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 ShortAxisFitting::getSegmentLengths(ShortAxisOptimizationInput* input) {
int ctr = 0;
double* lengthArray = *(input->result);
double* initialSegmentLengths = input->initialSegmentLengths;
double coord[3];
Cmiss_field_id coordinates_rc = input->coordinates_rc;
Cmiss_field_cache_id cache = input->cache;
std::vector<Cmiss_node_id>& cmiss_nodes(*input->cmiss_nodes);
double** segmentNodes = input->segmentNodes;
int frame = input->frame;
//for (int frame = 0; frame < input->numberOfModelFrames; frame++)
{
double time = ((double) frame) / ((double) input->numberOfModelFrames);
if (frame == (input->numberOfModelFrames - 1))
{
time = 1.0;
}
Cmiss_field_cache_set_time(cache, time);
for (int seg = 0; seg < input->NUMBER_OF_SEGMENTS; seg++)
{
Cmiss_field_cache_set_node(cache, cmiss_nodes[segmentNodes[seg][0]]);
Cmiss_field_evaluate_real(coordinates_rc, cache, 3, coord);
Point3D start(coord);
Cmiss_field_cache_set_node(cache, cmiss_nodes[segmentNodes[seg][1]]);
Cmiss_field_evaluate_real(coordinates_rc, cache, 3, coord);
Point3D end(coord);
lengthArray[ctr++] = start.distance(end);
}
}
ctr = 0;
double error = 0;
if (initialSegmentLengths != NULL)
{
//for (int frame = 0; frame < input->numberOfModelFrames; frame++)
{
for (int seg = 0; seg < input->NUMBER_OF_SEGMENTS; seg++)
{
error += fabs(initialSegmentLengths[ctr] - lengthArray[ctr]);
ctr++;
}
}
}
input->segmentMatchError = error;
}
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);
}
std::vector<std::string> StrainMeasures::getSegmentStrains(std::string fieldName) {
std::vector<std::string> strains(19);
Cmiss_field_id field = Cmiss_field_module_find_field_by_name(field_module, fieldName.c_str());
//Compute strains
unsigned int numSegments = mySegments->size();
double temp_array1[3];
double temp_array2[3];
//#define printcoord
#ifdef printcoord
#include "MeshTopology.h"
std::vector<Cmiss_node_id> myNodes(100);
Cmiss_nodeset_id nodeset = Cmiss_field_module_find_nodeset_by_name(field_module, "cmiss_nodes");
Cmiss_node_iterator_id nodeIterator = Cmiss_nodeset_create_node_iterator(nodeset);
Cmiss_node_id node = Cmiss_node_iterator_next(nodeIterator);
if (node != 0) {
double temp_array[3];
while (node) {
int node_id = Cmiss_node_get_identifier(node);
myNodes[node_id - 1] = node;
node = Cmiss_node_iterator_next(nodeIterator);
}
}
Cmiss_nodeset_destroy(&nodeset);
Cmiss_node_iterator_destroy(&nodeIterator);
std::vector<int> Nodes(27);
Nodes[8] = aplaxNodes8;
Nodes[7] = aplaxNodes7;
Nodes[6] = aplaxNodes6;
Nodes[5] = aplaxNodes5;
Nodes[4] = aplaxNodes4;
Nodes[3] = aplaxNodes3;
Nodes[2] = aplaxNodes2;
Nodes[1] = aplaxNodes1;
Nodes[0] = aplaxNodes0;
Nodes[9] = tchNodes0;
Nodes[10] = tchNodes1;
Nodes[11] = tchNodes2;
Nodes[12] = tchNodes3;
Nodes[13] = tchNodes4;
Nodes[14] = tchNodes5;
Nodes[15] = tchNodes6;
Nodes[16] = tchNodes7;
Nodes[17] = tchNodes8;
Nodes[18] = fchNodes0;
Nodes[19] = fchNodes1;
Nodes[20] = fchNodes2;
Nodes[21] = fchNodes3;
Nodes[22] = fchNodes4;
Nodes[23] = fchNodes5;
Nodes[24] = fchNodes6;
Nodes[25] = fchNodes7;
Nodes[26] = fchNodes8;
#endif
std::vector<std::vector<double> > aplaxLengths;
std::vector<std::vector<double> > tchLengths;
std::vector<std::vector<double> > fchLengths;
double denomj = (numberOfModelFrames_ - 1.0);
for (int i = 0; i < numberOfModelFrames_; i++) {
std::vector<double> cLengths;
double time = ((double) i) / denomj;
Cmiss_field_cache_set_time(fieldCache, time);
#ifdef printcoord
std::cout<<"Frame "<<i<<"\t"<<time<<"\t"<<mySegments->at(0).xia[2]<<std::endl;
#endif
for (int j = 0; j < numSegments; j++) {
WallSegment& seg = mySegments->at(j);
//The the lengths
temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
temp_array2[0] = temp_array2[1] = temp_array2[2] = 0.0;
//Since cmiss id starts at 1 subtract 1 from seg.elemeid?
//Note that accessing some computed field (those that involve gradients), with multiple versions leads to gradient set to 0 warning
Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementida - 1], 3, seg.xia);
Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementidb - 1], 3, seg.xib);
Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array2);
Point3D p1(temp_array1);
Point3D p2(temp_array2);
double dist = p1.distance(p2);
#ifdef printcoord
{
int nodeCtr = (j / 8) * 9 + j % 8;
Cmiss_field_cache_set_node(fieldCache, myNodes[Nodes[nodeCtr]]);
temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
Point3D p3(temp_array1);
Cmiss_field_cache_set_node(fieldCache, myNodes[Nodes[nodeCtr + 1]]);
temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
Point3D p4(temp_array1);
std::cout << p1 << "\t" << p2 << " = " << dist << "\t:\t Value at " << Nodes[nodeCtr] + 1 << "\t" << p3 << "\t" << p1.distance(p3) << "\t" << Nodes[nodeCtr + 1] + 1
<< "\t" << p4 << "\t" << p2.distance(p4) << "\t distance \t " << p3.distance(p4) << std::endl;
}
#endif
cLengths.push_back(dist);
}
for (int segc = 0; segc < numSegments / 8; segc++) {
int offset = segc * 8;
std::vector<double> sLengths;
sLengths.push_back(cLengths[0 + offset] + (1 / 3.0 - 1 / 4.0) * 4 * cLengths[1 + offset]);
sLengths.push_back((1.0 - (1 / 3.0 - 1 / 4.0)) * 4 * cLengths[1 + offset] + (2 / 3.0 - 1 / 2.0) * 4 * cLengths[2 + offset]);
sLengths.push_back((1.0 - (2 / 3.0 - 1 / 2.0)) * 4 * cLengths[2 + offset] + cLengths[3 + offset]);
sLengths.push_back(cLengths[4 + offset] + (1.0 - (2 / 3.0 - 1 / 2.0)) * 4 * cLengths[5 + offset]);
sLengths.push_back((2 / 3.0 - 1 / 2.0) * 4 * cLengths[5 + offset] + (1.0 - (1 / 3.0 - 1 / 4.0)) * 4 * cLengths[6 + offset]);
sLengths.push_back((1 / 3.0 - 1 / 4.0) * 4 * cLengths[6 + offset] + cLengths[7 + offset]);
if (segc == 0)
aplaxLengths.push_back(sLengths);
else if (segc == 1)
tchLengths.push_back(sLengths);
else
fchLengths.push_back(sLengths);
}
}
std::vector<double> avgStrains(numberOfModelFrames_, 0.0);
for (int segc = 0; segc < numSegments / 8; segc++) {
std::vector<std::vector<double> > dstrains;
std::vector<std::vector<double> > distances;
if (segc == 0)
distances = aplaxLengths;
else if (segc == 1)
distances = tchLengths;
else if (segc == 2)
distances = fchLengths;
std::vector<double>& initStrain = distances[0];
for (int frame = 1; frame < numberOfModelFrames_; frame++) { //Compute Strains
std::vector<double>& curStrainLengths = distances[frame];
std::vector<double> curStrain;
double c = 0;
unsigned int ulimit = initStrain.size();
for (int j = 0; j < ulimit; j++) {
c = 100.0 * (curStrainLengths[j] - initStrain[j]) / initStrain[j];
curStrain.push_back(c);
}
dstrains.push_back(curStrain);
}
std::vector<std::string> strainSeries;
for (int j = 0; j < initStrain.size(); j++) {
std::ostringstream ss;
ss << 0.0; //For init step
int denom = numberOfModelFrames_ - 1;
double maxStrain = dstrains[denom - 1][j];
//Note that frame goes from 1 to heart.numberOfModelFrames_ when computing strain
//so shift down by 1
for (int i = 0; i < denom; i++) { //Compute Strains
//Drift compensate
double stc = dstrains[i][j] - (i + 1) * maxStrain / denom;
ss << "," << stc;
avgStrains[i] += stc;
}
strainSeries.push_back(ss.str());
}
if (segc == 0) {
strains[2 - 1] = strainSeries[5];
strains[8 - 1] = strainSeries[4];
strains[17 - 1] = strainSeries[3];
strains[18 - 1] = strainSeries[2];
strains[11 - 1] = strainSeries[1];
strains[5 - 1] = strainSeries[0];
} else if (segc == 2) {
strains[3 - 1] = strainSeries[0];
strains[9 - 1] = strainSeries[1];
strains[14 - 1] = strainSeries[2];
strains[16 - 1] = strainSeries[3];
strains[12 - 1] = strainSeries[4];
strains[6 - 1] = strainSeries[5];
} else if (segc == 1) {
strains[4 - 1] = strainSeries[0];
strains[10 - 1] = strainSeries[1];
strains[15 - 1] = strainSeries[2];
strains[13 - 1] = strainSeries[3];
strains[7 - 1] = strainSeries[4];
strains[1 - 1] = strainSeries[5];
}
}
#ifdef printcoord
std::cout << "Linear 3D " << fieldName << std::endl;
for (int i = 1; i < 100; i++)
Cmiss_node_destroy(&myNodes[i]);
#endif
//Add the average strain
//Num strain segments depends on the number of active segments (6 strain segments per view, which has 8 active segments)
double denom = (numSegments / 8) * 6;
std::ostringstream ss;
ss << 0.0; //For init step
for (int i = 0; i < numberOfModelFrames_ - 1; i++) { //Compute the Average
ss << "," << avgStrains[i] / denom;
}
strains[18] = ss.str();
//Check if model PGS should be calculated
if (computeModelPGS) {
double max = fabs(avgStrains[0]);
int idx = 0;
for (int i = 1; i < numberOfModelFrames_ - 1; i++) {
if (fabs(avgStrains[i]) > max) {
max = fabs(avgStrains[i]);
idx = i;
}
}
modelPGS = avgStrains[idx] / denom;
computeModelPGS = false; //set it so that it is not computed in subsequent calls
}
Cmiss_field_destroy(&field);
return strains;
}
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);
}
}
ShortAxisFitting::ShortAxisFitting(std::vector<std::string> mesh, std::vector<std::vector<Point3D> > markers) :
inputMesh(mesh), saxMarkers(markers) {
numberOfModelFrames_ = mesh.size();
cmiss_nodes.resize(98);
//Load the mesh
//Initialise cmgui and get context
context_ = Cmiss_context_create("saxfit");
//This required for using the cmiss_context_execute_command
Cmiss_context_enable_user_interface(context_, NULL);
/**< Handle to the context */
Cmiss_region_id root_region = Cmiss_context_get_default_region(context_);
std::string region_name = "heart";
// Create a heart region
Cmiss_region_id heart_region = Cmiss_region_create_child(root_region, region_name.c_str());
// Read in the heart model spaced over the number of model frames
for (unsigned int i = 0; i < numberOfModelFrames_ - 1; i++)
{
double time = static_cast<double>(i) / numberOfModelFrames_;
Cmiss_stream_information_id stream_information = Cmiss_region_create_stream_information(root_region);
Cmiss_stream_information_region_id stream_information_region = Cmiss_stream_information_cast_region(stream_information);
Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, mesh[i].c_str(), mesh[i].length());
Cmiss_stream_information_region_set_resource_attribute_real(stream_information_region, stream_resource, CMISS_STREAM_INFORMATION_REGION_ATTRIBUTE_TIME, time);
Cmiss_region_read(root_region, stream_information);
Cmiss_stream_resource_destroy(&stream_resource);
Cmiss_stream_information_destroy(&stream_information);
Cmiss_stream_information_region_destroy(&stream_information_region);
}
// Wrap the end point add another set of nodes at time 1.0
{
Cmiss_stream_information_id stream_information = Cmiss_region_create_stream_information(root_region);
Cmiss_stream_information_region_id stream_information_region = Cmiss_stream_information_cast_region(stream_information);
Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, mesh[0].c_str(), mesh[0].length());
int r = Cmiss_stream_information_region_set_resource_attribute_real(stream_information_region, stream_resource, CMISS_STREAM_INFORMATION_REGION_ATTRIBUTE_TIME, 1.0);
Cmiss_region_read(root_region, stream_information);
Cmiss_stream_resource_destroy(&stream_resource);
Cmiss_stream_information_destroy(&stream_information);
Cmiss_stream_information_region_destroy(&stream_information_region);
}
//Cmiss_region_id heart_region = Cmiss_region_find_child_by_name(root_region, region_name.c_str());
//Get the field module of the heart region
field_module_ = Cmiss_region_get_field_module(heart_region);
if (field_module_ != 0)
{
Cmiss_field_module_begin_change(field_module_);
// 'coordinates' is an assumed field in
// a rc coordinate system.
coordinates_rc_ = Cmiss_field_module_find_field_by_name(field_module_, "coordinates");
//Create the cache
cache = Cmiss_field_module_create_cache(field_module_);
Cmiss_field_module_end_change(field_module_);
//Get node handles
Cmiss_nodeset_id nodeset = Cmiss_field_module_find_nodeset_by_name(field_module_, "cmiss_nodes");
Cmiss_node_iterator_id nodeIterator = Cmiss_nodeset_create_node_iterator(nodeset);
Cmiss_node_id node = Cmiss_node_iterator_next(nodeIterator);
if (node != 0)
{
while (node)
{
int node_id = Cmiss_node_get_identifier(node);
cmiss_nodes[node_id - 1] = node;
node = Cmiss_node_iterator_next(nodeIterator);
}
}
Cmiss_nodeset_destroy(&nodeset);
Cmiss_node_iterator_destroy(&nodeIterator);
int endo[] =
{ 55, 57, 71, 73, 66, 67, 69, 60, 61, 63, 52, 53, 54, 56, 70, 72, 64, 65, 68, 58, 59, 62, 50, 51, 77, 84, 85, 81, 82, 83, 78, 79, 80, 74, 75, 76, 89, 96, 97, 93, 94, 95,
90, 91, 92, 86, 87, 88, 98 };
memcpy(endoNodeIds, endo, sizeof(int) * 49);
//int sax[] = { 73, 74, 75, 76, 83, 84, 80, 81, 82, 77, 78, 79 };
//int sax[] = { 79, 78, 77, 82, 81, 80, 84, 83, 76, 75, 74, 73 };
int sax[] = { 80, 81, 82, 77, 78, 79, 73, 74, 75, 76, 83, 84 };
memcpy(saxNodes, sax, sizeof(int) * NUMBER_OF_SAX_NODES);
segmentNodes = new double*[24];
for (int i = 0; i < 24; i++)
{
segmentNodes[i] = new double[2];
}
//Store the initial endo coordinates
const int NUMBER_OF_ENDO_NODES = 48; //Skip apex
double coord[3];
for(int frame = 0;frame<numberOfModelFrames_;frame++){
std::vector<Point3D> frameCoords;
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++)
{
Cmiss_field_cache_set_node(cache, cmiss_nodes[endoNodeIds[nc] - 1]);
Cmiss_field_evaluate_real(coordinates_rc_, cache, 3, coord);
Point3D start(coord);
frameCoords.push_back(start);
}
initEndoCoordinates.push_back(frameCoords);
}
Cmiss_field_module_end_change(field_module_);
}
//Set the segment node ids
segmentNodes[0][0] = aplaxNodes0;
segmentNodes[0][1] = aplaxNodes1;
segmentNodes[1][0] = aplaxNodes1;
segmentNodes[1][1] = aplaxNodes2;
segmentNodes[2][0] = aplaxNodes2;
segmentNodes[2][1] = aplaxNodes3;
segmentNodes[3][0] = aplaxNodes3;
segmentNodes[3][1] = aplaxNodes4;
segmentNodes[4][0] = aplaxNodes4;
segmentNodes[4][1] = aplaxNodes5;
segmentNodes[5][0] = aplaxNodes5;
segmentNodes[5][1] = aplaxNodes6;
segmentNodes[6][0] = aplaxNodes6;
segmentNodes[6][1] = aplaxNodes7;
segmentNodes[7][0] = aplaxNodes7;
segmentNodes[7][1] = aplaxNodes8;
segmentNodes[8][0] = tchNodes0;
segmentNodes[8][1] = tchNodes1;
segmentNodes[9][0] = tchNodes1;
segmentNodes[9][1] = tchNodes2;
segmentNodes[10][0] = tchNodes2;
segmentNodes[10][1] = tchNodes3;
segmentNodes[11][0] = tchNodes3;
segmentNodes[11][1] = tchNodes4;
segmentNodes[12][0] = tchNodes4;
segmentNodes[12][1] = tchNodes5;
segmentNodes[13][0] = tchNodes5;
segmentNodes[13][1] = tchNodes6;
segmentNodes[14][0] = tchNodes6;
segmentNodes[14][1] = tchNodes7;
segmentNodes[15][0] = tchNodes7;
segmentNodes[15][1] = tchNodes8;
segmentNodes[16][0] = fchNodes0;
segmentNodes[16][1] = fchNodes1;
segmentNodes[17][0] = fchNodes1;
segmentNodes[17][1] = fchNodes2;
segmentNodes[18][0] = fchNodes2;
segmentNodes[18][1] = fchNodes3;
segmentNodes[19][0] = fchNodes3;
segmentNodes[19][1] = fchNodes4;
segmentNodes[20][0] = fchNodes4;
segmentNodes[20][1] = fchNodes5;
segmentNodes[21][0] = fchNodes5;
segmentNodes[21][1] = fchNodes6;
segmentNodes[22][0] = fchNodes6;
segmentNodes[22][1] = fchNodes7;
segmentNodes[23][0] = fchNodes7;
segmentNodes[23][1] = fchNodes8;
//Compute the segment lengths
initialSegmentLengths = new double[NUMBER_OF_SEGMENTS * numberOfModelFrames_];
ShortAxisOptimizationInput input;
input.NUMBER_OF_SEGMENTS = NUMBER_OF_SEGMENTS;
input.cache = cache;
input.cmiss_nodes = &cmiss_nodes;
input.coordinates_rc = coordinates_rc_;
input.result = &initialSegmentLengths;
input.numberOfModelFrames = numberOfModelFrames_;
input.initialSegmentLengths = NULL;
input.segmentNodes = segmentNodes;
getSegmentLengths(&input);
//Compute the average rotation that of the sax markers
std::vector<Point3D>& iptCoord(saxMarkers[0]);
unsigned int numSaxMarkers = iptCoord.size();
Point3D saxCentroid(0, 0, 0);
for (int i = 0; i < numSaxMarkers; i++)
{
saxCentroid += iptCoord[i];
}
saxCentroid = saxCentroid*(-1.0/numSaxMarkers);
initFrame = iptCoord;
for (int i = 0; i < numSaxMarkers; i++)
{
initFrame[i]+=saxCentroid;
}
for(int frame = 0;frame<numberOfModelFrames_;frame++){
std::vector<Point3D>& ipCoord(saxMarkers[frame]);
unsigned int numSaxMarkers = ipCoord.size();
Point3D saxcentroid(0, 0, 0);
for (int i = 0; i < numSaxMarkers; i++)
{
saxcentroid += ipCoord[i];
}
saxcentroid = saxcentroid*(-1.0/numSaxMarkers);
std::vector<Point3D> currentFrame(ipCoord);
for (int i = 0; i < numSaxMarkers; i++)
{
currentFrame[i]+=saxcentroid;
}
double avgAngle = 0.0;
for (int i = 0; i < numSaxMarkers; i++)
{
avgAngle += (atan2(currentFrame[i].z-initFrame[i].z,currentFrame[i].x-initFrame[i].x));
}
avgAngle /=numSaxMarkers;
targetDeltas.push_back(avgAngle);
std::cout<<frame<<"\t"<<avgAngle*180/M_PI<<std::endl;
}
//The initFrame markers should correspond to the initFrame of the mesh as that is what is used in the comparisons
initFrame.clear();
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(coordinates_rc_, cache, 3, coord);
Point3D start(coord);
initFrame.push_back(start);
sax_centroid += start;
}
sax_centroid = sax_centroid * (-1.0 / NUMBER_OF_SAX_NODES);
for (int seg = 0; seg < NUMBER_OF_SAX_NODES; seg++)
{
initFrame[seg] += sax_centroid;
}
}
else
{
std::cout << "--- No field module for heart region!!! (Short Axis Fitting)";
std::cout << "No field module " << std::endl;
throw -1;
}
Cmiss_region_destroy(&heart_region);
Cmiss_region_destroy(&root_region);
}
void ShortAxisFitting::fit() {
//Compute the segment lengths
double *tempSpace = new double[NUMBER_OF_SEGMENTS * numberOfModelFrames_];
memcpy(tempSpace, initialSegmentLengths, sizeof(double) * NUMBER_OF_SEGMENTS * numberOfModelFrames_);
ShortAxisOptimizationInput* input = new struct ShortAxisOptimizationInput;
input->numberOfModelFrames = numberOfModelFrames_;
input->NUMBER_OF_SEGMENTS = NUMBER_OF_SEGMENTS;
input->NUMBER_OF_SAX_NODES = NUMBER_OF_SAX_NODES;
input->field_module = field_module_;
input->coordinates_rc = coordinates_rc_;
input->cache = cache;
input->cmiss_nodes = &cmiss_nodes;
input->targetDeltas = &targetDeltas;
input->endoNodesIds = endoNodeIds;
input->segmentNodes = segmentNodes;
input->saxNodes = saxNodes;
input->initialSegmentLengths = initialSegmentLengths;
input->result = &tempSpace;
input->segmentMatchError = 0.0;
input->initFrame = &initFrame;
input->initEndoCoordinates = &initEndoCoordinates;
int nodegroups[][12] = {
{aplaxNodes0,aplaxNodes8,tchNodes0,tchNodes8,fchNodes0,fchNodes8,aplaxtchNode00,aplaxtchNode88,fchaplaxNode00,fchaplaxNode88,fchtchNode08,fchtchNode80},
{aplaxNodes1,aplaxNodes7,tchNodes1,tchNodes7,fchNodes1,fchNodes7,aplaxtchNode11,aplaxtchNode77,fchaplaxNode11,fchaplaxNode77,fchtchNode17,fchtchNode71},
{aplaxNodes2,aplaxNodes6,tchNodes2,tchNodes6,fchNodes2,fchNodes6,aplaxtchNode22,aplaxtchNode66,fchaplaxNode22,fchaplaxNode66,fchtchNode26,fchtchNode62},
{aplaxNodes3,aplaxNodes5,tchNodes3,tchNodes5,fchNodes3,fchNodes5,aplaxtchNode33,aplaxtchNode55,fchaplaxNode33,fchaplaxNode55,fchtchNode35,fchtchNode53}
};
// These variables define stopping conditions for the optimizer.
//
// We use very simple condition - |g|<=epsg
//
//Note that we do not want decimal accuracy, also the minimization problem never seems
//to reduce the error to zero, rather the order is in 10000.00
double epsg = 0.10;
double epsf = 0;
double epsx = 0;
double epso = 0.0010;
double epsi = 0.0010;
alglib::real_1d_array x;
alglib::real_1d_array bndl;
alglib::real_1d_array bndu;
//Create the initial and boundary vectors
int parameters = 4;
double* tempValues = new double[parameters];
for (int i = 0; i < parameters; i++)
{
tempValues[i] = -0.25;
}
bndl.setcontent(parameters, tempValues);
for (int i = 0; i < parameters; i++)
{
tempValues[i] = +0.25;
}
bndu.setcontent(parameters, tempValues);
alglib::minbleicstate state;
alglib::minbleicreport rep;
alglib::ae_int_t maxits = 0;
//
// This variable contains differentiation step
//
double diffstep = 1.0e-4;
for (int frame = 0; frame < numberOfModelFrames_; frame++)
{
input->frame = frame;
clock_t begin = clock();
tempValues[0] = 0.0;
tempValues[2] = targetDeltas[frame];
tempValues[1] = -targetDeltas[frame]/2;
tempValues[3] = -targetDeltas[frame]/2;
x.setcontent(parameters,tempValues);
//Compute the centroids
{
double coord[3];
double time = ((double) frame) / ((double) numberOfModelFrames_);
if (frame == (numberOfModelFrames_ - 1))
{
time = 1.0;
}
Cmiss_field_cache_set_time(cache, time);
//Compute the centroids
Point3D centroids[4];
for(int sc=0;sc<4;sc++){
for(int nc = 0;nc<12;nc++){
Cmiss_field_cache_set_node(cache, cmiss_nodes[nodegroups[sc][nc]]);
Cmiss_field_evaluate_real(coordinates_rc_, cache, 3, coord);
Point3D start(coord);
centroids[sc] += start;
}
input->centroids[sc] = centroids[sc]*(-1.0/12);
}
}
//
// Now we are ready to actually optimize something:
// * first we create optimizer
// * we add boundary constraints
// * we tune stopping conditions
// * and, finally, optimize and obtain results...
//
try
{
alglib::minbleiccreatef(x, diffstep, state);
alglib::minbleicsetbc(state, bndl, bndu);
alglib::minbleicsetinnercond(state, epsg, epsf, epsx);
alglib::minbleicsetoutercond(state, epso, epsi);
alglib::minbleicoptimize(state, optimize, NULL, input);
alglib::minbleicresults(state, x, rep);
setThetaDelta(input, x);
{
double coord[3];
{
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(coordinates_rc_, 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;
std::cout << "Frame " << frame << "\t" << x.tostring(5)<<"\t Result "<<avg*180/M_PI<<"\t Target "<<targetDeltas[frame]*180/M_PI<< std::endl;
}
}
} catch (alglib::ap_error& err)
{
std::cout << err.msg << std::endl;
}
clock_t end = clock();
double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;
std::cout << "Optimization took " << elapsed_secs << std::endl;
std::cout <<"Total Error "<< input->totalError << "\t segment error " << input->segmentMatchError << "\t thetaError " << input->thetaError << std::endl;
std::cout<<"*******************************************************************"<<std::endl;
}
delete[] tempSpace;
throw -1;
}
int setNode(Node& node)
{
return Cmiss_field_cache_set_node(id, node.getId());
}
