void
MultiviewRecognizerWithChangeDetection<PointT>::cleanupHVFilters() {
std::vector<size_t> view_ids_vector = getMapKeys(views_);
std::set<size_t> view_ids_set(view_ids_vector.begin(), view_ids_vector.end());
std::vector<size_t> removed_ids = getMapKeys(removed_points_history_);
for(size_t id_to_remove : removed_ids) {
if(view_ids_set.find(id_to_remove) == view_ids_set.end()) {
removed_points_history_.erase(id_to_remove);
removed_points_cumulated_history_.erase(id_to_remove);
}
}
}
std::vector<bool>
MultiviewRecognizerWithChangeDetection<PointT>::getHypothesisInViewsMask(ModelTPtr model, const Eigen::Matrix4f &pose, size_t origin_id) {
std::vector<size_t> sorted_view_ids = getMapKeys(views_);
std::sort(sorted_view_ids.begin(), sorted_view_ids.end());
size_t hypothesis_removed_since_view = id_ + 1; // assuming never removed (id_+1 = future)
for(std::vector<size_t>::iterator view_id = sorted_view_ids.begin(); view_id < sorted_view_ids.end(); view_id++) {
if(*view_id <= origin_id) {
continue; // hypothesis can not be removed before discovered
}
if(removed_points_history_[*view_id]->empty()) {
continue; // no changes were found in this view
}
CloudPtr model_aligned(new Cloud);
pcl::transformPointCloud(*model->assembled_, *model_aligned, pose);
int rem_support = v4r::ChangeDetector<PointT>::removalSupport(
removed_points_history_[*view_id], model_aligned, param_.tolerance_for_cloud_diff_, 1.1)->size();
PCL_INFO("Support for the removal of object [%s,%d]: %d\n", model->id_.c_str(), *view_id, rem_support);
if(rem_support > param_.min_points_for_hyp_removal_) {
hypothesis_removed_since_view = *view_id;
}
}
std::vector<bool> mask;
for(auto view : views_) {
mask.push_back(view.first >= origin_id && view.first < hypothesis_removed_since_view);
}
return mask;
}
/// validate the species
bool CKReader::validateSpecies(std::ostream& log) {
size_t nel = elements.size();
size_t nsp = species.size();
double tol;
log << newTask("validating species");
// check for undeclared elements
vector<string> esyms;
log << " checking that all species have been defined... ";
for (size_t k = 0; k < nsp; k++) {
Species& s = species[k];
if (s.valid == 0) {
log << endl << " species " << s.name << " undefined ";
s.valid = -1;
}
}
if (valid(species)) log << "OK" << endl;
else {
log << endl;
return false;
}
log << " checking that all species elements have been declared... ";
for (size_t k = 0; k < nsp; k++) {
Species& s = species[k];
getMapKeys(s.comp, esyms);
size_t nm = esyms.size();
for (size_t m = 0; m < nm; m++) {
size_t j;
for (j = 0; j < nel; j++) {
if (esyms[m] == elements[j].name) break;
}
if (j == nel) {
log << endl << " species "
<< s.name << ": undeclared element "
<< esyms[m];
s.valid = -1;
}
}
}
if (valid(species)) log << "OK" << endl;
else {
log << endl;
return false;
}
log << " checking consistency of species thermo data... ";
tol = 0.01;
if (checkThermo(log, species, tol)) log << "OK" << endl;
else {
log << endl;
return false;
}
return true;
}
/// print a summary of all reactions to the log file
bool CKReader::writeReactions(std::ostream& log) {
bool ok = true;
// int ns = species.size();
int nrxns = static_cast<int>(reactions.size());
log.flags(ios::unitbuf);
log.precision(6);
log << endl;
for (int n = 0; n < nrxns; n++) {
Reaction& r = reactions[n];
log << "reaction " << r.number << endl;
log << " ";
printReactionEquation(log, r);
log << endl;
// rate coefficient
if (r.isFalloffRxn) {
log << " high P rate coeff: ";
ok = ok && writeRateCoeff(r.kf, log) ;
log << " low P rate coeff: ";
ok = ok && writeRateCoeff(r.kf_aux, log);
ok = ok && writeFalloff(r.falloffType, r.falloffParameters, log);
}
else {
log << " rate coeff: ";
ok = ok && writeRateCoeff(r.kf, log);
}
if (r.isReversible && r.krev.A > 0) {
log << " reverse rate coeff: ";
ok = ok && writeRateCoeff(r.krev, log);
}
int ne = static_cast<int>(r.e3b.size());
if (ne > 0) {
vector<string> enhSpecies;
getMapKeys(r.e3b, enhSpecies);
log << " enhanced collision efficiencies:" << endl;
log << " ";
for (int nn = 0; nn < ne; nn++) {
log << enhSpecies[nn] << " "
<< r.e3b[enhSpecies[nn]];
if (nn < ne-1) log << ", ";
}
log << endl;
}
if (r.isDuplicate) log
<< " declared duplicate reaction. See reaction "
<< r.duplicate << "." << endl;
log << endl;
}
return ok;
}
int main (int argc, char ** argv)
{
printf ("YAJL TESTS\n");
printf ("==================\n\n");
modules = ksNew (0, KS_END);
elektraModulesInit (modules, 0);
init (argc, argv);
test_nextNotBelow ();
test_reverseLevel ();
test_countLevel ();
test_writing ();
test_json ("yajl/testdata_null.json", getNullKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_boolean.json", getBooleanKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_number.json", getNumberKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_string.json", getStringKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_maps.json", getMapKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_array.json", getArrayKeys (), ksNew (0, KS_END));
test_json ("yajl/testdata_below.json", getBelowKeys (), ksNew (0, KS_END));
test_json ("yajl/OpenICC_device_config_DB.json", getOpenICCKeys (), ksNew (0, KS_END));
// TODO currently do not have a KeySet, wait for C-plugin to make
// it easy to generate it..
test_readWrite ("yajl/empty_object.json", ksNew (0, KS_END));
test_readWrite ("yajl/empty_array.json", ksNew (0, KS_END));
test_readWrite ("yajl/top_level_string.json", ksNew (0, KS_END));
test_readWrite ("yajl/top_level_integer.json", ksNew (0, KS_END));
test_readWrite ("yajl/rfc_object.json", ksNew (0, KS_END));
test_readWrite ("yajl/rfc_array.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_mixed.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_in_array.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_in_array_anon_map.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_nested.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_broken.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_special_ending.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_outside.json", ksNew (0, KS_END));
test_readWrite ("yajl/keyframes_complex.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_mixed2.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_special_start.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_array_mixed3.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_empty_in_array.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_empty_in_map.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_empty_in_array1.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_empty_in_map2.json", ksNew (0, KS_END));
test_readWrite ("yajl/testdata_empty_in_map1.json", ksNew (0, KS_END));
elektraModulesClose (modules, 0);
ksDel (modules);
print_result ("test_yajl");
return nbError;
}
/**
* Check that all reactions balance.
* @param speciesData species property dataset used to look up
* elemental compositions.
* @param r list of reactions to check
* @param unbalanced list of integers specifying reaction numbers of
* unbalanced reactions.
* @return true if all reactions balance
* @todo use reaction number stored in reaction object
*/
bool checkBalance(std::ostream& f, speciesTable& speciesData,
reactionList& r, std::vector<int>& unbalanced, double tolerance)
{
int nrxn = static_cast<int>(r.size());
string rname, pname;
vector<string> elementSyms;
unsigned int m;
unbalanced.clear();
map<string, double> atoms;
for (int i = 0; i < nrxn; i++)
{
atoms.clear();
int nr = static_cast<int>(r[i].reactants.size());
int np = static_cast<int>(r[i].products.size());
int j;
double stoichCoeff;
for (j = 0; j < nr; j++)
{
rname = r[i].reactants[j].name;
stoichCoeff = r[i].reactants[j].number;
vector<Constituent>& elements = speciesData[rname].elements;
for (m = 0; m < elements.size(); m++)
{
atoms[elements[m].name] -= stoichCoeff * elements[m].number;
}
}
for (j = 0; j < np; j++)
{
pname = r[i].products[j].name;
stoichCoeff = r[i].products[j].number;
vector<Constituent>& elements = speciesData[pname].elements;
for (m = 0; m < elements.size(); m++)
{
atoms[elements[m].name] += stoichCoeff * elements[m].number;
}
}
double atms;
getMapKeys(atoms, elementSyms);
for (m = 0; m < elementSyms.size(); m++) {
atms = atoms[elementSyms[m]];
if (fabs(atms) > tolerance) {
//if (atoms[elementSyms[m]] != 0.0) {
// cout << "Reaction " << i+1 << " has an unbalanced element: "
// << elementSyms[m] << " "
// << atoms[elementSyms[m]] << endl;
unbalanced.push_back(i+1); break;
}
}
}
return (unbalanced.empty());
}
void test_nextNotBelow (void)
{
printf ("Test next not below\n");
KeySet * ks = getNullKeys ();
ksRewind (ks);
Key * k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/nullkey");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/nullkey");
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/second_nullkey");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/second_nullkey");
k = elektraNextNotBelow (ks);
succeed_if (k == 0, "not at end of keyset");
succeed_if (ksCurrent (ks) == 0, "not at end of keyset");
ksDel (ks);
ks = getBooleanKeys ();
ksRewind (ks);
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/boolean_key");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/boolean_key");
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/second_boolean_key");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/second_boolean_key");
k = elektraNextNotBelow (ks);
succeed_if (k == 0, "not at end of keyset");
succeed_if (ksCurrent (ks) == 0, "not at end of keyset");
ksDel (ks);
ks = getBelowKeys ();
ksRewind (ks);
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/fancy/path/below/v/y/z");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/fancy/path/below/v/y/z");
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/fancy/path/below/x/y/z");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/fancy/path/below/x/y/z");
k = elektraNextNotBelow (ks);
succeed_if (k == 0, "not at end of keyset");
succeed_if (ksCurrent (ks) == 0, "not at end of keyset");
ksDel (ks);
ks = getMapKeys ();
ksRewind (ks);
k = elektraNextNotBelow (ks);
succeed_if_equal (keyName (k), "user/tests/yajl/map/nested_map/second_string_key");
succeed_if_equal (keyName (ksCurrent (ks)), "user/tests/yajl/map/nested_map/second_string_key");
ksDel (ks);
}
