void
CDFBasis<d,dt>::evaluate
(const unsigned int derivative,
const RIndex& lambda,
const Array1D<double>& points, Array1D<double>& values)
{
values.resize(points.size());
for (unsigned int i(0); i < values.size(); i++) {
values[i] = evaluate(derivative, lambda, points[i]);
}
}
/*!
* Name : rayTraceFiller
* Description: Used to generate rachis segmentation
* Arguments : PROTO_INPUT : protobuf input containing segmented germline
* IMAGE_OUTPUT : float image containing intermediate rachis segmentation. This
* image needs to be post-processed (thresholding, throw out
* unconnected components).
* Syntax : ./segpipeline_FREEBSD 0 0 0 0 0 PROTO_INPUT 0 0 rayTraceFiller 32 IMAGE_OUTPUT 0 0 0 0 0 0 0 0
* Notes : This function has a random component, so you won't get the exact same result every time.
*/
void rayTraceFiller(TextIO* inputText, ImageIO* outputImage,
CallbackFunctions *cb) {
log(cb, 4, "Calculating rachis segmentation through ray tracing");
// generate full segmentation
Protobuf proto(cb);
proto.readProto(inputText);
Image3D<float> *I = new Image3D<float> (cb);
Array1D<float> color(cb);
proto.getList("protobuf_index", &color);
color + 1;
proto.drawSegmentationImage("full", I, &color);
// generate points spaced uniformly on a sphere
double Jiggle = 0.03 / sqrt(double(NUM_UNIFORM_POINTS_ON_SPHERE));
unsigned int Rounds = 5000;
points P("default", NUM_UNIFORM_POINTS_ON_SPHERE, Jiggle, Rounds);
Array1D<float> *xUniformP = new Array1D<float> (cb);
Array1D<float> *yUniformP = new Array1D<float> (cb);
Array1D<float> *zUniformP = new Array1D<float> (cb);
P.report(xUniformP, yUniformP, zUniformP);
// allocate rayScore. 0 if not yet checked, 1 if collision, 2 if no collision
int dimx, dimy, dimz;
I->getDimensions(dimx, dimy, dimz);
boost::multi_array<unsigned char, 4> *rayScore = new boost::multi_array<
unsigned char, 4>(
boost::extents[dimx][dimy][dimz][NUM_UNIFORM_POINTS_ON_SPHERE]);
// allocate array for progress bar
Array1D<float> *progress = new Array1D<float> (cb);
progress->resize(NUM_UNIFORM_POINTS_ON_SPHERE);
// do ray tracing
log(cb, 4, "Starting ray tracing");
#if defined USELIBDISPATCH
dispatch_apply(NUM_UNIFORM_POINTS_ON_SPHERE, dispatch_get_global_queue(0,0), ^(size_t ii) {
#else
for (int ii = 0; ii < NUM_UNIFORM_POINTS_ON_SPHERE; ii++) {
#endif
int i = (int) ii;
// get a discrete line
int xP = iround(LENGTH_BRESENHAM_LINE * (*xUniformP)(i));
int yP = iround(LENGTH_BRESENHAM_LINE * (*yUniformP)(i));
int zP = iround(LENGTH_BRESENHAM_LINE * (*zUniformP)(i));
Array1D<int> xLine(cb), yLine(cb), zLine(cb);
bresenhamLine(&xLine, &yLine, &zLine, xP, yP, zP);
// check if ray hits image boundary for every pixel in the image
for (int xc = 0; xc < dimx; xc++) {
for (int yc = 0; yc < dimy; yc++) {
for (int zc = 0; zc < dimz; zc++) {
// only do ray tracing if ray has not passed through point previously.
if ((*rayScore)[xc][yc][zc][i] == 0) {
// iterate over length of ray
for (int r = 0; r < yLine.size(); r++) {
int x = xc + xLine(r), y = yc + yLine(r), z = zc
+ zLine(r);
if (x >= 0 & x < dimx & y >= 0 & y < dimy & z >= 0
& z < dimz) { // check if ray in image boundary
if ((*I)(x, y, z) > float(BWTHRESH)) { // if collision detected, update collision information for all points on ray
for (int rr = 0; rr <= r; rr++) {
int xx = xc + xLine(rr), yy = yc
+ yLine(rr), zz = zc
+ zLine(rr);
(*rayScore)[xx][yy][zz][i] = 1;
}
break;
}
// else ray has reach image boundary
} else {
// update non-collision information on all points on the ray
for (int rr = 0; rr < r; rr++) {
int xx = xc + xLine(rr), yy = yc
+ yLine(rr), zz = zc + zLine(rr);
(*rayScore)[xx][yy][zz][i] = 2;
}
break; // break out of iteration over length of the ray
}
} // end iterate over length of ray
}
}
}
}
// update progress
(*progress)(i) = 1;
int progressOutOf100 = (int) (progress->sum()
/ NUM_UNIFORM_POINTS_ON_SPHERE * 100);
cb->progressReport(progressOutOf100);
#if defined USELIBDISPATCH
});
#else
}
Array1D<SampledMapping<2> >
evaluate(const LDomainJLBasis& basis,
const Index& lambda,
const int N)
{
Array1D<SampledMapping<2> > r(3);
// supp(psi_{j,e,c,k}) = 2^{-j}[k1-1,k1+1]x[k2-1,k2+1] cap Omega
FixedArray1D<Array1D<double>,2> values;
values[0].resize(N+1); // values in x-direction
values[1].resize(N+1); // values in y-direction
Array1D<double> knots;
knots.resize(N+1);
const double h = 1./N;
// patch Omega_0 = [-1,0]x[0,1]
for (int i = 0; i <= N; i++) {
values[0][i] = 0.;
values[1][i] = 0.;
}
if (lambda.k()[0] <= 0 && lambda.k()[1] >= 0) {
for (int i = 0; i <= N; i++)
knots[i] = -1.0+i*h;
evaluate(0, lambda.j(), lambda.e()[0], lambda.c()[0], lambda.k()[0], knots, values[0]);
for (int i = 0; i <= N; i++)
knots[i] = i*h;
evaluate(0, lambda.j(), lambda.e()[1], lambda.c()[1], lambda.k()[1], knots, values[1]);
}
r[0] = SampledMapping<2>(Point<2>(-1, 0), Point<2>(0,1), values);
// patch Omega_1 = [-1,0]x[-1,0]
for (int i = 0; i <= N; i++) {
values[0][i] = 0.;
values[1][i] = 0.;
}
if (lambda.k()[0] <= 0 && lambda.k()[1] <= 0) {
for (int i = 0; i <= N; i++)
knots[i] = -1.0+i*h;
evaluate(0, lambda.j(), lambda.e()[0], lambda.c()[0], lambda.k()[0], knots, values[0]);
evaluate(0, lambda.j(), lambda.e()[1], lambda.c()[1], lambda.k()[1], knots, values[1]);
}
r[1] = SampledMapping<2>(Point<2>(-1,-1), Point<2>(0,0), values);
// patch Omega_2 = [0,1]x[-1,0]
for (int i = 0; i <= N; i++) {
values[0][i] = 0.;
values[1][i] = 0.;
}
if (lambda.k()[0] >= 0 && lambda.k()[1] <= 0) {
for (int i = 0; i <= N; i++)
knots[i] = i*h;
evaluate(0, lambda.j(), lambda.e()[0], lambda.c()[0], lambda.k()[0], knots, values[0]);
for (int i = 0; i <= N; i++)
knots[i] = -1.0+i*h;
evaluate(0, lambda.j(), lambda.e()[1], lambda.c()[1], lambda.k()[1], knots, values[1]);
}
r[2] = SampledMapping<2>(Point<2>( 0,-1), Point<2>(1,0), values);
return r;
}
/*!
* Print simulation results to standard output
*/
void printSimulationResultsForTed_pedigreeDepth(PedigreeDepthStorage *pdStorage, bool cellProductionConstraintsMet, bool fecundityScheduleConstraintsMet, bool allConstraintsMet, ProgramOptionParser *opt) {
// print pedigree depth (i.e., value that Ted's optimizer is minimizing)
float valueBeingOptimized = 0;
string option_str(opt->fitnessMetric.c_str());
if (option_str.find("meanPedigreeDepthMeioticCells:")!=string::npos) {valueBeingOptimized = pdStorage->pd_AllCellsEnterMeioticRegion->mean();}
else if (strcmp(option_str.c_str(),"spermOocyteMean")==0) {valueBeingOptimized = pdStorage->pd_spermOocyte->mean();}
else if (strcmp(option_str.c_str(),"spermOocyteSum")==0) {valueBeingOptimized = pdStorage->pd_spermOocyteSum->mean();}
else if (strcmp(option_str.c_str(),"generationRate")==0) {float r = calculateGenerationFitness(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints,pdStorage->pd_spermOocyte->mean(),opt->deleteriousMutationRate,opt->maximalGenerationRate,opt->maximalPedigreeDepth);valueBeingOptimized = -r;}
else if (strcmp(option_str.c_str(),"generationRate2")==0) {float r = calculateGenerationFitness_selectionCoefficient(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints,pdStorage->pd_spermOocyte->mean(),opt->deleteriousMutationRate,opt->maximalGenerationRate,opt->maximalPedigreeDepth);valueBeingOptimized = -r;}
else {std::cerr << "Invalid choice of fitnessScoringMethod" << endl;exit(1);}
printf("%f\n",valueBeingOptimized);
// print whether cell production constraints (cpc) met
printf("%d\n", cellProductionConstraintsMet);
// print whether fecundity constraints (fc) met
printf("%d\n", fecundityScheduleConstraintsMet);
// print whether all constraints met
printf("%d\n", allConstraintsMet);
// print pedigree depth of individual simulations runs
if (option_str.find("meanPedigreeDepthMeioticCells:")!=string::npos) {pdStorage->pd_AllCellsEnterMeioticRegion->display();}
else if (strcmp(option_str.c_str(),"spermOocyteMean")==0) {pdStorage->pd_spermOocyte->display();}
else if (strcmp(option_str.c_str(),"spermOocyteSum")==0) {pdStorage->pd_spermOocyteSum->display();}
else if (strcmp(option_str.c_str(),"generationRate")==0) {
Array1D<float> output;
output.resize(pdStorage->pd_spermOocyte->size());
float r = calculateGenerationFitness(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints,pdStorage->pd_spermOocyte->mean(),opt->deleteriousMutationRate,opt->maximalGenerationRate,opt->maximalPedigreeDepth);
for (int i=0;i<pdStorage->pd_spermOocyte->size();i++) {
output(i) = -r;
}
output.display();
}
else if (strcmp(option_str.c_str(),"generationRate2")==0) {
Array1D<float> output;
output.resize(pdStorage->pd_spermOocyte->size());
float r = calculateGenerationFitness_selectionCoefficient(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints,pdStorage->pd_spermOocyte->mean(),opt->deleteriousMutationRate,opt->maximalGenerationRate,opt->maximalPedigreeDepth);
for (int i=0;i<pdStorage->pd_spermOocyte->size();i++) {
output(i) = -r;
}
output.display();
}
else {std::cerr << "Invalid choice of fitnessScoringMethod" << endl;exit(1);}
// print whether cell production constraint is met for individual simulation runs
Array2D<float>::array_index dimx_cellProduction,dimy_cellProduction;
pdStorage->simulatedCellProductionSchedule->getDimensions(dimx_cellProduction,dimy_cellProduction);
for (int x=0;x<dimx_cellProduction;x++) {
bool constraintsSatisfied=true;
for (int y=0;y<dimy_cellProduction;y++) {
if ((*pdStorage->simulatedCellProductionSchedule)(x,y)>(*pdStorage->cellProductionConstraints)(0,y)) {
constraintsSatisfied=false;
break;
}
}
if (opt->constraintMethod.compare("none")==0){
constraintsSatisfied=true;
}
printf("%d",constraintsSatisfied);
if (x!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
// print whether fecundity constraint is met for individual simulation runs
Array2D<float>::array_index dimx_simulatedFecundity, dimy_simulatedFecundity;
pdStorage->simulatedFecunditySchedule->getDimensions(dimx_simulatedFecundity,dimy_simulatedFecundity);
for (Array2D<float>::array_index x=0;x<dimx_simulatedFecundity;x++) {
bool constraintsSatisfied=true;
int sum_sim = 0;
int sum_sched = 0;
for (int y=0;y<dimy_simulatedFecundity;y++) {
if (y==0) { // check sperm constraint
int numSperm_sim = boost::math::iround((*pdStorage->simulatedFecunditySchedule)(x,y));
int numSperm_sched = opt->numSperm; // boost::math::iround((*pdStorage->fecundityConstraints)(0,y));
if (numSperm_sim!=numSperm_sched) {
constraintsSatisfied=false;
break;
}
} else { // check oocyte constraint
sum_sim+=ceil((*pdStorage->simulatedFecunditySchedule)(x,y));
sum_sched+=boost::math::iround((*pdStorage->fecundityConstraints)(y));
if (sum_sim<sum_sched) {
constraintsSatisfied=false;
break;
}
}
}
if (opt->constraintMethod.compare("none")==0){
constraintsSatisfied=true;
}
printf("%d",constraintsSatisfied);
if (x!=dimx_simulatedFecundity-1) {
printf(",");
}
}
printf("\n");
// print cell production time constraints for individual runs
for (int i=0;i<dimy_cellProduction;i++) {
printf("%f",(*pdStorage->cellProductionConstraints)(0,i));
if (i!=dimy_cellProduction-1) {
printf(",");
}
}
printf("\n");
// print cell production times for individual runs
for (int i=0;i<dimy_cellProduction;i++) {
for (int j=0;j<dimx_cellProduction;j++) {
printf("%f",(*pdStorage->simulatedCellProductionSchedule)(j,i));
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
// print fecundity constraints for individual runs
int sumConstraint=0;
for (int i=0;i<dimy_simulatedFecundity;i++) {
int constraint;
if (i==0) {
constraint = opt->numSperm;
} else {
constraint = boost::math::iround((*pdStorage->fecundityConstraints)(i));
}
sumConstraint+=constraint;
printf("%d",sumConstraint);
if (i!=dimy_simulatedFecundity-1) {
printf(",");
}
}
printf("\n");
// print fecundity for individual runs
Array1D<float> sumGamete;
sumGamete.resize(dimx_cellProduction);
for (int i=0;i<dimy_simulatedFecundity;i++) {
for (int j=0;j<dimx_cellProduction;j++) {
sumGamete(j)+=(*pdStorage->simulatedFecunditySchedule)(j,i);
printf("%d",boost::math::iround(sumGamete(j)));
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
}
/*!
* Print simulation results to standard output when MR constraints are not satisfied.
* These results fixed to very high pedigree depths / non-satisfied constraints
*/
void printSimulationResultsForTed_pedigreeDepth_badMR(PedigreeDepthStorage *pdStorage, ProgramOptionParser *opt) {
// print pedigree depth (i.e., value that Ted's optimizer is minimizing)
printf("999\n");
// print whether cell production constraints (cpc) met
printf("0\n");
// print whether fecundity constraints (fc) met
printf("0\n");
// print whether all constraints met
printf("0\n");
// print pedigree depth of individual simulations runs
Array1D<float> temp;
Array1D<float>::array_index numRuns = pdStorage->pd_AllCellsEnterMeioticRegion->size();
temp.resize(numRuns);
temp.fill(999);
temp.display();
// print whether cell production constraint is met for individual simulation runs
Array2D<float>::array_index dimx_cellProduction,dimy_cellProduction;
pdStorage->simulatedCellProductionSchedule->getDimensions(dimx_cellProduction,dimy_cellProduction);
for (int x=0;x<dimx_cellProduction;x++) {
printf("0");
if (x!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
// print whether fecundity constraint is met for individual simulation runs
Array2D<float>::array_index dimx_simulatedFecundity, dimy_simulatedFecundity;
pdStorage->simulatedFecunditySchedule->getDimensions(dimx_simulatedFecundity,dimy_simulatedFecundity);
for (Array2D<float>::array_index x=0;x<dimx_simulatedFecundity;x++) {
printf("%d",false);
if (x!=dimx_simulatedFecundity-1) {
printf(",");
}
}
printf("\n");
// print cell production time constraints for individual runs
for (int i=0;i<dimy_cellProduction;i++) {
printf("%f",(*pdStorage->cellProductionConstraints)(0,i));
if (i!=dimy_cellProduction-1) {
printf(",");
}
}
printf("\n");
// print cell production times for individual runs
for (int i=0;i<dimy_cellProduction;i++) {
for (int j=0;j<dimx_cellProduction;j++) {
printf("999");
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
// print fecundity constraints for individual runs
int sumConstraint=0;
for (int i=0;i<dimy_simulatedFecundity;i++) {
int constraint;
if (i==0) {
constraint = opt->numSperm;
} else {
constraint = boost::math::iround((*pdStorage->fecundityConstraints)(i));
}
sumConstraint+=constraint;
printf("%d",sumConstraint);
if (i!=dimy_simulatedFecundity-1) {
printf(",");
}
}
printf("\n");
// print fecundity for individual runs
Array1D<float> sumGamete;
sumGamete.resize(dimx_cellProduction);
for (int i=0;i<dimy_simulatedFecundity;i++) {
for (int j=0;j<dimx_cellProduction;j++) {
sumGamete(j)+=(*pdStorage->simulatedFecunditySchedule)(j,i);
printf("%d",boost::math::iround(sumGamete(j)));
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
}
/*!
* Print simulation results to standard output
*/
void printSimulationResults(PedigreeDepthStorage *pdStorage, int numSperm, bool cellProductionConstraintsMet, bool fecundityScheduleConstraintsMet, bool allConstraintsMet, ProgramOptionParser *opt) {
// print fitness metric values
printf("\n******************************\n");
printf("Fitness metrics:\n");
printf("pedigree depth sperm (mean) = %f\n",pdStorage->pd_sperm->mean());
printf("pedigree depth oocyte (mean) = %f\n",pdStorage->pd_oocyte->mean());
printf("pedigree depth sperm and oocyte (mean) = %f\n",pdStorage->pd_spermOocyte->mean());
printf("pedigree depth mitotic region (mean) = %f\n",pdStorage->pd_mitoticRegion->mean());
printf("pedigree depth meiotic region (mean) = %f\n",pdStorage->pd_meioticRegion->mean());
printf("pedigree depth whole germline (mean) = %f\n",pdStorage->pd_wholeGermline->mean());
printf("pedigree depth sperm (median) = %f\n",pdStorage->pd_sperm->perctile(0.5));
printf("pedigree depth oocyte (median) = %f\n",pdStorage->pd_oocyte->perctile(0.5));
printf("pedigree depth sperm and oocyte (median) = %f\n",pdStorage->pd_spermOocyte->perctile(0.5));
printf("pedigree depth mitotic region (median) = %f\n",pdStorage->pd_mitoticRegion->perctile(0.5));
printf("pedigree depth meiotic region (median) = %f\n",pdStorage->pd_meioticRegion->perctile(0.5));
printf("pedigree depth whole germline (median) = %f\n",pdStorage->pd_wholeGermline->perctile(0.5));
printf("pedigree depth sperm and oocyte (sum/numGametes) = %f\n",pdStorage->pd_spermOocyteSum->mean());
printf("pedigree depth of germline at egg laying = %f\n",pdStorage->pd_GermlineAtEggLaying->mean());
printf("pedigree depth of first N cells that entered meiotic region = %f\n",pdStorage->pd_AllCellsEnterMeioticRegion->mean());
// print generation rates
float r = calculateGenerationRate(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints);
float rFitness = calculateGenerationFitness(pdStorage->simulatedFecunditySchedule,pdStorage->fecundityConstraints,pdStorage->pd_spermOocyte->mean(),opt->deleteriousMutationRate,opt->maximalGenerationRate,opt->maximalPedigreeDepth);
printf("generation rate without pedigree depth contribution (hours^-1) = %f\n",r);
printf("negative generation rate with pedigree depth contribution (hours^-1, negative so minimization will optimize fitness) = %f\n",-rFitness); // negative so that minimization will optimize fitness
printf("\n");
// print timers
printf("Timers:\n");
printf("Number of cell divisions = %f\n",pdStorage->num_cellDivisions->mean());
printf("Number of cells that enter meiotic region = %f\n",pdStorage->num_meioticCellsProduced->mean());
printf("Time of first cell exiting meiotic region = %f\n",pdStorage->time_firstMeioticExit->mean());
printf("\n");
// print simulated fecundity schedule
Array2D<float>::array_index dummy,dimy_fecundity;
pdStorage->fecundityConstraints->getDimensions(dummy,dimy_fecundity);
printf("Simulated fecundity schedule:\n");
for (int i=0;i<dimy_fecundity;i++) {
float meanGametesProduced = pdStorage->simulatedFecunditySchedule->mean(i);
if (i==0) {
printf("%f sperm produced at %f hours (%d expected)\n",meanGametesProduced,(*pdStorage->fecundityConstraints)(0,i),numSperm);
} else {
printf("%f oocytes produced at %f hours (%d expected)\n",meanGametesProduced,(*pdStorage->fecundityConstraints)(0,i),(int)(*pdStorage->fecundityConstraints)(i));
}
}
printf("\n");
// print simulated cell exiting meiotic region schedule
printf("Simulated cells that hit end of meiotic region (and undergo apoptosis/oogenesis):\n");
for (int i=0;i<dimy_fecundity;i++) {
float meanCellDivisions = pdStorage->simulatedCellProductionSchedule_atFecundityBins->mean(i);
float meanNumCellsHitMeioticRegion = pdStorage->simulatedMeioticExitSchedule->mean(i);
printf("%f cell divisions, %f cells hit end of meiotic region at at %f hours\n",meanCellDivisions,meanNumCellsHitMeioticRegion,(*pdStorage->fecundityConstraints)(0,i));
}
printf("\n");
printf("theoretical oocyte probability = step*0:");
float total_numCellsHitMeioticRegion=0;
for (int i=1;i<dimy_fecundity;i++) {
float numCellsHitMeioticRegion = pdStorage->simulatedMeioticExitSchedule->mean(i);
float expectedNumberOocytes = (*pdStorage->fecundityConstraints)(i);
printf("%.3f",expectedNumberOocytes/numCellsHitMeioticRegion);
if (i!=dimy_fecundity-1) {
total_numCellsHitMeioticRegion += numCellsHitMeioticRegion;
printf("/%.2f:",total_numCellsHitMeioticRegion);
}
}
printf("\n\n");
// print simulated cell production schedule
printf("cell production schedule:\n");
Array2D<float>::array_index dimx_cellProduction,dimy_cellProduction;
pdStorage->simulatedCellProductionSchedule->getDimensions(dimx_cellProduction,dimy_cellProduction);
for (int i=0;i<dimy_cellProduction;i++) {
float time = pdStorage->simulatedCellProductionSchedule->mean(i);
float constraint = (*pdStorage->cellProductionConstraints)(0,i);
int cellDivisions = (int)(*pdStorage->cellProductionConstraints)(i);
printf("%d cell divisions at %f hours (constraint=%f)\n",cellDivisions,time,constraint);
}
printf("\n");
// print whether constraints were met
printf("cell production constraints met: %d\n", cellProductionConstraintsMet);
printf("fecundity constraints met: %d\n", fecundityScheduleConstraintsMet);
printf("all constraints met: %d\n", allConstraintsMet);
// pedigree depth for individual runs
printf("\n****** Individual Output ******\n");
printf("sperm/oocyte mean pedigree depth = ");
pdStorage->pd_spermOocyte->display();
// print whether cell production constraint is met for individual runs
printf("cell production constraint = ");
for (int x=0;x<dimx_cellProduction;x++) {
bool constraintsSatisfied=true;
for (int y=0;y<dimy_cellProduction;y++) {
if ((*pdStorage->simulatedCellProductionSchedule)(x,y)>(*pdStorage->cellProductionConstraints)(0,y)) {
constraintsSatisfied=false;
break;
}
}
if (opt->constraintMethod.compare("none")==0){
constraintsSatisfied=true;
}
printf("%d",constraintsSatisfied);
if (x!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
// print whether fecundity constraint is met for individual runs
Array2D<float>::array_index dimx_simulatedFecundity, dimy_simulatedFecundity;
printf("fecundity constraint = ");
pdStorage->simulatedFecunditySchedule->getDimensions(dimx_simulatedFecundity,dimy_simulatedFecundity);
for (Array2D<float>::array_index x=0;x<dimx_simulatedFecundity;x++) {
bool constraintsSatisfied=true;
int sum_sim = 0;
int sum_sched = 0;
for (int y=0;y<dimy_simulatedFecundity;y++) {
if (y==0) { // check sperm constraint
int numSperm_sim = boost::math::iround((*pdStorage->simulatedFecunditySchedule)(x,y));
int numSperm_sched = opt->numSperm; // boost::math::iround((*pdStorage->fecundityConstraints)(0,y));
if (numSperm_sim!=numSperm_sched) {
constraintsSatisfied=false;
break;
}
} else { // check oocyte constraint
sum_sim+=ceil((*pdStorage->simulatedFecunditySchedule)(x,y));
sum_sched+=boost::math::iround((*pdStorage->fecundityConstraints)(y));
if (sum_sim<sum_sched) {
constraintsSatisfied=false;
break;
}
}
}
if (opt->constraintMethod.compare("none")==0){
constraintsSatisfied=true;
}
printf("%d",constraintsSatisfied);
if (x!=dimx_simulatedFecundity-1) {
printf(",");
}
}
printf("\n");
for (int i=0;i<dimy_cellProduction;i++) {
printf("cell production time by simulation (constraint=%f) = ",(*pdStorage->cellProductionConstraints)(0,i));
for (int j=0;j<dimx_cellProduction;j++) {
printf("%f",(*pdStorage->simulatedCellProductionSchedule)(j,i));
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
int sumConstraint=0;
Array1D<float> sumGamete;
sumGamete.resize(dimx_cellProduction);
for (int i=0;i<dimy_simulatedFecundity;i++) {
int constraint;
if (i==0) {
constraint = opt->numSperm;
} else {
constraint = boost::math::iround((*pdStorage->fecundityConstraints)(i));
}
sumConstraint+=constraint;
printf("fecundity time by simulation (constraint=%d) = ",sumConstraint);
for (int j=0;j<dimx_cellProduction;j++) {
sumGamete(j)+=(*pdStorage->simulatedFecunditySchedule)(j,i);
printf("%d",boost::math::iround(sumGamete(j)));
if (j!=dimx_cellProduction-1) {
printf(",");
}
}
printf("\n");
}
}
