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merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008

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This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
This commit is contained in:
Greg Landrum
2008-07-05 07:42:38 +00:00
parent 4d75f40534
commit c9eb4e91e1
138 changed files with 10785 additions and 10112 deletions
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236
Code/SimDivPickers/Wrap/MaxMinPicker.cpp
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@@ -1,115 +1,121 @@
// $Id$
//
// Copyright (C) 2003-2007 Greg Landrum and Rational Discovery LLC
// @@ All Rights Reserved @@
//
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API
#include <boost/python.hpp>
#include <RDBoost/Wrap.h>
#include "Numeric/arrayobject.h"
#include <map>
#include <SimDivPickers/DistPicker.h>
#include <SimDivPickers/MaxMinPicker.h>
#include <iostream>
namespace python = boost::python;
namespace RDPickers {
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::INT_VECT MaxMinPicks(MaxMinPicker *picker,
python::numeric::array &distMat,
int poolSize,
int pickSize,
python::object firstPicks) {
if(pickSize>=poolSize){
throw ValueErrorException("pickSize must be less than poolSize");
}
PyArrayObject *copy;
copy = (PyArrayObject *)PyArray_ContiguousFromObject(distMat.ptr(),
PyArray_DOUBLE, 1,1);
double *dMat = (double *)copy->data;
RDKit::INT_VECT firstPickVect;
for(unsigned int i=0;i<python::extract<unsigned int>(firstPicks.attr("__len__")());++i){
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res=picker->pick(dMat, poolSize, pickSize,firstPickVect);
Py_DECREF(copy);
return res;
}
class pyobjFunctor {
public:
pyobjFunctor(python::object obj) : dp_obj(obj) {}
double operator()(unsigned int i,unsigned int j) {
double res;
std::pair<unsigned int ,unsigned int> idxPair(i,j);
if(this->d_cache.count(idxPair)>0){
res = this->d_cache[idxPair];
} else {
res=python::extract<double>(dp_obj(i,j));
this->d_cache[idxPair]=res;
}
return res;
}
private:
python::object dp_obj;
std::map<std::pair<unsigned int,unsigned int>,double> d_cache;
};
RDKit::INT_VECT LazyMaxMinPicks(MaxMinPicker *picker,
python::object distFunc,
int poolSize,
int pickSize,
python::object firstPicks) {
pyobjFunctor functor(distFunc);
RDKit::INT_VECT firstPickVect;
for(unsigned int i=0;i<python::extract<unsigned int>(firstPicks.attr("__len__")());++i){
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res=picker->lazyPick(functor, poolSize, pickSize,firstPickVect);
return res;
}
struct MaxMin_wrap {
static void wrap() {
python::class_<MaxMinPicker>("MaxMinPicker",
"A class for diversity picking of items using the MaxMin Algorithm\n")
.def("Pick", MaxMinPicks,
(python::arg("self"),python::arg("distMat"),python::arg("poolSize"),
python::arg("pickSize"),python::arg("firstPicks")=python::tuple()),
"Pick a subset of items from a pool of items using the MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604 \n\n"
"ARGUMENTS:\n"
" - distMat: 1D distance matrix (only the lower triangle elements)\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds the list)\n")
.def("LazyPick", LazyMaxMinPicks,
(python::arg("self"),python::arg("distFunc"),python::arg("poolSize"),
python::arg("pickSize"),python::arg("firstPicks")=python::tuple()),
"Pick a subset of items from a pool of items using the MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604 \n"
"ARGUMENTS:\n\n"
" - distFunc: a function that should take two indices and return the\n"
" distance between those two points.\n"
" NOTE: the implementation caches distance values, so the\n"
" client code does not need to do so; indeed, it should not.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds the list)\n")
;
};
};
}
void wrap_maxminpick() {
RDPickers::MaxMin_wrap::wrap();
}
// $Id$
//
// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
// @@ All Rights Reserved @@
//
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API
#include <boost/python.hpp>
#include <RDBoost/Wrap.h>
#include <boost/python/numeric.hpp>
#include "numpy/oldnumeric.h"
#include <map>
#include <SimDivPickers/DistPicker.h>
#include <SimDivPickers/MaxMinPicker.h>
#include <iostream>
namespace python = boost::python;
namespace RDPickers {
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::INT_VECT MaxMinPicks(MaxMinPicker *picker,
python::object distMat,
int poolSize,
int pickSize,
python::object firstPicks) {
if(pickSize>=poolSize){
throw ValueErrorException("pickSize must be less than poolSize");
}
if (!PyArray_Check(distMat.ptr())){
throw ValueErrorException("distance mat argument must be a numpy matrix");
}
PyArrayObject *copy;
copy = (PyArrayObject *)PyArray_ContiguousFromObject(distMat.ptr(),
PyArray_DOUBLE, 1,1);
double *dMat = (double *)copy->data;
RDKit::INT_VECT firstPickVect;
for(unsigned int i=0;i<python::extract<unsigned int>(firstPicks.attr("__len__")());++i){
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res=picker->pick(dMat, poolSize, pickSize,firstPickVect);
Py_DECREF(copy);
return res;
}
class pyobjFunctor {
public:
pyobjFunctor(python::object obj) : dp_obj(obj) {}
double operator()(unsigned int i,unsigned int j) {
double res;
std::pair<unsigned int ,unsigned int> idxPair(i,j);
if(this->d_cache.count(idxPair)>0){
res = this->d_cache[idxPair];
} else {
res=python::extract<double>(dp_obj(i,j));
this->d_cache[idxPair]=res;
}
return res;
}
private:
python::object dp_obj;
std::map<std::pair<unsigned int,unsigned int>,double> d_cache;
};
RDKit::INT_VECT LazyMaxMinPicks(MaxMinPicker *picker,
python::object distFunc,
int poolSize,
int pickSize,
python::object firstPicks) {
pyobjFunctor functor(distFunc);
RDKit::INT_VECT firstPickVect;
for(unsigned int i=0;i<python::extract<unsigned int>(firstPicks.attr("__len__")());++i){
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res=picker->lazyPick(functor, poolSize, pickSize,firstPickVect);
return res;
}
struct MaxMin_wrap {
static void wrap() {
python::class_<MaxMinPicker>("MaxMinPicker",
"A class for diversity picking of items using the MaxMin Algorithm\n")
.def("Pick", MaxMinPicks,
(python::arg("self"),python::arg("distMat"),python::arg("poolSize"),
python::arg("pickSize"),python::arg("firstPicks")=python::tuple()),
"Pick a subset of items from a pool of items using the MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604 \n\n"
"ARGUMENTS:\n"
" - distMat: 1D distance matrix (only the lower triangle elements)\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds the list)\n")
.def("LazyPick", LazyMaxMinPicks,
(python::arg("self"),python::arg("distFunc"),python::arg("poolSize"),
python::arg("pickSize"),python::arg("firstPicks")=python::tuple()),
"Pick a subset of items from a pool of items using the MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), 598-604 \n"
"ARGUMENTS:\n\n"
" - distFunc: a function that should take two indices and return the\n"
" distance between those two points.\n"
" NOTE: the implementation caches distance values, so the\n"
" client code does not need to do so; indeed, it should not.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds the list)\n")
;
};
};
}
void wrap_maxminpick() {
RDPickers::MaxMin_wrap::wrap();
}