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Fix indexing seg fault for Oxford Binary #18

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Fix indexing seg fault for Oxford Binary #18

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85 changes: 44 additions & 41 deletions include/modality/ebsd/idx.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -404,51 +404,54 @@ namespace emsphinx {

//loop over patterns indexing
std::vector< emsphinx::Result<Real> > res(om.size());//we need a result for each map
for(const size_t i : indices) {//loop over indices to index (may not be contiguous or in order)
if(0x00 != msk[i]) {//do we need to index and/or refine this point?
if(0x01 & msk[i]) {//reindexing requested
const bool ref = 0x02 & msk[i];//should we refine?
try {
idx[id]->indexImage((TPix*)ptr, res.data(), res.size(), ref);//index pattern
for(size_t j = 0; j < res.size(); j++) {
std::copy(res[j].qu, res[j].qu+4, om[j].qu[i].data());//save orientation
om[j].metric[i] = res[j].corr ;//save cross correlation
om[j].imQual[i] = res[j].iq ;//image quality
om[j].phase [i] = (uint_fast8_t)res[j].phase;//save phase
}
std::fill(ipf + 3 * i, ipf + 3 * i + 3, 0);
xtal::quat::rotateVector(res[0].qu, n, nx);
if (-1 == res[0].phase) {
std::fill(rgb, rgb + 3, Real(0));
} else {
om[0].phsList[res[0].phase].pg.ipfColor(nx, rgb, h2r);
const size_t numpatterns = pat->numPat();
for(const size_t i : indices){//loop over indices to index (may not be contiguous or in order)
if(i < numpatterns){ //don't index more patterns than there are
if(0x00 != msk[i]) {//do we need to index and/or refine this point?
if(0x01 & msk[i]) {//reindexing requested
const bool ref = 0x02 & msk[i];//should we refine?
try {
idx[id]->indexImage((TPix*)ptr, res.data(), res.size(), ref);//index pattern
for(size_t j = 0; j < res.size(); j++) {
std::copy(res[j].qu, res[j].qu+4, om[j].qu[i].data());//save orientation
om[j].metric[i] = res[j].corr ;//save cross correlation
om[j].imQual[i] = res[j].iq ;//image quality
om[j].phase [i] = (uint_fast8_t)res[j].phase;//save phase
}
std::fill(ipf + 3 * i, ipf + 3 * i + 3, 0);
xtal::quat::rotateVector(res[0].qu, n, nx);
if (-1 == res[0].phase) {
std::fill(rgb, rgb + 3, Real(0));
} else {
om[0].phsList[res[0].phase].pg.ipfColor(nx, rgb, h2r);
}
std::transform(rgb, rgb+3, ipf + 3 * i, [](const Real& v){return (char) std::round(v * 255);});
} catch (std::exception&) {// e) {
// std::cout << i << ": " << e.what() << '\n';//don't let one exception stop everything
for(size_t j = 0; j < res.size(); j++) {
om[j].qu[i].w = 1;
om[j].qu[i].x = om[j].qu[i].y = om[j].qu[i].z = 0;
om[j].metric[i] = 0;
om[j].imQual[i] = 0;
om[j].phase [i] = (uint_fast8_t)-1;
}
std::fill(ipf + 3 * i, ipf + 3 * i + 3, 0);
}
std::transform(rgb, rgb+3, ipf + 3 * i, [](const Real& v){return (char) std::round(v * 255);});
} catch (std::exception&) {// e) {
// std::cout << i << ": " << e.what() << '\n';//don't let one exception stop everything
for(size_t j = 0; j < res.size(); j++) {
om[j].qu[i].w = 1;
om[j].qu[i].x = om[j].qu[i].y = om[j].qu[i].z = 0;
om[j].metric[i] = 0;
om[j].imQual[i] = 0;
om[j].phase [i] = (uint_fast8_t)-1;
} else if(0x02 & msk[i]) {//only refinement requested
try {
//this currently only uses a single result but it could be modified
res[0].phase = om[0].phase[i];
std::copy(om[0].qu[i].data(), om[0].qu[i].data()+4, res[0].qu);//copy original orientation
idx[id]->refineImage((TPix*)ptr, res[0]);//refine orientation using pattern
std::copy(res[0].qu, res[0].qu+4, om[0].qu[i].data());//save orientation
om[0].metric[i] = res[0].corr ;//save cross correlation
om[0].imQual[i] = res[0].iq ;//image quality
} catch (std::exception&) {// e) {
// std::cout << i << ": " << e.what() << '\n';//don't let one exception stop everything
}
std::fill(ipf + 3 * i, ipf + 3 * i + 3, 0);
}
} else if(0x02 & msk[i]) {//only refinement requested
try {
//this currently only uses a single result but it could be modified
res[0].phase = om[0].phase[i];
std::copy(om[0].qu[i].data(), om[0].qu[i].data()+4, res[0].qu);//copy original orientation
idx[id]->refineImage((TPix*)ptr, res[0]);//refine orientation using pattern
std::copy(res[0].qu, res[0].qu+4, om[0].qu[i].data());//save orientation
om[0].metric[i] = res[0].corr ;//save cross correlation
om[0].imQual[i] = res[0].iq ;//image quality
} catch (std::exception&) {// e) {
// std::cout << i << ": " << e.what() << '\n';//don't let one exception stop everything
}
ctr++;//increment indexed pattern count
}
ctr++;//increment indexed pattern count
}
ptr += bytes;//move to next pattern
}
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11 changes: 7 additions & 4 deletions programs/index_ebsd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -163,14 +163,17 @@ try {
while(!pool.waitAll(uptFreq)) {
//get the time elapsed since we started (without resetting the reference point)
const double elapsed = t.poll(false);
const double percent = double(idxData.idxCtr) / idxData.numIdx;
const double rate = elapsed / percent;//estimate seconds per %
const double remaining = rate * (1.0 - percent);//estimate seconds left
double frac = double(idxData.idxCtr) / idxData.numIdx;
if(frac > 1.0){
frac = 1.0;
}
const double rate = elapsed / frac;//estimate seconds per %
const double remaining = rate * (1.0 - frac);//estimate seconds left

//print update
std::cout << '\r';
Timer::PrintSeconds(elapsed , std::cout);
std::cout << " elapsed, " << std::fixed << std::setprecision(1) << percent * 100 << "% complete, ";
std::cout << " elapsed, " << std::fixed << std::setprecision(1) << frac*100.0 << "% complete, ";
Timer::PrintSeconds(remaining, std::cout);
std::cout << " remaining ";
std::cout.flush();
Expand Down