File Coverage

pp-hmmpath.c

Criterion	Covered	Total	%
statement	33	54	61.1
branch	27	124	21.7
condition			n/a
subroutine			n/a
pod			n/a
total	60	178	33.7

#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-hmmpath.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_hmmpath_readdata(pdl_trans *__privtrans) {
  pdl_error PDL_err = {0, NULL, 0};
#line 80 "pp-hmmpath.c"
  if (!__privtrans->broadcast.incs) return PDL->make_error(PDL_EUSERERROR, "Error in hmmpath:" "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_psi = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,0,0);
  register PDL_Indx __tinc0_qfinal = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,1,0);
  register PDL_Indx __tinc0_path = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,2,0);
  register PDL_Indx __tinc1_psi = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,0,1);
  register PDL_Indx __tinc1_qfinal = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,1,1);
  register PDL_Indx __tinc1_path = PDL_BRC_INC(__privtrans->broadcast.incs,__tnpdls,2,1);
  #define PDL_BROADCASTLOOP_START_hmmpath_readdata PDL_BROADCASTLOOP_START( \
    readdata, \
    __privtrans->broadcast, \
    __privtrans->vtable, \
    psi_datap += __offsp[0]; \
    qfinal_datap += __offsp[1]; \
    path_datap += __offsp[2]; \
    , \
    (  ,psi_datap += __tinc1_psi - __tinc0_psi * __tdims0 \
    ,qfinal_datap += __tinc1_qfinal - __tinc0_qfinal * __tdims0 \
    ,path_datap += __tinc1_path - __tinc0_path * __tdims0 \
    ), \
    (  ,psi_datap += __tinc0_psi \
    ,qfinal_datap += __tinc0_qfinal \
    ,path_datap += __tinc0_path \
    ) \
  )
  #define PDL_BROADCASTLOOP_END_hmmpath_readdata PDL_BROADCASTLOOP_END( \
    __privtrans->broadcast, \
    psi_datap -= __tinc1_psi * __tdims1 + __offsp[0]; \
    qfinal_datap -= __tinc1_qfinal * __tdims1 + __offsp[1]; \
    path_datap -= __tinc1_path * __tdims1 + __offsp[2]; \
  )
  register PDL_Indx __inc_path_T = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,2,0)]; (void)__inc_path_T;
  register PDL_Indx __inc_psi_N = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,0,0)]; (void)__inc_psi_N;register PDL_Indx __inc_psi_T = __privtrans->inc_sizes[PDL_INC_ID(__privtrans->vtable,0,1)]; (void)__inc_psi_T;
  #ifndef PDL_DECLARE_PARAMS_hmmpath_1
  #define PDL_DECLARE_PARAMS_hmmpath_1(PDL_TYPE_OP,PDL_PPSYM_OP,PDL_TYPE_PARAM_qfinal,PDL_PPSYM_PARAM_qfinal,PDL_TYPE_PARAM_path,PDL_PPSYM_PARAM_path) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_OP, psi, (__privtrans->pdls[0]), 1, PDL_PPSYM_OP) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_PARAM_qfinal, qfinal, (__privtrans->pdls[1]), 1, PDL_PPSYM_PARAM_qfinal) \
    PDL_DECLARE_PARAMETER(PDL_TYPE_PARAM_path, path, (__privtrans->pdls[2]), 1, PDL_PPSYM_PARAM_path)
  #endif
  #define PDL_IF_BAD(t,f) f
  switch (__privtrans->__datatype) { /* Start generic switch */
    case PDL_F: {
      PDL_DECLARE_PARAMS_hmmpath_1(PDL_Float,F,PDL_Indx,N,PDL_Indx,N)
      PDL_BROADCASTLOOP_START_hmmpath_readdata    {
           /*-- Initialize: t==T-1: state_(t)==final() --*/
           int t = __privtrans->ind_sizes[1]-1;
           (path_datap)[0+(__inc_path_T*(t))] = (qfinal_datap)[0];

           /*-- Main: T-1 > t >= 0: Loop: time==t --*/
           for (t--; t>=0; t--) {
             int q_tp1   = (path_datap)[0+(__inc_path_T*(t+1))];
             (path_datap)[0+(__inc_path_T*(t))] = (psi_datap)[0+(__inc_psi_N*(q_tp1))+(__inc_psi_T*(t+1))];
           }
          }PDL_BROADCASTLOOP_END_hmmpath_readdata
    } break;
    case PDL_D: {
      PDL_DECLARE_PARAMS_hmmpath_1(PDL_Double,D,PDL_Indx,N,PDL_Indx,N)
      PDL_BROADCASTLOOP_START_hmmpath_readdata    {
           /*-- Initialize: t==T-1: state_(t)==final() --*/
           int t = __privtrans->ind_sizes[1]-1;
           (path_datap)[0+(__inc_path_T*(t))] = (qfinal_datap)[0];

           /*-- Main: T-1 > t >= 0: Loop: time==t --*/
           for (t--; t>=0; t--) {
             int q_tp1   = (path_datap)[0+(__inc_path_T*(t+1))];
             (path_datap)[0+(__inc_path_T*(t))] = (psi_datap)[0+(__inc_psi_N*(q_tp1))+(__inc_psi_T*(t+1))];
           }
          }PDL_BROADCASTLOOP_END_hmmpath_readdata
    } break;
    case PDL_LD: {
      PDL_DECLARE_PARAMS_hmmpath_1(PDL_LDouble,E,PDL_Indx,N,PDL_Indx,N)
      PDL_BROADCASTLOOP_START_hmmpath_readdata    {
           /*-- Initialize: t==T-1: state_(t)==final() --*/
           int t = __privtrans->ind_sizes[1]-1;
           (path_datap)[0+(__inc_path_T*(t))] = (qfinal_datap)[0];

           /*-- Main: T-1 > t >= 0: Loop: time==t --*/
           for (t--; t>=0; t--) {
             int q_tp1   = (path_datap)[0+(__inc_path_T*(t+1))];
             (path_datap)[0+(__inc_path_T*(t))] = (psi_datap)[0+(__inc_psi_N*(q_tp1))+(__inc_psi_T*(t+1))];
           }
          }PDL_BROADCASTLOOP_END_hmmpath_readdata
    } break;
    default: return PDL->make_error(PDL_EUSERERROR, "PP INTERNAL ERROR in hmmpath: 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_hmmpath_vtable_gentypes[] = { PDL_F, PDL_D, PDL_LD, -1 };
static PDL_Indx pdl_hmmpath_vtable_realdims[] = { 2, 0, 1 };
static char *pdl_hmmpath_vtable_parnames[] = { "psi","qfinal","path" };
static short pdl_hmmpath_vtable_parflags[] = {
  0,
  PDL_PARAM_ISTYPED,
  PDL_PARAM_ISCREAT|PDL_PARAM_ISOUT|PDL_PARAM_ISTYPED|PDL_PARAM_ISWRITE
};
static pdl_datatypes pdl_hmmpath_vtable_partypes[] = { -1, PDL_IND, PDL_IND };
static PDL_Indx pdl_hmmpath_vtable_realdims_starts[] = { 0, 2, 2 };
static PDL_Indx pdl_hmmpath_vtable_realdims_ind_ids[] = { 0, 1, 1 };
static char *pdl_hmmpath_vtable_indnames[] = { "N","T" };
pdl_transvtable pdl_hmmpath_vtable = {
  PDL_TRANS_DO_BROADCAST, 0, pdl_hmmpath_vtable_gentypes, 2, 3, NULL /*CORE21*/,
  pdl_hmmpath_vtable_realdims, pdl_hmmpath_vtable_parnames,
  pdl_hmmpath_vtable_parflags, pdl_hmmpath_vtable_partypes,
  pdl_hmmpath_vtable_realdims_starts, pdl_hmmpath_vtable_realdims_ind_ids, 3,
  2, pdl_hmmpath_vtable_indnames,
  NULL, pdl_hmmpath_readdata, NULL,
  NULL,
  0,"PDL::HMM::hmmpath"
};


pdl_error pdl_run_hmmpath(pdl  *psi,pdl  *qfinal,pdl  *path) {
  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_hmmpath_vtable);
  if (!__privtrans) return PDL->make_error_simple(PDL_EFATAL, "Couldn't create trans");
  __privtrans->pdls[0] = psi;
  __privtrans->pdls[1] = qfinal;
  __privtrans->pdls[2] = path;
  PDL_RETERROR(PDL_err, PDL->type_coerce(__privtrans));
  PDL_RETERROR(PDL_err, PDL->make_trans_mutual(__privtrans));
  return PDL_err;
}