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.../scitbx/math/boost_python/distributions.cpp | 60 +++++++++++++------
cctbx_sources/scitbx/rigid_body/spatial_lib.h | 1 +
cctbx_sources/scitbx/rigid_body/tardy.h | 4 +-
.../refinement/boost_python/weighting_schemes.cpp | 4 +-
.../smtbx/structure_factors/direct/standard_xray.h | 4 +-
5 files changed, 48 insertions(+), 25 deletions(-)
diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
index a676798..68818e7 100644
--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp
+++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
@@ -59,29 +59,51 @@ namespace {
{
typedef Distribution wt;
+ #define NEW_MEMBER(name) \
+ static FloatType name(wt const &self) { \
+ return boost::math::name(self); \
+ }
+
+ NEW_MEMBER(mean);
+ NEW_MEMBER(median);
+ NEW_MEMBER(mode);
+ NEW_MEMBER(variance);
+ NEW_MEMBER(standard_deviation);
+ NEW_MEMBER(skewness);
+ NEW_MEMBER(kurtosis);
+
+ #undef NEW_MEMBER
+
+ #define NEW_MEMBER(name) \
+ static FloatType name(wt const &self, FloatType arg) { \
+ return boost::math::name(self, arg); \
+ }
+
+ NEW_MEMBER(pdf);
+ NEW_MEMBER(cdf);
+ NEW_MEMBER(quantile);
+
+ #undef NEW_MEMBER
+
+ static scitbx::af::shared<FloatType> quantiles(wt const &self, std::size_t n) {
+ return scitbx::math::quantiles<FloatType>(self, n);
+ }
+
static void
wrap()
{
using namespace boost::python;
- def("mean", (FloatType(*)(wt const&)) boost::math::mean);
- def("median", (FloatType(*)(wt const&)) boost::math::median);
- def("mode", (FloatType(*)(wt const&)) boost::math::mode);
- def("variance", (FloatType(*)(wt const&)) boost::math::variance);
- def("standard_deviation",
- (FloatType(*)(wt const&)) boost::math::standard_deviation);
- def("skewness", (FloatType(*)(wt const&)) boost::math::skewness);
- def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis);
- def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf);
- def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf);
- def("quantile", (FloatType(*)(wt const&, FloatType const&))
- boost::math::quantile);
- def("quantiles",
-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306))
- (scitbx::af::shared<FloatType>(*)(wt const&, std::size_t)) quantiles
-#else
- quantiles<FloatType, wt>
-#endif
- );
+ def("mean" , mean);
+ def("median" , median);
+ def("mode" , mode);
+ def("variance" , variance);
+ def("standard_deviation", standard_deviation);
+ def("skewness" , skewness);
+ def("kurtosis" , kurtosis);
+ def("pdf" , pdf);
+ def("cdf" , cdf);
+ def("quantile" , quantile);
+ def("quantiles" , quantiles);
}
};
diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
index a084f0f..e377292 100755
--- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h
+++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
@@ -2,6 +2,7 @@
#define SCITBX_RIGID_BODY_SPATIAL_LIB_H
#include <scitbx/rotr3.h>
+#include <scitbx/rigid_body/matrix_helpers.h>
#include <scitbx/array_family/versa_matrix.h>
namespace scitbx { namespace rigid_body {
diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h
index 104f16b..a8f76cc 100755
--- a/cctbx_sources/scitbx/rigid_body/tardy.h
+++ b/cctbx_sources/scitbx/rigid_body/tardy.h
@@ -346,7 +346,7 @@ namespace tardy {
unsigned nb = this->bodies_size();
af::shared<af::small<ft, 7> > result((af::reserve(nb)));
af::shared<af::small<ft, 6> >
- tau_array = f_ext_as_tau(f_ext_array().const_ref());
+ tau_array = this->f_ext_as_tau(f_ext_array().const_ref());
for(unsigned ib=0;ib<nb;ib++) {
result.push_back(
this->bodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib]));
@@ -379,7 +379,7 @@ namespace tardy {
qdd_array()
{
if (!qdd_array_) {
- qdd_array_ = forward_dynamics_ab(
+ qdd_array_ = this->forward_dynamics_ab(
/*tau_array*/ af::const_ref<af::small<ft, 6> >(0, 0),
f_ext_array().const_ref(),
/*grav_accn*/ af::const_ref<ft>(0, 0));
diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
index ce0c27b..904e8d7 100644
--- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
+++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares {
: base_t(name, boost::python::no_init)
{
using namespace boost::python;
- def("__call__", &wt::operator(),
+ this->def("__call__", &wt::operator(),
(arg("fo_sq"), arg("sigma"), arg("fc_sq")));
- def("__call__", weights,
+ this->def("__call__", weights,
(arg("fo_sq"), arg("sigmas"), arg("fc_sq")));
}
};
diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
index 5e2df76..911bfde 100644
--- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
+++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
for (int k=0; k < hr_ht.groups.size(); ++k) {
hr_ht_group<float_type> const &g = hr_ht.groups[k];
float_type hrx = g.hr * scatterer.site;
- complex_type f = exp_i_2pi(hrx + g.ht);
+ complex_type f = this->exp_i_2pi(hrx + g.ht);
if (scatterer.flags.use_u_aniso()) {
float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);
f *= dw;
@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
for (int k=0; k < hr_ht.groups.size(); ++k) {
hr_ht_group<float_type> const &g = hr_ht.groups[k];
float_type hrx = g.hr * scatterer.site;
- complex_type f = exp_i_2pi(hrx + g.ht);
+ complex_type f = this->exp_i_2pi(hrx + g.ht);
float_type fa = f.real(), fb = f.imag();
if (scatterer.flags.use_u_aniso()) {
float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);
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