std::vector<OGRGeometry *> ogr_from_sfc(Rcpp::List sfc, OGRSpatialReference **sref) {
Rcpp::List wkblst = CPL_write_wkb(sfc, false);
std::vector<OGRGeometry *> g(sfc.length());
OGRSpatialReference *local_srs = NULL;
Rcpp::List crs = sfc.attr("crs");
Rcpp::IntegerVector epsg(1);
epsg[0] = crs["epsg"];
Rcpp::String p4s = crs["proj4string"];
if (p4s != NA_STRING) {
Rcpp::CharacterVector cv = crs["proj4string"];
local_srs = new OGRSpatialReference;
OGRErr err = local_srs->importFromProj4(cv[0]);
if (err != 0) {
local_srs->Release(); // #nocov
handle_error(err); // #nocov
}
}
for (int i = 0; i < wkblst.length(); i++) {
Rcpp::RawVector r = wkblst[i];
OGRErr err = OGRGeometryFactory::createFromWkb(&(r[0]), local_srs, &(g[i]),
r.length(), wkbVariantIso);
if (err != 0) {
if (local_srs != NULL) // #nocov
local_srs->Release(); // #nocov
handle_error(err); // #nocov
}
}
if (sref != NULL)
*sref = local_srs; // return and release later, or
else if (local_srs != NULL)
local_srs->Release(); // release now
return g;
}
// [[Rcpp::export]]
Rcpp::List mlist2clist(Rcpp::List mlist, int nthreads=1){
if (mlist.length()==0) Rcpp::stop("empty list is invalid");
int ncounts, nmarks, nbins = -1;
std::vector<std::string> foo;
listcubedim(mlist, &nbins, &ncounts, &nmarks, foo);
Rcpp::List newdnames(2); newdnames[0] = mlist.attr("names");
//allocate storage
Rcpp::List clist(ncounts);
for (int c = 0; c < ncounts; ++c){
Rcpp::IntegerMatrix mat(nmarks, nbins);
if (!Rf_isNull(newdnames[0])) mat.attr("dimnames") = newdnames;
clist[c] = mat;
}
//copy data
#pragma omp parallel for num_threads(nthreads) collapse(2)
for (int c = 0; c < ncounts; ++c){
for (int mark = 0; mark < nmarks; ++mark){
Vec<int> col = Mat<int>((SEXP)mlist[mark]).getCol(c);
MatRow<int> row = Mat<int>((SEXP)clist[c]).getRow(mark);
for (int bin = 0; bin < nbins; ++bin){
row[bin] = col[bin];
}
}
}
return clist;
}
// [[Rcpp::export]]
Rcpp::List clist2mlist(Rcpp::List clist, int nthreads=1){
if (clist.length()==0) Rcpp::stop("empty list is invalid");
int ncounts, nmarks, nbins = -1;
std::vector<std::string> rnames;
listcubedim(clist, &nmarks, &nbins, &ncounts, rnames);
//allocate storage
Rcpp::List mlist(nmarks);
for (int mark = 0; mark < nmarks; ++mark){
mlist[mark] = Rcpp::IntegerMatrix(nbins, ncounts);
}
if (rnames.size() > 0) mlist.attr("names") = rnames;
//copy data
#pragma omp parallel for num_threads(nthreads) collapse(2)
for (int c = 0; c < ncounts; ++c){
for (int mark = 0; mark < nmarks; ++mark){
MatRow<int> row = Mat<int>((SEXP)clist[c]).getRow(mark);
Vec<int> col = Mat<int>((SEXP)mlist[mark]).getCol(c);
for (int bin = 0; bin < nbins; ++bin){
col[bin] = row[bin];
}
}
}
return mlist;
}
// [[Rcpp::export]]
Rcpp::LogicalVector CPL_geos_is_simple(Rcpp::List sfc) {
GEOSContextHandle_t hGEOSCtxt = CPL_geos_init();
Rcpp::LogicalVector out(sfc.length());
std::vector<GEOSGeom> g = geometries_from_sfc(hGEOSCtxt, sfc);
for (size_t i = 0; i < g.size(); i++) {
out[i] = chk_(GEOSisSimple_r(hGEOSCtxt, g[i]));
GEOSGeom_destroy_r(hGEOSCtxt, g[i]);
}
CPL_geos_finish(hGEOSCtxt);
return out;
}
// [[Rcpp::export]]
Rcpp::IntegerVector CPL_gdal_dimension(Rcpp::List sfc, bool NA_if_empty = true) {
std::vector<OGRGeometry *> g = ogr_from_sfc(sfc, NULL);
Rcpp::IntegerVector out(sfc.length());
for (size_t i = 0; i < g.size(); i++) {
out[i] = g[i]->getDimension();
if (NA_if_empty && g[i]->IsEmpty())
out[i] = NA_INTEGER;
delete g[i];
}
return out;
}
// [[Rcpp::export]]
Rcpp::List CPL_geos_op(std::string op, Rcpp::List sfc,
double bufferDist = 0.0, int nQuadSegs = 30,
double dTolerance = 0.0, bool preserveTopology = false,
int bOnlyEdges = 1, double dfMaxLength = 0.0) {
GEOSContextHandle_t hGEOSCtxt = CPL_geos_init();
std::vector<GEOSGeom> g = geometries_from_sfc(hGEOSCtxt, sfc);
std::vector<GEOSGeom> out(sfc.length());
if (op == "buffer") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSBuffer_r(hGEOSCtxt, g[i], bufferDist, nQuadSegs));
} else if (op == "boundary") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSBoundary_r(hGEOSCtxt, g[i]));
} else if (op == "convex_hull") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSConvexHull_r(hGEOSCtxt, g[i]));
} else if (op == "union_cascaded") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSUnionCascaded_r(hGEOSCtxt, g[i]));
} else if (op == "simplify") {
for (size_t i = 0; i < g.size(); i++)
out[i] = preserveTopology ? chkNULL(GEOSTopologyPreserveSimplify_r(hGEOSCtxt, g[i], dTolerance)) :
chkNULL(GEOSSimplify_r(hGEOSCtxt, g[i], dTolerance));
} else if (op == "linemerge") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSLineMerge_r(hGEOSCtxt, g[i]));
} else if (op == "polygonize") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSPolygonize_r(hGEOSCtxt, &(g[i]), 1)); // xxx
} else if (op == "centroid") {
for (size_t i = 0; i < g.size(); i++) {
out[i] = chkNULL(GEOSGetCentroid_r(hGEOSCtxt, g[i]));
}
} else
#if GEOS_VERSION_MAJOR >= 3 && GEOS_VERSION_MINOR >= 4
if (op == "triangulate") {
for (size_t i = 0; i < g.size(); i++)
out[i] = chkNULL(GEOSDelaunayTriangulation_r(hGEOSCtxt, g[i], dTolerance, bOnlyEdges));
} else
#endif
throw std::invalid_argument("invalid operation"); // would leak g and out
for (size_t i = 0; i < g.size(); i++)
GEOSGeom_destroy_r(hGEOSCtxt, g[i]);
Rcpp::List ret(sfc_from_geometry(hGEOSCtxt, out)); // destroys out
CPL_geos_finish(hGEOSCtxt);
ret.attr("crs") = sfc.attr("crs");
return ret;
}
// [[Rcpp::export]]
Rcpp::NumericVector CPL_area(Rcpp::List sfc) {
std::vector<OGRGeometry *> g = ogr_from_sfc(sfc, NULL);
Rcpp::NumericVector out(sfc.length());
for (size_t i = 0; i < g.size(); i++) {
if (g[i]->getDimension() == 2) {
OGRSurface *a = (OGRSurface *) g[i];
out[i] = a->get_Area();
} else
out[i] = 0.0;
delete g[i];
}
return out;
}
void parseDataFrame(SEXP dataFrameObj, vector<Feature>& dataMatrix, vector<string>& sampleHeaders) {
Rcpp::DataFrame df(dataFrameObj);
//Rcpp::CharacterVector colNames = df.attr("names");
//Rcpp::CharacterVector rowNames = df.attr("row.names");
vector<string> featureHeaders = df.attr("names");
vector<string> foo = df.attr("row.names");
sampleHeaders = foo;
dataMatrix.resize( 0 );
//cout << "nf = " << featureHeaders.size() << endl;
//cout << "ns = " << sampleHeaders.size() << endl;
// Read one column of information, which in this case is assumed to be one sample
for ( size_t i = 0; i < featureHeaders.size(); ++i ) {
Rcpp::List vec = df[i];
assert(vec.length() == sampleHeaders.size() );
//cout << " " << foo[0] << flush;
//cout << " df[" << i << "].length() = " << vec.length() << endl;
if ( featureHeaders[i].substr(0,2) != "N:" ) {
vector<string> sVec(sampleHeaders.size());
for ( size_t j = 0; j < sampleHeaders.size(); ++j ) {
//cout << Rcpp::as<string>(vec[j]) << endl;
sVec[j] = Rcpp::as<string>(vec[j]);
}
if ( featureHeaders[i].substr(0,2) == "T:" ) {
bool doHash = true;
dataMatrix.push_back( Feature(sVec,featureHeaders[i],doHash) );
} else {
dataMatrix.push_back( Feature(sVec,featureHeaders[i]) );
}
} else {
vector<num_t> sVec(sampleHeaders.size());
for ( size_t j = 0; j < sampleHeaders.size(); ++j ) {
sVec[j] = Rcpp::as<num_t>(vec[j]);
}
dataMatrix.push_back( Feature(sVec,featureHeaders[i]) );
}
// cout << "df[" << j << "," << i << "] = " << Rcpp::as<num_t>(vec[j]) << endl;
// }
}
assert( dataMatrix.size() == featureHeaders.size() );
}
// [[Rcpp::export]]
Rcpp::NumericVector CPL_length(Rcpp::List sfc) {
std::vector<OGRGeometry *> g = ogr_from_sfc(sfc, NULL);
Rcpp::NumericVector out(sfc.length());
for (size_t i = 0; i < g.size(); i++) {
OGRwkbGeometryType gt = OGR_GT_Flatten(g[i]->getGeometryType());
if (gt == wkbLineString || gt == wkbCircularString || gt == wkbCompoundCurve || gt == wkbCurve) {
OGRCurve *a = (OGRCurve *) g[i];
out[i] = a->get_Length();
} else {
OGRGeometryCollection *a = (OGRGeometryCollection *) g[i];
out[i] = a->get_Length();
}
delete g[i];
}
return out;
}
SEXP collapsedList(Rcpp::List ll) {
if (ll.length() == 0) return R_NilValue;
Rcpp::List::iterator it = ll.begin();
switch(TYPEOF(*it)) {
case REALSXP: {
Rcpp::NumericVector v(ll.begin(), ll.end());
Rcpp::RObject ro = ll[0];
if (ro.hasAttribute("class")) {
Rcpp::CharacterVector cv = ro.attr("class");
if ((cv.size() == 1) && std::string(cv[0]) == "Date") {
Rcpp::DateVector dv(v);
return dv;
}
if ((cv.size() == 2) && std::string(cv[1]) == "POSIXt") {
Rcpp::DatetimeVector dtv(v);
return dtv;
}
}
return v;
break; // not reached ...
}
case INTSXP: {
Rcpp::IntegerVector v(ll.begin(), ll.end());
return v;
break; // not reached ...
}
case LGLSXP: {
Rcpp::LogicalVector v(ll.begin(), ll.end());
return v;
break; // not reached ...
}
case STRSXP: { // minor code smell that this is different :-/
int n = ll.size();
Rcpp::CharacterVector v(n);
for (int i=0; i<n; i++) {
std::string s = Rcpp::as<std::string>(ll[i]);
v[i] = s;
}
return v;
break; // not reached ...
}
}
return ll;
}
// [[Rcpp::export]]
Rcpp::List CPL_geos_binop(Rcpp::List sfc0, Rcpp::List sfc1, std::string op, double par = 0.0,
bool sparse = true) {
GEOSContextHandle_t hGEOSCtxt = CPL_geos_init();
std::vector<GEOSGeom> gmv0 = geometries_from_sfc(hGEOSCtxt, sfc0);
std::vector<GEOSGeom> gmv1 = geometries_from_sfc(hGEOSCtxt, sfc1);
Rcpp::List ret_list;
using namespace Rcpp; // so that later on the (i,_) works
if (op == "relate") { // character return matrix:
Rcpp::CharacterVector out(sfc0.length() * sfc1.length());
for (int i = 0; i < sfc0.length(); i++)
for (int j = 0; j < sfc1.length(); j++) {
char *cp = GEOSRelate_r(hGEOSCtxt, gmv0[i], gmv1[j]);
if (cp == NULL)
throw std::range_error("GEOS error in GEOSRelate_r");
out[j * sfc0.length() + i] = cp;
GEOSFree_r(hGEOSCtxt, cp);
}
out.attr("dim") = get_dim(sfc0.length(), sfc1.length());
ret_list = Rcpp::List::create(out);
} else if (op == "distance") { // return double matrix:
Rcpp::NumericMatrix out(sfc0.length(), sfc1.length());
for (size_t i = 0; i < gmv0.size(); i++)
for (size_t j = 0; j < gmv1.size(); j++) {
double dist = -1.0;
if (GEOSDistance_r(hGEOSCtxt, gmv0[i], gmv1[j], &dist) == 0)
throw std::range_error("GEOS error in GEOSDistance_r");
out(i,j) = dist;
}
ret_list = Rcpp::List::create(out);
} else {
// other cases: boolean return matrix, either dense or sparse
Rcpp::LogicalMatrix densemat;
if (! sparse) // allocate:
densemat = Rcpp::LogicalMatrix(sfc0.length(), sfc1.length());
Rcpp::List sparsemat(sfc0.length());
for (int i = 0; i < sfc0.length(); i++) { // row
// TODO: speed up contains, containsproperly, covers, and intersects with prepared geometry i
Rcpp::LogicalVector rowi(sfc1.length());
if (op == "intersects")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSIntersects_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "disjoint")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSDisjoint_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "touches")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSTouches_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "crosses")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSCrosses_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "within")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSWithin_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "contains")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSContains_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "overlaps")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSOverlaps_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "equals")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSEquals_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "covers")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSCovers_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "covered_by")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSCoveredBy_r(hGEOSCtxt, gmv0[i], gmv1[j]));
else if (op == "equals_exact")
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = chk_(GEOSEqualsExact_r(hGEOSCtxt, gmv0[i], gmv1[j], par));
/* else if (op == "is_within_distance") ==>> no C interface??
for (int j = 0; j < sfc1.length(); j++)
rowi(j) = gmv0[i]->isWithinDistance(gmv1[j].get(), par);
*/
else
throw std::range_error("wrong value for op"); // unlikely to happen unless user wants to
if (! sparse)
densemat(i,_) = rowi;
else
sparsemat[i] = get_which(rowi);
}
if (sparse)
ret_list = sparsemat;
else
ret_list = Rcpp::List::create(densemat);
}
for (size_t i = 0; i < gmv0.size(); i++)
GEOSGeom_destroy_r(hGEOSCtxt, gmv0[i]);
for (size_t i = 0; i < gmv1.size(); i++)
GEOSGeom_destroy_r(hGEOSCtxt, gmv1[i]);
CPL_geos_finish(hGEOSCtxt);
return ret_list;
}
//' rcpp_lines_as_network
//'
//' Return OSM data in Simple Features format
//'
//' @param sf_lines An sf collection of LINESTRING objects
//' @param pr Rcpp::DataFrame containing the weighting profile
//'
//' @return Rcpp::List objects of OSM data
//'
//' @noRd
// [[Rcpp::export]]
Rcpp::List rcpp_lines_as_network (const Rcpp::List &sf_lines,
Rcpp::DataFrame pr)
{
std::map <std::string, float> profile;
Rcpp::StringVector hw = pr [1];
Rcpp::NumericVector val = pr [2];
for (int i = 0; i != hw.size (); i ++)
profile.insert (std::make_pair (std::string (hw [i]), val [i]));
Rcpp::CharacterVector nms = sf_lines.attr ("names");
if (nms [nms.size () - 1] != "geometry")
throw std::runtime_error ("sf_lines have no geometry component");
if (nms [0] != "osm_id")
throw std::runtime_error ("sf_lines have no osm_id component");
int one_way_index = -1;
int one_way_bicycle_index = -1;
int highway_index = -1;
for (int i = 0; i < nms.size (); i++)
{
if (nms [i] == "oneway")
one_way_index = i;
if (nms [i] == "oneway.bicycle")
one_way_bicycle_index = i;
if (nms [i] == "highway")
highway_index = i;
}
Rcpp::CharacterVector ow = NULL;
Rcpp::CharacterVector owb = NULL;
Rcpp::CharacterVector highway = NULL;
if (one_way_index >= 0)
ow = sf_lines [one_way_index];
if (one_way_bicycle_index >= 0)
owb = sf_lines [one_way_bicycle_index];
if (highway_index >= 0)
highway = sf_lines [highway_index];
if (ow.size () > 0)
{
if (ow.size () == owb.size ())
{
for (unsigned i = 0; i != ow.size (); ++ i)
if (ow [i] == "NA" && owb [i] != "NA")
ow [i] = owb [i];
} else if (owb.size () > ow.size ())
ow = owb;
}
Rcpp::List geoms = sf_lines [nms.size () - 1];
std::vector<bool> isOneWay (geoms.length ());
std::fill (isOneWay.begin (), isOneWay.end (), false);
// Get dimension of matrix
size_t nrows = 0;
int ngeoms = 0;
for (auto g = geoms.begin (); g != geoms.end (); ++g)
{
// Rcpp uses an internal proxy iterator here, NOT a direct copy
Rcpp::NumericMatrix gi = (*g);
int rows = gi.nrow () - 1;
nrows += rows;
if (ngeoms < ow.size ())
{
if (!(ow [ngeoms] == "yes" || ow [ngeoms] == "-1"))
{
nrows += rows;
isOneWay [ngeoms] = true;
}
}
ngeoms ++;
}
Rcpp::NumericMatrix nmat = Rcpp::NumericMatrix (Rcpp::Dimension (nrows, 6));
Rcpp::CharacterMatrix idmat = Rcpp::CharacterMatrix (Rcpp::Dimension (nrows,
3));
nrows = 0;
ngeoms = 0;
int fake_id = 0;
for (auto g = geoms.begin (); g != geoms.end (); ++ g)
{
Rcpp::NumericMatrix gi = (*g);
std::string hway = std::string (highway [ngeoms]);
float hw_factor = profile [hway];
if (hw_factor == 0.0) hw_factor = 1e-5;
hw_factor = 1.0 / hw_factor;
Rcpp::List ginames = gi.attr ("dimnames");
Rcpp::CharacterVector rnms;
if (ginames.length () > 0)
rnms = ginames [0];
else
{
rnms = Rcpp::CharacterVector (gi.nrow ());
for (int i = 0; i < gi.nrow (); i ++)
rnms [i] = fake_id ++;
}
if (rnms.size () != gi.nrow ())
throw std::runtime_error ("geom size differs from rownames");
for (int i = 1; i < gi.nrow (); i ++)
{
float d = haversine (gi (i-1, 0), gi (i-1, 1), gi (i, 0),
gi (i, 1));
nmat (nrows, 0) = gi (i-1, 0);
nmat (nrows, 1) = gi (i-1, 1);
nmat (nrows, 2) = gi (i, 0);
nmat (nrows, 3) = gi (i, 1);
nmat (nrows, 4) = d;
nmat (nrows, 5) = d * hw_factor;
idmat (nrows, 0) = rnms (i-1);
idmat (nrows, 1) = rnms (i);
idmat (nrows, 2) = hway;
nrows ++;
if (isOneWay [ngeoms])
{
nmat (nrows, 0) = gi (i, 0);
nmat (nrows, 1) = gi (i, 1);
nmat (nrows, 2) = gi (i-1, 0);
nmat (nrows, 3) = gi (i-1, 1);
nmat (nrows, 4) = d;
nmat (nrows, 5) = d * hw_factor;
idmat (nrows, 0) = rnms (i);
idmat (nrows, 1) = rnms (i-1);
idmat (nrows, 2) = hway;
nrows ++;
}
}
ngeoms ++;
}
Rcpp::List res (2);
res [0] = nmat;
res [1] = idmat;
return res;
}