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RootSystem inital angle of base roots fixed
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Daniel Leitner committed Mar 16, 2023
1 parent f49787c commit 3078b41
Showing 1 changed file with 36 additions and 40 deletions.
76 changes: 36 additions & 40 deletions src/structural/Organ.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ std::shared_ptr<Organ> Organ::copy(std::shared_ptr<Organism> p)
/**
* @return the organs length from start node up to the node with index @param i.
*/
double Organ::getLength(int i) const
double Organ::getLength(int i) const
{
double l = 0.; // length until node i
if(hasRelCoord()){//is currently using relative coordinates?
Expand All @@ -91,7 +91,7 @@ double Organ::getLength(int i) const
}


/* @param realized FALSE: get theoretical organ length, INdependent from spatial resolution (dx() and dxMin())
/* @param realized FALSE: get theoretical organ length, INdependent from spatial resolution (dx() and dxMin())
* TRUE: get realized organ length, dependent from spatial resolution (dx() and dxMin())
* DEFAULT = TRUE
* @return The chosen type of organ length (realized or theoretical).
Expand Down Expand Up @@ -179,24 +179,24 @@ void Organ::addChild(std::shared_ptr<Organ> c)
*/
void Organ::addNode(Vector3d n, int id, double t, size_t index, bool shift)
{
if(!shift){//node added at the end of organ
if(!shift){//node added at the end of organ
nodes.push_back(n); // node
nodeIds.push_back(id); //unique id
nodeCTs.push_back(t); // exact creation time
}
else{//could be quite slow to insert, but we won t have that many (node-)tillers (?)
else{//could be quite slow to insert, but we won t have that many (node-)tillers (?)
nodes.insert(nodes.begin() + index, n);//add the node at index
//add a global index.
//add a global index.
//no need for the nodes to keep the same global index and makes the update of the nodes position for MappedPlant object more simple)
nodeIds.push_back(id);
nodeIds.push_back(id);
nodeCTs.insert(nodeCTs.begin() + index-1, t);
for(auto kid : children){//if carries children after the added node, update their "parent node index"
if(kid->parentNI >= index-1){
kid->moveOrigin(kid->parentNI + 1);
}

}

}
}

Expand All @@ -209,7 +209,7 @@ void Organ::moveOrigin(int idx)
{
this->parentNI = idx;
nodeIds.at(0) = getParent()->getNodeId(idx);

}

/**
Expand Down Expand Up @@ -295,7 +295,7 @@ void Organ::getOrgans(int ot, std::vector<std::shared_ptr<Organ>>& v, bool all)
//might have age <0 and node.size()> 1 when adding organ manuelly @see test_organ.py
bool forCarbon_limitedGrowth = (all && (this->getAge()>0));//when ask for "all" organs which have age > 0 even if nodes.size() == 1
bool notSeed = ( this->organType() != Organism::ot_seed);

if ((this->nodes.size()>1 || forCarbon_limitedGrowth)&& notBulb &&notSeed) {
if ((ot<0) || (ot==this->organType())) {
v.push_back(shared_from_this());
Expand Down Expand Up @@ -491,20 +491,20 @@ std::string Organ::toString() const
/**
* convert the nodes' positions from relative to absolute coordinates
*/
void Organ::rel2abs()
void Organ::rel2abs()
{

nodes[0] = getOrigin(); //recompute postiion of the first node

for(size_t i=1; i<nodes.size(); i++)
{
double sdx = nodes[i].length();
Vector3d newdx = getIncrement(nodes[i-1], sdx, i-1); //add tropism
nodes[i] = nodes[i-1].plus(newdx); //replace relative by absolute position
nodes[i] = nodes[i-1].plus(newdx); //replace relative by absolute position
}
moved = true; //update position of existing nodes in MappedSegments
//if carry children, update their pos

for(size_t i=0; i<children.size(); i++){
//if((children[i])->organType()!=Organism::ot_root){
(children[i])->rel2abs();
Expand All @@ -524,42 +524,38 @@ void Organ::abs2rel()
}
nodes[0] = Vector3d(0.,0.,0.);
moved = true; //update position of existing nodes in MappedSegments

for(size_t i=0; i<children.size(); i++){
//if((children[i])->organType()!=Organism::ot_root){
(children[i])->abs2rel();
//}
}//if carry children, update their pos

}

/**
* @return Current absolute heading of the organ at node n, based on initial heading, or segment before
*/
Vector3d Organ::getiHeading0() const
{

if(!getParent())
{
std::cout<<"Organ::getiHeading0(): for organ "<<getId()<<", type "<<organType()<<", no parent pointer found "<<std::flush;
std::cout<<"use own partial initial heading instead"<<std::endl;
return this->partialIHeading;
}
{
if (!getParent()) { // in case of class RootSystem base roots (tap, basal, shootborne) have no parent
Vector3d vparentHeading = Vector3d(0, 0, -1);
Matrix3d parentHeading = Matrix3d::ons(vparentHeading);
return parentHeading.times(this->partialIHeading);
}
Matrix3d parentHeading;
bool isBaseOrgan = (getParent()->organType()==Organism::ot_seed);
bool isShootBornRoot = ((getParent()->organType()==Organism::ot_stem)&&(organType()==Organism::ot_root));
if (isBaseOrgan||isShootBornRoot) { // from seed?
if (organType()==Organism::ot_root) {
if (organType()==Organism::ot_root) {
parentHeading = Matrix3d(Vector3d(0, 0, -1), Vector3d(0, -1, 0), Vector3d(-1, 0, 0));
}else{
parentHeading = Matrix3d(Vector3d(0, 0, 1), Vector3d(0, 1, 0), Vector3d(1, 0, 0));
}
}else
{
} else {
Vector3d vparentHeading = getParent()->heading(parentNI);
parentHeading = Matrix3d::ons(vparentHeading);
}

auto heading = parentHeading.column(0);
Vector3d new_heading = Matrix3d::ons(heading).times(this->partialIHeading);
return Matrix3d::ons(new_heading).column(0);
Expand All @@ -569,7 +565,7 @@ Vector3d Organ::getiHeading0() const
*/
Vector3d Organ::heading(int n ) const
{

if(n<0){n=nodes.size()-1 ;}
if ((nodes.size()>1)&&(n>0)) {
n = std::min(int(nodes.size()),n);
Expand Down Expand Up @@ -604,7 +600,7 @@ double Organ::orgVolume(double length_, bool realized) const
*/
Vector3d Organ::getIncrement(const Vector3d& p, double sdx, int n)
{

Vector3d h = heading(n);
Matrix3d ons = Matrix3d::ons(h);
Vector2d ab = getOrganRandomParameter()->f_tf->getHeading(p, ons, dx(), shared_from_this(), n+1);
Expand Down Expand Up @@ -656,22 +652,22 @@ void Organ::createSegments(double l, double dt, bool verbose, int PhytoIdx)
double shiftl = 0; // length produced by shift
int nn = nodes.size();
bool stemElongation = (PhytoIdx >= 0);//if we are doing internodal growth, PhytoIdx >= 0.
if( stemElongation){
if( stemElongation){
auto o = children.at(PhytoIdx);
nn = o->parentNI +1; //shift the last node of the phytomere n° PhytoIdx instead of the last node of the organ
}
}
if (firstCall||stemElongation) { // first call of createSegments (in Organ::simulate)
if(!stemElongation){firstCall = false;}
//don t move first node
bool notFirstNode = (nn>1);
bool notChildBaseNode = (children.empty() || (nn-1 != std::static_pointer_cast<Organ>(children.back())->parentNI));
// don't move a child base node unless you have phytomere expansion
if (notFirstNode && (notChildBaseNode || stemElongation) ) {
// don't move a child base node unless you have phytomere expansion
if (notFirstNode && (notChildBaseNode || stemElongation) ) {


Vector3d h;
Vector3d n2 = nodes.at(nn-2);

if(hasRelCoord())
{
h = nodes.at(nn-1);
Expand All @@ -684,7 +680,7 @@ void Organ::createSegments(double l, double dt, bool verbose, int PhytoIdx)
shiftl = std::min(dx()-olddx, l);
double sdx = olddx + shiftl; // length of new segment
// Vector3d newdxv = getIncrement(n2, sdx);

if(hasRelCoord())
{
nodes.at(nn-1) = Vector3d(sdx,0.,0.);//h.times(sdx);
Expand Down Expand Up @@ -714,7 +710,7 @@ void Organ::createSegments(double l, double dt, bool verbose, int PhytoIdx)
double sdx; // segment length (<=dx)
if (i<n) { // normal case
sdx = dx();
} else
} else
{ // last segment
sdx = l-n*dx();
if (sdx<dxMin()*(1-1e-10)) { //plant.lock()->getMinDx()) { // quit if l is too small
Expand Down

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