* newFactor = new Factor (myGroundVars,
+        factorClusters_[i]->getGroundFactors()[0]->getDistribution());
+    factorClusters_[i]->setRepresentativeFactor (newFactor);
+    fg->addFactor (newFactor);
+  }
+  return fg;
+}
+
+
+
+unsigned
+LiftedFG::getGroundEdgeCount (FactorCluster* fc, VarCluster* vc) const
+{
+  CFactorSet clusterGroundFactors = fc->getGroundFactors();
+  FgVarNode* var = vc->getGroundFgVarNodes()[0];
+  unsigned count = 0;
+  for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
+    if (clusterGroundFactors[i]->getIndexOf (var) != -1) {
+      count ++;
+    }
+  }
+  /*
+  CFgVarSet vars = vc->getGroundFgVarNodes();
+  for (unsigned i = 1; i < vars.size(); i++) {
+    FgVarNode* var = vc->getGroundFgVarNodes()[i];
+    unsigned count2 = 0;
+    for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
+      if (clusterGroundFactors[i]->getIndexOf (var) != -1) {
+        count2 ++;
+      }
+    }
+    if (count != count2) { cout << "oops!" << endl; abort(); }
+  }
+  */
+  return count;
+}
+
+
+
+void
+LiftedFG::printGroups (const VarSignMap& varGroups,
+                       const FactorSignMap& factorGroups) const
+{
+  cout << "variable groups:" << endl;
+  unsigned count = 0;
+  for (VarSignMap::const_iterator it = varGroups.begin();
+      it != varGroups.end(); it++) {
+    const FgVarSet& groupMembers = it->second;
+    if (groupMembers.size() > 0) {
+      cout << ++count << ": " ;
+      //if (groupMembers.size() > 1) {
+        for (unsigned i = 0; i < groupMembers.size(); i++) {
+          cout << groupMembers[i]->getLabel() << " " ;
+        }
+      //}
+      cout << endl;
+    }
+  }
+  cout << endl;
+  cout << "factor groups:" << endl;
+  count = 0;
+  for (FactorSignMap::const_iterator it = factorGroups.begin();
+      it != factorGroups.end(); it++) {
+    const FactorSet& groupMembers = it->second;
+    if (groupMembers.size() > 0) {
+      cout << ++count << ": " ;
+      //if (groupMembers.size() > 1) {
+        for (unsigned i = 0; i < groupMembers.size(); i++) {
+          cout << groupMembers[i]->getLabel() << " " ;
+        }
+    //}
+    cout << endl;
+    }
+  }
+}
+

packages/CLPBN/clpbn/bp/LiftedFG.h

@@ -0,0 +1,152 @@
+#ifndef BP_LIFTED_FG_H
+#define BP_LIFTED_FG_H
+
+#include <unordered_map>
+
+#include "FactorGraph.h"
+#include "FgVarNode.h"
+#include "Factor.h"
+#include "Shared.h"
+
+class VarCluster;
+class FactorCluster;
+class Distribution;
+
+typedef long                     Color;
+typedef vector<Color>            Signature;
+typedef vector<VarCluster*>      VarClusterSet;
+typedef vector<FactorCluster*>   FactorClusterSet;
+
+typedef map<string, FgVarSet>  VarSignMap;
+typedef map<string, FactorSet> FactorSignMap;
+
+typedef map<unsigned, vector<Color> > VarColorMap;
+typedef map<Distribution*, Color> DistColorMap;
+
+typedef map<Vid, VarCluster*> Vid2VarCluster;
+
+
+class VarCluster
+{
+  public:
+    VarCluster (CFgVarSet vs)
+    {
+      for (unsigned i = 0; i < vs.size(); i++) {
+        groundVars_.push_back (vs[i]);
+      }
+    }
+
+    void addFactorCluster (FactorCluster* fc)
+    {
+      factorClusters_.push_back (fc);
+    }
+
+    const FactorClusterSet& getFactorClusters (void) const
+    {
+      return factorClusters_;
+    }
+
+    FgVarNode* getRepresentativeVariable (void) const { return representVar_; }
+    void setRepresentativeVariable (FgVarNode* v)     { representVar_ = v; }
+    CFgVarSet getGroundFgVarNodes (void) const        { return groundVars_; }
+
+  private:
+    FgVarSet          groundVars_;
+    FactorClusterSet  factorClusters_;
+    FgVarNode*        representVar_;
+};
+
+
+class FactorCluster
+{
+  public:
+    FactorCluster (CFactorSet groundFactors, const VarClusterSet& vcs)
+    {
+      groundFactors_ = groundFactors;
+      varClusters_ = vcs;
+      for (unsigned i = 0; i < varClusters_.size(); i++) {
+        varClusters_[i]->addFactorCluster (this);
+      }
+    }
+ 
+    const VarClusterSet& getVarClusters (void) const
+    {
+      return varClusters_;
+    }
+  
+    bool containsGround (const Factor* f)
+    {
+      for (unsigned i = 0; i < groundFactors_.size(); i++) {
+        if (groundFactors_[i] == f) {
+          return true;
+        }
+      }
+      return false;
+    }
+
+    Factor* getRepresentativeFactor (void) const  { return representFactor_; }
+    void setRepresentativeFactor (Factor* f)      { representFactor_ = f; }
+    CFactorSet getGroundFactors (void) const      { return groundFactors_; }
+
+ 
+  private:
+    FactorSet      groundFactors_;
+    VarClusterSet  varClusters_;
+    Factor*        representFactor_;
+};
+
+
+class LiftedFG
+{
+  public:
+    LiftedFG (const FactorGraph&);
+   ~LiftedFG (void);
+
+    FactorGraph*    getCompressedFactorGraph (void);
+    unsigned        getGroundEdgeCount (FactorCluster*, VarCluster*) const;
+    void            printGroups (const VarSignMap& varGroups,
+                                 const FactorSignMap& factorGroups) const;
+
+    FgVarNode* getEquivalentVariable (Vid vid)
+    {
+      VarCluster* vc = vid2VarCluster_.find (vid)->second;
+      return vc->getRepresentativeVariable();
+    }
+  
+    const VarClusterSet&    getVariableClusters (void) { return varClusters_; }
+    const FactorClusterSet& getFactorClusters (void) { return factorClusters_; }
+ 
+  private:
+    string  getSignatureId (FgVarNode*) const;
+    string  getSignatureId (Factor*) const;
+
+    Color getFreeColor (void)           { return ++freeColor_ -1; }
+    Color getColor (FgVarNode* v) const { return varColors_[v->getIndex()]; }
+    Color getColor (Factor* f) const    { return factorColors_[f->getIndex()]; }
+
+    void setColor (FgVarNode* v, Color c)
+    {
+      varColors_[v->getIndex()] = c;
+    }
+
+    void setColor (Factor* f, Color  c)
+    {
+      factorColors_[f->getIndex()] = c;
+    }
+
+    VarCluster* getVariableCluster (Vid vid) const
+    {
+      return vid2VarCluster_.find (vid)->second;
+    }
+
+    Color               freeColor_;
+    vector<Color>       varColors_;
+    vector<Color>       factorColors_;
+    VarClusterSet       varClusters_;
+    FactorClusterSet    factorClusters_;
+    Vid2VarCluster      vid2VarCluster_;
+    const FactorGraph*  groundFg_;
+};
+
+#endif // BP_LIFTED_FG_H
+

packages/CLPBN/clpbn/bp/Makefile.in

@@ -50,28 +50,33 @@ CWD=$(PWD)
 HEADERS = \
 	$(srcdir)/GraphicalModel.h \
 	$(srcdir)/Variable.h \
+	$(srcdir)/Distribution.h \
 	$(srcdir)/BayesNet.h \
 	$(srcdir)/BayesNode.h \
-	$(srcdir)/Distribution.h \
+	$(srcdir)/LiftedFG.h \
 	$(srcdir)/CptEntry.h \
 	$(srcdir)/FactorGraph.h \
 	$(srcdir)/FgVarNode.h \
 	$(srcdir)/Factor.h \
 	$(srcdir)/Solver.h \
 	$(srcdir)/BPSolver.h \
-	$(srcdir)/BpNode.h \
+	$(srcdir)/BPNodeInfo.h \
 	$(srcdir)/SPSolver.h \
+  	$(srcdir)/CountingBP.h \
 	$(srcdir)/Shared.h \
 	$(srcdir)/xmlParser/xmlParser.h
-
+	
 CPP_SOURCES = \
 	$(srcdir)/BayesNet.cpp \
 	$(srcdir)/BayesNode.cpp \
 	$(srcdir)/FactorGraph.cpp \
 	$(srcdir)/Factor.cpp \
+	$(srcdir)/LiftedFG.cpp \
 	$(srcdir)/BPSolver.cpp \
-	$(srcdir)/BpNode.cpp \
+	$(srcdir)/BPNodeInfo.cpp \
 	$(srcdir)/SPSolver.cpp \
+	$(srcdir)/CountingBP.cpp \
+	$(srcdir)/Util.cpp \
 	$(srcdir)/HorusYap.cpp \
 	$(srcdir)/HorusCli.cpp \
 	$(srcdir)/xmlParser/xmlParser.cpp
@@ -82,22 +87,38 @@ OBJS = \
 	FactorGraph.o \
 	Factor.o \
 	BPSolver.o \
-	BpNode.o \
+	BPNodeInfo.o \
 	SPSolver.o \
-	HorusYap.o \
+	Util.o \
-	xmlParser.o
+	LiftedFG.o \
+	CountingBP.o \
+	HorusYap.o
+
+HCLI_OBJS = \
+	BayesNet.o \
+	BayesNode.o \
+	FactorGraph.o \
+	Factor.o \
+	BPSolver.o \
+  BPNodeInfo.o \
+	SPSolver.o \
+	Util.o \
+	LiftedFG.o \
+	CountingBP.o \
+	HorusCli.o \
+	xmlParser/xmlParser.o
 
 SOBJS=horus.@SO@
 
 
-all: $(SOBJS)
+all: $(SOBJS) hcli
 
 # default rule
 %.o : $(srcdir)/%.cpp
 	$(CXX) -c $(CXXFLAGS) $< -o $@
 
 
-xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
+xmlParser/xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
 	$(CXX) -c $(CXXFLAGS) $< -o $@
 
 
@@ -105,7 +126,7 @@ xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
 @DO_SECOND_LD@	@SHLIB_CXX_LD@ -o horus.@SO@ $(OBJS) @EXTRA_LIBS_FOR_SWIDLLS@
 
 
-hcli: $(OBJS)
+hcli: $(HCLI_OBJS)
 	$(CXX) -o hcli $(HCLI_OBJS)
 
 

packages/CLPBN/clpbn/bp/SPSolver.cpp

@@ -1,38 +1,77 @@
 #include <cassert>
-#include <algorithm>
+#include <limits>
+
 #include <iostream>
 
 #include "SPSolver.h"
 #include "FactorGraph.h"
 #include "FgVarNode.h"
 #include "Factor.h"
-
+#include "Shared.h"
-SPSolver* Link::klass = 0;
 
 
-SPSolver::SPSolver (const FactorGraph& fg) : Solver (&fg)
+SPSolver::SPSolver (FactorGraph& fg) : Solver (&fg)
 {
-  fg_           = &fg;
+  fg_ = &fg;
-  accuracy_     = 0.0001;
-  maxIter_      = 10000;
-  //schedule_     = S_SEQ_FIXED;
-  //schedule_     = S_SEQ_RANDOM;
-  //schedule_     = S_SEQ_PARALLEL;
-  schedule_     = S_MAX_RESIDUAL;
-  Link::klass   = this;
-  FgVarSet vars = fg_->getFgVarNodes();
-  for (unsigned i = 0; i < vars.size(); i++) {
-    msgs_.push_back (new MessageBanket (vars[i]));
-  }
 }
 
 
 
 SPSolver::~SPSolver (void)
 {
-  for (unsigned i = 0; i < msgs_.size(); i++) {
+  for (unsigned i = 0; i < varsI_.size(); i++) {
-    delete msgs_[i];
+    delete varsI_[i];
   }
+  for (unsigned i = 0; i < factorsI_.size(); i++) {
+    delete factorsI_[i];
+  }
+  for (unsigned i = 0; i < links_.size(); i++) {
+    delete links_[i];
+  }
+}
+
+
+
+void
+SPSolver::runTreeSolver (void)
+{
+  CFactorSet factors = fg_->getFactors();
+  bool finish = false;
+  while (!finish) {
+    finish = true;
+    for (unsigned i = 0; i < factors.size(); i++) {
+      CLinkSet links = factorsI_[factors[i]->getIndex()]->getLinks();
+      for (unsigned j = 0; j < links.size(); j++) {
+        if (!links[j]->messageWasSended()) {
+          if (readyToSendMessage(links[j])) {
+            links[j]->setNextMessage (getFactor2VarMsg (links[j]));
+            links[j]->updateMessage();
+          }
+          finish = false;
+        }
+      }
+    }
+  }
+}
+
+
+
+bool
+SPSolver::readyToSendMessage (const Link* link) const
+{
+  CFgVarSet factorVars = link->getFactor()->getFgVarNodes();
+  for (unsigned i = 0; i < factorVars.size(); i++) {
+    if (factorVars[i] != link->getVariable()) {
+      CLinkSet links = varsI_[factorVars[i]->getIndex()]->getLinks();
+      for (unsigned j = 0; j < links.size(); j++) {
+        if (links[j]->getFactor() != link->getFactor() &&
+            !links[j]->messageWasSended()) {
+          return false;
+        }
+      }
+    }
+  }
+  return true;
 }
 
 
@@ -40,62 +79,54 @@ SPSolver::~SPSolver (void)
 void
 SPSolver::runSolver (void)
 {
+  initializeSolver();
+  runTreeSolver();
+  return;
   nIter_ = 0;
-  vector<Factor*> factors = fg_->getFactors();
+  while (!converged() && nIter_ < SolverOptions::maxIter) {
-  for (unsigned i = 0; i < factors.size(); i++) {
+
-    FgVarSet neighbors = factors[i]->getFgVarNodes();
+    nIter_ ++;
-    for (unsigned j = 0; j < neighbors.size(); j++) {
+    if (DL >= 2) {
-      updateOrder_.push_back (Link (factors[i], neighbors[j]));
-    }
-  }
-  
-  while (!converged() && nIter_ < maxIter_) {
-    if (DL >= 1) {
       cout << endl;
       cout << "****************************************" ;
       cout << "****************************************" ;
       cout << endl;
-      cout << " Iteration " << nIter_ + 1 << endl;
+      cout << " Iteration " << nIter_ << endl;
       cout << "****************************************" ;
       cout << "****************************************" ;
       cout << endl;
     }
 
-    switch (schedule_) {
+    switch (SolverOptions::schedule) {
-
+      case SolverOptions::S_SEQ_RANDOM:
-      case S_SEQ_RANDOM:
+        random_shuffle (links_.begin(), links_.end());
-        random_shuffle (updateOrder_.begin(), updateOrder_.end());
         // no break
 
-      case S_SEQ_FIXED:
+      case SolverOptions::S_SEQ_FIXED:
-        for (unsigned c = 0; c < updateOrder_.size(); c++) {
+        for (unsigned i = 0; i < links_.size(); i++) {
-          Link& link = updateOrder_[c];
+          links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
-          calculateNextMessage (link.source, link.destination);
+          links_[i]->updateMessage();
-          updateMessage (updateOrder_[c]);
         }
         break;
 
-      case S_PARALLEL:
+      case SolverOptions::S_PARALLEL:
-        for (unsigned c = 0; c < updateOrder_.size(); c++) {
+        for (unsigned i = 0; i < links_.size(); i++) {
-          Link link = updateOrder_[c];
+          links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
-          calculateNextMessage (link.source, link.destination);
         }
-        for (unsigned c = 0; c < updateOrder_.size(); c++) {
+        for (unsigned i = 0; i < links_.size(); i++) {
-          Link link = updateOrder_[c];
+          links_[i]->updateMessage();
-          updateMessage (updateOrder_[c]);
         }
         break;
 
-      case S_MAX_RESIDUAL:
+      case SolverOptions::S_MAX_RESIDUAL:
         maxResidualSchedule();
         break;
     }
-
-    nIter_++;
   }
-  cout << endl;
+
-  if (DL >= 1) {
+  if (DL >= 2) {
-    if (nIter_ < maxIter_) {
+    cout << endl;
+    if (nIter_ < SolverOptions::maxIter) {
       cout << "Loopy Sum-Product converged in " ; 
       cout << nIter_ << " iterations" << endl;
     } else {
@@ -108,58 +139,168 @@ SPSolver::runSolver (void)
 
 
 ParamSet
-SPSolver::getPosterioriOf (const Variable* var) const
+SPSolver::getPosterioriOf (Vid vid) const
 {
-  assert (var);
+  assert (fg_->getFgVarNode (vid));
-  assert (var == fg_->getVariableById (var->getVarId()));
+  FgVarNode* var = fg_->getFgVarNode (vid);
-  assert (var->getIndex() < msgs_.size());
+  ParamSet probs;
 
-  ParamSet probs (var->getDomainSize(), 1);
   if (var->hasEvidence()) {
-    for (unsigned i = 0; i < probs.size(); i++) {
+    probs.resize (var->getDomainSize(), 0.0);
-      if ((int)i != var->getEvidence()) {
+    probs[var->getEvidence()] = 1.0;
-        probs[i] = 0;
-      }
-    }
-
   } else {
-
+    probs.resize (var->getDomainSize(), 1.0);
-    MessageBanket* mb = msgs_[var->getIndex()]; 
+    CLinkSet links = varsI_[var->getIndex()]->getLinks();
-    const FgVarNode* varNode  = fg_->getFgVarNodes()[var->getIndex()];
+    for (unsigned i = 0; i < links.size(); i++) {
-    vector<Factor*> neighbors = varNode->getFactors();
+      CParamSet msg = links[i]->getMessage();
-    for (unsigned i = 0; i < neighbors.size(); i++) {
-      const Message& msg = mb->getMessage (neighbors[i]);
       for (unsigned j = 0; j < msg.size(); j++) {
         probs[j] *= msg[j];
       }
     }
     Util::normalize (probs);
   }
-
   return probs;
 }
 
 
 
+ParamSet
+SPSolver::getJointDistributionOf (const VidSet& jointVids)
+{
+  FgVarSet jointVars;
+  unsigned dsize = 1;
+  for (unsigned i = 0; i < jointVids.size(); i++) {
+    FgVarNode* varNode = fg_->getFgVarNode (jointVids[i]);
+    dsize *= varNode->getDomainSize();
+    jointVars.push_back (varNode);
+  }
+
+  unsigned maxVid = std::numeric_limits<unsigned>::max();
+  FgVarNode* junctionVar = new FgVarNode (maxVid, dsize);
+  FgVarSet factorVars = { junctionVar };
+  for (unsigned i = 0; i < jointVars.size(); i++) {
+    factorVars.push_back (jointVars[i]);
+  }
+
+  unsigned nParams = dsize * dsize;
+  ParamSet params (nParams);
+  for (unsigned i = 0; i < nParams; i++) {
+    unsigned row = i / dsize;
+    unsigned col = i % dsize;
+    if (row == col) {
+      params[i] = 1;
+    } else {
+      params[i] = 0;
+    }
+  }
+
+  Distribution* dist = new Distribution (params, maxVid);
+  Factor* newFactor = new Factor (factorVars, dist);
+  fg_->addVariable (junctionVar);
+  fg_->addFactor (newFactor);
+
+  runSolver();
+  ParamSet results = getPosterioriOf (maxVid);
+  deleteJunction (newFactor, junctionVar);
+
+  return results;
+}
+
+
+
+void
+SPSolver::initializeSolver (void)
+{
+  fg_->setIndexes();
+
+  CFgVarSet vars = fg_->getFgVarNodes();
+  for (unsigned i = 0; i < varsI_.size(); i++) {
+    delete varsI_[i];
+  }
+  varsI_.reserve (vars.size());
+  for (unsigned i = 0; i < vars.size(); i++) {
+    varsI_.push_back (new SPNodeInfo());
+  }
+
+  CFactorSet factors = fg_->getFactors();
+  for (unsigned i = 0; i < factorsI_.size(); i++) {
+    delete factorsI_[i];
+  }
+  factorsI_.reserve (factors.size());
+  for (unsigned i = 0; i < factors.size(); i++) {
+    factorsI_.push_back (new SPNodeInfo());
+  }
+
+  for (unsigned i = 0; i < links_.size(); i++) {
+    delete links_[i];	
+  }
+  createLinks();
+
+  for (unsigned i = 0; i < links_.size(); i++) {
+    Factor* source  = links_[i]->getFactor();
+    FgVarNode* dest = links_[i]->getVariable();
+    varsI_[dest->getIndex()]->addLink (links_[i]);
+    factorsI_[source->getIndex()]->addLink (links_[i]);
+  }
+}
+
+
+
+void
+SPSolver::createLinks (void)
+{
+  CFactorSet factors = fg_->getFactors();
+  for (unsigned i = 0; i < factors.size(); i++) {
+    CFgVarSet neighbors = factors[i]->getFgVarNodes();
+    for (unsigned j = 0; j < neighbors.size(); j++) {
+      links_.push_back (new Link (factors[i], neighbors[j]));
+    }
+  }
+}
+
+
+
+void
+SPSolver::deleteJunction (Factor* f, FgVarNode* v)
+{
+  fg_->removeFactor (f);
+  f->freeDistribution();
+  delete f;
+  fg_->removeVariable (v);
+  delete v;
+}
+
+
+
 bool
 SPSolver::converged (void)
 {
+  // this can happen if the graph is fully disconnected
+  if (links_.size() == 0) {
+    return true;
+  }
   if (nIter_ == 0 || nIter_ == 1) {
     return false;
   }
   bool converged = true;
-  for (unsigned i = 0; i < updateOrder_.size(); i++) {
+  if (SolverOptions::schedule == SolverOptions::S_MAX_RESIDUAL) {
-    double residual = getResidual (updateOrder_[i]);
+    Param maxResidual = (*(sortedOrder_.begin()))->getResidual();
-    if (DL >= 1) {
+    if (maxResidual < SolverOptions::accuracy) {
-      cout << updateOrder_[i].toString();
+      converged = true;
-      cout << " residual = " << residual << endl;
+    } else {
-    }
-    if (residual > accuracy_) {
       converged = false;
-      if (DL == 0) {
+    }
-        break;
+  } else {
+    for (unsigned i = 0; i < links_.size(); i++) {
+      double residual = links_[i]->getResidual();
+      if (DL >= 2) {
+        cout << links_[i]->toString() + " residual = " << residual << endl;
       }
-    } 
+      if (residual > SolverOptions::accuracy) {
+        converged = false;
+        if (DL == 0) break;
+      }
+    }
   }
   return converged;
 }
@@ -169,127 +310,161 @@ SPSolver::converged (void)
 void
 SPSolver::maxResidualSchedule (void)
 {
-  if (nIter_ == 0) {
+  if (nIter_ == 1) {
-    for (unsigned c = 0; c < updateOrder_.size(); c++) {
+    for (unsigned i = 0; i < links_.size(); i++) {
-      Link& l = updateOrder_[c];
+      links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
-      calculateNextMessage (l.source, l.destination);
+      SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
-      if (DL >= 1) {
+      linkMap_.insert (make_pair (links_[i], it));
-        cout << updateOrder_[c].toString() << " residual = " ;
+      if (DL >= 2 && DL < 5) {
-        cout << getResidual (updateOrder_[c]) << endl;
+        cout << "calculating " << links_[i]->toString() << endl;
       }
     }
-    sort (updateOrder_.begin(), updateOrder_.end(), compareResidual);
+    return;
-  } else {
+  }
 
-    for (unsigned c = 0; c < updateOrder_.size(); c++) {
+  for (unsigned c = 0; c < links_.size(); c++) {
-      Link& link = updateOrder_.front();
+    if (DL >= 2) {
-      updateMessage (link); 
+      cout << endl << "current residuals:" << endl;
-      resetResidual (link);
+      for (SortedOrder::iterator it = sortedOrder_.begin();
+          it != sortedOrder_.end(); it ++) {
+        cout << "    " << setw (30) << left << (*it)->toString();
+        cout << "residual = " << (*it)->getResidual() << endl;
+      }
+    }
 
-      // update the messages that depend on message source --> destination
+    SortedOrder::iterator it = sortedOrder_.begin();
-      vector<Factor*> fstLevelNeighbors = link.destination->getFactors();
+    Link* link = *it;
-      for (unsigned i = 0; i < fstLevelNeighbors.size(); i++) {
+    if (DL >= 2) {
-        if (fstLevelNeighbors[i] != link.source) {
+      cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
-          FgVarSet sndLevelNeighbors;
+    }
-          sndLevelNeighbors = fstLevelNeighbors[i]->getFgVarNodes();
+    if (link->getResidual() < SolverOptions::accuracy) {
-          for (unsigned j = 0; j < sndLevelNeighbors.size(); j++) {
+      return;
-            if (sndLevelNeighbors[j] != link.destination) {
+    }
-              calculateNextMessage (fstLevelNeighbors[i], sndLevelNeighbors[j]);
+    link->updateMessage();
+    link->clearResidual();
+    sortedOrder_.erase (it);
+    linkMap_.find (link)->second = sortedOrder_.insert (link);
+
+    // update the messages that depend on message source --> destin
+    CFactorSet factorNeighbors = link->getVariable()->getFactors();
+    for (unsigned i = 0; i < factorNeighbors.size(); i++) {
+      if (factorNeighbors[i] != link->getFactor()) {
+        CLinkSet links = factorsI_[factorNeighbors[i]->getIndex()]->getLinks();
+        for (unsigned j = 0; j < links.size(); j++) {
+          if (links[j]->getVariable() != link->getVariable()) {
+            if (DL >= 2 && DL < 5) {
+              cout << "    calculating " << links[j]->toString() << endl;
             }
+            links[j]->setNextMessage (getFactor2VarMsg (links[j]));
+            LinkMap::iterator iter = linkMap_.find (links[j]);
+            sortedOrder_.erase (iter->second);
+            iter->second = sortedOrder_.insert (links[j]);
           }
         }
-      }  
+      }
-      sort (updateOrder_.begin(), updateOrder_.end(), compareResidual);
     }
   }
 }
 
 
 
-void
+ParamSet
-SPSolver::updateMessage (const Link& link)
+SPSolver::getFactor2VarMsg (const Link* link) const
 {
-  updateMessage (link.source, link.destination);
+  const Factor* src     = link->getFactor();
-}
+  const FgVarNode* dest = link->getVariable();
-
+  CFgVarSet neighbors = src->getFgVarNodes();
-
+  CLinkSet links = factorsI_[src->getIndex()]->getLinks();
-
+  // calculate the product of messages that were sent
-void
-SPSolver::updateMessage (const Factor* src, const FgVarNode* dest)
-{
-  msgs_[dest->getIndex()]->updateMessage (src);
-/*  cout << src->getLabel() << " --> " << dest->getLabel() << endl; 
-  cout << "    m: " ;
-  Message msg = msgs_[dest->getIndex()]->getMessage (src);
-  for (unsigned i = 0; i < msg.size(); i++) {
-    if (i != 0) cout << ", " ;
-    cout << msg[i];
-  }
-  cout << endl;
-*/
-}
-
-
-
-void
-SPSolver::calculateNextMessage (const Link& link)
-{
-  calculateNextMessage (link.source, link.destination);
-}
-
-
-void
-SPSolver::calculateNextMessage (const Factor* src, const FgVarNode* dest)
-{
-  FgVarSet neighbors = src->getFgVarNodes(); 
-  // calculate the product of MessageBankets sended
   // to factor `src', except from var `dest'
-  Factor result = *src;
+  Factor result (*src);
-  for (unsigned i = 0; i < neighbors.size(); i++) {
+  Factor temp;
-    if (neighbors[i] != dest) {
+  if (DL >= 5) {
-      Message msg (neighbors[i]->getDomainSize(), 1);
+    cout << "calculating " ;
-      calculateVarFactorMessage (neighbors[i], src, msg);
+    cout << src->getLabel() << " --> " << dest->getLabel();
-      result *= Factor (neighbors[i], msg);
+    cout << endl;
-    }
   }
-  // marginalize all vars except `dest'
   for (unsigned i = 0; i < neighbors.size(); i++) {
-    if (neighbors[i] != dest) {
+    if (links[i]->getVariable() != dest) {
-      result.marginalizeVariable (neighbors[i]);
+      if (DL >= 5) {
-    }
+        cout << "    message from " << links[i]->getVariable()->getLabel();
-  }
+        cout << ":  " ;
-  msgs_[dest->getIndex()]->setNextMessage (src, result.getParameters());
+        ParamSet p = getVar2FactorMsg (links[i]);
-}
+        cout << endl;
-
+        Factor temp2 (links[i]->getVariable(), p);
-
+        temp.multiplyByFactor (temp2);
-
+        temp2.freeDistribution();
-void
-SPSolver::calculateVarFactorMessage (const FgVarNode* src,
-                                     const Factor* dest,
-                                     Message& placeholder) const
-{
-  assert (src->getDomainSize() == (int)placeholder.size());
-  if (src->hasEvidence()) {
-    for (unsigned i = 0; i < placeholder.size(); i++) {
-      if ((int)i != src->getEvidence()) {
-        placeholder[i] = 0.0;
       } else {
-        placeholder[i] = 1.0;
+        Factor temp2 (links[i]->getVariable(), getVar2FactorMsg (links[i]));
-      }
+        temp.multiplyByFactor (temp2);
-    }
+        temp2.freeDistribution();
-
-  } else {
-
-    MessageBanket* mb = msgs_[src->getIndex()];
-    vector<Factor*> neighbors = src->getFactors();
-    for (unsigned i = 0; i < neighbors.size(); i++) {
-      if (neighbors[i] != dest) {
-        const Message& fromFactor = mb->getMessage (neighbors[i]);
-        for (unsigned j = 0; j < fromFactor.size(); j++) {
-          placeholder[j] *= fromFactor[j];
-        }
       }
     }
   }
+  if (links.size() >= 2) {
+    result.multiplyByFactor (temp, &(src->getCptEntries()));
+    if (DL >= 5) {
+      cout << "    message product: " ;
+      cout << Util::parametersToString (temp.getParameters()) << endl;
+      cout << "    factor product:  " ;
+      cout << Util::parametersToString (src->getParameters());
+      cout << " x " ;
+      cout << Util::parametersToString (temp.getParameters());
+      cout << " = " ;
+      cout << Util::parametersToString (result.getParameters()) << endl;
+    }
+    temp.freeDistribution();
+  }
+
+  for (unsigned i = 0; i < links.size(); i++) {
+    if (links[i]->getVariable() != dest) {
+      result.removeVariable (links[i]->getVariable());
+    }
+  }
+  if (DL >= 5) {
+    cout << "    final message:   " ;
+    cout << Util::parametersToString (result.getParameters()) << endl << endl;
+  }
+  ParamSet msg = result.getParameters();
+  result.freeDistribution();
+  return msg;
+}
+
+
+
+ParamSet
+SPSolver::getVar2FactorMsg (const Link* link) const
+{
+  const FgVarNode* src = link->getVariable();
+  const Factor* dest   = link->getFactor();
+  ParamSet msg;
+  if (src->hasEvidence()) {
+    msg.resize (src->getDomainSize(), 0.0);
+    msg[src->getEvidence()] = 1.0;
+    if (DL >= 5) {
+      cout << Util::parametersToString (msg);
+    }
+  } else {
+    msg.resize (src->getDomainSize(), 1.0);
+  }
+  if (DL >= 5) {
+    cout << Util::parametersToString (msg);
+  }
+  CLinkSet links = varsI_[src->getIndex()]->getLinks();
+  for (unsigned i = 0; i < links.size(); i++) {
+    if (links[i]->getFactor() != dest) {
+      CParamSet msgFromFactor = links[i]->getMessage();
+      for (unsigned j = 0; j < msgFromFactor.size(); j++) {
+        msg[j] *= msgFromFactor[j];
+      }
+      if (DL >= 5) {
+        cout << " x " << Util::parametersToString (msgFromFactor);
+      }
+    }
+  }
+  if (DL >= 5) {
+    cout << " = " << Util::parametersToString (msg);
+  }
+  return msg;
 }
 

packages/CLPBN/clpbn/bp/SPSolver.h

@@ -1,10 +1,8 @@
-#ifndef BP_SPSOLVER_H
+#ifndef BP_SP_SOLVER_H
-#define BP_SPSOLVER_H
+#define BP_SP_SOLVER_H
 
-#include <cmath>
-#include <map>
 #include <vector>
-#include <string>
+#include <set>
 
 #include "Solver.h"
 #include "FgVarNode.h"
@@ -15,157 +13,118 @@ using namespace std;
 class FactorGraph;
 class SPSolver;
 
-struct Link
-{
-  Link (Factor* s, FgVarNode* d)
-  { 
-    source      = s;
-    destination = d;
-  }
-  string toString (void) const
-  {
-    stringstream ss;
-    ss << source->getLabel() << " --> " ;
-    ss << destination->getLabel();
-    return ss.str();
-  }
-  Factor*           source;
-  FgVarNode*        destination;
-  static SPSolver*  klass;
-};
 
-
+class Link
-
-class MessageBanket
 {
   public:
-    MessageBanket (const FgVarNode* var)
+    Link (Factor* f, FgVarNode* v)
+    { 
+      factor_ = f;
+      var_    = v;
+      currMsg_.resize (v->getDomainSize(), 1);
+      nextMsg_.resize (v->getDomainSize(), 1);
+      msgSended_ = false;
+      residual_ = 0.0;
+    }
+  
+    void setMessage (ParamSet msg)
     {
-      vector<Factor*> sources = var->getFactors();
+      Util::normalize (msg);
-      for (unsigned i = 0; i < sources.size(); i++) {
+      residual_ = Util::getMaxNorm (currMsg_, msg);
-        indexMap_.insert (make_pair (sources[i], i));
+      currMsg_ = msg;
-        currMsgs_.push_back (Message(var->getDomainSize(), 1));
-        nextMsgs_.push_back (Message(var->getDomainSize(), -10));
-        residuals_.push_back (0.0);
-      }
     }
 
-    void updateMessage (const Factor* source)
+    void setNextMessage (CParamSet msg)
     {
-      unsigned idx = getIndex(source);
+      nextMsg_ = msg;
-      currMsgs_[idx] = nextMsgs_[idx];
+      Util::normalize (nextMsg_);
+      residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
     }
 
-    void setNextMessage (const Factor* source, const Message& msg)
+    void updateMessage (void) 
     {
-      unsigned idx = getIndex(source);
+      currMsg_ = nextMsg_;
-      nextMsgs_[idx] = msg;
+      msgSended_ = true;
-      residuals_[idx] = computeResidual (source);
     }
 
-    const Message& getMessage (const Factor* source) const
+    string toString (void) const
     {
-      return currMsgs_[getIndex(source)];
+      stringstream ss;
-    }
+      ss << factor_->getLabel();
-
+      ss << " -- " ;
-    double getResidual (const Factor* source) const
+      ss << var_->getLabel();
-    {
+      return ss.str();
-      return residuals_[getIndex(source)];
-    }
-    
-    void resetResidual (const Factor* source)
-    {
-      residuals_[getIndex(source)] = 0.0;
     }
 
+    Factor*      getFactor (void) const        { return factor_; }
+    FgVarNode*   getVariable (void) const      { return var_; }
+    CParamSet    getMessage (void) const       { return currMsg_; }
+    bool         messageWasSended (void) const { return msgSended_; }
+    double       getResidual (void) const      { return residual_; }
+    void         clearResidual (void)          { residual_ = 0.0; }
+ 
   private:
-    double computeResidual (const Factor* source)
+    Factor*      factor_;
-    {
+    FgVarNode*   var_;
-      double change = 0.0;
+    ParamSet     currMsg_;
-      unsigned idx  = getIndex (source);
+    ParamSet     nextMsg_;
-      const Message& currMessage = currMsgs_[idx];
+    bool         msgSended_;
-      const Message& nextMessage = nextMsgs_[idx];
+    double       residual_;
-      for (unsigned i = 0; i < currMessage.size(); i++) {
-        change += abs (currMessage[i] - nextMessage[i]);
-      }
-      return change;
-    }
- 
-    unsigned getIndex (const Factor* factor) const
-    {
-      assert (factor);
-      assert (indexMap_.find(factor) != indexMap_.end());
-      return indexMap_.find(factor)->second;
-    }
- 
-    typedef map<const Factor*, unsigned> IndexMap;
-
-    IndexMap               indexMap_;
-    vector<Message>        currMsgs_;
-    vector<Message>        nextMsgs_;
-    vector<double>         residuals_;
 };
 
 
+class SPNodeInfo
+{
+  public:
+    void         addLink (Link* link)         { links_.push_back (link); }
+    CLinkSet     getLinks (void)              { return links_; }
+
+  private:
+    LinkSet      links_;
+};
+
 
 class SPSolver : public Solver
 {
   public:
-    SPSolver (const FactorGraph&);
+    SPSolver (FactorGraph&);
-   ~SPSolver (void);
+    virtual ~SPSolver (void);
 
-    void            runSolver (void);
+    void              runSolver (void);
-    ParamSet        getPosterioriOf (const Variable* var) const;
+    virtual ParamSet  getPosterioriOf (Vid) const;
+    ParamSet          getJointDistributionOf (CVidSet);
+ 
+  protected:
+    virtual void      initializeSolver (void);
+    void              runTreeSolver (void);
+    bool              readyToSendMessage (const Link*) const;
+    virtual void      createLinks (void);
+    virtual void      deleteJunction (Factor*, FgVarNode*);
+    bool              converged (void);
+    virtual void      maxResidualSchedule (void);
+    virtual ParamSet  getFactor2VarMsg (const Link*) const;
+    virtual ParamSet  getVar2FactorMsg (const Link*) const;
 
-  private:
+    struct CompareResidual {
-    bool            converged (void);
+      inline bool operator() (const Link* link1, const Link* link2)
-    void            maxResidualSchedule (void);
+      {
-    void            updateMessage (const Link&);
+        return link1->getResidual() > link2->getResidual();
-    void            updateMessage (const Factor*, const FgVarNode*);
+      }
-    void            calculateNextMessage (const Link&);
+    };
-    void            calculateNextMessage (const Factor*, const FgVarNode*);
+
-    void            calculateVarFactorMessage (
+    FactorGraph*         fg_;
-                         const FgVarNode*, const Factor*, Message&) const;
+    LinkSet              links_;
-    double          getResidual (const Link&) const;
+    vector<SPNodeInfo*>  varsI_;
-    void            resetResidual (const Link&) const;
+    vector<SPNodeInfo*>  factorsI_;
-    friend bool     compareResidual (const Link&, const Link&);
+    unsigned             nIter_;
+
+    typedef multiset<Link*, CompareResidual> SortedOrder;
+    SortedOrder sortedOrder_;
+
+    typedef map<Link*, SortedOrder::iterator> LinkMap;
+    LinkMap linkMap_;
 
-    const FactorGraph*          fg_;
-    vector<MessageBanket*>      msgs_;
-    Schedule                    schedule_;
-    int                         nIter_;
-    double                      accuracy_;
-    int                         maxIter_;
-    vector<Link>                updateOrder_;
 };
 
-
+#endif // BP_SP_SOLVER_H
-
-inline double
-SPSolver::getResidual (const Link& link) const
-{
-  MessageBanket* mb = Link::klass->msgs_[link.destination->getIndex()];
-  return mb->getResidual (link.source);
-}
-
-
-
-inline void
-SPSolver::resetResidual (const Link& link) const
-{
-  MessageBanket* mb = Link::klass->msgs_[link.destination->getIndex()];
-  mb->resetResidual (link.source);
-}
-
-
-
-inline bool
-compareResidual (const Link& link1, const Link& link2)
-{
-  MessageBanket* mb1 = Link::klass->msgs_[link1.destination->getIndex()];
-  MessageBanket* mb2 = Link::klass->msgs_[link2.destination->getIndex()];
-  return mb1->getResidual(link1.source) > mb2->getResidual(link2.source);
-}
-
-#endif
 

packages/CLPBN/clpbn/bp/Shared.h

@@ -2,14 +2,15 @@
 #define BP_SHARED_H
 
 #include <cmath>
-#include <iostream>
-#include <fstream>
 #include <cassert>
 #include <vector>
 #include <map>
 #include <unordered_map>
 
-// Macro to disallow the copy constructor and operator= functions
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+
 #define DISALLOW_COPY_AND_ASSIGN(TypeName) \
   TypeName(const TypeName&);               \
   void operator=(const TypeName&)
@@ -19,61 +20,162 @@ using namespace std;
 class Variable;
 class BayesNode;
 class FgVarNode;
+class Factor;
+class Link;
+class Edge;
 
 typedef double                             Param;
 typedef vector<Param>                      ParamSet;
-typedef vector<Param>                      Message;
+typedef const ParamSet&                    CParamSet;
+typedef unsigned                           Vid;
+typedef vector<Vid>                        VidSet;
+typedef const VidSet&                      CVidSet;
 typedef vector<Variable*>                  VarSet;
-typedef vector<BayesNode*>                 NodeSet;
+typedef vector<BayesNode*>                 BnNodeSet;
+typedef const BnNodeSet&                   CBnNodeSet;
 typedef vector<FgVarNode*>                 FgVarSet;
+typedef const FgVarSet&                    CFgVarSet;
+typedef vector<Factor*>                    FactorSet;
+typedef const FactorSet&                   CFactorSet;
+typedef vector<Link*>                      LinkSet;
+typedef const LinkSet&                     CLinkSet;
+typedef vector<Edge*>                      EdgeSet;
+typedef const EdgeSet&                     CEdgeSet;
 typedef vector<string>                     Domain;
-typedef vector<unsigned>                   DomainConf;
+typedef vector<unsigned>                   DConf;
-typedef pair<unsigned, unsigned>           DomainConstr;
+typedef pair<unsigned, unsigned>           DConstraint;
-typedef unordered_map<unsigned, unsigned>  IndexMap;
+typedef map<unsigned, unsigned> IndexMap;
 
-
+// level of debug information
-//extern unsigned DL;
 static const unsigned DL = 0;
 
-// number of digits to show when printing a parameter
+static const int NO_EVIDENCE = -1;
-static const unsigned PRECISION = 10;
 
-// shared by bp and sp solver
+// number of digits to show when printing a parameter
-enum Schedule
+static const unsigned PRECISION = 5;
+
+static const bool     EXPORT_TO_DOT   = false;
+static const unsigned EXPORT_MIN_SIZE = 30;
+
+
+namespace SolverOptions
 {
-  S_SEQ_FIXED,
+  enum Schedule
-  S_SEQ_RANDOM,
+  {
-  S_PARALLEL,
+    S_SEQ_FIXED,
-  S_MAX_RESIDUAL
+    S_SEQ_RANDOM,
+    S_PARALLEL,
+    S_MAX_RESIDUAL
+  };
+  extern bool      runBayesBall;
+  extern bool      convertBn2Fg;
+  extern bool      compressFactorGraph;
+  extern Schedule  schedule;
+  extern double    accuracy;
+  extern unsigned  maxIter;
+}
+
+
+namespace Util
+{
+  void normalize (ParamSet&);
+  void pow (ParamSet&, unsigned);
+  double getL1dist (CParamSet, CParamSet);
+  double getMaxNorm (CParamSet, CParamSet);
+  bool isInteger (const string&);
+  string parametersToString (CParamSet);
+  vector<DConf> getDomainConfigurations (const VarSet&);
+  vector<string> getInstantiations (const VarSet&);
 };
 
 
 struct NetInfo
 {
-  NetInfo (unsigned c, double t)
+  NetInfo (void)
   { 
-    counting    = c;
+    counting    = 0;
-    solvingTime = t;
+    nIters      = 0;
+    solvingTime = 0.0;
   }
   unsigned  counting;
   double    solvingTime;
+  unsigned  nIters;
 };
 
+
+struct CompressInfo
+{ 
+  CompressInfo (unsigned a, unsigned b, unsigned c,
+                unsigned d, unsigned e) {
+    nUncVars     = a; 
+    nUncFactors  = b; 
+    nCompVars    = c;
+    nCompFactors = d;
+    nNeighborlessVars = e;
+  }
+  unsigned nUncVars;
+  unsigned nUncFactors;
+  unsigned nCompVars;
+  unsigned nCompFactors;
+  unsigned nNeighborlessVars;
+};
+
+
 typedef map<unsigned, NetInfo> StatisticMap; 
-
-
 class Statistics
 {
   public:
 
-    static void updateStats (unsigned size, double time)
+    static void updateStats (unsigned size, unsigned nIters, double time)
     {
-      StatisticMap::iterator it  = stats_.find(size);
+      StatisticMap::iterator it  = stats_.find (size);
       if (it == stats_.end()) {
-        stats_.insert (make_pair (size, NetInfo (1, 0.0)));
+        it = (stats_.insert (make_pair (size, NetInfo()))).first;
       } else {
         it->second.counting ++;
+        it->second.nIters += nIters;
         it->second.solvingTime += time;
+        totalOfIterations += nIters;
+          if (nIters > maxIterations) { 
+          maxIterations = nIters;
+        }
+      }
+    }
+
+    static void updateCompressingStats (unsigned nUncVars,
+                                        unsigned nUncFactors,
+                                        unsigned nCompVars, 
+                                        unsigned nCompFactors,
+                                        unsigned nNeighborlessVars) {
+      compressInfo_.push_back (CompressInfo (
+          nUncVars, nUncFactors, nCompVars, nCompFactors, nNeighborlessVars));
+    }
+
+    static void printCompressingStats (const char* fileName)
+    {
+      ofstream out (fileName);
+      if (!out.is_open()) {
+        cerr << "error: cannot open file to write at " ;
+        cerr << "BayesNet::printCompressingStats()" << endl;
+        abort();
+      }
+      out << "--------------------------------------" ;
+      out << "--------------------------------------" << endl;
+      out << " Compression Stats" << endl;
+      out << "--------------------------------------" ;
+      out << "--------------------------------------" << endl;
+      out << left;
+      out << "Uncompress   Compressed   Uncompress   Compressed   Neighborless";
+      out << endl;
+      out << "Vars         Vars         Factors      Factors      Vars" ;
+      out << endl;
+      for (unsigned i = 0; i < compressInfo_.size(); i++) {
+        out << setw (13) << compressInfo_[i].nUncVars;
+        out << setw (13) << compressInfo_[i].nCompVars;
+        out << setw (13) << compressInfo_[i].nUncFactors;
+        out << setw (13) << compressInfo_[i].nCompFactors;
+        out << setw (13) << compressInfo_[i].nNeighborlessVars;
+        out << endl;
       }
     }
 
@@ -84,20 +186,12 @@ class Statistics
       return it->second.counting;
     }
 
-    static void updateIterations (unsigned nIters)
-    {
-      totalOfIterations += nIters;
-      if (nIters > maxIterations) { 
-        maxIterations = nIters;
-      }
-    }
-
     static void writeStats (void)
     {
       ofstream out ("../../stats.txt");
       if (!out.is_open()) {
         cerr << "error: cannot open file to write at " ;
-        cerr << "Statistics:::updateStats()" << endl;
+        cerr << "Statistics::updateStats()" << endl;
         abort();
       }
       unsigned avgIterations = 0;
@@ -117,17 +211,24 @@ class Statistics
       out << "   average iterations:         " << avgIterations      << endl;
       out << "total solving time             " << totalSolvingTime   << endl;
       out << endl;
-      out << "Network Size\tCounting\tSolving Time\tAverage Time" << endl;
+      out << left << endl;
+      out << setw (15) << "Network Size" ;
+      out << setw (15) << "Counting" ;
+      out << setw (15) << "Solving Time" ;
+      out << setw (15) << "Average Time" ;
+      out << setw (15) << "#Iterations" ;
+      out << endl;
       for (StatisticMap::iterator it = stats_.begin();
           it != stats_.end(); it++) {
-        out << it->first;
+        out << setw (15) << it->first;
-        out << "\t\t" << it->second.counting;
+        out << setw (15) << it->second.counting;
-        out << "\t\t" << it->second.solvingTime;
+        out << setw (15) << it->second.solvingTime;
         if (it->second.counting > 0) {
-          out << "\t\t" << it->second.solvingTime / it->second.counting;
+          out << setw (15) << it->second.solvingTime / it->second.counting;
         } else {
-          out << "\t\t0.0" ;
+          out << setw (15) << "0.0" ;
         }
+        out << setw (15) << it->second.nIters;
         out << endl;
       }
       out.close();
@@ -142,62 +243,8 @@ class Statistics
     static StatisticMap stats_;
     static unsigned maxIterations;
     static unsigned totalOfIterations;
-
+    static vector<CompressInfo> compressInfo_;
 };
 
-
+#endif //BP_SHARED_H
-
-class Util
-{
-  public:
-    static void normalize (ParamSet& v)
-    {
-     double sum = 0.0;
-      for (unsigned i = 0; i < v.size(); i++) {
-        sum += v[i];
-      }
-      assert (sum != 0.0);
-      for (unsigned i = 0; i < v.size(); i++) {
-        v[i] /= sum;
-      }
-    }
-
-    static double getL1dist (const ParamSet& v1, const ParamSet& v2)
-    {
-      assert (v1.size() == v2.size());
-      double dist = 0.0;
-      for (unsigned i = 0; i < v1.size(); i++) {
-        dist += abs (v1[i] - v2[i]);
-      }
-      return dist;
-    }
-
-    static double getMaxNorm (const ParamSet& v1, const ParamSet& v2)
-    {
-      assert (v1.size() == v2.size());
-      double max = 0.0;
-      for (unsigned i = 0; i < v1.size(); i++) {
-        double diff = abs (v1[i] - v2[i]);
-        if (diff > max) {
-          max = diff;
-        }
-      }
-      return max;
-    }
-
-    static bool isInteger (const string& s)
-    {
-      stringstream ss1 (s);
-      stringstream ss2;
-      int integer;
-      ss1 >> integer;
-      ss2 << integer;
-      return (ss1.str() == ss2.str());
-    }
-};
-
-
-//unsigned Statistics::totalOfIterations  = 0;
-
-#endif
 

packages/CLPBN/clpbn/bp/Solver.h

@@ -15,19 +15,30 @@ class Solver
     {
       gm_ = gm;
     }
+    virtual ~Solver() {} // to call subclass destructor
     virtual void     runSolver (void) = 0;
-    virtual ParamSet getPosterioriOf  (const Variable*) const = 0;
+    virtual ParamSet getPosterioriOf  (Vid) const = 0;
+    virtual ParamSet getJointDistributionOf (const VidSet&) = 0;
 
-    void printPosterioriOf (const Variable* var) const
+    void printAllPosterioris (void) const
     {
+      VarSet vars = gm_->getVariables();
+      for (unsigned i = 0; i < vars.size(); i++) {
+        printPosterioriOf (vars[i]->getVarId());
+      }
+    }
+
+    void printPosterioriOf (Vid vid) const
+    {
+      Variable* var = gm_->getVariable (vid);
       cout << endl;
       cout << setw (20) << left << var->getLabel() << "posteriori" ;
       cout << endl;
       cout << "------------------------------" ;
       cout << endl;
       const Domain& domain = var->getDomain();
-      ParamSet results = getPosterioriOf (var);
+      ParamSet results = getPosterioriOf (vid);
-      for (int xi = 0; xi < var->getDomainSize(); xi++) {
+      for (unsigned xi = 0; xi < var->getDomainSize(); xi++) {
         cout << setw (20) << domain[xi];
         cout << setprecision (PRECISION) << results[xi];
         cout << endl;
@@ -35,16 +46,35 @@ class Solver
       cout << endl;
     }
 
-    void printAllPosterioris (void) const
+    void printJointDistributionOf (const VidSet& vids)
     {
-      VarSet vars = gm_->getVariables();
+      const ParamSet& jointDist = getJointDistributionOf (vids);
-      for (unsigned i = 0; i < vars.size(); i++) {
+      cout << endl;
-        printPosterioriOf (vars[i]);
+      cout << "joint distribution of " ;
+      VarSet vars;
+      for (unsigned i = 0; i < vids.size() - 1; i++) {
+        Variable* var = gm_->getVariable (vids[i]);
+        cout << var->getLabel() << ", " ;
+        vars.push_back (var);
       }
+      Variable* var = gm_->getVariable (vids[vids.size() - 1]);
+      cout << var->getLabel() ;
+      vars.push_back (var);
+      cout << endl;
+      cout << "------------------------------" ;
+      cout << endl;
+      const vector<string>& domainConfs = Util::getInstantiations (vars);
+      for (unsigned i = 0; i < jointDist.size(); i++) {
+        cout << left << setw (20) << domainConfs[i];
+        cout << setprecision (PRECISION) << jointDist[i];
+        cout << endl;
+      }
+      cout << endl;
     }
 
   private:
-     const GraphicalModel* gm_;
+    const GraphicalModel* gm_;
 };
 
-#endif
+#endif //BP_SOLVER_H
+

packages/CLPBN/clpbn/bp/Util.cpp

@@ -0,0 +1,191 @@
+#include <sstream>
+
+#include "Variable.h"
+#include "Shared.h"
+
+namespace SolverOptions {
+
+bool runBayesBall         = false;
+bool convertBn2Fg         = true;
+bool compressFactorGraph  = true;
+Schedule schedule = S_SEQ_FIXED;
+//Schedule schedule = S_SEQ_RANDOM;
+//Schedule schedule = S_PARALLEL;
+//Schedule schedule = S_MAX_RESIDUAL;
+double accuracy  = 0.0001;
+unsigned maxIter = 1000; //FIXME
+
+}
+
+
+
+unsigned Statistics::numCreatedNets      = 0;
+unsigned Statistics::numSolvedPolyTrees  = 0;
+unsigned Statistics::numSolvedLoopyNets  = 0;
+unsigned Statistics::numUnconvergedRuns  = 0;
+unsigned Statistics::maxIterations       = 0;
+unsigned Statistics::totalOfIterations   = 0;
+vector<CompressInfo> Statistics::compressInfo_;
+StatisticMap Statistics::stats_;
+
+
+
+namespace Util {
+
+void
+normalize (ParamSet& v)
+{
+  double sum = 0.0;
+  for (unsigned i = 0; i < v.size(); i++) {
+    sum += v[i];
+  }
+  assert (sum != 0.0);
+  for (unsigned i = 0; i < v.size(); i++) {
+    v[i] /= sum;
+  }
+}
+
+
+void
+pow (ParamSet& v, unsigned expoent)
+{
+  for (unsigned i = 0; i < v.size(); i++) {
+    double value = 1;
+    for (unsigned j = 0; j < expoent; j++) {
+      value *= v[i];
+    }
+    v[i] = value;
+  }
+}
+
+
+double
+getL1dist (const ParamSet& v1, const ParamSet& v2)
+{
+  assert (v1.size() == v2.size());
+  double dist = 0.0;
+  for (unsigned i = 0; i < v1.size(); i++) {
+    dist += abs (v1[i] - v2[i]);
+  }
+  return dist;
+}
+
+
+double
+getMaxNorm (const ParamSet& v1, const ParamSet& v2)
+{
+  assert (v1.size() == v2.size());
+  double max = 0.0;
+  for (unsigned i = 0; i < v1.size(); i++) {
+    double diff = abs (v1[i] - v2[i]);
+    if (diff > max) {
+      max = diff;
+    }
+  }
+  return max;
+}
+
+
+bool
+isInteger (const string& s)
+{
+  stringstream ss1 (s);
+  stringstream ss2;
+  int integer;
+  ss1 >> integer;
+  ss2 << integer;
+  return (ss1.str() == ss2.str());
+}
+
+
+
+string
+parametersToString (CParamSet v)
+{
+  stringstream ss;  
+  ss << "[" ; 
+  for (unsigned i = 0; i < v.size() - 1; i++) {
+    ss << v[i] << ", " ;
+  }
+  if (v.size() != 0) {
+    ss << v[v.size() - 1];
+  }
+  ss << "]" ;
+  return ss.str();
+}
+
+
+
+vector<DConf>
+getDomainConfigurations (const VarSet& vars)
+{
+  unsigned nConfs = 1;
+  for (unsigned i = 0; i < vars.size(); i++) {
+    nConfs *= vars[i]->getDomainSize();
+  }
+
+  vector<DConf> confs (nConfs);
+  for (unsigned i = 0; i < nConfs; i++) {
+    confs[i].resize (vars.size());
+  }
+
+  unsigned nReps = 1;
+  for (int i = vars.size() - 1; i >= 0; i--) {
+    unsigned index = 0;
+    while (index < nConfs) {
+      for (unsigned j = 0; j < vars[i]->getDomainSize(); j++) {
+        for (unsigned r = 0; r < nReps; r++) {
+          confs[index][i] = j; 
+          index++;
+        }
+      }
+    }
+    nReps *= vars[i]->getDomainSize();
+  }
+  return confs;
+}
+
+
+vector<string>
+getInstantiations (const VarSet& vars)
+{
+  //FIXME handle variables without domain
+  /*
+  char c = 'a' ;
+  const DConf& conf = entries[i].getDomainConfiguration();
+  for (unsigned j = 0; j < conf.size(); j++) {
+    if (j != 0) ss << "," ;
+    ss << c << conf[j] + 1;
+    c ++;
+  }
+  */
+  unsigned rowSize  = 1;
+  for (unsigned i = 0; i < vars.size(); i++) {
+    rowSize *= vars[i]->getDomainSize();
+  }
+
+  vector<string> headers (rowSize);
+
+  unsigned nReps = 1;
+  for (int i = vars.size() - 1; i >= 0; i--) {
+    Domain domain = vars[i]->getDomain();
+    unsigned index = 0;
+    while (index < rowSize) {
+      for (unsigned j = 0; j < vars[i]->getDomainSize(); j++) {
+        for (unsigned r = 0; r < nReps; r++) {
+          if (headers[index] != "") {
+            headers[index] = domain[j] + ", " + headers[index];
+          } else {
+            headers[index] = domain[j];
+          }
+          index++;
+        }
+      }
+    }
+    nReps *= vars[i]->getDomainSize();
+  }
+  return headers;
+}
+
+}
+

packages/CLPBN/clpbn/bp/Variable.h

@@ -1,9 +1,10 @@
-#ifndef BP_GENERIC_VARIABLE_H
+#ifndef BP_VARIABLE_H
-#define BP_GENERIC_VARIABLE_H
+#define BP_VARIABLE_H
+
+#include <algorithm>
 
 #include <sstream>
 
-#include <algorithm>
 #include "Shared.h"
 
 using namespace std;
@@ -12,33 +13,61 @@ class Variable
 {
   public:
 
-    Variable (unsigned varId)
+    Variable (const Variable* v)
     {
-      this->varId_      = varId;
+      vid_ = v->getVarId();
-      this->dsize_      = 0;
+      dsize_ = v->getDomainSize();
-      this->evidence_   = -1;
+      if (v->hasDomain()) {
-      this->label_      = 0;
+        domain_ = v->getDomain();
+        dsize_ = domain_.size();
+      } else {
+        dsize_ = v->getDomainSize();
+      }
+      evidence_ = v->getEvidence();
+      if (v->hasLabel()) {
+        label_ = new string (v->getLabel());
+      } else {
+        label_ = 0;
+      }
     }
 
-    Variable (unsigned varId, unsigned dsize, int evidence = -1)
+    Variable (Vid vid)
+    {
+      this->vid_       = vid;
+      this->dsize_     = 0;
+      this->evidence_  = NO_EVIDENCE;
+      this->label_     = 0;
+    }
+
+    Variable (Vid vid, unsigned dsize, int evidence = NO_EVIDENCE,
+                                       const string& lbl = string())
     {
       assert (dsize != 0);
       assert (evidence < (int)dsize);
-      this->varId_      = varId;
+      this->vid_       = vid;
-      this->dsize_      = dsize;
+      this->dsize_     = dsize;
-      this->evidence_   = evidence;
+      this->evidence_  = evidence;
-      this->label_      = 0;
+      if (!lbl.empty()) {
+        this->label_   = new string (lbl);
+      } else {
+        this->label_   = 0;
+      }
     }
 
-    Variable (unsigned varId, const Domain& domain, int evidence = -1)
+    Variable (Vid vid, const Domain& domain, int evidence = NO_EVIDENCE,
+                                             const string& lbl = string())
     {
       assert (!domain.empty());
       assert (evidence < (int)domain.size());
-      this->varId_      = varId;
+      this->vid_       = vid;
-      this->dsize_      = domain.size();
+      this->dsize_     = domain.size();
-      this->domain_     = domain;
+      this->domain_    = domain;
-      this->evidence_   = evidence;
+      this->evidence_  = evidence;
-      this->label_      = 0;
+      if (!lbl.empty()) {
+        this->label_   = new string (lbl);
+      } else {
+        this->label_   = 0;
+      }
     }
 
    ~Variable (void)
@@ -46,19 +75,19 @@ class Variable
       delete label_;
     }
 
-    unsigned       getVarId (void) const       { return varId_; }
+    unsigned   getVarId (void) const       { return vid_; }
-    unsigned       getIndex (void) const       { return index_; }
+    unsigned   getIndex (void) const       { return index_; }
-    void           setIndex (unsigned idx)     { index_ = idx; }
+    void       setIndex (unsigned idx)     { index_ = idx; }
-    int            getDomainSize (void) const  { return dsize_; }
+    unsigned   getDomainSize (void) const  { return dsize_; }
-    bool           hasEvidence (void) const    { return evidence_ != -1; }
+    bool       hasEvidence (void) const    { return evidence_ != NO_EVIDENCE; }
-    int            getEvidence (void) const    { return evidence_; }
+    int        getEvidence (void) const    { return evidence_; }
-    bool           hasDomain (void)            { return !domain_.empty(); }
+    bool       hasDomain (void) const      { return !domain_.empty(); }
-    bool           hasLabel (void)             { return label_ != 0; }
+    bool       hasLabel (void) const       { return label_ != 0; }
 
-   bool isValidStateIndex (int index)
+    bool isValidStateIndex (int index)
-   {
+    {
-     return index >= 0 && index < dsize_;
+      return index >= 0 && index < (int)dsize_;
-   }
+    }
 
     bool isValidState (const string& state)
     {
@@ -70,7 +99,7 @@ class Variable
       assert (dsize_ != 0);
       if (domain_.size() == 0) {
         Domain d;
-        for (int i = 0; i < dsize_; i++) {
+        for (unsigned i = 0; i < dsize_; i++) {
           stringstream ss;
           ss << "x" << i ;
           d.push_back (ss.str());
@@ -110,7 +139,7 @@ class Variable
       }
     }
 
-    void setLabel (string label)
+    void setLabel (const string& label)
     {
       label_ = new string (label);
     }
@@ -119,25 +148,25 @@ class Variable
     {
       if (label_ == 0) {
         stringstream ss;
-        ss << "v" << varId_;
+        ss << "v" << vid_;
         return ss.str();
       } else {
         return *label_;
       }
     }
 
-  protected:
-    unsigned       varId_;
-    string*        label_;
-    unsigned       index_;
-    int            evidence_;
 
   private:
     DISALLOW_COPY_AND_ASSIGN (Variable);
-    Domain         domain_;
+
-    int            dsize_;
+    Vid         vid_;
+    unsigned    dsize_;
+    int         evidence_;
+    Domain      domain_;
+    string*     label_;
+    unsigned    index_;
 
 };
 
-#endif // BP_GENERIC_VARIABLE_H
+#endif // BP_VARIABLE_H
 

packages/CLPBN/clpbn/bp/examples/1parentNchilds.yap

@@ -0,0 +1,34 @@
+
+:- use_module(library(clpbn)).
+
+:- set_clpbn_flag(solver, bp).
+
+%
+%         R 
+%       / | \
+%      /  |  \ 
+%     A   B   C
+%
+
+
+r(R) :-
+    { R = r with p([t, f], [0.35, 0.65]) }.
+
+a(A) :-
+    r(R),
+    child_dist(R,Dist),
+    { A = a with Dist }.
+
+b(B) :-
+    r(R),
+    child_dist(R,Dist),
+    { B = b with Dist }.
+
+c(C) :-
+    r(R),
+    child_dist(R,Dist),
+    { C = c with Dist }.
+
+
+child_dist(R, p([t, f], [0.3, 0.4, 0.25, 0.05], [R])).
+

packages/CLPBN/clpbn/bp/examples/bp-example.xml

@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="US-ASCII"?>
+
+<!--
+
+     A     B
+      \   /
+       \ / 
+        C
+
+-->
+
+<BIF VERSION="0.3">
+<NETWORK>
+<NAME>Neapolitan</NAME>
+
+<VARIABLE TYPE="nature">
+	<NAME>A</NAME>
+	<OUTCOME>a1</OUTCOME>
+	<OUTCOME>a2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>B</NAME>
+	<OUTCOME>b1</OUTCOME>
+	<OUTCOME>b2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>C</NAME>
+	<OUTCOME>c1</OUTCOME>
+	<OUTCOME>c2</OUTCOME>
+</VARIABLE>
+
+<DEFINITION>
+	<FOR>A</FOR>
+	<TABLE> .695 .305 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>B</FOR>
+	<TABLE> .25 .75 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>C</FOR>
+	<GIVEN>A</GIVEN>
+	<GIVEN>B</GIVEN>
+	<TABLE> .2 .8 .45 .55 .32 .68 .7 .3 </TABLE>
+</DEFINITION>
+
+</NETWORK>
+</BIF>
+

packages/CLPBN/clpbn/bp/examples/burglary-alarm.uai

@@ -9,10 +9,10 @@ MARKOV
 2 4 2
 
 2
- .001 .009
+ .001 .999
 
 2
- .002 .008 
+ .002 .998 
 
 8
  .95 .94 .29 .001

packages/CLPBN/clpbn/bp/examples/burglary-alarm.xml

@@ -49,12 +49,12 @@
 
 <DEFINITION>
 	<FOR>B</FOR>
-	<TABLE> .001 .009 </TABLE>
+	<TABLE> .001 .999 </TABLE>
 </DEFINITION>
 
 <DEFINITION>
 	<FOR>E</FOR>
-	<TABLE> .002 .008 </TABLE>
+	<TABLE> .002 .998 </TABLE>
 </DEFINITION>
 
 <DEFINITION>

packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap

@@ -1,54 +1,29 @@
 
 :- use_module(library(clpbn)).
 
-:- set_clpbn_flag(solver, vel).
+:- set_clpbn_flag(solver, bp).
 
-%
+r(R) :- r_cpt(RCpt),
-%    B     E
+        { R = r with p([r1, r2], RCpt) }.
-%     \   /
-%      \ / 
-%       A 
-%      / \
-%     /   \
-%    J     M
-%
 
+t(T) :- t_cpt(TCpt),
+        { T = t with p([t1, t2], TCpt) }.
 
-b(B) :-
+a(A) :- r(R), t(T), a_cpt(ACpt),
-    b_table(BDist),
+        { A = a with p([a1, a2], ACpt, [R, T]) }.
-    { B = b with p([b1, b2], BDist) }.
 
-e(E) :-
+j(J) :- a(A), j_cpt(JCpt),
-    e_table(EDist),
+        { J = j with p([j1, j2], JCpt, [A]) }.
-    { E = e with p([e1, e2], EDist) }.
 
-a(A) :-
+m(M) :- a(A), m_cpt(MCpt),
-    b(B),
+        { M = m with p([m1, m2], MCpt, [A]) }.
-    e(E),
-    a_table(ADist),
-    { A = a with p([a1, a2], ADist, [B, E]) }.
-
-j(J):-
-    a(A),
-    j_table(JDist),
-    { J = j with p([j1, j2], JDist, [A]) }.
-
-m(M):-
-    a(A),
-    m_table(MDist),
-    { M = m with p([m1, m2], MDist, [A]) }.
     
-
+r_cpt([0.001, 0.999]).
-b_table([0.001, 0.009]).
+t_cpt([0.002, 0.998]).
-
+a_cpt([0.95, 0.94, 0.29, 0.001,
-e_table([0.002, 0.008]).
+       0.05, 0.06, 0.71, 0.999]).
-
+j_cpt([0.9, 0.05,
-a_table([0.95, 0.94, 0.29, 0.001,
+       0.1, 0.95]).
-         0.05, 0.06, 0.71, 0.999]).
+m_cpt([0.7, 0.01,
-
+       0.3, 0.99]).
-j_table([0.9, 0.05,
-         0.1, 0.95]).
-
-m_table([0.7, 0.01,
-         0.3, 0.99]).
 

packages/CLPBN/clpbn/bp/examples/convergence.xml

@@ -16,34 +16,37 @@
 
 <VARIABLE TYPE="nature">
 	<NAME>A</NAME>
-	<OUTCOME></OUTCOME>
+	<OUTCOME>a1</OUTCOME>
+	<OUTCOME>a2</OUTCOME>
 </VARIABLE>
 
 <VARIABLE TYPE="nature">
 	<NAME>B</NAME>
-	<OUTCOME></OUTCOME>
+	<OUTCOME>b1</OUTCOME>
+	<OUTCOME>b2</OUTCOME>
 </VARIABLE>
 
 <VARIABLE TYPE="nature">
 	<NAME>C</NAME>
-	<OUTCOME></OUTCOME>
+	<OUTCOME>c1</OUTCOME>
+	<OUTCOME>c2</OUTCOME>
 </VARIABLE>
 
 <DEFINITION>
 	<FOR>A</FOR>
-	<TABLE>1</TABLE>
+	<TABLE>.695 .305</TABLE>
 </DEFINITION>
 
 <DEFINITION>
 	<FOR>B</FOR>
-	<TABLE>1</TABLE>
+	<TABLE>0.25 0.75</TABLE>
 </DEFINITION>
 
 <DEFINITION>
 	<FOR>C</FOR>
 	<GIVEN>A</GIVEN>
 	<GIVEN>B</GIVEN>
-	<TABLE>1</TABLE>
+	<TABLE>0.2 0.8 0.45 0.55 0.32 0.68 0.7 0.3</TABLE>
 </DEFINITION>
 
 </NETWORK>

packages/CLPBN/clpbn/bp/examples/lambda fail.xml

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="US-ASCII"?>
+
+<!--
+
+  P1  P2  P3
+   \  |  /
+    \ | / 
+      -  
+      C
+
+-->
+
+<BIF VERSION="0.3">
+<NETWORK>
+
+<NAME>Simple Convergence</NAME>
+<VARIABLE TYPE="nature">
+	<NAME>P1</NAME>
+	<OUTCOME>p1</OUTCOME>
+	<OUTCOME>p2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>P2</NAME>
+	<OUTCOME>p1</OUTCOME>
+	<OUTCOME>p2</OUTCOME>
+	<OUTCOME>p3</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>P3</NAME>
+	<OUTCOME>p1</OUTCOME>
+	<OUTCOME>p2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>C</NAME>
+	<OUTCOME>c1</OUTCOME>
+	<OUTCOME>c2</OUTCOME>
+</VARIABLE>
+
+<DEFINITION>
+	<FOR>P1</FOR>
+	<TABLE>.695 .305</TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>P2</FOR>
+	<TABLE>0.2 0.3 0.5</TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>P3</FOR>
+	<TABLE>0.25 0.75</TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>C</FOR>
+	<GIVEN>P1</GIVEN>
+	<GIVEN>P2</GIVEN>
+	<GIVEN>P3</GIVEN>
+	<TABLE>0.2 0.8 0.45 0.55 0.32 0.68 0.7 0.3 0.3 0.7 0.55 0.45 0.22 0.78 0.25 0.75 0.11 0.89 0.34 0.66 0.1 0.9 0.6 0.4</TABLE>
+</DEFINITION>
+
+</NETWORK>
+</BIF>
+

packages/CLPBN/clpbn/bp/examples/neapolitan.yap

@@ -2,6 +2,7 @@
 :- use_module(library(clpbn)).
 
 :- set_clpbn_flag(solver, bp).
+%:- set_clpbn_flag(solver, jt).
 
 %
 %     B     F

packages/CLPBN/clpbn/bp/examples/sp-example.uai

@@ -0,0 +1,17 @@
+MARKOV
+3
+2 2 2
+3
+1 0
+1 1
+3 2 0 1
+
+2
+ .695 .305
+
+2
+ .25 .75
+
+8
+ 0.2 0.45 0.32 0.7
+ 0.8 0.55 0.68 0.3

packages/CLPBN/clpbn/bp/examples/test_bn.xml

@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="US-ASCII"?>
+
+<!--
+ 
+ A   B   C
+  \  |  /
+   \ | /
+     D
+   / | \
+  /  |  \
+ E   F   G
+
+-->
+
+<BIF VERSION="0.3">
+<NETWORK>
+<NAME>Node with several parents and childs</NAME>
+
+<VARIABLE TYPE="nature">
+	<NAME>A</NAME>
+	<OUTCOME>a1</OUTCOME>
+	<OUTCOME>a2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>B</NAME>
+	<OUTCOME>b1</OUTCOME>
+	<OUTCOME>b2</OUTCOME>
+	<OUTCOME>b3</OUTCOME>
+	<OUTCOME>b4</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>C</NAME>
+	<OUTCOME>c1</OUTCOME>
+	<OUTCOME>c2</OUTCOME>
+	<OUTCOME>c3</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>D</NAME>
+	<OUTCOME>d1</OUTCOME>
+	<OUTCOME>d2</OUTCOME>
+	<OUTCOME>d3</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>E</NAME>
+	<OUTCOME>e1</OUTCOME>
+	<OUTCOME>e2</OUTCOME>
+	<OUTCOME>e3</OUTCOME>
+	<OUTCOME>e4</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>F</NAME>
+	<OUTCOME>f1</OUTCOME>
+	<OUTCOME>f2</OUTCOME>
+	<OUTCOME>f3</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>G</NAME>
+	<OUTCOME>g1</OUTCOME>
+	<OUTCOME>g2</OUTCOME>
+</VARIABLE>
+
+
+<DEFINITION>
+	<FOR>A</FOR>
+	<TABLE> .1 .2 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>B</FOR>
+	<TABLE> .01 .02 .03 .04 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>C</FOR>
+	<TABLE> .11 .22 .33 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>D</FOR>
+	<GIVEN>A</GIVEN>
+	<GIVEN>B</GIVEN>
+	<GIVEN>C</GIVEN>
+	<TABLE>
+      .522 .008 .99 .01 .2 .8 .003 .457 .423 .007 .92 .04 .5 .232 .033 .227 .112 .048 .91 .21 .24 .18 .005 .227
+      .212 .04 .59 .21 .6 .1 .023 .215 .913 .017 .96 .01 .55 .422 .013 .417 .272 .068 .61 .11 .26 .28 .205 .322 
+      .142 .028 .19 .11 .5 .67 .013 .437 .163 .067 .12 .06 .1 .262 .063 .167 .512 .028 .11 .41 .14 .68 .015 .92  
+    </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>E</FOR>
+	<GIVEN>D</GIVEN>
+	<TABLE> 
+      .111 .11 .1
+      .222 .22 .2
+      .333 .33 .3
+      .444 .44 .4
+    </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>F</FOR>
+	<GIVEN>D</GIVEN>
+	<TABLE> 
+      .112 .111 .110
+      .223 .222 .221
+      .334 .333 .332
+    </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>G</FOR>
+	<GIVEN>D</GIVEN>
+	<TABLE>
+      .101 .102 .103
+      .201 .202 .203
+    </TABLE>
+</DEFINITION>
+
+</NETWORK>
+</BIF>
+

packages/CLPBN/clpbn/bp/examples/test_mk.uai

@@ -0,0 +1,36 @@
+MARKOV
+5
+4 2 3 2 3
+7
+1 0
+1 1
+1 2
+1 3
+1 4
+2 0 1
+4 1 2 3 4
+
+4
+ 0.1 0.7 0.43 0.22
+
+2
+ 0.2 0.6
+
+3
+ 0.3 0.5 0.2
+
+2
+ 0.15 0.75
+
+3
+ 0.25 0.45 0.15
+
+8
+ 0.210 0.333 0.457 0.4
+ 0.811 0.000 0.189 0.89
+
+36
+ 0.1 0.15 0.2 0.25 0.3 0.45 0.5 0.55 0.65 0.7 0.75 0.9
+ 0.11 0.22 0.33 0.44 0.55 0.66 0.77 0.88 0.91 0.93 0.95 0.97
+ 0.42 0.22 0.33 0.44 0.15 0.36 0.27 0.28 0.21 0.13 0.25 0.17
+

packages/CLPBN/clpbn/bp/examples/ve_example.xml

@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="US-ASCII"?>
+
+<!--
+
+    A     B
+     \   /
+      \ / 
+       C 
+       |
+       |
+       D
+
+-->
+
+
+<BIF VERSION="0.3">
+<NETWORK>
+<NAME>Simple Loop</NAME>
+
+<VARIABLE TYPE="nature">
+	<NAME>A</NAME>
+	<OUTCOME>a1</OUTCOME>
+	<OUTCOME>a2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>B</NAME>
+	<OUTCOME>b1</OUTCOME>
+	<OUTCOME>b2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>C</NAME>
+	<OUTCOME>c1</OUTCOME>
+	<OUTCOME>c2</OUTCOME>
+</VARIABLE>
+
+<VARIABLE TYPE="nature">
+	<NAME>D</NAME>
+	<OUTCOME>d1</OUTCOME>
+	<OUTCOME>d2</OUTCOME>
+</VARIABLE>
+
+<DEFINITION>
+	<FOR>A</FOR>
+	<TABLE> .001 .009 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>B</FOR>
+	<TABLE> .002 .008 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>C</FOR>
+	<GIVEN>A</GIVEN>
+	<GIVEN>B</GIVEN>
+	<TABLE> .95 .05 .94 .06 .29 .71 .001 .999 </TABLE>
+</DEFINITION>
+
+<DEFINITION>
+	<FOR>D</FOR>
+	<GIVEN>C</GIVEN>
+	<TABLE> .9 .1 .05 .95  </TABLE>
+</DEFINITION>
+
+</NETWORK>
+</BIF>
+

packages/PLStream/pl-write.c

@@ -884,6 +884,15 @@ writePrimitive(term_t t, write_options *options)
     return writeString(t, options);
 #endif /* O_STRING */
 
+#if __YAP_PROLOG__
+  {
+    number n;
+    n.type = V_INTEGER;
+    n.value.i = 0;
+    return WriteNumber(&n, options);
+  }
+#endif
+
   assert(0);
   fail;
 }

packages/PLStream/pl-yap.c

@@ -1121,6 +1121,9 @@ Yap_StreamPosition(IOSTREAM *st)
   return StreamPosition(st);
 }
 
+IOSTREAM   *STD_PROTO(Yap_Scurin, (void));
+int    STD_PROTO(Yap_dowrite, (Term, IOSTREAM *, int, int));
+
 IOSTREAM *
 Yap_Scurin(void)
 {
@@ -1128,6 +1131,32 @@ Yap_Scurin(void)
   return Scurin;
 }
 
+int 
+Yap_dowrite(Term t, IOSTREAM *stream, int flags, int priority)
+     /* term to be written			 */
+     /* consumer				 */
+     /* write options			 */
+{			
+  CACHE_REGS
+    int swi_flags;
+  int res;
+  Int slot = Yap_InitSlot(t PASS_REGS);  
+
+  swi_flags = 0;
+  if (flags & Quote_illegal_f)
+    swi_flags |= PL_WRT_QUOTED;
+  if (flags & Handle_vars_f)
+    swi_flags |= PL_WRT_NUMBERVARS;
+  if (flags & Use_portray_f)
+    swi_flags |= PL_WRT_PORTRAY;
+  if (flags & Ignore_ops_f)
+    swi_flags |= PL_WRT_IGNOREOPS;
+  
+  res =  PL_write_term(stream, slot, priority, swi_flags);
+  Yap_RecoverSlots(1 PASS_REGS);
+  return res;
+}
+
 
 #if THREADS
 
@@ -1178,6 +1207,7 @@ error:
   return rc;
 }
 
+
 int
 recursiveMutexInit(recursiveMutex *m)
 {

packages/RDF

@@ -1 +1 @@
-Subproject commit cee6c346ba77e046ef1873b9d8c88c52c3baae2d
+Subproject commit a5d2a3755f86ebffd8eb6e2a6921790d299eab30

packages/clib

@@ -1 +1 @@
-Subproject commit f6fce313722d2f69e5ce6074f304ce05065bbf40
+Subproject commit a6f0f4ec7d5fd51ca8b268b8392da9b20bfd1b44

packages/http

@@ -1 +1 @@
-Subproject commit 3f7eee803d46071f10804010f7266b3864bab7e6
+Subproject commit 2a0843683e8790d8129fa4bad99c82a5fcaf441b

packages/plunit

@@ -1 +1 @@
-Subproject commit aa90b8f8a67e605e82566b719a8f20d125598bd2
+Subproject commit 2daa5b9942a9fc22005ec48b6560f8596f33d995

packages/semweb

@@ -1 +1 @@
-Subproject commit 2229eb3807b21497ffd680686ceeeddeac9f57fb
+Subproject commit e3c7eb9a9a54d6a9069396ecd1c3b537a8f6165a

packages/sgml

@@ -1 +1 @@
-Subproject commit babcbfe9cc5ab269cd5fd4f024e9d57bd3d0a8db
+Subproject commit f1c3ef54f4d9431ba5b4188cb72ca3056d20b202

packages/tai/Makefile.in

@@ -1,59 +0,0 @@
-#
-# default base directory for YAP installation
-# (EROOT for architecture-dependent files)
-#
-prefix = @prefix@
-exec_prefix = @exec_prefix@
-ROOTDIR = $(prefix)
-EROOTDIR = @exec_prefix@
-abs_top_builddir = @abs_top_builddir@
-#
-# where the binary should be
-#
-BINDIR = $(EROOTDIR)/bin
-#
-# where YAP should look for libraries
-#
-LIBDIR=@libdir@
-YAPLIBDIR=@libdir@/Yap
-#
-#
-DEFS=@DEFS@ -D_YAP_NOT_INSTALLED_=1
-CC=@CC@
-CFLAGS= @SHLIB_CFLAGS@ $(YAP_EXTRAS) $(DEFS) -I$(srcdir) -I../.. -I$(srcdir)/../../include -I$(srcdir)/../PLStream -I$(srcdir)/../PLStream/windows -I$(srcdir)/../../H
-#
-#
-# You shouldn't need to change what follows.
-#
-INSTALL=@INSTALL@
-INSTALL_DATA=@INSTALL_DATA@
-INSTALL_PROGRAM=@INSTALL_PROGRAM@
-SHELL=/bin/sh
-RANLIB=@RANLIB@
-srcdir=@srcdir@
-SO=@SO@
-#4.1VPATH=@srcdir@:@srcdir@/OPTYap
-CWD=$(PWD)
-#
-
-OBJS=pl-tai.o
-SOBJS=pl-tai.@SO@
-
-#in some systems we just create a single object, in others we need to
-# create a libray
-
-all: $(SOBJS) 
-
-pl-tai.o: $(srcdir)/pl-tai.c
-	(cd libtai ; $(MAKE))
-	$(CC) -c $(CFLAGS) $(srcdir)/pl-tai.c -o pl-tai.o
-
-@DO_SECOND_LD@pl-tai.@SO@: pl-tai.o
-@DO_SECOND_LD@	@SHLIB_LD@ $(LDFLAGS) -o pl-tai.@SO@ pl-tai.o libtai/libtai.a @EXTRA_LIBS_FOR_SWIDLLS@
-
-install: all
-	$(INSTALL_PROGRAM) $(SOBJS) $(DESTDIR)$(YAPLIBDIR)
-
-clean:
-	rm -f *.o *~ $(OBJS) $(SOBJS) *.BAK
-	-(cd libtai && $(MAKE) clean)

packages/zlib

@@ -1 +1 @@
-Subproject commit deea4bfdf7041387e91eca37978a5c8db9287eda
+Subproject commit 109bf1d224009dc049ab12a0fbbb50511ef8e1fb

pl/consult.yap

@@ -1050,6 +1050,8 @@ make :-
 	fail.
 make.
 
+make_library_index(_Directory).
+
 '$file_name'(Stream,F) :-
 	stream_property(Stream, file_name(F)), !.
 '$file_name'(user_input,user_output).

pl/debug.yap

@@ -495,7 +495,7 @@ debugging :-
 	'$continue_debugging'(no, '$execute_nonstop'(G,M)).
 '$spycall'(G, M, CalledFromDebugger, InRedo) :-
 	'$flags'(G,M,F,F),
-	F /\ 0x18402000 =\= 0, !, % dynamic procedure, logical semantics, user-C, or source
+	F /\ 0x08402000 =\= 0, !, % dynamic procedure, logical semantics, or source
 	% use the interpreter
 	CP is '$last_choice_pt',
 	'$clause'(G, M, Cl, _),

pl/errors.yap

@@ -245,22 +245,15 @@ print_message(Severity, Msg) :-
 	'$notrace'(user:portray_message(Severity, Msg)), !.
 % This predicate has more hooks than a pirate ship!
 print_message(Severity, Term) :-
-	(
+	% first step at hook processing
-	 (
+	'$message_to_lines'(Term, Lines),
-	  '$oncenotrace'(user:generate_message_hook(Term, [], Lines)) ->
+	(   nonvar(Term),
-	  true
+	    '$oncenotrace'(user:message_hook(Term, Severity, Lines))
-	 ;
+	->
-	  '$oncenotrace'(prolog:message(Term, Lines, [])) ->
+           true
-	  true
+	;
-	 ;
+	   '$print_system_message'(Term, Severity, Lines)
-	 '$messages':generate_message(Term, Lines, [])
+	), !.
-	 )
-	->  (   nonvar(Term),
-		'$oncenotrace'(user:message_hook(Term, Severity, Lines))
-	    ->  !
-	    ;   !, '$print_system_message'(Term, Severity, Lines)
-	    )
-	).
 print_message(silent, _) :-  !.
 print_message(_, error(syntax_error(syntax_error(_,between(_,L,_),_,_,_,_,StreamName)),_)) :-  !,
 	format(user_error,'SYNTAX ERROR at ~a, close to ~d~n',[StreamName,L]).
@@ -271,6 +264,14 @@ print_message(_, loaded(A, F, _, Time, Space)) :- !,
 print_message(_, Term) :-
 	format(user_error,'~q~n',[Term]).
 
+'$message_to_lines'(Term, Lines) :-
+	'$oncenotrace'(user:generate_message_hook(Term, [], Lines)), !.
+'$message_to_lines'(Term, Lines) :-
+	'$oncenotrace'(prolog:message(Term, Lines, [])), !.
+'$message_to_lines'(Term, Lines) :-
+	'$messages':generate_message(Term, Lines, []), !.
+	
+
 %	print_system_message(+Term, +Level, +Lines)
 %
 %	Print the message if the user did not intecept the message.

pl/messages.yap

@@ -69,6 +69,10 @@ generate_message(debug) --> !,
 	[ debug ].
 generate_message(trace) --> !,
 	[ trace ].
+generate_message(error(Error,Context)) -->
+	{ Error = existence_error(procedure,_) }, !,	
+	system_message(error(Error,Context)),
+	stack_dump(error(Error,Context)).
 generate_message(error(Error,context(Cause,Extra))) -->
 	system_message(error(Error,Cause)),
 	stack_dump(error(Error,context(Cause,Extra))).
@@ -130,8 +134,6 @@ system_message(no_match(P)) -->
 	[ 'No matching predicate for ~w.' - [P] ].
 system_message(leash([A|B])) -->
 	[ 'Leashing set to ~w.' - [[A|B]] ].
-system_message(existence_error(prolog_flag,F)) -->
-	[ 'Prolog Flag ~w: new Prolog flags must be created using create_prolog_flag/3.' - [F] ].
 system_message(singletons([SV],P)) -->
 	[ 'Singleton variable ~s in ~q.' - [SV,P] ].
 system_message(singletons(SVs,P)) -->
@@ -159,14 +161,18 @@ system_message(error(context_error(Goal,Who),Where)) -->
 system_message(error(domain_error(DomainType,Opt), Where)) -->
 	[ 'DOMAIN ERROR- ~w: ' - Where],
 	domain_error(DomainType, Opt).
+system_message(error(existence_error(directory,Key), Where)) -->
+	[ 'EXISTENCE ERROR- ~w: ~w not an existing directory' - [Where,Key] ].
+system_message(error(existence_error(key,Key), Where)) -->
+	[ 'EXISTENCE ERROR- ~w: ~w not an existing key' - [Where,Key] ].
+system_message(existence_error(prolog_flag,F)) -->
+	[ 'Prolog Flag ~w: new Prolog flags must be created using create_prolog_flag/3.' - [F] ].
 system_message(error(existence_error(prolog_flag,P), Where)) --> !,
 	[ 'EXISTENCE ERROR- ~w: prolog flag ~w is undefined' - [Where,P] ].
 system_message(error(existence_error(procedure,P), context(Call,Parent))) --> !,
 	[ 'EXISTENCE ERROR- procedure ~w is undefined, called from context  ~w~n                 Goal was ~w' - [P,Parent,Call] ].
 system_message(error(existence_error(stream,Stream), Where)) -->
 	[ 'EXISTENCE ERROR- ~w: ~w not an open stream' - [Where,Stream] ].
-system_message(error(existence_error(key,Key), Where)) -->
-	[ 'EXISTENCE ERROR- ~w: ~w not an existing key' - [Where,Key] ].
 system_message(error(existence_error(thread,Thread), Where)) -->
 	[ 'EXISTENCE ERROR- ~w: ~w not a running thread' - [Where,Thread] ].
 system_message(error(existence_error(variable,Var), Where)) -->