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// $Id: HierarchicalClusterPicker.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API
#include <boost/python.hpp>
#include <boost/python/numeric.hpp>
#include "numpy/oldnumeric.h"
#include <RDBoost/Wrap.h>
#include <SimDivPickers/DistPicker.h>
#include <SimDivPickers/HierarchicalClusterPicker.h>
namespace python = boost::python;
namespace RDPickers {
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::INT_VECT HierarchicalPicks(HierarchicalClusterPicker *picker,
python::object &distMat,
int poolSize,
int pickSize) {
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;
// it's painful to have to copy the input matrix, but the
// picker itself will step on the distance matrix, so use
// CopyFromObject here instead of ContiguousFromObject
copy = (PyArrayObject *)PyArray_CopyFromObject(distMat.ptr(),
PyArray_DOUBLE, 1,1);
double *dMat = (double *)copy->data;
RDKit::INT_VECT res=picker->pick(dMat, poolSize, pickSize);
Py_DECREF(copy);
return res;
}
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::VECT_INT_VECT HierarchicalClusters(HierarchicalClusterPicker *picker,
python::object &distMat,
int poolSize,
int pickSize) {
if (!PyArray_Check(distMat.ptr())){
throw ValueErrorException("distance mat argument must be a numpy matrix");
}
// REVIEW: check pickSize < poolSize, otherwise throw_value_error()
PyArrayObject *copy;
// it's painful to have to copy the input matrix, but the
// picker itself will step on the distance matrix, so use
// CopyFromObject here instead of ContiguousFromObject
copy = (PyArrayObject *)PyArray_CopyFromObject(distMat.ptr(),
PyArray_DOUBLE, 1,1);
double *dMat = (double *)copy->data;
RDKit::VECT_INT_VECT res=picker->cluster(dMat, poolSize, pickSize);
Py_DECREF(copy);
return res;
}
struct HierarchCP_wrap {
static void wrap() {
std::string docString = "A class for diversity picking of items using Hierarchical Clustering\n";
python::class_<HierarchicalClusterPicker>("HierarchicalClusterPicker",
docString.c_str(),
python::init<HierarchicalClusterPicker::ClusterMethod>
(python::args("clusterMethod")))
.def("Pick", HierarchicalPicks,
"Pick a diverse subset of items from a pool of items using hierarchical clustering\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")
.def("Cluster", HierarchicalClusters,
"Return a list of clusters of item from the pool using hierachical clustering\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")
;
python::enum_<HierarchicalClusterPicker::ClusterMethod>("ClusterMethod")
.value("WARD", HierarchicalClusterPicker::WARD)
.value("SLINK", HierarchicalClusterPicker::SLINK)
.value("CLINK", HierarchicalClusterPicker::CLINK)
.value("UPGMA", HierarchicalClusterPicker::UPGMA)
.value("MCQUITTY", HierarchicalClusterPicker::MCQUITTY)
.value("GOWER", HierarchicalClusterPicker::GOWER)
.value("CENTROID", HierarchicalClusterPicker::CENTROID)
;
};
};
}
void wrap_HierarchCP() {
RDPickers::HierarchCP_wrap::wrap();
}
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