From a3dbf0899f9a077c025136336b597ae9b22e414f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Fri, 26 Feb 2016 10:34:38 +0000
Subject: [PATCH] Basic vesicle is dumped and restored, however, memory is not ok.
---
src/restore.c | 93 +++++++++++++++++++++++++++++++++++++++++++++-
1 files changed, 90 insertions(+), 3 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index d8542ac..94e2621 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -10,11 +10,14 @@
#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);
@@ -37,17 +40,48 @@
if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
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");
exit(0);
vesicle_free(vesicle);
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;
@@ -194,3 +228,56 @@
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;
+ for(i=0;i<3;i++) token[i]=strtok(pts," ");
+ 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;
+ for(i=0;i<2;i++) token[i]=strtok(b," ");
+ 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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