From e87e4e4fcbba57d36dfd17b92f413ccf2c1b322a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 29 Feb 2016 08:20:59 +0000
Subject: [PATCH] Fixed restoration (partially)
---
src/restore.c | 232 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
1 files changed, 228 insertions(+), 4 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index f7725b4..74b0ef6 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -8,10 +8,16 @@
#include <snapshot.h>
#include <zlib.h>
#include "vesicle.h"
+#include "vertex.h"
+#include "triangle.h"
+#include "bond.h"
+#include "energy.h"
+#include "initial_distribution.h"
+
ts_bool parseDump(char *dumpfname) {
xmlDocPtr doc;
- xmlNodePtr cur;
- ts_vesicle *vesicle;
+ xmlNodePtr cur, cur1,cur2;
+ ts_vesicle *vesicle=NULL;
doc = xmlParseFile(dumpfname);
@@ -32,20 +38,55 @@
cur = cur->xmlChildrenNode;
while (cur != NULL) {
if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
- *vesicle=parseTrisurfTag(doc, cur);
+ vesicle=parseTrisurfTag(doc, cur);
}
-
+ // START Point Position data & Bonds
+ if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){
+ cur1 = cur->xmlChildrenNode;
+ while(cur1!=NULL){
+ if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
+ cur2=cur1->xmlChildrenNode;
+ while(cur2!=NULL){
+ if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
+ fprintf(stderr,"Found point data\n");
+ if(vesicle!=NULL)
+ parseXMLVertexPosition(vesicle, doc, cur);
+ }
+ if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
+ fprintf(stderr,"Found cell(Bonds) data\n");
+ if(vesicle!=NULL)
+ parseXMLBonds(vesicle, doc, cur);
+ }
+ cur2=cur2->next;
+ }
+ }
+ cur1 = cur1->next;
+ }
+ }
+ // END Point Position data & Bonds
cur = cur->next;
}
xmlFreeDoc(doc);
+ init_normal_vectors(vesicle->tlist);
+ mean_curvature_and_energy(vesicle);
+
+/* TODO: cells, polymeres, filaments, core, tape */
+
fprintf(stderr,"Restoration completed\n");
+ vesicle_free(vesicle);
exit(0);
return TS_SUCCESS;
}
+
+
+/* this is a parser of additional data in xml */
ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){
fprintf(stderr,"Parsing trisurf tag\n");
+ xmlNodePtr child;
+
+#ifdef COMPRESS
/* base64decode */
size_t cLen;
/*size_t tLen;
@@ -77,6 +118,7 @@
fprintf(stderr,"%s\n",subtree);
free(subtree);
+#endif
/*parse xml subtree */
xmlChar *nvtx, *npoly, *nfono;
nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
@@ -88,5 +130,187 @@
xmlFree(nvtx);
xmlFree(npoly);
xmlFree(nfono);
+
+ child = cur->xmlChildrenNode;
+ while (child != NULL) {
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"vtxn"))){
+ parseTrisurfVtxn(vesicle->vlist, doc, child);
+ }
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
+ parseTrisurfTria(vesicle, doc, child);
+ }
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
+ parseTrisurfTriaNeigh(vesicle, doc, child);
+ }
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
+ parseTrisurfTristar(vesicle, doc, child);
+ }
+
+ child = child->next;
+ }
+
+
+
return vesicle;
}
+
+
+
+/* Low level tags parsers */
+
+ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){
+
+ xmlChar *chari;
+ xmlChar *neighs;
+ char *n;
+ char *token;
+ ts_uint neighi;
+ ts_uint i;
+ chari = xmlGetProp(cur, (xmlChar *)"idx");
+ i=atoi((char *)chari);
+ xmlFree(chari);
+ ts_vertex *vtx=vlist->vtx[i];
+ neighs = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ //fprintf(stderr,"Found neigh for vtx %u that seems to have index %u with neighs=%s\n",i,vtx->idx,neighs);
+
+ n=(char *)neighs;
+ token=strtok(n," ");
+ while(token!=NULL){
+ neighi=atoi(token);
+ //fprintf(stderr,"%u", neighi);
+ vtx_add_neighbour(vtx,vlist->vtx[neighi]);
+ token=strtok(NULL," ");
+ }
+ xmlFree(neighs);
+ return TS_SUCCESS;
+}
+
+ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *triangles;
+ char *tria;
+ char *vtx[3];
+
+ ts_uint i,j;
+ triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ tria=(char *)triangles;
+ vtx[0]=strtok(tria," ");
+ for(i=1;i<3;i++) vtx[i]=strtok(NULL," ");
+ j=0;
+ while(vtx[2]!=NULL){
+ triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
+ for(i=0;i<3;i++) vtx[i]=strtok(NULL," ");
+ j++;
+ }
+ fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);
+
+ xmlFree(triangles);
+ return TS_SUCCESS;
+}
+
+
+ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *triangles;
+ char *tria;
+ char *ntria[3];
+ ts_uint i,j;
+ triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ tria=(char *)triangles;
+ ntria[0]=strtok(tria," ");
+ for(i=1;i<3;i++) ntria[i]=strtok(NULL," ");
+ j=0;
+ while(ntria[2]!=NULL){
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
+ j++;
+ for(i=0;i<3;i++) ntria[i]=strtok(NULL," ");
+ }
+ fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);
+
+ xmlFree(triangles);
+ return TS_SUCCESS;
+}
+
+
+ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
+
+ xmlChar *chari;
+ xmlChar *tristar;
+ char *t;
+ char *token;
+ ts_uint neighi;
+ ts_uint i;
+ chari = xmlGetProp(cur, (xmlChar *)"idx");
+ i=atoi((char *)chari);
+ xmlFree(chari);
+ ts_vertex *vtx=vesicle->vlist->vtx[i];
+ tristar = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+// fprintf(stderr,"Found tristar for vtx %u that seems to have index %u with tristar=%s\n",i,vtx->idx,tristar);
+
+ t=(char *)tristar;
+ token=strtok(t," ");
+ while(token!=NULL){
+ neighi=atoi(token);
+ //fprintf(stderr,"%u", neighi);
+ vertex_add_tristar(vtx,vesicle->tlist->tria[neighi]);
+ token=strtok(NULL," ");
+ }
+ xmlFree(tristar);
+ return TS_SUCCESS;
+}
+
+
+/* this is a parser of vertex positions and bonds from main xml data */
+ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
+ xmlNodePtr child = cur->xmlChildrenNode;
+ xmlChar *points;
+ char *pts;
+ int i, idx;
+ char *token[3];
+ while (child != NULL) {
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
+ points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
+ pts=(char *)points;
+ token[0]=strtok(pts," ");
+ for(i=1;i<3;i++) token[i]=strtok(NULL," ");
+ idx=0;
+ while(token[0]!=NULL){
+ vesicle->vlist->vtx[idx]->x=atof(token[0]);
+ vesicle->vlist->vtx[idx]->y=atof(token[1]);
+ vesicle->vlist->vtx[idx]->z=atof(token[2]);
+ for(i=0;i<3;i++) token[i]=strtok(NULL," ");
+ idx++;
+ }
+ xmlFree(points);
+ }
+ child=child->next;
+ }
+ return TS_SUCCESS;
+}
+ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
+ xmlNodePtr child = cur->xmlChildrenNode;
+ xmlChar *bonds;
+ char *b;
+ int i, idx;
+ char *token[2];
+ while (child != NULL) {
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
+ bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
+ b=(char *)bonds;
+ token[0]=strtok(b," ");
+ token[1]=strtok(NULL," ");
+ idx=0;
+ while(token[0]!=NULL){
+ bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
+ for(i=0;i<2;i++) token[i]=strtok(NULL," ");
+ idx++;
+ }
+ xmlFree(bonds);
+ }
+ child=child->next;
+ }
+ return TS_SUCCESS;
+}
+
+
+
--
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