void ShortAxisFitting::setThetaDelta(ShortAxisOptimizationInput* input, const alglib::real_1d_array& x) {
Cmiss_field_module_id field_module = (input->field_module);
std::vector<Cmiss_node_id>& cmiss_nodes(*(input->cmiss_nodes));
Cmiss_field_id coordinate = (input->coordinates_rc);
Cmiss_field_cache_id cache = (input->cache);
double* initialSegmentLengths = input->initialSegmentLengths;
int* saxNodes = input->saxNodes;
int numberOfModelFrames = input->numberOfModelFrames;
int NUMBER_OF_SEGMENTS = input->NUMBER_OF_SEGMENTS;
int NUMBER_OF_SAX_NODES = input->NUMBER_OF_SAX_NODES;
double** result = input->result; //This is expected to be preallocated for heap efficiency
int* endoNodeIds = input->endoNodesIds;
const int NUMBER_OF_ENDO_NODES = 48; //Ignore the apex
int ctr = 0;
double coord[3];
int frame = input->frame;
Point3D centroids[4];
centroids[0] = input->centroids[0];
centroids[1] = input->centroids[1];
centroids[2] = input->centroids[2];
centroids[3] = input->centroids[3];
//First 12 endo nodes saxcentroid 0, next 12 1...
//Set the theta variation in x to the mesh
{
Cmiss_field_module_begin_change(field_module);
{
double time = ((double) frame) / ((double) numberOfModelFrames);
if (frame == (numberOfModelFrames - 1))
{
time = 1.0;
}
Cmiss_field_cache_set_time(cache, time);
for (int nc = 0; nc < NUMBER_OF_ENDO_NODES; nc++)
{
ctr = nc/12;
double deltaTheta = ((int)(x[ctr]*100000))/100000.0;
Cmiss_field_cache_set_node(cache, cmiss_nodes[endoNodeIds[nc] - 1]);
Cmiss_field_evaluate_real(coordinate, cache, 3, coord);
Point3D start(coord);
start = start + centroids[nc/12];
double nTheta = atan2(start.z, start.x) + deltaTheta;
double dist = sqrt(start.x * start.x + start.z * start.z);
coord[0] = dist * cos(nTheta) - centroids[nc/12].x;
coord[2] = dist * sin(nTheta) - centroids[nc/12].z;
Cmiss_field_assign_real(coordinate, cache, 3, coord);
}
}
Cmiss_field_module_end_change(field_module);
}
}
void StrainMeasures::embedStrainOnElements(std::string fieldname, std::vector<std::string>& strain) {
const unsigned int num_strains = numberOfModelFrames_;
double times[1024];
for (unsigned int j = 0; j < num_strains; j++) {
times[j] = static_cast<double>(j) / (num_strains - 1.0);
}
Cmiss_time_sequence_id time_sequence = Cmiss_field_module_get_matching_time_sequence(field_module, num_strains, times);
Cmiss_field_module_begin_change(field_module);
//Create Node template
Cmiss_nodeset_id nodeset = Cmiss_field_module_find_nodeset_by_name(field_module, "cmiss_nodes");
Cmiss_node_template_id nodeTemplate = Cmiss_nodeset_create_node_template(nodeset);
//Create the field
Cmiss_field_id strainField = Cmiss_field_module_create_field(field_module, fieldname.c_str(), "finite number_of_components 1 component_names value");
if (!strainField) {
std::cout << "Unable to create field " << fieldname << std::endl;
return;
}
Cmiss_node_template_define_field(nodeTemplate, strainField);
Cmiss_node_template_define_time_sequence(nodeTemplate, strainField, time_sequence);
//Create Element template
Cmiss_mesh_id mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, 3);
Cmiss_element_template_id element_template = Cmiss_mesh_create_element_template(mesh);
Cmiss_element_template_set_shape_type(element_template, CMISS_ELEMENT_SHAPE_CUBE);
Cmiss_element_template_set_number_of_nodes(element_template, 1);
Cmiss_element_basis_id constant_basis = Cmiss_field_module_create_element_basis(field_module, 3, CMISS_BASIS_FUNCTION_CONSTANT);
const int local_node_index = 1;
Cmiss_element_template_define_field_simple_nodal(element_template, strainField, -1, constant_basis, 1, &local_node_index);
Cmiss_element_basis_destroy(&constant_basis);
//Map strains to elements
std::map<int, int> elemStrainMap; //Cmiss element no is mapped to strain array number
//APLAX
elemStrainMap[3] = elemStrainMap[10] = 1; //Array id base 0
elemStrainMap[15] = elemStrainMap[22] = 18; //Average of strain ids 2 and 8
elemStrainMap[27] = elemStrainMap[34] = 12;
elemStrainMap[39] = elemStrainMap[46] = 17;
elemStrainMap[40] = elemStrainMap[45] = 17;
elemStrainMap[28] = elemStrainMap[33] = 10;
elemStrainMap[16] = elemStrainMap[21] = 19; //Average of strain ids 11 and 5
elemStrainMap[4] = elemStrainMap[9] = 4;
//TCH
elemStrainMap[11] = elemStrainMap[12] = 2; //Array id base 0
elemStrainMap[23] = elemStrainMap[24] = 20; //Average of strain ids 3 and 9
elemStrainMap[35] = elemStrainMap[36] = 8;
elemStrainMap[47] = elemStrainMap[48] = 16;
elemStrainMap[41] = elemStrainMap[42] = 16;
elemStrainMap[17] = elemStrainMap[18] = 11;
elemStrainMap[29] = elemStrainMap[30] = 21; //Average of strain ids 12 and 6
elemStrainMap[5] = elemStrainMap[6] = 5;
//FCH
elemStrainMap[1] = elemStrainMap[2] = 3; //Array id base 0
elemStrainMap[13] = elemStrainMap[14] = 22; //Average of 10 and 4
elemStrainMap[25] = elemStrainMap[26] = 4;
elemStrainMap[37] = elemStrainMap[38] = 23; //Average of strains 14 and 15
elemStrainMap[43] = elemStrainMap[44] = 24; //Average of strains 16 and 13
elemStrainMap[31] = elemStrainMap[32] = 6;
elemStrainMap[19] = elemStrainMap[20] = 25; //Average of strains 7 and 1
elemStrainMap[7] = elemStrainMap[8] = 0;
std::vector<std::string> allStrain = strain;
//Add the additional strains 18 - 23
std::string s2 = strain[1];
std::string s8 = strain[7];
std::string s11 = strain[10];
std::string s5 = strain[5];
std::string s9 = strain[8];
std::string s3 = strain[2];
std::string s12 = strain[11];
std::string s6 = strain[6];
std::string s10 = strain[9];
std::string s4 = strain[3];
std::string s14 = strain[13];
std::string s15 = strain[14];
std::string s16 = strain[15];
std::string s13 = strain[12];
std::string s1 = strain[0];
std::string s7 = strain[6];
std::vector<std::string> compute;
compute.push_back(s2);
compute.push_back(s8);
compute.push_back(s11);
compute.push_back(s5);
compute.push_back(s9);
compute.push_back(s3);
compute.push_back(s12);
compute.push_back(s6);
compute.push_back(s10);
compute.push_back(s4);
compute.push_back(s14);
compute.push_back(s15);
compute.push_back(s16);
compute.push_back(s13);
compute.push_back(s7);
compute.push_back(s1);
for (int cptc = 0; cptc < 16; cptc += 2) {
std::vector<std::string> strain1;
std::vector<std::string> strain2;
std::ostringstream ss;
boost::split(strain1, compute[cptc], boost::is_any_of(","));
boost::split(strain2, compute[cptc + 1], boost::is_any_of(","));
for (unsigned int j = 0; j < num_strains - 1; j++) {
double value1 = atof(strain1[j].c_str());
double value2 = atof(strain2[j].c_str());
ss << (value1 + value2) * 0.5 << ",";
}
ss << "0.0";
allStrain.push_back(ss.str());
}
for (unsigned int i = 0; i < num_elements; i++) {
Cmiss_node_id temporaryNode = Cmiss_nodeset_create_node(nodeset, extraNodeStartID++, nodeTemplate);
Cmiss_element_template_set_node(element_template, 1, temporaryNode); //Link node with the element
Cmiss_element_merge(elements[i], element_template);
Cmiss_field_cache_set_node(fieldCache, temporaryNode);
std::vector<std::string> strains;
boost::split(strains, allStrain[elemStrainMap[i + 1]], boost::is_any_of(","));
for (unsigned int j = 0; j < num_strains; j++) {
double value = atof(strains[j].c_str());
double time = times[j];
Cmiss_field_cache_set_time(fieldCache, time);
Cmiss_field_assign_real(strainField,fieldCache,1,&value);
}
Cmiss_node_destroy(&temporaryNode);
}
Cmiss_field_module_end_change(field_module);
Cmiss_field_destroy(&strainField);
Cmiss_element_template_destroy(&element_template);
Cmiss_node_template_destroy(&nodeTemplate);
Cmiss_nodeset_destroy(&nodeset);
//Calling the following leads to the error ERROR: DESTROY(FE_time_sequence). Positive access_count
//Cmiss_time_sequence_destroy(&time_sequence);
}
void ShortAxisFitting::optimize(const alglib::real_1d_array& x, double& func, void* ptr) {
struct ShortAxisOptimizationInput* input = static_cast<struct ShortAxisOptimizationInput*>(ptr);
Cmiss_field_module_id field_module = (input->field_module);
std::vector<Cmiss_node_id>& cmiss_nodes(*(input->cmiss_nodes));
std::vector<double>& targetDeltas(*(input->targetDeltas));
Cmiss_field_id coordinate = (input->coordinates_rc);
Cmiss_field_cache_id cache = (input->cache);
double* initialSegmentLengths = input->initialSegmentLengths;
int* saxNodes = input->saxNodes;
int numberOfModelFrames = input->numberOfModelFrames;
int NUMBER_OF_SEGMENTS = input->NUMBER_OF_SEGMENTS;
int NUMBER_OF_SAX_NODES = input->NUMBER_OF_SAX_NODES;
double** result = input->result; //This is expected to be preallocated for heap efficiency
int* endoNodeIds = input->endoNodesIds;
const int NUMBER_OF_ENDO_NODES = 48; //Ignore the apex
int ctr = 0;
double coord[3];
int frame = input->frame;
std::vector<Point3D>& resetCoord(input->initEndoCoordinates->at(frame));
std::vector<Point3D>& initFrame(*input->initFrame);
setThetaDelta(input, x);
//Compute the theta error
double thetaError = 0.0;
//for (int frame = 0; frame < numberOfModelFrames; frame++)
{
double time = ((double) frame) / ((double) numberOfModelFrames);
if (frame == (numberOfModelFrames - 1))
{
time = 1.0;
}
Cmiss_field_cache_set_time(cache, time);
std::vector<Point3D> sax;
Point3D sax_centroid(0, 0, 0);
for (int seg = 0; seg < NUMBER_OF_SAX_NODES; seg++)
{
Cmiss_field_cache_set_node(cache, cmiss_nodes[saxNodes[seg]]);
Cmiss_field_evaluate_real(coordinate, cache, 3, coord);
Point3D start(coord);
sax.push_back(start);
sax_centroid += start;
}
sax_centroid = sax_centroid * (1.0 / NUMBER_OF_SAX_NODES);
double avg = 0.0;
for (int seg = 0; seg < NUMBER_OF_SAX_NODES; seg++)
{
Vector3D trans = sax[seg] - sax_centroid;
double denom = trans.x- initFrame[seg].x;
double nuem = trans.z- initFrame[seg].z;
double ltheta = atan2(nuem, denom);
if(fabs(denom)<1.0e-6 && fabs(nuem)<1.0e-6){
ltheta = 0.0;
}
avg += ltheta;
}
avg /=NUMBER_OF_SAX_NODES;
thetaError +=fabs(avg-targetDeltas[frame]);
input->thetaError = avg;
}
//Compute the segment error
getSegmentLengths(input);
double segmentMatchError = input->segmentMatchError;
func = segmentMatchError + thetaError;
if(segmentMatchError>2.0)
func = 1.0e+30;
input->totalError = func;
//Reset coordinates to original
{
Cmiss_field_module_begin_change(field_module);
{
double time = ((double) frame) / ((double) numberOfModelFrames);
if (frame == (numberOfModelFrames - 1))
{
time = 1.0;
}
Cmiss_field_cache_set_time(cache, time);
for (int nc = 0; nc < NUMBER_OF_ENDO_NODES; nc++)
{
coord[0] = resetCoord[nc].x;
coord[1] = resetCoord[nc].y;
coord[2] = resetCoord[nc].z;
Cmiss_field_cache_set_node(cache, cmiss_nodes[endoNodeIds[nc] - 1]);
Cmiss_field_assign_real(coordinate, cache, 3, coord);
}
}
Cmiss_field_module_end_change(field_module);
}
}
inline int Field::assignReal(FieldCache& cache, int numberOfValues, const double *values)
{
return Cmiss_field_assign_real(id, cache.getId(), numberOfValues,
values);
}
