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implemented fix for wrong prefixes
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@schochastics
schochastics committed Sep 23, 2024
1 parent 44737d7 commit 16bcee9
Showing 1 changed file with 102 additions and 101 deletions.
203 changes: 102 additions & 101 deletions src/init.cpp
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Original file line number Diff line number Diff line change
@@ -1,130 +1,131 @@
#include "QuadCensus.h"
#include <stdexcept>
#include <stdlib.h> // for NULL

#include <fstream>
#include <stdexcept>

#include <stdlib.h> // for NULL
#include <Rinternals.h>
#include "QuadCensus.h"
#define R_NO_REMAP
#include <R_ext/Rdynload.h>
#include <Rinternals.h>

using namespace std;
using namespace oaqc;

static SEXP c_to_r(const unsigned int* const rMap, const unsigned long * orbit,
unsigned int size, unsigned long orbitCount) {
const unsigned long len = size * orbitCount;
SEXP rvec = PROTECT(allocVector(REALSXP, len));
// set dimensions
SEXP dim = PROTECT(allocVector(INTSXP, 2));
INTEGER(dim)[0] = size;
INTEGER(dim)[1] = orbitCount;
setAttrib(rvec, R_DimSymbol, dim);
// copy (cast and transpose) data
double * data = REAL(rvec);
unsigned int j = 0;

for (unsigned int o = 0; o < orbitCount; ++o){
for (unsigned int i = 0; i < size; ++i) {
unsigned int pos = i;
if (rMap != NULL) {
pos = rMap[i];
}
data[j++] = (double) orbit[pos * orbitCount + o];
}
}
UNPROTECT(2);
return rvec;
static SEXP c_to_r(const unsigned int* const rMap, const unsigned long* orbit,
unsigned int size, unsigned long orbitCount) {
const unsigned long len = size * orbitCount;
SEXP rvec = PROTECT(Rf_allocVector(REALSXP, len));
// set dimensions
SEXP dim = PROTECT(Rf_allocVector(INTSXP, 2));
INTEGER(dim)[0] = size;
INTEGER(dim)[1] = orbitCount;
Rf_setAttrib(rvec, R_DimSymbol, dim);
// copy (cast and transpose) data
double* data = REAL(rvec);
unsigned int j = 0;

for (unsigned int o = 0; o < orbitCount; ++o) {
for (unsigned int i = 0; i < size; ++i) {
unsigned int pos = i;
if (rMap != NULL) {
pos = rMap[i];
}
data[j++] = (double)orbit[pos * orbitCount + o];
}
}
UNPROTECT(2);
return rvec;
}

static void write_to_file(string fName, const unsigned int* const rMap,
const unsigned long * orbit, unsigned int size,
unsigned long orbitCount) {
ofstream writer;
// open the writer
writer.open(fName.c_str());
if (!writer.is_open()) {
throw ios_base::failure("cannot open " + fName);
}
for (unsigned int o = 0; o < orbitCount - 1; ++o) {
writer << "orbit_" << o << ";";
}
writer << "orbit_" << (orbitCount - 1) << std::endl;

for (unsigned int i = 0; i < size; ++i) {
unsigned int pos = i;
if (rMap != NULL) {
pos = rMap[i];
}
for (unsigned int o = 0; o < orbitCount - 1; ++o) {
writer << orbit[pos * orbitCount + o] << ";";
}
writer << orbit[pos * orbitCount + orbitCount - 1] << std::endl;
}
// flush and close
writer.flush();
writer.close();
const unsigned long* orbit, unsigned int size,
unsigned long orbitCount) {
ofstream writer;
// open the writer
writer.open(fName.c_str());
if (!writer.is_open()) {
throw ios_base::failure("cannot open " + fName);
}
for (unsigned int o = 0; o < orbitCount - 1; ++o) {
writer << "orbit_" << o << ";";
}
writer << "orbit_" << (orbitCount - 1) << std::endl;

for (unsigned int i = 0; i < size; ++i) {
unsigned int pos = i;
if (rMap != NULL) {
pos = rMap[i];
}
for (unsigned int o = 0; o < orbitCount - 1; ++o) {
writer << orbit[pos * orbitCount + o] << ";";
}
writer << orbit[pos * orbitCount + orbitCount - 1] << std::endl;
}
// flush and close
writer.flush();
writer.close();
}

static void write_results(SEXP& a_value, SEXP& a_names, unsigned int& sIndex,
const unsigned int n, const unsigned int m, QuadCensus& qc,
string& filePrefix, string rType) {

if (!filePrefix.empty()) {
write_to_file(filePrefix + "_n_orbits_" + rType + ".csv",
qc.getMapping(), qc.nOrbits(), n, qc.getNOrbitCount());
write_to_file(filePrefix + "_e_orbits_" + rType + ".csv", NULL,
qc.eOrbits(), m, qc.getEOrbitCount());
}
SET_STRING_ELT(a_names, sIndex, mkChar(("n_orbits_" + rType).c_str()));
SET_VECTOR_ELT(a_value, sIndex,
c_to_r(qc.getMapping(), qc.nOrbits(), n, qc.getNOrbitCount()));
++sIndex;
SET_STRING_ELT(a_names, sIndex, mkChar(("e_orbits_" + rType).c_str()));
SET_VECTOR_ELT(a_value, sIndex,
c_to_r(NULL, qc.eOrbits(), m, qc.getEOrbitCount()));
++sIndex;
const unsigned int n, const unsigned int m,
QuadCensus& qc, string& filePrefix, string rType) {
if (!filePrefix.empty()) {
write_to_file(filePrefix + "_n_orbits_" + rType + ".csv", qc.getMapping(),
qc.nOrbits(), n, qc.getNOrbitCount());
write_to_file(filePrefix + "_e_orbits_" + rType + ".csv", NULL,
qc.eOrbits(), m, qc.getEOrbitCount());
}
SET_STRING_ELT(a_names, sIndex, Rf_mkChar(("n_orbits_" + rType).c_str()));
SET_VECTOR_ELT(a_value, sIndex,
c_to_r(qc.getMapping(), qc.nOrbits(), n, qc.getNOrbitCount()));
++sIndex;
SET_STRING_ELT(a_names, sIndex, Rf_mkChar(("e_orbits_" + rType).c_str()));
SET_VECTOR_ELT(a_value, sIndex,
c_to_r(NULL, qc.eOrbits(), m, qc.getEOrbitCount()));
++sIndex;
}

extern "C" SEXP entry(SEXP a_n, SEXP a_edges, SEXP a_freqFlag, SEXP a_file) {
const unsigned int n = INTEGER(a_n)[0];
const unsigned int m = length(a_edges) / 2;
const int * edges = INTEGER(a_edges);
string filePrefix(CHAR(STRING_ELT(a_file, 0)));
const bool wNonIndFreq = LOGICAL(a_freqFlag)[0];
const unsigned int n = INTEGER(a_n)[0];
const unsigned int m = length(a_edges) / 2;
const int* edges = INTEGER(a_edges);
string filePrefix(CHAR(STRING_ELT(a_file, 0)));
const bool wNonIndFreq = LOGICAL(a_freqFlag)[0];

unsigned int res_size;
if (wNonIndFreq) {
res_size = 4;
} else {
res_size = 2;
}
QuadCensus qc(n, m, edges);
unsigned int res_size;
if (wNonIndFreq) {
res_size = 4;
} else {
res_size = 2;
}
QuadCensus qc(n, m, edges);

SEXP value = PROTECT(allocVector(VECSXP, res_size)); // VECSXP == list
SEXP names = PROTECT(allocVector(STRSXP, res_size));
SEXP value = PROTECT(Rf_allocVector(VECSXP, res_size)); // VECSXP == list
SEXP names = PROTECT(Rf_allocVector(STRSXP, res_size));

unsigned int pos = 0;
unsigned int pos = 0;

if (wNonIndFreq) {
write_results(value, names, pos, n, m, qc, filePrefix, "non_ind");
}
if (wNonIndFreq) {
write_results(value, names, pos, n, m, qc, filePrefix, "non_ind");
}

qc.calcInducedFrequencies();
qc.calcInducedFrequencies();

write_results(value, names, pos, n, m, qc, filePrefix, "ind");
write_results(value, names, pos, n, m, qc, filePrefix, "ind");

setAttrib(value, R_NamesSymbol, names);
Rf_setAttrib(value, R_NamesSymbol, names);

UNPROTECT(2);
return value;
UNPROTECT(2);
return value;
}

#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n}
#define CALLDEF(name, n) {#name, (DL_FUNC) & name, n}

static const R_CallMethodDef CallEntries[] = {
CALLDEF(entry, 4), { NULL, NULL, 0 } };
static const R_CallMethodDef CallEntries[] = {CALLDEF(entry, 4),
{NULL, NULL, 0}};

extern "C" void R_init_oaqc(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
extern "C" void R_init_oaqc(DllInfo* dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
}

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