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;
}
std::vector<std::string> StrainMeasures::getSixteenSegmentTorsions(double wall_xi) {
//The measure of change due to helix rotation between the walls
//Setup segments
const double base_start = 1.0;
const double mid_start = 0.7;
const double apex_start = 0.5;
const double apex_end = 0.001;
const double wall_epi = 1.0;
if (wall_xi == 1.0)
wall_xi = 0.99;
std::vector<WallSegment> segments;
//APLAX
const double apexAngle = 0.0;
//Base
WallSegment seg1(3, 7); //Segment 2
seg1.setXIA(apexAngle, 0.5 * (base_start + mid_start), wall_xi);
seg1.setXIB(apexAngle, 0.5 * (base_start + mid_start), wall_epi);
WallSegment seg2(5, 1); //Segment 5
seg2.setXIA(apexAngle, 0.5 * (base_start + mid_start), wall_xi);
seg2.setXIB(apexAngle, 0.5 * (base_start + mid_start), wall_epi);
//Mid
WallSegment seg3(7, 11); //Segment 8
seg3.setXIA(apexAngle, 0.5 * (mid_start + apex_start), wall_xi);
seg3.setXIB(apexAngle, 0.5 * (mid_start + apex_start), wall_epi);
WallSegment seg4(5, 9); //Segment 11
seg4.setXIA(apexAngle, 0.5 * (mid_start + apex_start), wall_xi);
seg4.setXIB(apexAngle, 0.5 * (mid_start + apex_start), wall_epi);
//Apex
WallSegment seg5(12, 16); //Segment 13
seg5.setXIA(0.8, 0.5 * (apex_start + apex_end), wall_xi);
seg5.setXIB(0.8, 0.5 * (apex_start + apex_end), wall_epi);
WallSegment seg6(9, 13); //Segment 15
seg6.setXIA(0.1, 0.5 * (apex_start + apex_end), wall_xi);
seg6.setXIB(0.1, 0.5 * (apex_start + apex_end), wall_epi);
//TCH
const double tchAngle = 2.5 / 3.0;
//Base
WallSegment tseg1(4, 8); //Segment 3
tseg1.setXIA(tchAngle, 0.5 * (base_start + mid_start), wall_xi);
tseg1.setXIB(tchAngle, 0.5 * (base_start + mid_start), wall_epi);
WallSegment tseg2(6, 2); //Segment 6
tseg2.setXIA(tchAngle, 0.5 * (base_start + mid_start), wall_xi);
tseg2.setXIB(tchAngle, 0.5 * (base_start + mid_start), wall_epi);
//Mid
WallSegment tseg3(8, 12); //Segment 9
tseg3.setXIA(tchAngle, 0.5 * (mid_start + apex_start), wall_xi);
tseg3.setXIB(tchAngle, 0.5 * (mid_start + apex_start), wall_epi);
WallSegment tseg4(6, 10); //Segment 12
tseg4.setXIA(tchAngle, 0.5 * (mid_start + apex_start), wall_xi);
tseg4.setXIB(tchAngle, 0.5 * (mid_start + apex_start), wall_epi);
//Apex
WallSegment tseg5(12, 16); //Segment 14
tseg5.setXIA(tchAngle, 0.5 * (apex_start + apex_end), wall_xi);
tseg5.setXIB(tchAngle, 0.5 * (apex_start + apex_end), wall_epi);
WallSegment tseg6(10, 14); //Segment 16
tseg6.setXIA(tchAngle, 0.5 * (apex_start + apex_end), wall_xi);
tseg6.setXIB(tchAngle, 0.5 * (apex_start + apex_end), wall_epi);
//FCH
const double fchAngle = 1.0 / 3.0;
//Base
WallSegment fseg1(1, 5); //Segment 4
fseg1.setXIA(fchAngle, 0.5 * (base_start + mid_start), wall_xi);
fseg1.setXIB(fchAngle, 0.5 * (base_start + mid_start), wall_epi);
WallSegment fseg2(7, 3); //Segment 1
fseg2.setXIA(fchAngle, 0.5 * (base_start + mid_start), wall_xi);
fseg2.setXIB(fchAngle, 0.5 * (base_start + mid_start), wall_epi);
//Mid
WallSegment fseg3(5, 9); //Segment 10
fseg3.setXIA(fchAngle, 0.5 * (mid_start + apex_start), wall_xi);
fseg3.setXIB(fchAngle, 0.5 * (mid_start + apex_start), wall_epi);
WallSegment fseg4(7, 11); //Segment 7
fseg4.setXIA(fchAngle, 0.5 * (mid_start + apex_start), wall_xi);
fseg4.setXIB(fchAngle, 0.5 * (mid_start + apex_start), wall_epi);
//Apex
WallSegment fseg5(9, 13); //Segment 14+15
fseg5.setXIA(fchAngle, apex_start, wall_xi);
fseg5.setXIB(fchAngle, apex_end, wall_epi);
WallSegment fseg6(11, 15); //Segment 13+16
fseg6.setXIA(fchAngle, apex_start, wall_xi);
fseg6.setXIB(fchAngle, apex_end, wall_epi);
segments.clear();
segments.push_back(fseg2); //1
segments.push_back(seg1); //2
segments.push_back(tseg1); //3
segments.push_back(fseg1); //4
segments.push_back(seg2); //5
segments.push_back(tseg2); //6
segments.push_back(fseg4); //7
segments.push_back(seg3); //8
segments.push_back(tseg3); //9
segments.push_back(fseg3); //10
segments.push_back(seg4); //11
segments.push_back(tseg4); //12
segments.push_back(seg5); //13
segments.push_back(tseg5); //14
segments.push_back(seg6); //15
segments.push_back(tseg6); //16
//Setup the active strain segments
int aplaxStrainIds[] = { 1, 7, 12, 14, 10, 4 };
int tchStrainIds[] = { 2, 8, 13, 15, 11, 5 };
int fchStrainIds[] = { 0, 6, 9, 3 };
int activeStrainSegments[16];
unsigned int totalActiveSegments = 0;
memset(activeStrainSegments, 0, sizeof(int) * 16);
for (int i = 0; i < 6; i++)
activeStrainSegments[aplaxStrainIds[i]] = 1;
totalActiveSegments += 6;
for (int i = 0; i < 6; i++)
activeStrainSegments[tchStrainIds[i]] = 1;
totalActiveSegments += 6;
for (int i = 0; i < 4; i++)
activeStrainSegments[fchStrainIds[i]] = 1;
totalActiveSegments += 4;
//Compute the strain for each segment over time
unsigned int samples = numberOfModelFrames_;
double* length = new double[samples];
double* nstrain = new double[numberOfModelFrames_];
double* avgstrain = new double[numberOfModelFrames_];
double temp_array[3], temp_array1[3];
unsigned int numSegments = segments.size();
memset(avgstrain, 0, numberOfModelFrames_ * sizeof(double));
std::vector<std::string> strains;
std::stringstream ss;
//Setup the header
for (unsigned int i = 0; i < numSegments; i++) {
WallSegment& seg = segments[i];
for (unsigned int dt = 0; dt < samples; dt++) {
double time = ((double) dt) / (samples - 1.0);
Cmiss_field_cache_set_time(fieldCache, time);
temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
//Since cmiss id starts at 1 subtract 1 from seg.elementid?
Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementida - 1], 3, seg.xia);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, temp_array);
Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementida - 1], 3, seg.xib);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, temp_array1);
length[dt] = fabs(temp_array1[2]);
}
ss << " 0.0";
avgstrain[0] = 0.0;
for (unsigned int dt = 1; dt < samples - 1; dt++) {
nstrain[dt] = length[dt] - length[0];
ss << "," << nstrain[dt];
avgstrain[dt] += nstrain[dt] * activeStrainSegments[i];
}
ss << "," << nstrain[0];
avgstrain[numberOfModelFrames_ - 1] += nstrain[0] * activeStrainSegments[i];
strains.push_back(ss.str());
//Clear the buffer
ss.str("");
}
ss << avgstrain[0];
for (unsigned int dt = 1; dt < numberOfModelFrames_; dt++) {
ss << "," << avgstrain[dt] / totalActiveSegments;
}
strains.push_back(ss.str());
delete[] length;
delete[] nstrain;
delete[] avgstrain;
return strains;
}
std::vector<std::string> StrainMeasures::getLinearDistortion(double* wall_xi, unsigned int cnt, double power) {
unsigned int xdiscret = 25;
unsigned int ydiscret = 25;
//Create points of interest array
double **pointsOfInterest_x = new double*[xdiscret + 1];
double **pointsOfInterest_y = new double*[xdiscret + 1];
for (unsigned int i = 0; i <= xdiscret; i++) {
pointsOfInterest_x[i] = new double[ydiscret + 1];
pointsOfInterest_y[i] = new double[ydiscret + 1];
}
double delx = 1.0 / xdiscret;
double dely = 1.0 / ydiscret;
for (unsigned int xd = 0; xd <= xdiscret; xd++) {
double xinc = xd * delx;
if (xinc == 0.0)
xinc = 0.001;
if (xinc == 1.0)
xinc = 0.99;
for (unsigned int yd = 0; yd <= ydiscret; yd++) {
double yinc = yd * dely;
if (yinc == 0.0)
yinc = 0.001;
if (yinc == 1.0)
yinc = 0.99;
pointsOfInterest_x[xd][yd] = xinc;
pointsOfInterest_y[xd][yd] = yinc;
}
}
Cmiss_field_id principleStarinsField = Cmiss_field_module_find_field_by_name(field_module, "principal_strains");
double temp_array[3];
double coordinates[3];
long nan_count = 0;
std::vector<std::string> results;
std::vector<LevelSet*>* coordSets = new std::vector<LevelSet*>();
std::vector<LevelSet*>* deformSets = new std::vector<LevelSet*>();
for (unsigned int ls = 0; ls < cnt; ls++) {
coordSets->clear();
deformSets->clear();
for (unsigned int mt = 0; mt < numberOfModelFrames_; mt++) {
double time = ((double) mt) / (numberOfModelFrames_ - 1.0);
LevelSet* myCoordLevelSet = new LevelSet(num_elements, xdiscret + 1, ydiscret + 1);
LevelSet* myDeformLevelSet = new LevelSet(num_elements, xdiscret + 1, ydiscret + 1, 1);
Cmiss_field_cache_set_time(fieldCache, time);
nan_count = 0;
for (unsigned int xd = 0; xd <= xdiscret; xd++) {
for (unsigned int yd = 0; yd <= ydiscret; yd++) {
for (unsigned int elementId = 0; elementId < num_elements; elementId++) {
coordinates[0] = pointsOfInterest_x[xd][yd];
coordinates[1] = pointsOfInterest_y[xd][yd];
coordinates[2] = wall_xi[ls];
//std::cout<<coordinates[0]<<" "<<coordinates[1]<<" "<<coordinates[2]<<std::endl;
temp_array[0] = temp_array[1] = temp_array[2] = 0.0;
Cmiss_field_cache_set_mesh_location(fieldCache, elements[elementId], 3, coordinates);
Cmiss_field_evaluate_real(principleStarinsField, fieldCache, 3, temp_array);
double result = getLocalDeformation(temp_array, &nan_count);
myDeformLevelSet->setData(elementId, xd, yd, &result, 1);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, temp_array);
myCoordLevelSet->setData(elementId, xd, yd, temp_array, 3);
}
}
}
coordSets->push_back(myCoordLevelSet);
deformSets->push_back(myDeformLevelSet);
}
std::stringstream ss;
unsigned int numpoints = coordSets->size();
for (unsigned int i = 0; i < numpoints; i++) {
LevelSet* myCoordLevelSet = coordSets->at(i);
LevelSet* myDeformLevelSet = deformSets->at(i);
ss << myDeformLevelSet->getLPSum(0, power) / myCoordLevelSet->getArea();
if (i < (numpoints - 1))
ss << ",";
delete myCoordLevelSet;
delete myDeformLevelSet;
}
results.push_back(ss.str());
}
//Clean up
delete deformSets;
delete coordSets;
for (unsigned int i = 0; i <= xdiscret; i++) {
delete[] pointsOfInterest_x[i];
delete[] pointsOfInterest_y[i];
}
delete[] pointsOfInterest_x;
delete[] pointsOfInterest_y;
Cmiss_field_destroy(&principleStarinsField);
return results;
}
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;
}
std::vector<std::string> StrainMeasures::getRadialStrains(double wall_xi, ViewTypeEnum type) {
std::vector<std::string> strains(18, "");
std::vector<double> avgStrains(numberOfModelFrames_, 0.0);
std::ostringstream strain;
//Note with respect to the model apex base is x-axis
//choose y-z as xy
//Compute the XI values for the circles
const int allelemIds[][6][3] = { { { 47, 0, 0 }, { 46, 15, 31 }, { 14, 30, 46 }, { 45, 0, 0 }, { 48, 13, 29 }, { 16, 32, 48 } }, { { 43, 0, 0 }, { 42, 11, 27 }, { 14, 30, 46 },
{ 41, 0, 0 }, { 44, 9, 25 }, { 12, 28, 44 } }, { { 39, 0, 0 }, { 38, 7, 23 }, { 14, 30, 46 }, { 37, 0, 0 }, { 40, 5, 21 }, { 8, 24, 40 } } };
const double elemStarts[][3] = { { 0, 0, 0 }, { 0.5, 0, 0 }, { 0.0, 0, 0 }, { 0, 0, 0 }, { 0.5, 0, 0 }, { 0, 0, 0 } };
const double elemEnds[][3] = { { 1, 1, 1 }, { 1, 1, 1 }, { 1, 1, 0.5 }, { 1, 1, 1 }, { 1, 1, 1 }, { 1, 1, 0.5 } };
double discretization = 0.02;
int typedepth = 0;
if (type == SAXAPEX)
typedepth = 2;
else if (type == SAXMID)
typedepth = 1;
double depth = 0.0; //Get the central cross section
std::vector<std::vector<double*> > eCPTS;
std::vector<std::vector<int> > eELEM;
for (int elemDepth = 0; elemDepth < 6; elemDepth++) {
std::vector<double*> cpts;
std::vector<int> cel;
for (int eid = 0; eid < 3; eid++) {
if (allelemIds[typedepth][elemDepth][eid] > 0) {
int elemID = allelemIds[typedepth][elemDepth][eid] - 1;
for (double xs = elemStarts[elemDepth][eid]; xs < elemEnds[elemDepth][eid]; xs += discretization) {
Point3D xiCoord(xs, depth, wall_xi);
cpts.push_back(xiCoord.ToArray());
cel.push_back(elemID);
}
}
}
eCPTS.push_back(cpts);
eELEM.push_back(cel);
}
unsigned int nStrains = eCPTS.size();
for (int ns = 0; ns < nStrains; ns++) {
std::vector<double*>& cpts = eCPTS[ns];
std::vector<int>& cel = eELEM[ns];
unsigned int npts = cpts.size();
std::vector<double> circums;
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
double time = ((double) frame) / (numberOfModelFrames_ - 1.0);
Cmiss_field_cache_set_time(fieldCache, time);
//Compute the circle coordinates
std::vector<Point3D> pts;
double coord[3];
for (int j = 0; j < npts; j++) {
Cmiss_field_cache_set_mesh_location(fieldCache, elements[cel[j]], 3, cpts[j]);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, coord);
coord[1] = 0.0;
pts.push_back(Point3D(coord[0], coord[1], coord[2]));
}
double distance = 0;
for (int j = 1; j < npts; j++) {
distance += pts[j - 1].distance(pts[j]);
}
circums.push_back(distance);
}
//Free mem
for (int j = 0; j < npts; j++) {
delete[] cpts[j];
}
double initValue = circums[0];
strain.str("");
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
double stv = (circums[frame] - initValue) / initValue;
strain << stv << ",";
avgStrains[frame] += stv;
}
std::string lvstr = strain.str();
strains[ns] = (lvstr.substr(0, lvstr.length() - 1));
}
//Push the average strain
strain.str("");
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
strain << avgStrains[frame] / numberOfModelFrames_ << ",";
}
std::string lvstr = strain.str();
strains[17] = (lvstr.substr(0, lvstr.length() - 1)); //Location of average strain
return strains;
}
std::string StrainMeasures::getCircumferentialStrain(double wall_xi, ViewTypeEnum type) {
std::ostringstream strain;
//Note with respect to the model apex base is x-axis
//choose y-z as xy
//Compute the XI values for the circles
// xi x(1 inc),height(1 dec),y(=xi)
const int elemIds[][12] = { { 14, 30, 46, 15, 31, 47, 16, 32, 48, 13, 29, 45 }, { 10, 26, 42, 11, 27, 13, 12, 28, 44, 9, 25, 41 },
{ 6, 22, 38, 7, 23, 39, 8, 24, 40, 5, 21, 37 }, { 2, 18, 34, 3, 19, 35, 4, 20, 36, 1, 17, 33 } };
double discretization = 0.02;
int elemDepth = 2;
double depth = 0.0;
switch (type) {
case SAXAPEX: {
elemDepth = 2;
depth = 0.5;
break;
}
case SAXMID: {
elemDepth = 1;
depth = 0.5;
break;
}
case SAXBASE: {
elemDepth = 0;
depth = 0.01;
break;
}
}
std::vector<double*> cpts;
std::vector<int> cel;
for (int eid = 0; eid < 12; eid++) {
int elemID = elemIds[elemDepth][eid] - 1;
for (double xs = 0.0; xs < 1.0; xs += discretization) {
Point3D xiCoord(xs, depth, wall_xi);
cpts.push_back(xiCoord.ToArray());
cel.push_back(elemID);
}
}
unsigned int npts = cpts.size();
std::vector<double> circums;
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
double time = ((double) frame) / (numberOfModelFrames_ - 1.0);
Cmiss_field_cache_set_time(fieldCache, time);
//Compute the circle coordinates
std::vector<Point3D> pts;
double coord[3];
for (int j = 0; j < npts; j++) {
Cmiss_field_cache_set_mesh_location(fieldCache, elements[cel[j]], 3, cpts[j]);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, coord);
coord[1] = 0.0;
pts.push_back(Point3D(coord[0], coord[1], coord[2]));
}
LVChamberCircle circle(pts);
circums.push_back(circle.getCircumference());
}
//Free mem
for (int j = 0; j < npts; j++) {
delete[] cpts[j];
}
double initValue = circums[0];
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
strain << (circums[frame] - initValue) / initValue << ",";
}
std::string lvstr = strain.str();
//Remove the last "," seperator
return lvstr.substr(0, lvstr.length() - 1);
}
std::string StrainMeasures::getLVVolume(double xi) {
//Compute the LV circles
std::vector<std::vector<Point3D> > circleXI;
std::vector<std::vector<int> > circleElem;
std::ostringstream lvVolume;
//Note with respect to the model apex base is x-axis
//choose y-z as xy
//Compute the XI values for the circles
// xi x(1 inc),height(1 dec),y(=xi)
const int elemIds[][12] = { { 14, 30, 46, 15, 31, 47, 16, 32, 48, 13, 29, 45 }, { 10, 26, 42, 11, 27, 13, 12, 28, 44, 9, 25, 41 },
{ 6, 22, 38, 7, 23, 39, 8, 24, 40, 5, 21, 37 }, { 2, 18, 34, 3, 19, 35, 4, 20, 36, 1, 17, 33 } };
double discretization = 0.05;
for (int elemDepth = 0; elemDepth < 4; elemDepth++) {
for (double depth = 1.0; depth >= discretization; depth -= discretization) {
std::vector<Point3D> cpts;
std::vector<int> cel;
for (int eid = 0; eid < 12; eid++) {
int elemID = elemIds[elemDepth][eid] - 1;
for (double xs = 0.0; xs < 1.0; xs += discretization) {
cpts.push_back(Point3D(xs, depth, xi));
cel.push_back(elemID);
}
}
circleXI.push_back(cpts);
circleElem.push_back(cel);
}
}
unsigned int numCircles = circleXI.size();
double minVolume = -1.0; //Compute Ejection fraction
double endVolume = 0.0; //as using smallest and end volume
for (int frame = 0; frame < numberOfModelFrames_; frame++) {
double time = ((double) frame) / (numberOfModelFrames_ - 1.0);
std::vector<LVChamberCircle> circles;
Cmiss_field_cache_set_time(fieldCache, time);
//Compute the circles
for (int i = 0; i < numCircles; i++) {
std::vector<Point3D>& circlexi = circleXI[i];
std::vector<int>& cel = circleElem[i];
std::vector<Point3D> cpts;
unsigned int npts = circlexi.size();
double coord[3];
for (int j = 0; j < npts; j++) {
double* xcoord = circlexi[j].ToArray();
Cmiss_field_cache_set_mesh_location(fieldCache, elements[cel[j]], 3, xcoord);
Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, coord);
cpts.push_back(Point3D(coord[0], coord[1], coord[2]));
delete[] xcoord;
}
circles.push_back(LVChamberCircle(cpts));
}
//Compute the volume for the existing circles
double volume = 0.0;
numCircles = circles.size();
for (int i = 0; i < numCircles - 1; i++) {
volume += circles[i].getVolume(circles[i + 1]);
}
if (minVolume < 0.0 || volume < minVolume) {
minVolume = volume;
}
endVolume = volume;
lvVolume << volume << ",";
}
if (xi < 0.001) {
ejectionFraction = (endVolume - minVolume) / endVolume;
}
std::string lvstr = lvVolume.str();
//Remove the last "," seperator
return lvstr.substr(0, lvstr.length() - 1);
}
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;
}
inline int Field::evaluateReal(FieldCache& cache, int numberOfValues, double *outValues)
{
return Cmiss_field_evaluate_real(id, cache.getId(), numberOfValues, outValues);
}
