/* vim: set ts=4 sts=4 sw=4 noet : */
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#include <string.h>
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#include "general.h"
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#include <stdio.h>
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#include "initial_distribution.h"
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#include "vesicle.h"
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#include "dumpstate.h"
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#include <libxml/parser.h>
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#include <libxml/tree.h>
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#include "vertex.h"
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#include "energy.h"
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ts_vesicle *vtk2vesicle(char *filename, ts_tape *tape){
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ts_uint nshell=tape->nshell;
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ts_uint ncmax1=tape->ncxmax;
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ts_uint ncmax2=tape->ncymax;
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ts_uint ncmax3=tape->nczmax;
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ts_double stepsize=tape->stepsize;
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ts_uint no_vertices=5*nshell*nshell+2;
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ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
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vesicle->nshell=nshell;
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parse_vtk(filename, vesicle);
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exit(1);
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return vesicle;
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}
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ts_bool parse_vtk(char *filename, ts_vesicle *vesicle){
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xmlDoc *doc;
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xmlNode *root_element=NULL;
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xmlNode *cur_node = NULL;
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doc = xmlReadFile(filename, NULL, 0);
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root_element=xmlDocGetRootElement(doc);
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cur_node=root_element->children;
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while(cur_node!=NULL){
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// fprintf(stderr,"Node name is: %s\n",cur_node->name);
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if(strcmp((char *)cur_node->name,"UnstructuredGrid")==0) break;
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cur_node=cur_node->next;
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}
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cur_node=cur_node->children;
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while(cur_node!=NULL){
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// fprintf(stderr,"Node name is: %s\n",cur_node->name);
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cur_node=cur_node->next;
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if(strcmp((char *)cur_node->name,"Piece")==0) break;
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}
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cur_node=cur_node->children;
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while(cur_node!=NULL){
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//fprintf(stderr,"Node name is: %s\n",cur_node->name);
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cur_node=cur_node->next;
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if(strcmp((char *)cur_node->name,"PointData")==0) vtk_index2vesicle(cur_node->children->next->children, vesicle);
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if(strcmp((char *)cur_node->name,"Points")==0) vtk_coordinates(cur_node->children->next->children,vesicle);
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if(strcmp((char *)cur_node->name,"Cells")==0) {
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vtk_neighbours(cur_node->children->next->children,vesicle);
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break; //segfaults, because it finds another cells. Why?
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}
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}
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//we have vertices and neighbour relations all set, but unordered. Let's do bonds, ordering, triangles...
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vesicle->vlist = vtk_sort_neighbours(vesicle->blist,vesicle->vlist);
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init_triangles(vesicle);
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init_triangle_neighbours(vesicle);
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init_common_vertex_triangle_neighbours(vesicle);
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init_normal_vectors(vesicle->tlist);
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mean_curvature_and_energy(vesicle);
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ts_fprintf(stdout,"restoring from vtk dump finished!\n");
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return TS_SUCCESS;
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}
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ts_bool vtk_index2vesicle(xmlNode *node, ts_vesicle *vesicle){
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//fprintf(stderr, "vsebina: %s\n",node->content);
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ts_uint i;
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char *token;
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token = strtok((char *)node->content, " ");
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for(i=0;i<vesicle->vlist->n;i++){
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vesicle->vlist->vtx[i]->idx=atoi(token);
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token=strtok(NULL," ");
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}
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//fprintf(stderr,"idx[11]=%d\n",vesicle->vlist->vtx[11]->idx);
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return TS_SUCCESS;
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}
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ts_bool vtk_coordinates(xmlNode *node, ts_vesicle *vesicle){
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//fprintf(stderr, "vsebina: %s\n",node->content);
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ts_uint i;
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char *token;
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token = strtok((char *)node->content, " ");
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for(i=0;i<vesicle->vlist->n;i++){
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vesicle->vlist->vtx[i]->x=atof(token);
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// fprintf(stderr,"%e, ",atof(token));
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token=strtok(NULL," ");
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vesicle->vlist->vtx[i]->y=atof(token);
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token=strtok(NULL,"\n");
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vesicle->vlist->vtx[i]->z=atof(token);
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if(i>0) token=strtok(NULL," ");
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}
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return TS_SUCCESS;
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}
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ts_bool vtk_neighbours(xmlNode *node, ts_vesicle *vesicle){
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// fprintf(stderr, "vsebina: %s\n",node->content);
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ts_uint i;
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ts_uint idx1, idx2;
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char *token;
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token = strtok((char *)node->content, " ");
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for(i=0;i<3*(vesicle->vlist->n-2);i++){
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idx1=atoi(token);
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token=strtok(NULL,"\n");
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idx2=atoi(token);
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vtx_add_neighbour(vesicle->vlist->vtx[idx1], vesicle->vlist->vtx[idx2]);
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vtx_add_neighbour(vesicle->vlist->vtx[idx2], vesicle->vlist->vtx[idx1]);
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fprintf(stderr, "%d. povezujem %d in %d\n",i,idx1,idx2);
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if(i>0) token=strtok(NULL," ");
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}
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return TS_SUCCESS;
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}
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/* this is almost exact copy of init_sort_neighbours */
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ts_vertex_list *vtk_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){
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ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
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ts_uint i,l,j,jj,jjj,k=0;
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ts_double eps=0.001; // Take a look if EPS from math.h can be used
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/*lets initialize memory for temporary vertex_list. Should we write a function instead */
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ts_vertex_list *tvlist=vertex_list_copy(vlist);
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ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */
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ts_double dist2; // Square of distance of neighbours
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ts_double direct; // Something, dont know what, but could be normal of some kind
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for(i=1;i<=vlist->n;i++){
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k++; // WHY i IS NOT GOOD??
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vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
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jjj=1;
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jj=1;
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for(l=2;l<=vtx[i]->neigh_no;l++){
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for(j=2;j<=vtx[i]->neigh_no;j++){
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dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
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direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
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// TODO: check if fabs can be used with all floating point types!!
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if( (direct>0.0) && (j!=jjj) ){
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vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
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jjj=jj;
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jj=j;
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// break;
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}
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}
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}
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if(vtx[i]->neigh_no!=tvtx[i]->neigh_no){
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fprintf(stderr,"Hej! pri vtx=%d se razikuje stevilo sosedov (prej=%d, potem=%d)\n",i, vtx[i]->neigh_no, tvtx[i]->neigh_no);
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}
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}
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if(eps>dist2);
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/* We use the temporary vertex for our main vertices and we abandon main
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* vertices, because their neighbours are not correctly ordered */
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// tvtx=vlist->vtx;
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// vlist->vtx=tvtx;
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// tvlist->vtx=vtx;
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vtx_list_free(vlist);
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/* Let's make a check if the number of bonds is correct */
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if((blist->n)!=3*(tvlist->n-2)){
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ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
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fatal("Number of bonds is not 3*(no_vertex-2).",4);
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}
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return tvlist;
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}
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