void list_keys(py::dict dict)
{
std::cout << py::len(dict.items()) << " keys in dict:" << std::endl;
for(int i=0; i<py::len(dict.items()); ++i)
{
std::cout << std::string(py::extract<std::string>(dict.items()[i][0]))
<< std::endl;
}
}
INT_VECT EmbedMultipleConfs(
ROMol &mol, unsigned int numConfs, unsigned int maxAttempts, int seed,
bool clearConfs, bool useRandomCoords, double boxSizeMult, bool randNegEig,
unsigned int numZeroFail, double pruneRmsThresh, python::dict &coordMap,
double forceTol, bool ignoreSmoothingFailures, bool enforceChirality,
int numThreads, bool useExpTorsionAnglePrefs, bool useBasicKnowledge,
bool printExpTorsionAngles) {
std::map<int, RDGeom::Point3D> pMap;
python::list ks = coordMap.keys();
unsigned int nKeys = python::extract<unsigned int>(ks.attr("__len__")());
for (unsigned int i = 0; i < nKeys; ++i) {
unsigned int id = python::extract<unsigned int>(ks[i]);
pMap[id] = python::extract<RDGeom::Point3D>(coordMap[id]);
}
std::map<int, RDGeom::Point3D> *pMapPtr = 0;
if (nKeys) {
pMapPtr = &pMap;
}
INT_VECT res;
{
NOGIL gil;
DGeomHelpers::EmbedMultipleConfs(
mol, res, numConfs, numThreads, maxAttempts, seed, clearConfs,
useRandomCoords, boxSizeMult, randNegEig, numZeroFail, pruneRmsThresh,
pMapPtr, forceTol, ignoreSmoothingFailures, enforceChirality,
useExpTorsionAnglePrefs, useBasicKnowledge, printExpTorsionAngles);
}
return res;
}
boost::shared_ptr<ecto::module_<T> > inspect(boost::python::tuple args,
boost::python::dict kwargs)
{
typedef ecto::module_<T> module_t;
namespace bp = boost::python;
//SHOW();
boost::shared_ptr<module_t> mm(new module_t());
ecto::module * m = mm.get();
m->declare_params();
bp::list l = kwargs.items();
for (int j = 0; j < bp::len(l); ++j)
{
bp::object key = l[j][0];
bp::object value = l[j][1];
std::string keystring = bp::extract<std::string>(key);
std::string valstring =
bp::extract<std::string>(value.attr("__repr__")());
m->parameters.at(keystring).set(value);
}
m->declare_io();
return mm;
}
static void writeKeyValueMap(
PolymorphicSharedPtr<KeyspaceStorage>& inStorage,
boost::python::dict& keysAndValues
)
{
map<SharedState::Key, KeyState> state;
boost::python::list keys = keysAndValues.keys();
long len = boost::python::len(keys);
for (long k = 0; k < len; k++)
{
state[boost::python::extract<SharedState::Key>(keys[k])()] =
KeyState(
null() << ValueType(
null() << PythonWrapper<SharedState::View>::pyToJsonOrError(keysAndValues[keys[k]]),
UniqueId()
),
null() << UniqueId(),
std::map<UniqueId, PartialEvent>()
);
}
inStorage->writeStateExternal(state);
}
/**
* If an output workspace was created then extract it from the given dictionary
* @param locals A dictionary possibly containing an 'output' reference
* @return A pointer to the output workspace if created, otherwise an empty
* pointer
*/
boost::shared_ptr<API::Workspace> RunPythonScript::extractOutputWorkspace(
const boost::python::dict &locals) const {
using namespace API;
using namespace boost::python;
// Might be None, string or a workspace object
auto pyoutput = locals.get("output");
if (isNone(pyoutput))
return Workspace_sptr();
auto ptrExtract = ExtractWorkspace(pyoutput);
if (ptrExtract.check()) {
return ptrExtract();
} else {
extract<std::string> extractString(pyoutput);
if (extractString.check()) {
// Will raise an error if the workspace does not exist as the user
// requested
// an output workspace
// but didn't create one.
return AnalysisDataService::Instance().retrieve(extractString());
} else {
throw std::runtime_error(
"Invalid type assigned to 'output' variable. Must "
"be a string or a Workspace object");
}
}
}
unsigned int Compute2DCoords(RDKit::ROMol &mol, bool canonOrient,
bool clearConfs, python::dict &coordMap,
unsigned int nFlipsPerSample = 3,
unsigned int nSamples = 100, int sampleSeed = 100,
bool permuteDeg4Nodes = false,
double bondLength = -1.0) {
RDGeom::INT_POINT2D_MAP cMap;
cMap.clear();
python::list ks = coordMap.keys();
for (unsigned int i = 0;
i < python::extract<unsigned int>(ks.attr("__len__")()); i++) {
unsigned int id = python::extract<unsigned int>(ks[i]);
if (id >= mol.getNumAtoms()) {
throw_value_error("atom index out of range");
}
cMap[id] = python::extract<RDGeom::Point2D>(coordMap[id]);
}
double oBondLen = RDDepict::BOND_LEN;
if (bondLength > 0) {
RDDepict::BOND_LEN = bondLength;
}
unsigned int res;
res = RDDepict::compute2DCoords(mol, &cMap, canonOrient, clearConfs,
nFlipsPerSample, nSamples, sampleSeed,
permuteDeg4Nodes);
if (bondLength > 0) {
RDDepict::BOND_LEN = oBondLen;
}
return res;
}
void Serializable::pyUpdateAttrs(const boost::python::dict& d){
boost::python::list l=d.items(); size_t ll=boost::python::len(l); if(ll==0) return;
for(size_t i=0; i<ll; i++){
boost::python::tuple t=boost::python::extract<boost::python::tuple>(l[i]);
string key=boost::python::extract<string>(t[0]);
pySetAttr(key,t[1]);
}
callPostLoad();
}
/**
* @param mapping A Python dictionary instance
* @return A new C++ PropertyManager instance
*/
boost::shared_ptr<Kernel::PropertyManager>
createPropertyManager(const boost::python::dict &mapping) {
auto pmgr = boost::make_shared<PropertyManager>();
#if PY_MAJOR_VERSION >= 3
object view(mapping.attr("items")());
object itemIter(handle<>(PyObject_GetIter(view.ptr())));
#else
object itemIter(mapping.attr("iteritems")());
#endif
auto length = len(mapping);
for (ssize_t i = 0; i < length; ++i) {
const object keyValue(handle<>(PyIter_Next(itemIter.ptr())));
const std::string cppkey = extract<std::string>(keyValue[0])();
pmgr->declareProperty(PropertyWithValueFactory::create(cppkey, keyValue[1],
Direction::Input));
}
return pmgr;
}
void clientW::connect(const std::string& uri, const boost::python::dict& query){
std::map<std::string, std::string> newmap;
int len = boost::python::len(query);
boost::python::list keys = query.keys();
for(int i=0; i < len; i++) {
std::string k = boost::python::extract<std::string>(keys[i]);
newmap[k] = boost::python::extract<std::string>(query[k]);
}
this->client::connect(uri,newmap);
}
map<string,double> extract_solution(boost::python::dict pySol)
{
boost::python::list sol_keys = pySol.keys();
map<string,double> sol;
for(int iter = 0; iter < len(sol_keys); ++iter)
{
boost::python::extract<std::string> key(sol_keys[iter]);
boost::python::extract<double> value(pySol[sol_keys[iter]]);
sol[key] = value;
}
return sol;
}
static mapnik::attributes dict2attr(boost::python::dict const& d)
{
using namespace boost::python;
mapnik::attributes vars;
mapnik::transcoder tr_("utf8");
boost::python::list keys=d.keys();
for (int i=0; i < len(keys); ++i)
{
std::string key = extract<std::string>(keys[i]);
object obj = d[key];
if (PyUnicode_Check(obj.ptr()))
{
PyObject* temp = PyUnicode_AsUTF8String(obj.ptr());
if (temp)
{
#if PY_VERSION_HEX >= 0x03000000
char* c_str = PyBytes_AsString(temp);
#else
char* c_str = PyString_AsString(temp);
#endif
vars[key] = tr_.transcode(c_str);
Py_DecRef(temp);
}
continue;
}
extract<std::string> ex0(obj);
if (ex0.check())
{
vars[key] = tr_.transcode(ex0().c_str());
continue;
}
extract<mapnik::value_integer> ex2(obj);
if (ex2.check())
{
vars[key] = ex2();
continue;
}
extract<double> ex3(obj);
if (ex3.check())
{
vars[key] = ex3();
continue;
}
extract<mapnik::value_bool> ex1(obj);
if (ex1.check())
{
vars[key] = ex1();
continue;
}
}
return vars;
}
map<string,Vec4d> extract_targets(boost::python::dict target_positions)
{
boost::python::list target_keys = target_positions.keys();
map<string,Vec4d> target;
for( int iter = 0; iter < len(target_keys); ++iter)
{
boost::python::extract<std::string> key(target_keys[iter]);
boost::python::list value = boost::python::extract<boost::python::list>(target_positions[target_keys[iter]]);
Vec4d v;
assert(len(value) == 4);
for(int jter = 0; jter < len(value); ++jter)
v.values[jter] = boost::python::extract<double>(value[jter]);
target[key] = v;
}
return target;
}
//---------------------------------------------------------------------------
boost::property_tree::ptree make_ptree(const boost::python::dict &args) {
using namespace boost::python;
boost::property_tree::ptree p;
for(stl_input_iterator<tuple> arg(args.items()), end; arg != end; ++arg) {
const char *name = extract<const char*>((*arg)[0]);
const char *type = extract<const char*>((*arg)[1].attr("__class__").attr("__name__"));
if (strcmp(type, "int") == 0)
p.put(name, extract<int>((*arg)[1]));
else
p.put(name, extract<float>((*arg)[1]));
}
return p;
}
const std::string PugAPI::map(const std::string node, const boost::python::dict& d) const
{
QVariantMap qmap;
boost::python::list keys = (boost::python::list)d.iterkeys();
for (int i = 0; i < boost::python::len(keys); i++) {
boost::python::object obj = d[keys[i]];
if (PyString_Check(obj.ptr())) {
qmap[QString::fromStdString(boost::python::extract<std::string>(keys[i]))] = QString::fromStdString(boost::python::extract<std::string>(obj));
} else if (PyInt_Check(obj.ptr())) {
qmap[QString::fromStdString(boost::python::extract<std::string>(keys[i]))] = QVariant(boost::python::extract<int>(obj));
}
// ignore things we can't convert
}
QString qresult = m_root->map(QString::fromStdString(node), qmap);
return qresult.toStdString();
}
void add_mrfenergy_class(py::dict cls_dict, py::object key, const std::string& suffix)
{
typedef typename T::LocalSize LocalSize;
typedef typename T::NodeData NodeData;
typedef typename T::EdgeData EdgeData;
// NodeId is a pointer to a private struct Node. These lines
// mask NodeId as an integer value (numeric_pointer).
typedef numeric_pointer (MRFEnergy<T>::*add_node_type)(LocalSize, NodeData);
typedef void (MRFEnergy<T>::*add_edge_type)(numeric_pointer, numeric_pointer, EdgeData);
// Export the MRFEnergy class for the given T.
py::object c = py::class_<MRFEnergy<T> >(("MRFEnergy"+suffix).c_str(), "MRF energy representation.",
py::init<typename T::GlobalSize>())
.def("add_node", (add_node_type)(&MRFEnergy<T>::AddNode),
(py::arg("local_size"), py::arg("node_data")))
.def("add_edge", (add_edge_type)(&MRFEnergy<T>::AddEdge),
(py::arg("nodeid1"), py::arg("nodeid2"), py::arg("edge_data")))
.def("minimize_trw", &minimize_trw<T>,
"Minimize the energy of the MRF using TRW.",
(py::arg("self"), py::arg("eps")=-1, py::arg("itermax")=50,
py::arg("printiter")=5, py::arg("printminiter")=0, py::arg("details")=false))
.def("minimize_bp", &minimize_bp<T>,
"Minimize the energy of the MRF using BP.",
(py::arg("self"), py::arg("eps")=-1, py::arg("itermax")=50,
py::arg("printiter")=5, py::arg("printminiter")=0, py::arg("details")=false))
.def("zero_messages", &MRFEnergy<T>::ZeroMessages)
.def("set_automatic_ordering", &MRFEnergy<T>::SetAutomaticOrdering)
.def("add_grid_nodes", &add_grid_nodes<T>,
(py::arg("unary_terms"), py::arg("axis")=0))
.def("add_grid_edges", &add_grid_edges<T>,
(py::arg("nodeids"), py::arg("edge_data")))
.def("add_grid_edges_direction", &add_grid_edges_direction<T>,
(py::arg("nodeis"), py::arg("edge_data"), py::arg("direction")))
.def("add_grid_edges_direction_local", &add_grid_edges_direction_local<T>,
(py::arg("nodeis"), py::arg("edge_data"), py::arg("direction"), py::arg("axis")=0))
.def("get_solution", &get_solution<T>,
(py::arg("nodeids")));
cls_dict.attr("__setitem__")(key, c);
}
PXR_NAMESPACE_OPEN_SCOPE
bool
SdfFileFormatArgumentsFromPython(
const boost::python::dict& dict,
SdfLayer::FileFormatArguments* args,
std::string* errMsg)
{
SdfLayer::FileFormatArguments argsMap;
typedef SdfLayer::FileFormatArguments::key_type ArgKeyType;
typedef SdfLayer::FileFormatArguments::mapped_type ArgValueType;
const boost::python::object items = dict.items();
for (boost::python::ssize_t i = 0; i < len(items); ++i) {
boost::python::extract<ArgKeyType> keyExtractor(items[i][0]);
if (!keyExtractor.check()) {
if (errMsg) {
*errMsg = "All file format argument keys must be strings";
}
return false;
}
boost::python::extract<ArgValueType> valueExtractor(items[i][1]);
if (!valueExtractor.check()) {
if (errMsg) {
*errMsg = "All file format argument values must be strings";
}
return false;
}
argsMap[keyExtractor()] = valueExtractor();
}
args->swap(argsMap);
return true;
}
