void AdhesionFlexPlugin::update(CC3DXMLElement *_xmlData, bool _fullInitFlag){
automaton = potts->getAutomaton();
ASSERT_OR_THROW("CELL TYPE PLUGIN WAS NOT PROPERLY INITIALIZED YET. MAKE SURE THIS IS THE FIRST PLUGIN THAT YOU SET", automaton)
set<unsigned char> cellTypesSet;
//scanning Adhesion Molecule names
CC3DXMLElementList adhesionMoleculeNameXMLVec=_xmlData->getElements("AdhesionMolecule");
vector<string> adhesionMoleculeNameVec;
set<string> adhesionMoleculeNameSet;
moleculeNameIndexMap.clear();
for (int i = 0 ; i<adhesionMoleculeNameXMLVec.size(); ++i){
string moleculeName=adhesionMoleculeNameXMLVec[i]->getAttribute("Molecule");
if (! adhesionMoleculeNameSet.insert(moleculeName).second){
ASSERT_OR_THROW(string("Duplicate molecule Name=")+moleculeName+ " specified in AdhesionMolecule section ", false);
}
adhesionMoleculeNameVec.push_back(moleculeName);
moleculeNameIndexMap.insert(make_pair(moleculeName,i));
}
numberOfAdhesionMolecules=moleculeNameIndexMap.size();
if (!sim->getRestartEnabled()){
adhesionMoleculeDensityVecMedium=vector<float>(numberOfAdhesionMolecules,0.0);
}
cerr<<"numberOfAdhesionMolecules="<<numberOfAdhesionMolecules<<endl;
//scannning AdhesionMoleculeDensity section
CC3DXMLElementList adhesionMoleculeDensityXMLVec=_xmlData->getElements("AdhesionMoleculeDensity");
typeToAdhesionMoleculeDensityMap.clear();
std::map<int,std::vector<float> >::iterator mitr;
for (int i = 0 ; i<adhesionMoleculeDensityXMLVec.size(); ++i){
int typeId=automaton->getTypeId(adhesionMoleculeDensityXMLVec[i]->getAttribute("CellType"));
cerr<<"typeId="<<typeId<<endl;
mitr=typeToAdhesionMoleculeDensityMap.find(typeId);
if (mitr==typeToAdhesionMoleculeDensityMap.end()){
typeToAdhesionMoleculeDensityMap.insert(make_pair(typeId,vector<float>(numberOfAdhesionMolecules,0.0)));
cerr<<"typeToAdhesionMoleculeDensityMap[typeId].size()="<<typeToAdhesionMoleculeDensityMap[typeId].size()<<endl;
}
string moleculeName=adhesionMoleculeDensityXMLVec[i]->getAttribute("Molecule");
cerr<<"moleculeName="<<moleculeName<<endl;
if(moleculeNameIndexMap.find(moleculeName)==moleculeNameIndexMap.end()){
ASSERT_OR_THROW(string("Molecule Name=")+moleculeName+" was not declared in the AdhesionMolecule section",false);
}
cerr<<"moleculeNameIndexMap[moleculeName]="<<moleculeNameIndexMap[moleculeName]<<endl;
cerr<<"adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble(Density)="<<adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble("Density")<<endl;
cerr<<"typeToAdhesionMoleculeDensityMap[typeId].size()="<<typeToAdhesionMoleculeDensityMap[typeId].size()<<endl;
typeToAdhesionMoleculeDensityMap[typeId][moleculeNameIndexMap[moleculeName]]=adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble("Density");
cerr<<"AFTER ASSIGNING DENSITY"<<endl;
}
//scanning BindingFormula section
CC3DXMLElement * bindingFormulaXMLElem=_xmlData->getFirstElement("BindingFormula");
formulaString=bindingFormulaXMLElem->getFirstElement("Formula")->getText(); //formula string
CC3DXMLElement * variablesSectionXMLElem=bindingFormulaXMLElem->getFirstElement("Variables");
//cerr<<"formulaString="<<formulaString<<endl;
//here we can add options depending on variables input - for now it is har-coded to accept only matrix of bindingParameters
bindingParameters.clear() ; //have to clear binding parameters
CC3DXMLElement * adhesionInteractionMatrixXMLElem = variablesSectionXMLElem->getFirstElement("AdhesionInteractionMatrix");
CC3DXMLElementList bindingParameterXMLVec = adhesionInteractionMatrixXMLElem->getElements("BindingParameter");
for (int i = 0 ; i<bindingParameterXMLVec.size(); ++i){
setBindingParameter(bindingParameterXMLVec[i]->getAttribute("Molecule1") , bindingParameterXMLVec[i]->getAttribute("Molecule2"), bindingParameterXMLVec[i]->getDouble());
}
//vectorized variables for convenient parallel access
unsigned int maxNumberOfWorkNodes=pUtils->getMaxNumberOfWorkNodesPotts();
molecule1Vec.assign(maxNumberOfWorkNodes,0.0);
molecule2Vec.assign(maxNumberOfWorkNodes,0.0);
pVec.assign(maxNumberOfWorkNodes,mu::Parser());
for (int i = 0 ; i< maxNumberOfWorkNodes ; ++i){
pVec[i].DefineVar("Molecule1",&molecule1Vec[i]);
pVec[i].DefineVar("Molecule2",&molecule2Vec[i]);
pVec[i].SetExpr(formulaString);
}
// p=mu::Parser(); //using new parser
// //setting up muParser
// p.DefineVar("Molecule1", &molecule1);
// p.DefineVar("Molecule2", &molecule2);
// p.SetExpr(formulaString);
//scanning NeighborOrder or Depth
//Here I initialize max neighbor index for direct acces to the list of neighbors
boundaryStrategy=BoundaryStrategy::getInstance();
maxNeighborIndex=0;
if(_xmlData->getFirstElement("Depth")){
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromDepth(_xmlData->getFirstElement("Depth")->getDouble());
//cerr<<"got here will do depth"<<endl;
}else{
//cerr<<"got here will do neighbor order"<<endl;
if(_xmlData->getFirstElement("NeighborOrder")){
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(_xmlData->getFirstElement("NeighborOrder")->getUInt());
cerr<<"maxNeighborIndex="<<maxNeighborIndex<<endl;
}else{
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
}
}
cerr<<"sizeBindingArray="<<moleculeNameIndexMap.size()<<endl;
//initializing binding parameter array
int sizeBindingArray=moleculeNameIndexMap.size();
int indexBindingArray ;
bindingParameterArray.clear();
bindingParameterArray.assign(sizeBindingArray,vector<double>(sizeBindingArray,0.0));
bindingParameters_t::iterator bmitr;
for(int i = 0 ; i < sizeBindingArray ; ++i)
for(int j = 0 ; j < sizeBindingArray ; ++j){
indexBindingArray= getIndex(i,j);
bmitr=bindingParameters.find(indexBindingArray);
if(bmitr!=bindingParameters.end()){
bindingParameterArray[i][j] = bmitr->second;
}
}
for(int i = 0 ; i < sizeBindingArray ; ++i)
for(int j = 0 ; j < sizeBindingArray ; ++j){
cerr<<"bindingParameterArray["<<i<<"]["<<j<<"]="<<bindingParameterArray[i][j]<<endl;
}
}
void FiPySolver::update(CC3DXMLElement *_xmlData, bool _fullInitFlag){
//notice, only basic steering is enabled for PDE solvers - changing diffusion constants, do -not-diffuse to types etc...
// Coupling coefficients cannot be changed and also there is no way to allocate extra fields while simulation is running
if(potts->getDisplayUnitsFlag()){
Unit diffConstUnit=powerUnit(potts->getLengthUnit(),2)/potts->getTimeUnit();
Unit decayConstUnit=1/potts->getTimeUnit();
Unit secretionConstUnit=1/potts->getTimeUnit();
CC3DXMLElement * unitsElem=_xmlData->getFirstElement("Units");
if (!unitsElem){ //add Units element
unitsElem=_xmlData->attachElement("Units");
}
if(unitsElem->getFirstElement("DiffusionConstantUnit")){
unitsElem->getFirstElement("DiffusionConstantUnit")->updateElementValue(diffConstUnit.toString());
}else{
unitsElem->attachElement("DiffusionConstantUnit",diffConstUnit.toString());
}
if(unitsElem->getFirstElement("DecayConstantUnit")){
unitsElem->getFirstElement("DecayConstantUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("DecayConstantUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("DeltaXUnit")){
unitsElem->getFirstElement("DeltaXUnit")->updateElementValue(potts->getLengthUnit().toString());
}else{
unitsElem->attachElement("DeltaXUnit",potts->getLengthUnit().toString());
}
if(unitsElem->getFirstElement("DeltaTUnit")){
unitsElem->getFirstElement("DeltaTUnit")->updateElementValue(potts->getTimeUnit().toString());
}else{
unitsElem->attachElement("DeltaTUnit",potts->getTimeUnit().toString());
}
if(unitsElem->getFirstElement("CouplingCoefficientUnit")){
unitsElem->getFirstElement("CouplingCoefficientUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("CouplingCoefficientUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("SecretionUnit")){
unitsElem->getFirstElement("SecretionUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("SecretionUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("SecretionOnContactUnit")){
unitsElem->getFirstElement("SecretionOnContactUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("SecretionOnContactUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("ConstantConcentrationUnit")){
unitsElem->getFirstElement("ConstantConcentrationUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("ConstantConcentrationUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("DecayConstantUnit")){
unitsElem->getFirstElement("DecayConstantUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("DecayConstantUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("DeltaXUnit")){
unitsElem->getFirstElement("DeltaXUnit")->updateElementValue(potts->getLengthUnit().toString());
}else{
unitsElem->attachElement("DeltaXUnit",potts->getLengthUnit().toString());
}
if(unitsElem->getFirstElement("DeltaTUnit")){
unitsElem->getFirstElement("DeltaTUnit")->updateElementValue(potts->getTimeUnit().toString());
}else{
unitsElem->attachElement("DeltaTUnit",potts->getTimeUnit().toString());
}
if(unitsElem->getFirstElement("CouplingCoefficientUnit")){
unitsElem->getFirstElement("CouplingCoefficientUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("CouplingCoefficientUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("UptakeUnit")){
unitsElem->getFirstElement("UptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("UptakeUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("RelativeUptakeUnit")){
unitsElem->getFirstElement("RelativeUptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("RelativeUptakeUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("MaxUptakeUnit")){
unitsElem->getFirstElement("MaxUptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("MaxUptakeUnit",decayConstUnit.toString());
}
}
diffSecrFieldTuppleVec.clear();
bcSpecVec.clear();
bcSpecFlagVec.clear();
CC3DXMLElementList diffFieldXMLVec=_xmlData->getElements("DiffusionField");
for(unsigned int i = 0 ; i < diffFieldXMLVec.size() ; ++i ){
diffSecrFieldTuppleVec.push_back(DiffusionSecretionFiPyFieldTupple());
DiffusionData & diffData=diffSecrFieldTuppleVec[diffSecrFieldTuppleVec.size()-1].diffData;
SecretionData & secrData=diffSecrFieldTuppleVec[diffSecrFieldTuppleVec.size()-1].secrData;
if(diffFieldXMLVec[i]->findElement("DiffusionData"))
diffData.update(diffFieldXMLVec[i]->getFirstElement("DiffusionData"));
if(diffFieldXMLVec[i]->findElement("SecretionData"))
secrData.update(diffFieldXMLVec[i]->getFirstElement("SecretionData"));
if(diffFieldXMLVec[i]->findElement("ReadFromFile"))
readFromFileFlag=true;
//boundary conditions parsing
bcSpecFlagVec.push_back(false);
bcSpecVec.push_back(BoundaryConditionSpecifier());
if (diffFieldXMLVec[i]->findElement("BoundaryConditions")){
bcSpecFlagVec[bcSpecFlagVec.size()-1]=true;
BoundaryConditionSpecifier & bcSpec = bcSpecVec[bcSpecVec.size()-1];
CC3DXMLElement * bcSpecElem = diffFieldXMLVec[i]->getFirstElement("BoundaryConditions");
CC3DXMLElementList planeVec = bcSpecElem->getElements("Plane");
for(unsigned int ip = 0 ; ip < planeVec.size() ; ++ip ){
ASSERT_OR_THROW ("Boundary Condition specification Plane element is missing Axis attribute",planeVec[ip]->findAttribute("Axis"));
string axisName=planeVec[ip]->getAttribute("Axis");
int index=0;
if (axisName=="x" ||axisName=="X" ){
index=0;
}
if (axisName=="y" ||axisName=="Y" ){
index=2;
}
if (axisName=="z" ||axisName=="Z" ){
index=4;
}
if (planeVec[ip]->findElement("Periodic")){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::PERIODIC;
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::PERIODIC;
}else {
//if (planeVec[ip]->findElement("ConstantValue")){
CC3DXMLElementList cvVec=planeVec[ip]->getElements("ConstantValue");
CC3DXMLElementList cdVec=planeVec[ip]->getElements("ConstantDerivative");
for (unsigned int v = 0 ; v < cvVec.size() ; ++v ){
string planePos=cvVec[v]->getAttribute("PlanePosition");
double value=cvVec[v]->getAttributeAsDouble("Value");
changeToLower(planePos);
if (planePos=="min"){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::CONSTANT_VALUE;
bcSpec.values[index]=value;
}else if (planePos=="max"){
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::CONSTANT_VALUE;
bcSpec.values[index+1]=value;
}else{
ASSERT_OR_THROW("PlanePosition attribute has to be either max on min",false);
}
}
if (cvVec.size()<=1){
for (unsigned int d = 0 ; d < cdVec.size() ; ++d ){
string planePos=cdVec[d]->getAttribute("PlanePosition");
double value=cdVec[d]->getAttributeAsDouble("Value");
changeToLower(planePos);
if (planePos=="min"){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::CONSTANT_DERIVATIVE;
bcSpec.values[index]=value;
}else if (planePos=="max"){
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::CONSTANT_DERIVATIVE;
bcSpec.values[index+1]=value;
}else{
ASSERT_OR_THROW("PlanePosition attribute has to be either max on min",false);
}
}
}
}
}
}
}
if(_xmlData->findElement("Serialize")){
serializeFlag=true;
if(_xmlData->getFirstElement("Serialize")->findAttribute("Frequency")){
serializeFrequency=_xmlData->getFirstElement("Serialize")->getAttributeAsUInt("Frequency");
}
cerr<<"serialize Flag="<<serializeFlag<<endl;
}
if(_xmlData->findElement("ReadFromFile")){
readFromFileFlag=true;
cerr<<"readFromFileFlag="<<readFromFileFlag<<endl;
}
for(int i = 0 ; i < diffSecrFieldTuppleVec.size() ; ++i){
diffSecrFieldTuppleVec[i].diffData.setAutomaton(automaton);
diffSecrFieldTuppleVec[i].secrData.setAutomaton(automaton);
diffSecrFieldTuppleVec[i].diffData.initialize(automaton);
diffSecrFieldTuppleVec[i].secrData.initialize(automaton);
}
///assigning member method ptrs to the vector
for(unsigned int i = 0 ; i < diffSecrFieldTuppleVec.size() ; ++i){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec.assign(diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.size(),0);
unsigned int j=0;
for(set<string>::iterator sitr=diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.begin() ; sitr != diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.end() ; ++sitr){
if((*sitr)=="Secretion"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteSingleField;
++j;
}
else if((*sitr)=="SecretionOnContact"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteOnContactSingleField;
++j;
}
else if((*sitr)=="ConstantConcentration"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteConstantConcentrationSingleField;
++j;
}
}
}
}