File Coverage

pp-hmmfw.c

Criterion	Covered	Total	%
statement	53	84	63.1
branch	44	184	23.9
condition			n/a
subroutine			n/a
pod			n/a
total	97	268	36.1

#line 453 "lib/PDL/PP.pm"
/*
 * THIS FILE WAS GENERATED BY PDL::PP from HMM.pd! Do not modify!
 */

#define PDL_FREE_CODE(trans, destroy, comp_free_code, ntpriv_free_code) \
    if (destroy) { \
	comp_free_code \
    } \
    if ((trans)->dims_redone) { \
	ntpriv_free_code \
    }

#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"
#include "pdl.h"
#include "pdlcore.h"
#define PDL PDL_HMM
extern Core* PDL; /* Structure hold core C functions */
#line 23 "pp-hmmfw.c"

#include

/*#define DEBUG_ALPHA*/
/*#define DEBUG_BETA*/
/*#define DEBUG_VITERBI*/


/* logadd(x,y) = log(exp(x)+exp(y))
 *   + Code from Manning & Schütze (1997), Sec. 9.4, page 337
 *
 * LOG_BIG = log(1E31)
 */
#define LOG_BIG    71.3801378828154
#define LOG_ZERO  -1E+38
#define LOG_ONE    0
#define LOG_NONE   1
static inline double logadd1(double x, double y) {
  if      (y-x > LOG_BIG) return y;
  else if (x-y > LOG_BIG) return x;
  /*else        return min(x,y) + log(exp(x-min(x,y)) + exp(y-min(x,y))); */
  else if (x
  else          return y        + log(exp(x-y)        + 1);
}
static inline double logadd0(double x, double y) {
  return log(exp(x)+exp(y));
}

/* logdiff(x,y) = log(exp(x)-exp(y))
 *   + adapted from above
 *   + always returns positive (i.e. symmetric difference)
 */
static inline double logdiff1(double x, double y) {
  if      (y-x > LOG_BIG) { return y; }
  else if (x-y > LOG_BIG) { return x; }
  /*else        { return max(x,y) + log(exp(max(x,y)-max(x,y)) - exp(min(x,y)-max(x,y))); } */
  /*                   = max(x,y) + log( 1 - exp(min(x,y)-max(x,y))); } */
  else if (x>y) { return x        + log( 1 - exp(y-x)); }
  else          { return y        + log( 1 - exp(x-y)); }
}
static inline double logdiff0(double x, double y) {
  return log(x>y ? (exp(x)-exp(y)) : (exp(y)-exp(x)));
}

/*
#define logadd(x,y) logadd0(x,y)
#define logdiff(x,y) logdiff0(x,y)
*/

#define logadd(x,y) logadd1(x,y)
#define logdiff(x,y) logdiff1(x,y)


#line 1857 "lib/PDL/PP.pm"
pdl_error pdl_hmmfw_readdata(pdl_trans *__privtrans) {
  pdl_error PDL_err = {0, NULL, 0};
#line 80 "pp-hmmfw.c"
  register PDL_Indx __N_size = __privtrans->ind_sizes[1];
  if (!__privtrans->broadcast.incs) return PDL->make_error(PDL_EUSERERROR, "Error in hmmfw:" "broadcast.incs NULL");
  /* broadcastloop declarations */
  int __brcloopval;
  register PDL_Indx __tind0,__tind1; /* counters along dim */
  register PDL_Indx __tnpdls = __privtrans->broadcast.npdls;
  /* dims here are how many steps along those dims */
  register PDL_Indx __tinc0_a = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,0,0);
  register PDL_Indx __tinc0_b = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,1,0);
  register PDL_Indx __tinc0_pi = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,2,0);
  register PDL_Indx __tinc0_o = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,3,0);
  register PDL_Indx __tinc0_alpha = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,4,0);
  register PDL_Indx __tinc1_a = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,0,1);
  register PDL_Indx __tinc1_b = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,1,1);
  register PDL_Indx __tinc1_pi = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,2,1);
  register PDL_Indx __tinc1_o = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,3,1);
  register PDL_Indx __tinc1_alpha = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,4,1);
  #define PDL_BROADCASTLOOP_START_hmmfw_readdata PDL_BROADCASTLOOP_START( \
    readdata, \
    __privtrans->broadcast, \
    __privtrans->vtable, \
    a_datap += __offsp[0]; \
    b_datap += __offsp[1]; \
    pi_datap += __offsp[2]; \
    o_datap += __offsp[3]; \
    alpha_datap += __offsp[4]; \
    , \
    (  ,a_datap += __tinc1_a - __tinc0_a * __tdims0 \
    ,b_datap += __tinc1_b - __tinc0_b * __tdims0 \
    ,pi_datap += __tinc1_pi - __tinc0_pi * __tdims0 \
    ,o_datap += __tinc1_o - __tinc0_o * __tdims0 \
    ,alpha_datap += __tinc1_alpha - __tinc0_alpha * __tdims0 \
    ), \
    (  ,a_datap += __tinc0_a \
    ,b_datap += __tinc0_b \
    ,pi_datap += __tinc0_pi \
    ,o_datap += __tinc0_o \
    ,alpha_datap += __tinc0_alpha \
    ) \
  )
  #define PDL_BROADCASTLOOP_END_hmmfw_readdata PDL_BROADCASTLOOP_END( \
    __privtrans->broadcast, \
    a_datap -= __tinc1_a * __tdims1 + __offsp[0]; \
    b_datap -= __tinc1_b * __tdims1 + __offsp[1]; \
    pi_datap -= __tinc1_pi * __tdims1 + __offsp[2]; \
    o_datap -= __tinc1_o * __tdims1 + __offsp[3]; \
    alpha_datap -= __tinc1_alpha * __tdims1 + __offsp[4]; \
  )
  register PDL_Indx __inc_a_N0 = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,0,0)]; (void)__inc_a_N0;register PDL_Indx __inc_a_N1 = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,0,1)]; (void)__inc_a_N1;
  register PDL_Indx __inc_alpha_N = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,4,0)]; (void)__inc_alpha_N;register PDL_Indx __inc_alpha_T = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,4,1)]; (void)__inc_alpha_T;
  register PDL_Indx __inc_b_N = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,1,0)]; (void)__inc_b_N;register PDL_Indx __inc_b_M = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,1,1)]; (void)__inc_b_M;
  register PDL_Indx __inc_o_T = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,3,0)]; (void)__inc_o_T;
  register PDL_Indx __inc_pi_N = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,2,0)]; (void)__inc_pi_N;
  #ifndef PDL_DECLARE_PARAMS_hmmfw_1
  #define PDL_DECLARE_PARAMS_hmmfw_1(PDL_TYPE_OP,PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, a, (__privtrans->pdls[0]), 1, PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, b, (__privtrans->pdls[1]), 1, PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, pi, (__privtrans->pdls[2]), 1, PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, o, (__privtrans->pdls[3]), 1, PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, alpha, (__privtrans->pdls[4]), 1, PDL_PPSYM_OP)
  #endif
  #define PDL_IF_BAD(t,f) f
  switch (__privtrans->__datatype) { /* Start generic switch */
    case PDL_F: {
      PDL_DECLARE_PARAMS_hmmfw_1(PDL_Float,F)
      PDL_BROADCASTLOOP_START_hmmfw_readdata    {
           /*-- Initialize: t==0 --*/
           int i,j,t, o_tp1 = (o_datap)[0+(__inc_o_T*(0))];
           {/* Open N */ PDL_EXPAND2(register PDL_Indx N=0, __N_stop=(__N_size)); for(; N<__N_stop; N+=1) {
               (alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))] = (pi_datap)[0+(__inc_pi_N*(N))] + (b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
               printf("INIT: j=%u,t=0,o=%d:  pi(j=%u)=%.2e  b(j=%u,o=%d)=%.2e  alpha(j=%u,t=0)=%.2e\n",
            	  n,o_tp1,
            	  n,      exp((pi_datap)[0+(__inc_pi_N*(N))]),
            	  n,o_tp1 exp((b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))]),
            	  n,      exp((alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))])
            	 );
               #endif
             }} /* Close N */

           #ifdef DEBUG_ALPHA
           printf("\n\n");
           #endif

           /*-- Loop: time t>0 --*/
           for (t=0; t < __privtrans->ind_sizes[2]-1; t++) {
             o_tp1 = (o_datap)[0+(__inc_o_T*(t+1))];

             /*-- Loop: state_(t+1)==j --*/
             for (j=0; j<__privtrans->ind_sizes[1]; j++) {
               PDL_Float alpha_j_tp1 = (PDL_Float)LOG_ZERO;


               /*-- Loop: state_t==i --*/
               for (i=0; i<__privtrans->ind_sizes[1]; i++) {
                 alpha_j_tp1 = logadd( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))],  alpha_j_tp1 );

                 #ifdef DEBUG_ALPHA
                  printf("i=%u,j=%u,t=%u,o=%d:  alpha(i=%u,t=%u)=%.2e  a(i=%u,j=%u)=%.2e  b(j=%u,o=%d)=%.2e  prod=%.2e  sum=%.2e\n",
          	       i,j,t,o_tp1,
          	       i,t,     exp((alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))]),
          	       i,j,     exp((a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))]),
          	       j,o_tp1, exp((b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))]),
          	       exp( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))] ), exp(alpha_j_tp1));
                 #endif
               }

               /*-- Storage: alpha(time=t+1, state=j) --*/
               (alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))] = alpha_j_tp1 + (b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
                printf("----> alpha(j=%u,t=%u)=%.2E\n", j,t+1, exp((alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))]));
               #endif
             }
             #ifdef DEBUG_ALPHA
              printf("\n\n");
             #endif
           }
          }PDL_BROADCASTLOOP_END_hmmfw_readdata
    } break;
    case PDL_D: {
      PDL_DECLARE_PARAMS_hmmfw_1(PDL_Double,D)
      PDL_BROADCASTLOOP_START_hmmfw_readdata    {
           /*-- Initialize: t==0 --*/
           int i,j,t, o_tp1 = (o_datap)[0+(__inc_o_T*(0))];
           {/* Open N */ PDL_EXPAND2(register PDL_Indx N=0, __N_stop=(__N_size)); for(; N<__N_stop; N+=1) {
               (alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))] = (pi_datap)[0+(__inc_pi_N*(N))] + (b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
               printf("INIT: j=%u,t=0,o=%d:  pi(j=%u)=%.2e  b(j=%u,o=%d)=%.2e  alpha(j=%u,t=0)=%.2e\n",
            	  n,o_tp1,
            	  n,      exp((pi_datap)[0+(__inc_pi_N*(N))]),
            	  n,o_tp1 exp((b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))]),
            	  n,      exp((alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))])
            	 );
               #endif
             }} /* Close N */

           #ifdef DEBUG_ALPHA
           printf("\n\n");
           #endif

           /*-- Loop: time t>0 --*/
           for (t=0; t < __privtrans->ind_sizes[2]-1; t++) {
             o_tp1 = (o_datap)[0+(__inc_o_T*(t+1))];

             /*-- Loop: state_(t+1)==j --*/
             for (j=0; j<__privtrans->ind_sizes[1]; j++) {
               PDL_Double alpha_j_tp1 = (PDL_Double)LOG_ZERO;


               /*-- Loop: state_t==i --*/
               for (i=0; i<__privtrans->ind_sizes[1]; i++) {
                 alpha_j_tp1 = logadd( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))],  alpha_j_tp1 );

                 #ifdef DEBUG_ALPHA
                  printf("i=%u,j=%u,t=%u,o=%d:  alpha(i=%u,t=%u)=%.2e  a(i=%u,j=%u)=%.2e  b(j=%u,o=%d)=%.2e  prod=%.2e  sum=%.2e\n",
          	       i,j,t,o_tp1,
          	       i,t,     exp((alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))]),
          	       i,j,     exp((a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))]),
          	       j,o_tp1, exp((b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))]),
          	       exp( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))] ), exp(alpha_j_tp1));
                 #endif
               }

               /*-- Storage: alpha(time=t+1, state=j) --*/
               (alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))] = alpha_j_tp1 + (b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
                printf("----> alpha(j=%u,t=%u)=%.2E\n", j,t+1, exp((alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))]));
               #endif
             }
             #ifdef DEBUG_ALPHA
              printf("\n\n");
             #endif
           }
          }PDL_BROADCASTLOOP_END_hmmfw_readdata
    } break;
    case PDL_LD: {
      PDL_DECLARE_PARAMS_hmmfw_1(PDL_LDouble,E)
      PDL_BROADCASTLOOP_START_hmmfw_readdata    {
           /*-- Initialize: t==0 --*/
           int i,j,t, o_tp1 = (o_datap)[0+(__inc_o_T*(0))];
           {/* Open N */ PDL_EXPAND2(register PDL_Indx N=0, __N_stop=(__N_size)); for(; N<__N_stop; N+=1) {
               (alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))] = (pi_datap)[0+(__inc_pi_N*(N))] + (b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
               printf("INIT: j=%u,t=0,o=%d:  pi(j=%u)=%.2e  b(j=%u,o=%d)=%.2e  alpha(j=%u,t=0)=%.2e\n",
            	  n,o_tp1,
            	  n,      exp((pi_datap)[0+(__inc_pi_N*(N))]),
            	  n,o_tp1 exp((b_datap)[0+(__inc_b_N*(N))+(__inc_b_M*(o_tp1))]),
            	  n,      exp((alpha_datap)[0+(__inc_alpha_N*(N))+(__inc_alpha_T*(0))])
            	 );
               #endif
             }} /* Close N */

           #ifdef DEBUG_ALPHA
           printf("\n\n");
           #endif

           /*-- Loop: time t>0 --*/
           for (t=0; t < __privtrans->ind_sizes[2]-1; t++) {
             o_tp1 = (o_datap)[0+(__inc_o_T*(t+1))];

             /*-- Loop: state_(t+1)==j --*/
             for (j=0; j<__privtrans->ind_sizes[1]; j++) {
               PDL_LDouble alpha_j_tp1 = (PDL_LDouble)LOG_ZERO;


               /*-- Loop: state_t==i --*/
               for (i=0; i<__privtrans->ind_sizes[1]; i++) {
                 alpha_j_tp1 = logadd( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))],  alpha_j_tp1 );

                 #ifdef DEBUG_ALPHA
                  printf("i=%u,j=%u,t=%u,o=%d:  alpha(i=%u,t=%u)=%.2e  a(i=%u,j=%u)=%.2e  b(j=%u,o=%d)=%.2e  prod=%.2e  sum=%.2e\n",
          	       i,j,t,o_tp1,
          	       i,t,     exp((alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))]),
          	       i,j,     exp((a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))]),
          	       j,o_tp1, exp((b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))]),
          	       exp( (alpha_datap)[0+(__inc_alpha_N*(i))+(__inc_alpha_T*(t))] + (a_datap)[0+(__inc_a_N0*(i))+(__inc_a_N1*(j))] ), exp(alpha_j_tp1));
                 #endif
               }

               /*-- Storage: alpha(time=t+1, state=j) --*/
               (alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))] = alpha_j_tp1 + (b_datap)[0+(__inc_b_N*(j))+(__inc_b_M*(o_tp1))];

               #ifdef DEBUG_ALPHA
                printf("----> alpha(j=%u,t=%u)=%.2E\n", j,t+1, exp((alpha_datap)[0+(__inc_alpha_N*(j))+(__inc_alpha_T*(t+1))]));
               #endif
             }
             #ifdef DEBUG_ALPHA
              printf("\n\n");
             #endif
           }
          }PDL_BROADCASTLOOP_END_hmmfw_readdata
    } break;
    default: return PDL->make_error(PDL_EUSERERROR, "PP INTERNAL ERROR in hmmfw: unhandled datatype(%d), only handles (FDE)! PLEASE MAKE A BUG REPORT\n", __privtrans->__datatype);
  }
  #undef PDL_IF_BAD
  return PDL_err;
}

static pdl_datatypes pdl_hmmfw_vtable_gentypes[] = { PDL_F, PDL_D, PDL_LD, -1 };
static PDL_Indx pdl_hmmfw_vtable_realdims[] = { 2, 2, 1, 1, 2 };
static char *pdl_hmmfw_vtable_parnames[] = { "a","b","pi","o","alpha" };
static short pdl_hmmfw_vtable_parflags[] = {
  0,
  0,
  0,
  0,
  PDL_PARAM_ISCREAT|PDL_PARAM_ISOUT|PDL_PARAM_ISWRITE
};
static pdl_datatypes pdl_hmmfw_vtable_partypes[] = { -1, -1, -1, -1, -1 };
static PDL_Indx pdl_hmmfw_vtable_realdims_starts[] = { 0, 2, 4, 5, 6 };
static PDL_Indx pdl_hmmfw_vtable_realdims_ind_ids[] = { 1, 1, 1, 0, 1, 2, 1, 2 };
static char *pdl_hmmfw_vtable_indnames[] = { "M","N","T" };
pdl_transvtable pdl_hmmfw_vtable = {
  PDL_TRANS_DO_BROADCAST, 0, pdl_hmmfw_vtable_gentypes, 4, 5, NULL /*CORE21*/,
  pdl_hmmfw_vtable_realdims, pdl_hmmfw_vtable_parnames,
  pdl_hmmfw_vtable_parflags, pdl_hmmfw_vtable_partypes,
  pdl_hmmfw_vtable_realdims_starts, pdl_hmmfw_vtable_realdims_ind_ids, 8,
  3, pdl_hmmfw_vtable_indnames,
  NULL, pdl_hmmfw_readdata, NULL,
  NULL,
  0,"PDL::HMM::hmmfw"
};


pdl_error pdl_run_hmmfw(pdl  *a,pdl  *b,pdl  *pi,pdl  *o,pdl  *alpha) {
  pdl_error PDL_err = {0, NULL, 0};
  if (!PDL) return (pdl_error){PDL_EFATAL, "PDL core struct is NULL, can't continue",0};
  pdl_trans *__privtrans = PDL->create_trans(&pdl_hmmfw_vtable);
  if (!__privtrans) return PDL->make_error_simple(PDL_EFATAL, "Couldn't create trans");
  __privtrans->pdls[0] = a;
  __privtrans->pdls[1] = b;
  __privtrans->pdls[2] = pi;
  __privtrans->pdls[3] = o;
  __privtrans->pdls[4] = alpha;
  PDL_RETERROR(PDL_err, PDL->type_coerce(__privtrans));
  PDL_RETERROR(PDL_err, PDL->make_trans_mutual(__privtrans));
  return PDL_err;
}