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feature.cc
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feature.cc
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//#include "network.h"
#include <cmath>
#include "feature.h"
#include "general.h"
using namespace std;
int FEATURE::createFeatures(ATOM_NETWORK *uc,VORONOI_NETWORK *origVNet, DIJKSTRA_NETWORK *origDNet, std::fstream &output, int initIndex,char *name){
nfeatures = 0;
features = std::vector<int> ();
feature_node_mapping = std::vector<int> ();
segmentChannel(uc);
if(nfeatures == 0){
std::cerr << "Error occurred during channel segmentation. No features were found." << "\n"
<< "Exiting..." << "\n";
exit(1);
}
std::vector< std::vector<int> > nodesForFeatures = std::vector < std::vector<int> > (nfeatures, std::vector<int> ());
std::vector<FEATURE> featChannels = std::vector<FEATURE> ();
for(unsigned int i = 0; i < feature_node_mapping.size(); i++){
nodesForFeatures[feature_node_mapping[i]].push_back(reverseIDMappings.find(i)->second);
}
int zeroVecs [3][3] = {{0, 0, 0},{ 0, 0, 0}, {0, 0, 0}};
for(int i = 0; i < nfeatures; i++){
DIJKSTRA_NETWORK featNet;
DIJKSTRA_NETWORK::filterDnetEdges(nodesForFeatures[i], origVNet, &featNet);
std::vector<bool> infoStorage; std::vector<CHANNEL> channels;
findChannels(&featNet, &infoStorage, &channels);
int dim;
if(channels.size() != 0){
dim = channels[0].dimensionality;
featChannels.push_back(FEATURE(nodesForFeatures[i], origDNet, dim, channels[0].basis));
}
else{
dim = 0;
featChannels.push_back(FEATURE(nodesForFeatures[i], origDNet, 0, zeroVecs));
}
featChannels[i].writeToVMD("feature", initIndex + i, output);
std::cout << "@@ " << name << " Feature " << initIndex + i << " volume = " << featChannels[i].calculateVolume() << "\n";
featChannels[i].calculateSurfaceArea(uc,&nodes,&feature_node_mapping,i,name,initIndex + i);
}
return nfeatures;
}
int FEATURE::createSegments(ATOM_NETWORK *uc,VORONOI_NETWORK *origVNet, DIJKSTRA_NETWORK *origDNet, std::fstream &output, int initIndex){
nsegments = 0;
segments = std::vector<int> ();
segmentChannel(uc);
if(nsegments == 0){
std::cerr << "Error occurred during channel segmentation. No segments were found." << "\n"
<< "Exiting..." << "\n";
exit(1);
}
std::vector< std::vector<int> > nodesForSegments = std::vector < std::vector<int> > (nsegments, std::vector<int> ());
std::vector<CHANNEL> segChannels = std::vector<CHANNEL> ();
for(unsigned int i = 0; i < segments.size(); i++){
nodesForSegments[segments[i]].push_back(reverseIDMappings.find(i)->second);
}
int zeroVecs [3][3] = {{0, 0, 0},{ 0, 0, 0}, {0, 0, 0}};
for(int i = 0; i < nsegments; i++){
DIJKSTRA_NETWORK segNet;
DIJKSTRA_NETWORK::filterDnetEdges(nodesForSegments[i], origVNet, &segNet);
std::vector<bool> infoStorage; std::vector<CHANNEL> channels;
findChannels(&segNet, &infoStorage, &channels);
int dim;
if(channels.size() != 0){
dim = channels[0].dimensionality;
segChannels.push_back(CHANNEL(nodesForSegments[i], origDNet, dim, channels[0].basis));
}
else{
dim = 0;
segChannels.push_back(CHANNEL(nodesForSegments[i], origDNet, 0, zeroVecs));
}
segChannels[i].writeToVMD("segment", initIndex + i, output);
}
return nsegments;
}
void FEATURE::segmentChannel(ATOM_NETWORK *uc){
int i;
cout << "Current channel has " << nodes.size() << " nodes" << "\n";
for(i=0;i<(int)nodes.size();i++)
{
segments.push_back(-1);
};
nsegments=0;
while(segment_findMaxNode()>-1)
{
// segment_growSegment_start(uc,segment_findMaxNode());
segment_distBasedSegmentation(uc);
};
cout << "Initial number of segments (minima) " << nsegments << "\n";
/*
fstream output1;
output1.open("segments.zvis",fstream::out);
segment_saveVis(output1);
output1.close();
*/
//segment_identify_connections(); // analyzes connectivity of each segment to find segment's 'faces' - connection between segments
//merge_segments(); // analyze segments and merge if neccesary
//merge_nothing(); // this function copies segments into features
merge_singlenode_segments();
//calculateVolumeForAllFeatures(); // calculate volume of each segment
/* Print results */
cout << "\n" << "Segment info (ID - r):"<<"\n";
for(i=0;i<(int)segment_max_r.size();i++)
{
cout << i<< " " << segment_max_r[i] << "\n";
};
cout << "\n" << "Segment connection info (from to radii merge_stat):"<<"\n";
/*
for(i=0;i<(int)segment_conn.size();i++)
{
cout << segment_conn.at(i).from_seg << " " << segment_conn.at(i).to_seg << " " <<segment_conn.at(i).max_radius << " " << segment_conn.at(i).merged << "\n";
};
cout << "\n" << "Total number of segment connecting edges : "<< segment_conn_fulllist.size() <<"\n";
cout << "\n" << "Segment info vs features (segment ID - feature ID):"<<"\n";
for(i=0;i<nsegments;i++)
{
cout << i<< " " << segment_merge_list[i] << "\n";
};
*/
cout << "\n" << "Features info (ID - r - volume):"<<"\n";
for(i=0;i<(int)feature_max_r.size();i++)
{
// cout << i<< " " << feature_max_r[i] << " " << feature_volume[i] << "\n";
cout << i<< " " << feature_max_r[i] << "\n";
};
/*
cout << "\n" << "Features connection info (from to radii ):"<<"\n";
for(i=0;i<(int)feature_conn.size();i++)
{
cout << feature_conn.at(i).from_seg << " " << feature_conn.at(i).to_seg << " " <<feature_conn.at(i).max_radius << "\n";
};
*/
} // end of segmentChannel
/* find node with largest max_radius that is not assigned to any segment yet */
int FEATURE::segment_findMaxNode(){
int i;
int nd=-1;
double min=0;
for(i=0;i<(int)nodes.size();i++)
{
if(segments[i]==-1&&nodes.at(i).max_radius>min)
{
nd=i;
min=nodes.at(i).max_radius;
};
};
return nd;
} // end of segment_findMaxNode()
/* NEW segmentation rountine based on distance criterion */
/* this function needs to have a pointer to unit cell to run distance calcluations
* please call setUnitCellPointer() prior to this function */
void FEATURE::segment_distBasedSegmentation(ATOM_NETWORK *uc)
{
UnitCellPtr=uc;
int cur_maxId; // id of current max node
double cur_r;
int i;
double scale_factor=1.1;
if(UnitCellPtr==NULL) {cout<< "no distance pointer set";abort();};
do{
/* clear variable */
segments.clear();
segment_max_r.clear();
for(i=0;i<(int)nodes.size();i++)
{
segments.push_back(-1);
};
nsegments=0;
/* adjust scale factor */
scale_factor-=0.05;
if(scale_factor==0.5)
{
cerr << "Segmentation failed. Aborting" << "\n";
abort();
};
/* perform segmentation */
while(segment_findMaxNode()>-1)
{
cur_maxId=segment_findMaxNode();
cur_r=nodes.at(cur_maxId).max_radius;
segments[cur_maxId]=nsegments; // assign new segment number to a nw segment
segment_max_r.push_back(nodes.at(cur_maxId).max_radius); //store maximum r in a segment
// now assign all nodes with close distance to the current node
for(i=0;i<(int)nodes.size();i++)
{
if(UnitCellPtr->calcDistanceXYZ(nodes.at(cur_maxId).x,nodes.at(cur_maxId).y,nodes.at(cur_maxId).z,nodes.at(i).x,nodes.at(i).y,nodes.at(i).z)<scale_factor*cur_r)
{
segments[i]=nsegments;
};
};
nsegments++;
};
}while(validateSegmentation()==0);
//}while(scale_factor>0.5);
cout << " no segments after segment_distBasedSegmentation: " << nsegments << "\n";
} // end of segment_distBasedSegmentation()
/* this function validates current segmentation
* valid segments are build from interconnected nodes only */
int FEATURE::validateSegmentation(){
int i;
int valid=1;
for(i=0;i<nsegments;i++)
{
if(validateSegment(i)==0)
{
valid=0;
break;
};
}
return valid;
} // end of CHANNEL::validateSegmentation()
int FEATURE::validateSegment(int segid){
int i;
int id,conn_to;
int nvisited=0;
int valid=1;
vector <int> nodelist;
vector <int> visited;
vector <int> heap;
/* count nodes and init heap */
for(i=0;i<(int)nodes.size();i++)
{
if(segments[i]==segid)
{
nodelist.push_back(i);
// visited.push_back(-1);
};
visited.push_back(-1);
};
heap.push_back(nodelist[0]);
visited[nodelist[0]]=1;
nvisited++;
/* investigate connections by adding them to heap */
while(nvisited<(int)nodelist.size())
{
if(heap.size()==0)
{
valid=0;
break;
};
id=heap.back();heap.pop_back();
/* current node is id, investigate its connections, add to heap */
for(i=0;i<(int)nodes.at(id).connections.size();i++)
{
conn_to=nodes.at(id).connections.at(i).to;
if(segments[conn_to]==segid&&visited[conn_to]==-1) // if connected to other node within same segment and not visited, add to heap
{
heap.push_back(conn_to);
nvisited++;
visited[conn_to]=1;
};
};
};
return valid;
}// end of CHANNEL::validateSegment()
/* grow and assign segments starting from a node that has a largest radii */
void FEATURE::segment_growSegment_start(ATOM_NETWORK *uc, int nodeid){
segments[nodeid]=nsegments; // assign new segment number to a nw segment
segment_max_r.push_back(nodes.at(nodeid).max_radius); //store maximum r in a segment
segment_growSegment_cont(uc,nodeid,nodeid);
nsegments++;
}// end of segment_growSegment()
/*
class CONN{
public:
int from, to; // IDs of nodes involved in connectioon
double length; // Length of edge
double max_radius; // Radius of largest spherical probe that can travel along edge
DELTA_POS deltaPos; // Change in unit cell
*/
/* initnodeid is id of a nod that was a seed for this segment */
void FEATURE::segment_growSegment_cont(ATOM_NETWORK *uc,int initnodeid,int nodeid){
int i,j;
int conn_to;
int update_conn_flag; // segment connection updated or new
double r;
SEGCONN segcon;
/* this if makes sure that segment is grown only within the sphere marked by the shere located on the seed node */
if(uc->calcDistanceXYZ(nodes.at(initnodeid).x,nodes.at(initnodeid).y,nodes.at(initnodeid).z,nodes.at(nodeid).x,nodes.at(nodeid).y,nodes.at(nodeid).z)<SPHERE_SCALE*nodes.at(initnodeid).max_radius)
{
segments[nodeid]=nsegments;
r=nodes.at(nodeid).max_radius;
for(i=0;i<(int)nodes.at(nodeid).connections.size();i++)
{
conn_to=nodes.at(nodeid).connections.at(i).to;
if(segments[conn_to]==-1) // investigate connection to nodes not yet assigned to any segments
{
// if(nodes.at(conn_to).max_radius<r&&(nodes.at(conn_to).max_radius/nodes.at(nodeid).connections.at(i).max_radius)<NODE_R_EDGE_R_RATIO)
{
segment_growSegment_cont(uc,initnodeid,conn_to);
}
;
//
/*
else if(nodes.at(conn_to).max_radius==r&&
((nodes.at(conn_to).max_radius/nodes.at(nodeid).connections.at(i).max_radius)<1.05||
(r/nodes.at(nodeid).connections.at(i).max_radius)<1.05)
)
{
segment_growSegment_cont(conn_to);
};
*/
} // end if(segments[conn_to]==-1)
else if(segments[conn_to]!=-1&&segments[conn_to]!=nsegments) // do if encounter segment-segment boundary
{
segcon.from=nodeid; // assign value to new segment connection
segcon.to=conn_to;
segcon.from_seg=nsegments;
segcon.to_seg=segments[conn_to];
segcon.max_radius=nodes.at(nodeid).connections.at(i).max_radius;
segcon.length=nodes.at(nodeid).connections.at(i).length;
segcon.merged=0;
segment_conn_fulllist.push_back(segcon); // store every intersegment connection
// this will be used to identify features
// connecting different segments
if(segment_conn.size()==0) {segment_conn.push_back(segcon);}
else
{
update_conn_flag=0;
for(j=0;j<(int)segment_conn.size();j++)
{
// if((segment_conn.at(j).from==nodeid&&segment_conn.at(j).to==conn_to)||(segment_conn.at(j).from==conn_to&&segment_conn.at(j).to==nodeid))
if((segment_conn.at(j).from_seg==nsegments&&segment_conn.at(j).to_seg==segments[conn_to])
||(segment_conn.at(j).from_seg==segments[conn_to]&&segment_conn.at(j).to==nsegments))
{
update_conn_flag=1;
if(segment_conn.at(j).max_radius<nodes.at(nodeid).connections.at(i).max_radius)
segment_conn.at(j).max_radius=nodes.at(nodeid).connections.at(i).max_radius;
};
/* else
{
segment_conn.push_back(segcon);
}; */
};
if(update_conn_flag==0) segment_conn.push_back(segcon);
}; // end else if(segment_conn.size()==0)
}; // end of else if
};
}; // closes if(calculatedistance)....
}
/* segment detection algorithm identified only one (major) connection to other segment (with an edge with the largest corresponding r)
* we need to post-process intersegment connecting nodes (ones with edges connecting to other segments) to obtain this info */
/* INFO
vector <SEGCONN> segment_conn_fulllist; // lists all connections (edges) briging different segments
// this will be used to determine topology of segments
vector < vector<int> > segment_faces_conn; // list of 'faces' for each segment, faces are clusters of edges that connect to another segment
vector < vector<double> > segment_faces_max_r; // max r for each segment's face
*/
void FEATURE::segment_identify_connections(){
int i,j,k;
int nfaces;
vector <int> segfaces;
vector <double> segfaces_max_r;
vector <int> nodes_in_segment; // list IDs of nodes assigned to segment
vector <int> face_nodes_in_segment; // list IDs of nodes assigned to segment and located on segment's "face", that is
// nodes with connections to other segments
vector <int> connected_segment_for_face_nodes_in_segment; // for each node, if it is a face node, store segment id to which it is connected
vector <SEGCONN> edges_from_segment; // list of edges that connect the current segment to other segments
SEGCONN segc; // inter-segment connection
vector <int> edges_in_face; // for each edge connecting to other semgent assign to a face, this svector stores face id for each edge
/* loop over all segments and identify all connections to other segments */
for(i=0;i<nsegments;i++)
{
nodes_in_segment.clear();
edges_from_segment.clear();
for(j=0;j<(int)nodes.size();j++)
{
if(segments[j]==i) nodes_in_segment.push_back(j);
};
face_nodes_in_segment.clear();
connected_segment_for_face_nodes_in_segment.clear();
face_nodes_in_segment.resize(nodes_in_segment.size(),0);
connected_segment_for_face_nodes_in_segment.resize(nodes_in_segment.size(),-1);
for(j=0;j<(int)nodes_in_segment.size();j++)
{
for(k=0;k<(int)nodes.at(nodes_in_segment[j]).connections.size();k++)
{
if(segments[nodes.at(nodes_in_segment[j]).connections.at(k).to]!=i)
{
face_nodes_in_segment[j]++;
connected_segment_for_face_nodes_in_segment[j]=segments[nodes.at(nodes_in_segment[j]).connections.at(k).to];
segc.from=nodes_in_segment[j]; // this is ID id in channel)
segc.to=nodes.at(nodes_in_segment[j]).connections.at(k).to; // node id in channel
segc.from_seg=i;
segc.to_seg=segments[nodes.at(nodes_in_segment[j]).connections.at(k).to];
segc.max_radius=nodes.at(nodes_in_segment[j]).connections.at(k).max_radius;
segc.deltaPos=nodes.at(nodes_in_segment[j]).connections.at(k).deltaPos;
edges_from_segment.push_back(segc);
};
};
};
// now connected_segment_for_face_nodes_in_segment has a list of segments each node in the current segment is conneed to (-1 if not)
// we need now to find "clusters" of these nodes that will correspond to different connections;
// edges_from_segment stores all edges going out from a segment to other segments
int nedges_tobe_assigned=edges_from_segment.size();
edges_in_face.clear();
edges_in_face.resize(nedges_tobe_assigned,-1);
nfaces=0;
int neigh_seg; // id of neighboring segment
// while(nedges_tobe_assigned>-1)
{
for(k=0;k<(int)edges_from_segment.size();k++)
{
if(edges_in_face[k]==-1) // find first edge not assigned to face
{
neigh_seg=edges_from_segment[k].to_seg;
edges_in_face[k]=nfaces;
nedges_tobe_assigned--;
segment_identify_connections_recurr(&nodes_in_segment,&edges_in_face,&nedges_tobe_assigned,nfaces,neigh_seg,&edges_from_segment,k);
nfaces++;
};
// nfaces++;
};
};
/*
cout << "Segment " << i <<": " << nodes_in_segment.size() << " nodes, " << edges_in_face.size() << " edges, " << nfaces << " faces, nodes-to-go " << nedges_tobe_assigned << "\n";
for(k=0;k<(int)edges_from_segment.size();k++)
{
cout << "Edge " << edges_from_segment[k].from << " " << edges_from_segment[k].to << " Segments:" << edges_from_segment[k].from_seg << " " << edges_from_segment[k].to_seg << " "; edges_from_segment[k].deltaPos.print();
};
*/
}; // end of loop over all segments
} // end of segment_identify_connections()
/* segment_identify_connections_recurr() identifed edges that belong to particular face
* */
void FEATURE::segment_identify_connections_recurr(vector <int> *nodeid,vector <int> *edgeinface,int *nodes_togo,int curr_face,int curr_neigh_seg, vector <SEGCONN> *edges,int curr_edge)
{
int i;
// check node at current edge, if not assigned to face, assign, consider its neighbors
for(i=0;i<(int)edges->size();i++)
{
if(i!=curr_edge&&edgeinface->at(i)==-1) // only consider if not yet assigned to face
{
//only consider pairs of edges that connect to the same segment
if(curr_neigh_seg==edges->at(i).to_seg&&edges->at(curr_edge).deltaPos.equals(edges->at(i).deltaPos))
{
// for two edges connecting to another segment, two edges are on the same face
// only if starting nodes of this face overlap
// int node1id=nodeid->at(edges->at(curr_edge).from);
// int node2id=nodeid->at(edges->at(i).from);
// int node1id=(edges->at(curr_edge).from);
// int node2id=(edges->at(i).from);
// if(nodes[node1id].max_radius+nodes[node2id].max_radius>calcEuclideanDistance(nodes[node1id].x,nodes[node1id].y,nodes[node1id].z,nodes[node2id].x,nodes[node2id].y,nodes[node2id].z))
{ // starting nodes of edges overlap, assign edge to the current face
edgeinface->at(i)=curr_face;
*nodes_togo=(*nodes_togo)--;
segment_identify_connections_recurr(nodeid,edgeinface,nodes_togo,curr_face,curr_neigh_seg,edges,i);
};
}; // end of if - overlapping nodes
}; // end of if - the same segments
}; // end of loop over all edges
} // end of segment_identify_connections_recurr()
/* updated a vector with stores segment id for each node in voronoi network */
/* if flag==1 that it does the same but for features not segments */
void FEATURE::update_node_segmentinfo(vector <int> *segid,int *curr_id,int flag)
{
int i;
//loop over all nodes in channel system and update voronoi network nodes
for(i=0;i<(int)nodes.size();i++)
{
if(flag==0)
{
segid->at(reverseIDMappings[i])=segments[i]+(*curr_id);
}else{
segid->at(reverseIDMappings[i])=feature_node_mapping[i]+(*curr_id);
};
};
if(flag==0) {
*curr_id+=nsegments;
}else{
*curr_id+=nfeatures;
};
} // end of update_node_segmentinfo()
/* This function does perform "fake" merging - all segments are being copied as features
* this is done to use all datastrucutres created for features to analyze segments
*/
void FEATURE::merge_nothing()
{
int i;
nfeatures=nsegments;
for(i=0;i<nsegments;i++)
{
features.push_back(i);
feature_max_r.push_back(segment_max_r[i]);
};
for(i=0;i<(int)nodes.size();i++)
{
feature_node_mapping.push_back(segments[i]);
};
cout << "After merging nothing, nfeatures = " << nfeatures << "\n";
}
/* This is new merging that just mergest single node semgents */
void FEATURE::merge_singlenode_segments()
{
int i,j,k;
int mink=0;
int count;
int nsingle=0;
double min=0;
vector <int> nodelist; // list of nodes in current segment
vector <int> tobemerged; // flag for nodes to be merged with other segments
vector <int> tobeextended; // flag for nodes that will be extended by toher nodes
vector <int> listofsinglenodesegments;
vector <int> tobemerged_segments;
tobemerged.resize(nodes.size(),-1);
tobeextended.resize(nodes.size(),0);
tobemerged_segments.resize(nsegments,0);
for(i=0;i<nsegments;i++)
{
nodelist.clear();
for(j=0;j<(int)nodes.size();j++)
{
if(segments[j]==i) nodelist.push_back(j);
};
if(nodelist.size()==1)
{
if(tobeextended[nodelist[0]]==0) // if the current node is not planned to be extended with other node, merge with others
{
tobemerged_segments[i]=1; // mark current segment as one to e merged
for(k=0;k<(int)nodes.at(nodelist[0]).connections.size();k++) // iterate over all connections to find closes node
{
if(k==0) {min=nodes.at(nodelist[0]).connections.at(k).length;mink=nodes.at(nodelist[0]).connections.at(k).to;};
if(k>0&&nodes.at(nodelist[0]).connections.at(k).length<min)
{
mink=nodes.at(nodelist[0]).connections.at(k).to;
min=nodes.at(nodelist[0]).connections.at(k).length;
};
};
// shortest connection leads to mink
if(tobemerged[mink]>-1) mink=tobemerged[mink]; // if node to which we are going to merge the current node
// also will be merged, merge into the other node
tobemerged[nodelist[0]]=mink; // curr node to be connected to mink
tobeextended[mink]=1;
tobeextended[nodelist[0]]=1; // "write protect" current node
nsingle++;
};
};
};
/* now merging */
nfeatures=nsegments-nsingle;
feature_node_mapping.resize(nodes.size(),-1);
count=0;
for(i=0;i<nsegments;i++)
{
if(tobemerged_segments[i]==0)
{
features.push_back(count);
feature_max_r.push_back(segment_max_r[i]);
for(j=0;j<(int)nodes.size();j++)
{
if(segments[j]==i) feature_node_mapping[j]=count;
};
count++;
};
};
count=0;
for(i=0;i<(int)nodes.size();i++)
{
if(tobemerged[i]>-1)
{
feature_node_mapping[i]=feature_node_mapping[tobemerged[i]];
count++;
};
};
for(i=0;i<(int)nodes.size();i++)
{
if(feature_node_mapping[i]==-1)
{
cout << "Feature construction failed. Abort."<< "\n";abort();
}
}
cout << "After merging single segments, nfeatures = " << nfeatures << "\n";
} // end of merge_singlenode_segments()
int FEATURE::number_nodes_in_segment(int segid)
{
int i;
int count=0;
for(i=0;i<(int)nodes.size();i++)
{
if(segments[i]==segid) count++;
};
return count;
}
/* merge_segments function goes over all identified segments and tries to merge some into larger blocks */
void FEATURE::merge_segments()
{
int i;
int current_segment;
SEGCONN featcon;
segment_merge_list.resize(nsegments,-1);
nfeatures=0;
/* loop over all segment connections and mark ones to be merge
* Merging criteria - restriction is smaller than % of average max radii for each segment
* */
for(i=0;i<(int)segment_conn.size();i++)
{
if(segment_conn.at(i).max_radius>FEAT_NODE_R_EDGE_R_RATIO*0.5*(segment_max_r[(segment_conn.at(i).from_seg)]+segment_max_r[(segment_conn.at(i).to_seg)]))
segment_conn.at(i).merged=1;
/* new function to merge short edges: */
// if(segment_conn.at(i).length<max(segment_max_r[(segment_conn.at(i).from_seg)],segment_max_r[(segment_conn.at(i).to_seg)]))
// segment_conn.at(i).merged=1;
};
/* after connections of to-be-merged segments have been identified, we build
* features, this includes 'flood fill' of segments */
do{
//find first segment not assigned to feature
current_segment=merge_findNotAssignedFragment();
//creature new feature
features.push_back(nfeatures); // number of segments after merging
//grow
// cout << current_segment << "\n";
merge_newSegmentGrow(current_segment);
//increase counter (number of segments)
nfeatures++;
}while(merge_findNotAssignedFragment()!=-1);
// update feature radii vector
feature_max_r.resize(nfeatures,0);
for(i=0;i<(int)segment_merge_list.size();i++)
{
if(feature_max_r[segment_merge_list[i]]<segment_max_r[i]) feature_max_r[segment_merge_list[i]]=segment_max_r[i];
};
// update feature information on all nodes in a channel
for(i=0;i<(int)nodes.size();i++)
{
feature_node_mapping.push_back(segment_merge_list[segments[i]]);
};
/* having identified features we need to convert segments connectivity info
* into feature connectivity */
for(i=0;i<(int)segment_conn.size();i++)
{
if(segment_conn.at(i).merged!=1)
{
featcon.from_seg=segment_merge_list[segment_conn.at(i).from_seg];
featcon.to_seg=segment_merge_list[segment_conn.at(i).to_seg];
featcon.max_radius=segment_conn.at(i).max_radius;
feature_conn.push_back(featcon);
};
};
} // end of CHANNEL:merge_segments()
void FEATURE::merge_newSegmentGrow(int segid)
{
int k;
int conn_to;
segment_merge_list[segid]=nfeatures;
for(k=0;k<(int)segment_conn.size();k++)
{
if((segment_conn.at(k).from_seg==segid||segment_conn.at(k).to_seg==segid)&&segment_conn.at(k).merged==1)
{
if(segment_conn.at(k).from_seg==segid)
{conn_to=segment_conn.at(k).to_seg;}
else {conn_to=segment_conn.at(k).from_seg;};
if(segment_merge_list.at(conn_to)==-1) merge_newSegmentGrow(conn_to);
}; // end if
}; //end for loop
}// end of merge_newSegmentGrow
int FEATURE::merge_findNotAssignedFragment()
{
int i;
int r=-1;
for(i=segment_merge_list.size()-1;i>-1;i--)
{
if(segment_merge_list.at(i)==-1) r=i;
};
return r;
} //end merge_findNotAssignedFragment()
void FEATURE::segment_saveVis(fstream &output)
{
int k;
if(!output.is_open()){
cerr << "Error: File stream needed to print segment information was not open." << "\n"
<< "Exiting ..." << "\n";
exit(1);
}
else{
for(k=0;k<nsegments;k++)
{
output << "\n" << "Segment " << k << " with max_r of " << segment_max_r.at(k) << "\n";
// Draw the components located in each unit cell
for(unsigned int i = 0; i < unitCells.size(); i++){
vector<int> nodeIDs = ucNodes.at(i);
DELTA_POS disp = unitCells.at(i);
// Iterate over all nodes in the unit cell
for(unsigned int j = 0; j < nodeIDs.size(); j++){
DIJKSTRA_NODE curNode = nodes.at(nodeIDs.at(j));
if(segments.at(nodeIDs.at(j))==k)
{
// Find node coordinates
double xCoord = curNode.x + v_a.x*disp.x + v_b.x*disp.y + v_c.x*disp.z;
double yCoord = curNode.y + v_a.y*disp.x + v_b.y*disp.y + v_c.y*disp.z;
double zCoord = curNode.z + v_a.z*disp.x + v_b.z*disp.y + v_c.z*disp.z;
// Command used to draw node
// output << "draw sphere {" << xCoord << " " << yCoord << " " << zCoord << "} radius " << curNode.max_radius << "\n";
output << "draw sphere {" << xCoord << " " << yCoord << " " << zCoord << "} radius " << 0.1 << "\n";
};//printing segment block
} // ends for loop
}
}
}
}
/** Calcluate volume of channel/segment/feature
* It uses reconstructed feature, puts it in a box
* and performs MC integration */
double FEATURE::calculateVolume(){
long int i,j,counter=0;
double volume;
XYZ max,min;
XYZ box;
XYZ pt;
srand(randSeed2);
SPHERE sph;
vector <SPHERE> object; // a vector of spheres that define object (segemnt/feature/channel)
// Draw the components located in each unit cell
for(unsigned int i = 0; i < unitCells.size(); i++){
vector<int> nodeIDs = ucNodes.at(i);
DELTA_POS disp = unitCells.at(i);
// Iterate over all nodes in the unit cell
for(unsigned int j = 0; j < nodeIDs.size(); j++){
DIJKSTRA_NODE curNode = nodes.at(nodeIDs.at(j));
// Find node coordinates
if(dimensionality<1)
{ // if feature is not a channel, use reconstrcted feature
sph.x = curNode.x + v_a.x*disp.x + v_b.x*disp.y + v_c.x*disp.z;
sph.y = curNode.y + v_a.y*disp.x + v_b.y*disp.y + v_c.y*disp.z;
sph.z = curNode.z + v_a.z*disp.x + v_b.z*disp.y + v_c.z*disp.z;
} else {
sph.x = nodes.at(nodeIDs.at(j)).x;sph.y = nodes.at(nodeIDs.at(j)).y;sph.z = nodes.at(nodeIDs.at(j)).z;
// cout << "draw sphere { " << sph.x << " " << sph.y << " " << sph.z << " } radius 0.1 " << "\n";
};
sph.r = SPHERE_SCALE*curNode.max_radius;
object.push_back(sph);
if(object.size()==1)
{ // first sphere added
min.x=sph.x-sph.r;max.x=sph.x+sph.r;
min.y=sph.y-sph.r;max.y=sph.y+sph.r;
min.z=sph.z-sph.r;max.z=sph.z+sph.r;
}else
{
if(min.x>(sph.x-sph.r)) min.x=sph.x-sph.r;
if(max.x<(sph.x+sph.r)) max.x=sph.x+sph.r;
if(min.y>(sph.y-sph.r)) min.y=sph.y-sph.r;
if(max.y<(sph.y+sph.r)) max.y=sph.y+sph.r;
if(min.z>(sph.z-sph.r)) min.z=sph.z-sph.r;
if(max.z<(sph.z+sph.r)) max.z=sph.z+sph.r;
};
}
} // end of analysis of object
box.x=max.x-min.x;
box.y=max.y-min.y;
box.z=max.z-min.z;
volume=box.x*box.y*box.z;
cout << "Segment Box volume= " << volume << "\n";
// Now MC integration of volume
// example of random generation
// // double theta = (rand()*1.0/RAND_MAX)*2*pi;
for(i=0;i<N_MC_SAMPLE;i++)
{
pt.x = (rand()*1.0/RAND_MAX)*box.x+min.x;
pt.y = (rand()*1.0/RAND_MAX)*box.y+min.y;
pt.z = (rand()*1.0/RAND_MAX)*box.z+min.z;
for(j=0;j<(int)object.size();j++)
{
if(calcEuclideanDistance(pt.x,pt.y,pt.z,object[j].x,object[j].y,object[j].z)<object[j].r)
{
counter++;
break;
};
};