move widely duplicated math functions into m.h header

5 files changed, 20 insertions, 36 deletions

diff --git a/gi/pf/base_distributions.cc b/gi/pf/base_distributions.cc
index d362fd76..d9761005 100644
--- a/gi/pf/base_distributions.cc
+++ b/gi/pf/base_distributions.cc
@@ -59,7 +59,7 @@ prob_t PhraseConditionalUninformativeUnigramBase::p0(const vector<WordID>& vsrc,
   const int flen = vsrc.size() - start_src;
   const int elen = vtrg.size() - start_trg;
   prob_t p;
-  p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
+  p.logeq(Md::log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
   //p.logeq(log_poisson(elen, 1));       // elen | flen          ~Pois(flen + 0.01)
   for (int i = 0; i < elen; ++i)
     p *= u(vtrg[i + start_trg]);                        // draw e_i             ~Uniform
@@ -73,7 +73,7 @@ prob_t PhraseConditionalUninformativeBase::p0(const vector<WordID>& vsrc,
   const int elen = vtrg.size() - start_trg;
   prob_t p;
   //p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-  p.logeq(log_poisson(elen, 1));       // elen | flen          ~Pois(flen + 0.01)
+  p.logeq(Md::log_poisson(elen, 1));       // elen | flen          ~Pois(flen + 0.01)
   for (int i = 0; i < elen; ++i)
     p *= kUNIFORM_TARGET;                        // draw e_i             ~Uniform
   return p;
@@ -113,7 +113,7 @@ prob_t PhraseConditionalBase::p0(const vector<WordID>& vsrc,
   const int elen = vtrg.size() - start_trg;
   prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
   prob_t p;
-  p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
+  p.logeq(Md::log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
   for (int i = 0; i < elen; ++i) {               // for each position i in e-RHS
     const WordID trg = vtrg[i + start_trg];
     prob_t tp = prob_t::Zero();
@@ -139,9 +139,9 @@ prob_t PhraseJointBase::p0(const vector<WordID>& vsrc,
   const int elen = vtrg.size() - start_trg;
   prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
   prob_t p;
-  p.logeq(log_poisson(flen, 1.0));               // flen                 ~Pois(1)
+  p.logeq(Md::log_poisson(flen, 1.0));               // flen                 ~Pois(1)
                                                  // elen | flen          ~Pois(flen + 0.01)
-  prob_t ptrglen; ptrglen.logeq(log_poisson(elen, flen + 0.01));
+  prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01));
   p *= ptrglen;
   p *= kUNIFORM_SOURCE.pow(flen);                // each f in F ~Uniform
   for (int i = 0; i < elen; ++i) {               // for each position i in E
@@ -171,9 +171,9 @@ prob_t PhraseJointBase_BiDir::p0(const vector<WordID>& vsrc,
   prob_t uniform_trg_alignment; uniform_trg_alignment.logeq(-log(elen + 1));
 
   prob_t p1;
-  p1.logeq(log_poisson(flen, 1.0));               // flen                 ~Pois(1)
+  p1.logeq(Md::log_poisson(flen, 1.0));               // flen                 ~Pois(1)
                                                  // elen | flen          ~Pois(flen + 0.01)
-  prob_t ptrglen; ptrglen.logeq(log_poisson(elen, flen + 0.01));
+  prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01));
   p1 *= ptrglen;
   p1 *= kUNIFORM_SOURCE.pow(flen);                // each f in F ~Uniform
   for (int i = 0; i < elen; ++i) {               // for each position i in E
@@ -193,9 +193,9 @@ prob_t PhraseJointBase_BiDir::p0(const vector<WordID>& vsrc,
   }
 
   prob_t p2;
-  p2.logeq(log_poisson(elen, 1.0));               // elen                 ~Pois(1)
+  p2.logeq(Md::log_poisson(elen, 1.0));               // elen                 ~Pois(1)
                                                  // flen | elen          ~Pois(flen + 0.01)
-  prob_t psrclen; psrclen.logeq(log_poisson(flen, elen + 0.01));
+  prob_t psrclen; psrclen.logeq(Md::log_poisson(flen, elen + 0.01));
   p2 *= psrclen;
   p2 *= kUNIFORM_TARGET.pow(elen);                // each f in F ~Uniform
   for (int i = 0; i < flen; ++i) {               // for each position i in E
@@ -227,9 +227,9 @@ JumpBase::JumpBase() : p(200) {
     for (int j = min_jump; j <= max_jump; ++j) {
       prob_t& cp = cpd[j];
       if (j < 0)
-        cp.logeq(log_poisson(1.5-j, 1));
+        cp.logeq(Md::log_poisson(1.5-j, 1));
       else if (j > 0)
-        cp.logeq(log_poisson(j, 1));
+        cp.logeq(Md::log_poisson(j, 1));
       cp.poweq(0.2);
       z += cp;
     }
diff --git a/gi/pf/base_distributions.h b/gi/pf/base_distributions.h
index a23ac32b..0d597c5c 100644
--- a/gi/pf/base_distributions.h
+++ b/gi/pf/base_distributions.h
@@ -13,24 +13,7 @@
 #include "prob.h"
 #include "tdict.h"
 #include "sampler.h"
-
-inline double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-inline double log_binom_coeff(unsigned n, unsigned k) {
-  assert(n >= k);
-  if (n == k) return 0.0;
-  return lgamma(n + 1) - lgamma(k + 1) - lgamma(n - k + 1);
-}
-
-// http://en.wikipedia.org/wiki/Negative_binomial_distribution
-inline double log_negative_binom(unsigned x, unsigned r, double p) {
-  assert(p > 0.0);
-  assert(p < 1.0);
-  return log_binom_coeff(x + r - 1, x) + r * log(1 - p) + x * log(p);
-}
+#include "m.h"
 
 inline std::ostream& operator<<(std::ostream& os, const std::vector<WordID>& p) {
   os << '[';
@@ -68,7 +51,7 @@ struct Model1 {
 struct PoissonUniformUninformativeBase {
   explicit PoissonUniformUninformativeBase(const unsigned ves) : kUNIFORM(1.0 / ves) {}
   prob_t operator()(const TRule& r) const {
-    prob_t p; p.logeq(log_poisson(r.e_.size(), 1.0));
+    prob_t p; p.logeq(Md::log_poisson(r.e_.size(), 1.0));
     prob_t q = kUNIFORM; q.poweq(r.e_.size());
     p *= q;
     return p;
diff --git a/gi/pf/conditional_pseg.h b/gi/pf/conditional_pseg.h
index 0aa5e8e0..2e9e38fc 100644
--- a/gi/pf/conditional_pseg.h
+++ b/gi/pf/conditional_pseg.h
@@ -6,6 +6,7 @@
 #include <boost/functional/hash.hpp>
 #include <iostream>
 
+#include "m.h"
 #include "prob.h"
 #include "ccrp_nt.h"
 #include "mfcr.h"
@@ -210,7 +211,7 @@ struct ConditionalParallelSegementationModel {
 
   prob_t AlignProbability(unsigned span) const {
     prob_t p;
-    p.logeq(aligns.logprob(span, log_poisson(span, 1.0)));
+    p.logeq(aligns.logprob(span, Md::log_poisson(span, 1.0)));
     return p;
   }
 
diff --git a/gi/pf/pfdist.cc b/gi/pf/pfdist.cc
index ef08a165..3d578db2 100644
--- a/gi/pf/pfdist.cc
+++ b/gi/pf/pfdist.cc
@@ -315,7 +315,7 @@ struct BackwardEstimate {
       for (int i = 0; i < src_cov.size(); ++i)
         if (!src_cov[i]) r.push_back(src_[i]);
       const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
+      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
       for (unsigned j = trg_cov; j < trg_.size(); ++j) {
         prob_t p;
         for (unsigned i = 0; i < r.size(); ++i)
@@ -352,7 +352,7 @@ struct BackwardEstimateSym {
         if (!src_cov[i]) r.push_back(src_[i]);
       r.push_back(0);  // NULL word
       const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
+      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
       for (unsigned j = trg_cov; j < trg_.size(); ++j) {
         prob_t p;
         for (unsigned i = 0; i < r.size(); ++i)
@@ -367,7 +367,7 @@ struct BackwardEstimateSym {
       r.pop_back();
       const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0));
       prob_t inv;
-      inv.logeq(log_poisson(r.size(), trg_.size() - trg_cov));
+      inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov));
       for (unsigned i = 0; i < r.size(); ++i) {
         prob_t p;
         for (unsigned j = trg_cov - 1; j < trg_.size(); ++j)
diff --git a/gi/pf/pfnaive.cc b/gi/pf/pfnaive.cc
index acba9d22..e1a53f5c 100644
--- a/gi/pf/pfnaive.cc
+++ b/gi/pf/pfnaive.cc
@@ -77,7 +77,7 @@ struct BackwardEstimateSym {
         r.push_back(src_[i]);
       r.push_back(0);  // NULL word
       const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
+      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
       for (unsigned j = trg_cov; j < trg_.size(); ++j) {
         prob_t p;
         for (unsigned i = 0; i < r.size(); ++i)
@@ -92,7 +92,7 @@ struct BackwardEstimateSym {
       r.pop_back();
       const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0));
       prob_t inv;
-      inv.logeq(log_poisson(r.size(), trg_.size() - trg_cov));
+      inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov));
       for (unsigned i = 0; i < r.size(); ++i) {
         prob_t p;
         for (unsigned j = trg_cov - 1; j < trg_.size(); ++j)