/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: getBottomDataProperty
* Signature: ()Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;
*/
JNIEXPORT jobject JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_getBottomDataProperty
(JNIEnv * env, jobject obj)
{
TRACE_JNI("getBottomDataProperty");
TJNICache* J = getJ(env,obj);
return J->DataProperty(J->getDName("http://www.w3.org/2002/07/owl#bottomDataProperty"));
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: getDataTop
* Signature: ()Luk/ac/manchester/cs/factplusplus/DataTypePointer;
*/
JNIEXPORT jobject JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_getDataTop
(JNIEnv * env, jobject obj)
{
TRACE_JNI("getDataTop");
TJNICache* J = getJ(env,obj);
return J->DataType(J->EM->DataTop());
}
bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
if (index < atoms_.size()) {
Vector3d velRot;
Mat3x3d skewMat;;
Vector3d ref = refCoords_[index];
Vector3d ji = getJ();
Mat3x3d I = getI();
skewMat(0, 0) =0;
skewMat(0, 1) = ji[2] /I(2, 2);
skewMat(0, 2) = -ji[1] /I(1, 1);
skewMat(1, 0) = -ji[2] /I(2, 2);
skewMat(1, 1) = 0;
skewMat(1, 2) = ji[0]/I(0, 0);
skewMat(2, 0) =ji[1] /I(1, 1);
skewMat(2, 1) = -ji[0]/I(0, 0);
skewMat(2, 2) = 0;
velRot = (getA() * skewMat).transpose() * ref;
vel =getVel() + velRot;
return true;
} else {
std::cerr << index << " is an invalid index, current rigid body contains "
<< atoms_.size() << "atoms" << std::endl;
return false;
}
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: addArg
* Signature: (Luk/ac/manchester/cs/factplusplus/Pointer;)V
*/
JNIEXPORT void JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_addArg
(JNIEnv * env, jobject obj, jobject arg)
{
TRACE_JNI("addArg");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
J->EM->addArg(getExpr(env,arg));
}
void try_flip_2_edge(int *g, int gsize, int &best_count_2, std::vector<int> &best_K, int best_start, int *nd, bool flip_new){
int i;
int j;
int k;
int l;
int cnt;
size_t m;
size_t n;
size_t sz = best_K.size();
best_count_2 = BIGCOUNT;
for(m=best_start; m<sz; m++){
for(n=m+1; n<sz; n++){
/*
flip
*/
i = getI(best_K[m]);
j = getJ(best_K[m]);
k = getI(best_K[n]);
l = getJ(best_K[n]);
g[ i*gsize + j ] = 1 - g[ i*gsize + j ];
g[ k*gsize + l ] = 1 - g[ k*gsize + l ];
cnt = CliqueCount(g, gsize, flip_new);
if( cnt < best_count_2 ){
best_count_2 = cnt;
nd[0] = i;
nd[1] = j;
nd[2] = k;
nd[3] = l;
}
/*
unflip
*/
g[ i*gsize + j ] = 1 - g[ i*gsize + j ];
g[ k*gsize + l ] = 1 - g[ k*gsize + l ];
}
}
}
void operator()() {
id = threadId();
wait();
// ++j;
j = getJ()+1;
std::cout << "Hello " << "World " << "from "
<< id // std::this_thread::get_id()
<< " where j is " << j
<< " start is " << Hi::start << std::endl;
}
void dcfeed::calcTR (nr_double_t) {
nr_double_t l = getPropertyDouble ("L");
nr_double_t r, v;
nr_double_t i = real (getJ (VSRC_1));
setState (fState, i * l);
integrate (fState, l, r, v);
setD (VSRC_1, VSRC_1, -r);
setE (VSRC_1, v);
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askEquivalentDataProperties
* Signature: (Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;)[Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askEquivalentDataProperties
(JNIEnv * env, jobject obj, jobject arg)
{
TRACE_JNI("askEquivalentDataProperties");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<DataPropertyPolicy> actor(J);
PROCESS_QUERY ( J->K->getEquivalentRoles ( getRODRoleExpr(env,arg), actor ) );
return actor.getSynonyms();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askSameAs
* Signature: (Luk/ac/manchester/cs/factplusplus/IndividualPointer;)[Luk/ac/manchester/cs/factplusplus/IndividualPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askSameAs
(JNIEnv * env, jobject obj, jobject arg)
{
TRACE_JNI("askSameAs");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<IndividualPolicy</*plain=*/true> > actor(J);
PROCESS_QUERY ( J->K->getSameAs ( getROIndividualExpr(env,arg), actor ) );
return actor.getSynonyms();
}
void cccs::calcTR (nr_double_t t) {
nr_double_t T = getPropertyDouble ("T");
if (T > 0.0) {
T = t - T;
nr_double_t g = getPropertyDouble ("G");
nr_double_t i = getJ (VSRC_1, T);
setI (NODE_2, -g * i);
setI (NODE_3, +g * i);
}
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askDataPropertyDomain
* Signature: (Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;Z)[[Luk/ac/manchester/cs/factplusplus/ClassPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askDataPropertyDomain
(JNIEnv * env, jobject obj, jobject arg, jboolean direct)
{
TRACE_JNI("askDataPropertyDomain");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<ClassPolicy> actor(J);
PROCESS_QUERY ( J->K->getDRoleDomain ( getRODRoleExpr(env,arg), direct, actor ) );
return actor.getElements();
}
void ServiceWalker::onNewTile()
{
Walker::onNewTile();
std::set<Building*> reachedBuildings = getReachedBuildings(getI(), getJ());
for (std::set<Building*>::iterator itBuilding = reachedBuildings.begin(); itBuilding != reachedBuildings.end(); ++itBuilding)
{
Building &building = **itBuilding;
building.applyService(*this);
}
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askDisjointClasses
* Signature: (Luk/ac/manchester/cs/factplusplus/ClassPointer;)[[Luk/ac/manchester/cs/factplusplus/ClassPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askDisjointClasses
(JNIEnv * env, jobject obj, jobject arg)
{
TRACE_JNI("askDisjointClasses");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<ClassPolicy> actor(J);
const TConceptExpr* p = getROConceptExpr(env,arg);
PROCESS_QUERY ( J->K->getDisjointConcepts(p,actor) );
return actor.getElements();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askInstancesGrouped
* Signature: (Luk/ac/manchester/cs/factplusplus/ClassPointer;Z)[[Luk/ac/manchester/cs/factplusplus/IndividualPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askInstancesGrouped
(JNIEnv * env, jobject obj, jobject arg, jboolean direct)
{
TRACE_JNI("askInstancesGrouped");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<IndividualPolicy</*plain=*/false> > actor(J);
const TConceptExpr* p = getROConceptExpr(env,arg);
PROCESS_QUERY ( direct ? J->K->getDirectInstances(p,actor) : J->K->getInstances(p,actor) );
return actor.getElements();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askIndividualTypes
* Signature: (Luk/ac/manchester/cs/factplusplus/IndividualPointer;Z)[[Luk/ac/manchester/cs/factplusplus/ClassPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askIndividualTypes
(JNIEnv * env, jobject obj, jobject arg, jboolean direct)
{
TRACE_JNI("askIndividualTypes");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<ClassPolicy> actor(J);
const TIndividualExpr* p = getROIndividualExpr(env,arg);
PROCESS_QUERY ( J->K->getTypes(p,direct,actor) );
return actor.getElements();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askSubDataProperties
* Signature: (Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;Z)[[Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askSubDataProperties
(JNIEnv * env, jobject obj, jobject arg, jboolean direct)
{
TRACE_JNI("askSubDataProperties");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<DataPropertyPolicy> actor(J);
const TDRoleExpr* p = getRODRoleExpr(env,arg);
PROCESS_QUERY ( J->K->getSubRoles(p,direct,actor) );
return actor.getElements();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askSuperClasses
* Signature: (Luk/ac/manchester/cs/factplusplus/ClassPointer;Z)[[Luk/ac/manchester/cs/factplusplus/ClassPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askSuperClasses
(JNIEnv * env, jobject obj, jobject arg, jboolean direct)
{
MemoryStatistics MS("getSuperClasses");
TRACE_JNI("askSuperClasses");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
JTaxonomyActor<ClassPolicy> actor(J);
const TConceptExpr* p = getROConceptExpr(env,arg);
PROCESS_QUERY ( J->K->getSupConcepts(p,direct,actor) );
return actor.getElements();
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askDataProperties
* Signature: (Luk/ac/manchester/cs/factplusplus/IndividualPointer;)[Luk/ac/manchester/cs/factplusplus/DataPropertyPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askDataProperties
(JNIEnv * env, jobject obj, jobject arg)
{
TRACE_JNI("askDataProperties");
TRACE_ARG(env,obj,arg);
TJNICache* J = getJ(env,obj);
ReasoningKernel::NamesVector Rs;
PROCESS_QUERY ( J->K->getRelatedRoles ( getROIndividualExpr(env,arg), Rs, /*data=*/true, /*needI=*/false ) );
std::vector<TExpr*> acc;
for ( ReasoningKernel::NamesVector::const_iterator p = Rs.begin(), p_end = Rs.end(); p < p_end; ++p )
acc.push_back(J->getDName((*p)->getName()));
return J->buildArray ( acc, J->DataPropertyPointer );
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: askRelatedIndividuals
* Signature: (Luk/ac/manchester/cs/factplusplus/IndividualPointer;Luk/ac/manchester/cs/factplusplus/ObjectPropertyPointer;)[Luk/ac/manchester/cs/factplusplus/IndividualPointer;
*/
JNIEXPORT jobjectArray JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_askRelatedIndividuals
(JNIEnv * env, jobject obj, jobject arg1, jobject arg2)
{
TRACE_JNI("askRelatedIndividuals");
TRACE_ARG(env,obj,arg1);
TRACE_ARG(env,obj,arg2);
TJNICache* J = getJ(env,obj);
ReasoningKernel::NamesVector Js;
PROCESS_QUERY ( J->K->getRoleFillers ( getROIndividualExpr(env,arg1), getROORoleExpr(env,arg2), Js ) );
std::vector<TExpr*> acc;
for ( ReasoningKernel::NamesVector::const_iterator p = Js.begin(), p_end = Js.end(); p < p_end; ++p )
acc.push_back(J->getIName((*p)->getName()));
return J->buildArray ( acc, J->IndividualPointer );
}
void inductor::calcTR (nr_double_t) {
nr_double_t l = getPropertyDouble ("L");
nr_double_t r, v;
nr_double_t i = real (getJ (VSRC_1));
/* apply initial condition if requested */
if (getMode () == MODE_INIT && isPropertyGiven ("I")) {
i = getPropertyDouble ("I");
}
setState (fState, i * l);
integrate (fState, l, r, v);
setD (VSRC_1, VSRC_1, -r);
setE (VSRC_1, v);
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: getBuiltInDataType
* Signature: (Ljava/lang/String;)Luk/ac/manchester/cs/factplusplus/DataTypePointer;
*/
JNIEXPORT jobject JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_getBuiltInDataType
(JNIEnv * env, jobject obj, jstring str)
{
TRACE_JNI("getBuiltInDataType");
TRACE_STR(env,str);
TJNICache* J = getJ(env,obj);
JString name(env,str);
std::string DTName(name());
if ( DTName == "http://www.w3.org/2000/01/rdf-schema#Literal" ||
DTName == "http://www.w3.org/2000/01/rdf-schema#anySimpleType" ||
DTName == "http://www.w3.org/2001/XMLSchema#anyType" ||
DTName == "http://www.w3.org/2001/XMLSchema#anySimpleType" )
return J->DataType(J->EM->DataTop());
if ( DTName == "http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral" ||
DTName == "http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral" ||
DTName == "http://www.w3.org/2001/XMLSchema#string" ||
DTName == "http://www.w3.org/2001/XMLSchema#anyURI" ||
DTName == "http://www.w3.org/2001/XMLSchema#ID" )
return J->DataType(J->EM->getStrDataType());
if ( DTName == "http://www.w3.org/2001/XMLSchema#integer" ||
DTName == "http://www.w3.org/2001/XMLSchema#int" ||
DTName == "http://www.w3.org/2001/XMLSchema#long" ||
DTName == "http://www.w3.org/2001/XMLSchema#nonNegativeInteger" ||
DTName == "http://www.w3.org/2001/XMLSchema#positiveInteger" ||
DTName == "http://www.w3.org/2001/XMLSchema#negativeInteger" ||
DTName == "http://www.w3.org/2001/XMLSchema#short" ||
DTName == "http://www.w3.org/2001/XMLSchema#byte" )
return J->DataType(J->EM->getIntDataType());
if ( DTName == "http://www.w3.org/2001/XMLSchema#float" ||
DTName == "http://www.w3.org/2001/XMLSchema#double" ||
DTName == "http://www.w3.org/2001/XMLSchema#real" ||
DTName == "http://www.w3.org/2001/XMLSchema#decimal" )
return J->DataType(J->EM->getRealDataType());
if ( DTName == "http://www.w3.org/2001/XMLSchema#boolean" )
return J->DataType(J->EM->getBoolDataType());
if ( DTName == "http://www.w3.org/2001/XMLSchema#dateTimeAsLong" )
return J->DataType(J->EM->getTimeDataType());
std::stringstream err;
err << "Unsupported datatype '" << DTName.c_str() << "'";
Throw ( env, err.str().c_str() );
return (jobject)0;
}
void Well::setRefDepthFromCompletions() const {
size_t timeStep = m_creationTimeStep;
while (true) {
auto completions = getCompletions( timeStep );
if (completions->size() > 0) {
auto firstCompletion = completions->get(0);
double depth = m_grid->getCellDepth( firstCompletion->getI() , firstCompletion->getJ() , firstCompletion->getK());
m_refDepth.setValue( depth );
break;
} else {
timeStep++;
if (timeStep >= m_timeMap->size())
throw std::invalid_argument("No completions defined for well: " + name() + " can not infer reference depth");
}
}
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: getDataValue
* Signature: (Ljava/lang/String;Luk/ac/manchester/cs/factplusplus/DataTypePointer;)Luk/ac/manchester/cs/factplusplus/DataValuePointer;
*/
JNIEXPORT jobject JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_getDataValue__Ljava_lang_String_2Luk_ac_manchester_cs_factplusplus_DataTypePointer_2
(JNIEnv * env, jobject obj, jstring str, jobject type)
{
TRACE_JNI("getDataValue");
TRACE_STR(env,str);
TJNICache* J = getJ(env,obj);
JString name(env,str);
jobject ret = (jobject)0;
try
{
ret = J->DataValue ( J->EM->DataValue ( name(), getDataTypeExpr(env,type) ) );
}
catch (const EFPPCantRegName&)
{
Throw ( env, "FaCT++ Kernel: Can not register new data value" );
}
return ret;
}
/*
* Class: uk_ac_manchester_cs_factplusplus_FaCTPlusPlus
* Method: getNamedClass
* Signature: (Ljava/lang/String;)Luk/ac/manchester/cs/factplusplus/ClassPointer;
*/
JNIEXPORT jobject JNICALL Java_uk_ac_manchester_cs_factplusplus_FaCTPlusPlus_getNamedClass
(JNIEnv * env, jobject obj, jstring str)
{
TRACE_JNI("getNamedClass");
TRACE_STR(env,str);
TJNICache* J = getJ(env,obj);
JString name(env,str);
jobject ret = (jobject)0;
try
{
ret = J->Class(J->getCName(name()));
}
catch (const EFPPCantRegName&)
{
Throw ( env, "FaCT++ Kernel: Can not register new class name" );
}
return ret;
}
void biastee::calcTR (nr_double_t) {
nr_double_t l = getPropertyDouble ("L");
nr_double_t c = getPropertyDouble ("C");
nr_double_t g, r, v;
nr_double_t i = real (getJ (VSRC_1));
setState (fState, i * l);
integrate (fState, l, r, v);
setD (VSRC_1, VSRC_1, -r);
setE (VSRC_1, v);
v = real (getV (NODE_1) - getV (NODE_2));
setState (qState, c * v);
integrate (qState, c, g, i);
setY (NODE_1, NODE_1, +g); setY (NODE_2, NODE_2, +g);
setY (NODE_1, NODE_2, -g); setY (NODE_2, NODE_1, -g);
setI (NODE_1 , -i);
setI (NODE_2 , +i);
}
void SundialsInterface::init(const Dict& opts) {
// Call the base class method
Integrator::init(opts);
// If sensitivity equations, make sure derivative_of_ is available
casadi_assert_message(ns_==0 || !derivative_of_.is_null(),
"Not implemented.");
// Default options
abstol_ = 1e-8;
reltol_ = 1e-6;
max_num_steps_ = 10000;
stop_at_end_ = true;
use_precon_ = true;
max_krylov_ = 10;
linear_solver_ = "csparse";
string newton_scheme = "direct";
quad_err_con_ = false;
string interpolation_type = "hermite";
steps_per_checkpoint_ = 20;
disable_internal_warnings_ = false;
max_multistep_order_ = 5;
second_order_correction_ = true;
step0_ = 0;
max_order_ = 0;
nonlin_conv_coeff_ = 0;
// Read options
for (auto&& op : opts) {
if (op.first=="abstol") {
abstol_ = op.second;
} else if (op.first=="reltol") {
reltol_ = op.second;
} else if (op.first=="max_num_steps") {
max_num_steps_ = op.second;
} else if (op.first=="stop_at_end") {
stop_at_end_ = op.second;
} else if (op.first=="use_preconditioner") {
use_precon_ = op.second;
} else if (op.first=="max_krylov") {
max_krylov_ = op.second;
} else if (op.first=="newton_scheme") {
newton_scheme = op.second.to_string();
} else if (op.first=="linear_solver") {
linear_solver_ = op.second.to_string();
} else if (op.first=="linear_solver_options") {
linear_solver_options_ = op.second;
} else if (op.first=="quad_err_con") {
quad_err_con_ = op.second;
} else if (op.first=="interpolation_type") {
interpolation_type = op.second.to_string();
} else if (op.first=="steps_per_checkpoint") {
steps_per_checkpoint_ = op.second;
} else if (op.first=="disable_internal_warnings") {
disable_internal_warnings_ = op.second;
} else if (op.first=="max_multistep_order") {
max_multistep_order_ = op.second;
} else if (op.first=="second_order_correction") {
second_order_correction_ = op.second;
} else if (op.first=="step0") {
step0_ = op.second;
} else if (op.first=="max_order") {
max_order_ = op.second;
} else if (op.first=="nonlin_conv_coeff") {
nonlin_conv_coeff_ = op.second;
}
}
// Type of Newton scheme
if (newton_scheme=="direct") {
newton_scheme_ = SD_DIRECT;
} else if (newton_scheme=="gmres") {
newton_scheme_ = SD_GMRES;
} else if (newton_scheme=="bcgstab") {
newton_scheme_ = SD_BCGSTAB;
} else if (newton_scheme=="tfqmr") {
newton_scheme_ = SD_TFQMR;
} else {
casadi_error("Unknown Newton scheme: " + newton_scheme);
}
// Interpolation_type
if (interpolation_type=="hermite") {
interp_ = SD_HERMITE;
} else if (interpolation_type=="polynomial") {
interp_ = SD_POLYNOMIAL;
} else {
casadi_error("Unknown interpolation type: " + interpolation_type);
}
// Get or create Jacobians and linear system solvers
for (bool backward : {false, true}) {
// Skip backward?
if (backward && nrx_==0) continue;
// Get Jacobian function
Function J;
if (ns_==0) {
J = getJ(backward);
} else {
SundialsInterface* d = derivative_of_.get<SundialsInterface>();
casadi_assert(d!=0);
if (d->ns_==0) {
J = d->get_function(backward ? "jacB" : "jacF");
} else {
J = d->getJ(backward);
}
}
set_function(J, J.name(), true);
alloc_w(J.nnz_out(0), true);
}
// Allocate work vectors
alloc_w(np_, true); // p
alloc_w(nrp_, true); // rp
alloc_w(2*max(nx_+nz_, nrx_+nrz_), true); // v1, v2
// Allocate linear solvers
linsolF_ = Linsol("linsolF", linear_solver_, linear_solver_options_);
if (nrx_>0) {
linsolB_ = Linsol("linsolB", linear_solver_, linear_solver_options_);
}
}
Point Tile::getScreenPos() const
{
return Point( 30 * ( getI() + getJ()), 15 * (getI() - getJ()) );
}
//! @brief Returns the local reference system.
Ref3d3d XC::CrdTransf3d::getLocalReference(void) const
{
const Vector vI= getI();
const Vector vJ= getJ();
return Ref3d3d(getPosNodeI(),Vector3d(vI[0],vI[1],vI[2]),Vector3d(vJ[0],vJ[1],vJ[2]));
}
virtual void init(Voxel& voxel)
{
b0_index.clear();
for(unsigned int index = 0;index < voxel.bvalues.size();++index)
if(voxel.bvalues[index] == 0)
b0_index.push_back(index);
half_odf_size = voxel.ti.vertices_count/2;
float lambda = voxel.param[0];
unsigned int max_l = voxel.param[1];
const unsigned int R = ((max_l+1)*(max_l+2)/2);
std::vector<std::pair<int,int> > j_map(R);
for (int k = 0; k <= max_l; k += 2)
for (int m = -k; m <= k; ++m)
j_map[getJ(m,k)] = std::make_pair(m,k);
std::vector<float> Bt(R*voxel.bvectors.size());
for (unsigned int j = 0,index = 0; j < R; ++j)
for (unsigned int n = 0; n < voxel.bvectors.size(); ++n,++index)
{
float atan2_xy = std::atan2(voxel.bvectors[n][1],voxel.bvectors[n][0]);
if (atan2_xy < 0.0)
atan2_xy += 2.0*M_PI;
Bt[index] = Yj(j_map[j].second,j_map[j].first,std::acos(voxel.bvectors[n][2]),atan2_xy);
}
std::vector<float> UP(half_odf_size*R);
{
std::vector<float> U(half_odf_size*R);
for (unsigned int n = 0,index = 0; n < half_odf_size; ++n)
for (unsigned int j = 0; j < R; ++j,++index)
{
float atan2_xy = std::atan2(voxel.ti.vertices[n][1],voxel.ti.vertices[n][0]);
if (atan2_xy < 0.0)
atan2_xy += 2.0*M_PI;
U[index] = Yj(j_map[j].second,j_map[j].first,std::acos(voxel.ti.vertices[n][2]),atan2_xy);
}
std::vector<float> P(R*R);
for (unsigned int i = 0,index = 0; i < R; ++i,index += R+1)
P[index] = boost::math::legendre_p(j_map[i].second,0.0)*2.0*M_PI;
image::matrix::product(U.begin(),P.begin(),UP.begin(),image::dyndim(half_odf_size,R),image::dyndim(R,R));
}
std::vector<float> iB(Bt.size());
{
std::vector<float> BtB(R*R); // BtB = Bt * trans(Bt);
image::matrix::square(Bt.begin(),BtB.begin(),image::dyndim(R,voxel.bvectors.size()));
for (unsigned int i = 0,index = 0; i < R; ++i,index += R+1)
{
float l = j_map[i].second;
BtB[index] += l*l*(l+1.0)*(l+1.0)*lambda;
}
std::vector<unsigned int> pivot(R);
image::matrix::lu_decomposition(BtB.begin(),pivot.begin(),image::dyndim(R,R));
//iB = inv(BtB)*Bt;
image::matrix::lu_solve(BtB.begin(),pivot.begin(),Bt.begin(),iB.begin(),image::dyndim(R,R),image::dyndim(R,voxel.bvectors.size()));
}
UPiB.resize(half_odf_size*voxel.bvectors.size());
image::matrix::product(UP.begin(),iB.begin(),UPiB.begin(),image::dyndim(half_odf_size,R),image::dyndim(R,voxel.bvectors.size()));
}
Point Tile::getXY() const
{
return Point( 30 * ( getI() + getJ()), 15 * (getI() - getJ()) );
}
