void update_beagle_eigen(t_mod* mod)
{
assert(UNINITIALIZED != mod->b_inst);
int whichmodel = mod->whichmodel;
//We use Eigen Decomposition only for GTR models and AA datasets
if((mod->io->datatype == AA || whichmodel==GTR || whichmodel==CUSTOM) && mod->use_m4mod == NO)
{
//Beagle expects untransformed eigen-values (i.e. recall e_val is EXP() scaled, so we undo that)
phydbl* evals = (phydbl*)malloc(mod->ns * sizeof(phydbl));
int i;
for(i=0;i<mod->ns;++i) evals[i]=LOG(mod->eigen->e_val[i]);
int ret=-1;
if((sizeof(float)==sizeof(phydbl)))//Need to convert to doubles?
{
double* eigen_vects = float_to_double(mod->eigen->r_e_vect, mod->eigen->size*mod->eigen->size);
double* eigen_vects_inv = float_to_double(mod->eigen->l_e_vect, mod->eigen->size*mod->eigen->size);
double* eigen_vals = float_to_double(evals,mod->eigen->size);
ret = beagleSetEigenDecomposition(mod->b_inst,0,eigen_vects,eigen_vects_inv,eigen_vals);
Free(eigen_vects);Free(eigen_vects_inv);Free(eigen_vals);
} else {
ret = beagleSetEigenDecomposition(mod->b_inst,0,mod->eigen->r_e_vect,mod->eigen->l_e_vect,evals);
}
if(ret<0){
fprintf(stderr, "beagleSetEigenDecomposition() on instance %i failed:%i\n\n",mod->b_inst,ret);
Free(evals);
Exit("");
}
Free(evals);
}
}
unsigned int sw_location(char* hardwareId, float lat, float lon, float ele, int64_t eventDate,
uint8_t* buffer, size_t length, char* originator) {
pb_ostream_t stream = pb_ostream_from_buffer(buffer, length);
SiteWhere_Header header = { };
header.command = SiteWhere_Command_DEVICELOCATION;
if (originator != NULL) {
header.has_originator = true;
strcpy(header.originator, originator);
}
if (!pb_encode_delimited(&stream, SiteWhere_Header_fields, &header)) {
return 0;
}
SiteWhere_DeviceLocation location = { };
strcpy(location.hardwareId, hardwareId);
location.latitude = float_to_double(lat);
location.longitude = float_to_double(lon);
location.elevation = float_to_double(ele);
location.has_elevation = true;
if (eventDate != NULL) {
location.has_eventDate = true;
location.eventDate = eventDate;
}
if (!pb_encode_delimited(&stream, SiteWhere_DeviceLocation_fields, &location)) {
return 0;
}
return stream.bytes_written;
}
unsigned int sw_measurement(char* hardwareId, char* name, float value, int64_t eventDate,
uint8_t* buffer, size_t length, char* originator) {
pb_ostream_t stream = pb_ostream_from_buffer(buffer, length);
SiteWhere_Header header = { };
header.command = SiteWhere_Command_DEVICEMEASUREMENT;
if (originator != NULL) {
header.has_originator = true;
strcpy(header.originator, originator);
}
if (!pb_encode_delimited(&stream, SiteWhere_Header_fields, &header)) {
return 0;
}
SiteWhere_DeviceMeasurements measurements = { };
strcpy(measurements.hardwareId, hardwareId);
SiteWhere_Measurement measurement = { };
strcpy(measurement.measurementId, name);
measurement.measurementValue = float_to_double(value);
measurements.measurement[0] = measurement;
measurements.measurement_count = 1;
if (eventDate != NULL) {
measurements.has_eventDate = true;
measurements.eventDate = eventDate;
}
if (!pb_encode_delimited(&stream, SiteWhere_DeviceMeasurements_fields, &measurements)) {
return 0;
}
return stream.bytes_written;
}
double __extendsfdf2(float a)
{
float_t fa;
double_t res;
fa.val = a;
res.data = float_to_double(fa.data);
return res.val;
}
void update_beagle_ras(t_mod* mod)
{
assert(UNINITIALIZED != mod->b_inst);
int ret=-1;
if((sizeof(float)==sizeof(phydbl))) //Do we need to convert?
{
double* catg_rates = float_to_double(mod->ras->gamma_rr->v, mod->ras->n_catg);
ret = beagleSetCategoryRates(mod->b_inst, catg_rates);
Free(catg_rates);
if(ret<0){
fprintf(stderr, "beagleSetCategoryRates() on instance %i failed:%i\n\n",mod->b_inst,ret);
Exit("");
}
double* catg_wts = float_to_double(mod->ras->gamma_r_proba->v, mod->ras->n_catg);
if(!mod->optimizing_topology) {
ret = beagleSetCategoryWeights(mod->b_inst, 0, catg_wts);
Free(catg_wts);
if(ret<0){
fprintf(stderr, "beagleSetCategoryWeights() on instance %i failed:%i\n\n",mod->b_inst,ret);
Exit("");
}
}
}
else
{
ret = beagleSetCategoryRates(mod->b_inst, mod->ras->gamma_rr->v);
if(ret<0){
fprintf(stderr, "beagleSetCategoryRates() on instance %i failed:%i\n\n",mod->b_inst,ret);
Exit("");
}
if(!mod->optimizing_topology) {
ret = beagleSetCategoryWeights(mod->b_inst, 0, mod->ras->gamma_r_proba->v);
if(ret<0){
fprintf(stderr, "beagleSetCategoryWeights() on instance %i failed:%i\n\n",mod->b_inst,ret);
Exit("");
}
}
}
}
void update_beagle_efrqs(t_mod* mod)
{
assert(UNINITIALIZED != mod->b_inst);
int ret=-1;
if((sizeof(float)==sizeof(phydbl))) {
double* efrqs = float_to_double(mod->e_frq->pi->v, mod->ns);
ret = beagleSetStateFrequencies(mod->b_inst, 0, efrqs);
Free(efrqs);
} else {
ret = beagleSetStateFrequencies(mod->b_inst, 0, mod->e_frq->pi->v);
}
if(ret<0){
fprintf(stderr, "beagleSetStateFrequencies() on instance %i failed:%i\n\n",mod->b_inst,ret);
Exit("");
}
}
