| commit | author | age | ||
| 8c1bb1 | 1 | #include <stdio.h> |
| SP | 2 | #include <string.h> |
| 3 | #include <stdlib.h> | |
| 4 | #include <libxml/xmlmemory.h> | |
| 5 | #include <libxml/parser.h> | |
| 6 | #include <general.h> | |
| 7 | #include <restore.h> | |
| 8 | #include <snapshot.h> | |
| 9 | #include <zlib.h> | |
| 10 | #include "vesicle.h" | |
| 487968 | 11 | #include "vertex.h" |
| a011d2 | 12 | #include "triangle.h" |
| SP | 13 | |
| 8c1bb1 | 14 | ts_bool parseDump(char *dumpfname) { |
| SP | 15 | xmlDocPtr doc; |
| 8fa1c0 | 16 | xmlNodePtr cur, cur1,cur2; |
| SP | 17 | ts_vesicle *vesicle=NULL; |
| 8c1bb1 | 18 | |
| SP | 19 | doc = xmlParseFile(dumpfname); |
| 20 | ||
| 21 | if (doc == NULL ) { | |
| 22 | fatal("Dump file could not be found or parsed. It is correct file?",1); | |
| 23 | } | |
| 24 | ||
| 25 | cur = xmlDocGetRootElement(doc); | |
| 26 | ||
| 27 | if (cur == NULL) { | |
| 28 | fatal("Dump file is empty.",1); | |
| 29 | } | |
| 30 | ||
| 31 | if (xmlStrcmp(cur->name, (const xmlChar *) "VTKFile")) { | |
| 32 | fatal("document of the wrong type, root node != story",1); | |
| 33 | } | |
| 34 | ||
| 35 | cur = cur->xmlChildrenNode; | |
| 36 | while (cur != NULL) { | |
| 37 | if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){ | |
| 3c772b | 38 | vesicle=parseTrisurfTag(doc, cur); |
| 8c1bb1 | 39 | } |
| 8fa1c0 | 40 | // START Point Position data & Bonds |
| SP | 41 | if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){ |
| 42 | cur1 = cur->xmlChildrenNode; | |
| 43 | while(cur1!=NULL){ | |
| 44 | if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){ | |
| 45 | cur2=cur1->xmlChildrenNode; | |
| 46 | while(cur2!=NULL){ | |
| 47 | if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){ | |
| 48 | fprintf(stderr,"Found point data\n"); | |
| 49 | if(vesicle!=NULL) | |
| 50 | parseXMLVertexPosition(vesicle, doc, cur); | |
| 51 | } | |
| 52 | if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){ | |
| 53 | fprintf(stderr,"Found cell(Bonds) data\n"); | |
| 54 | } | |
| 55 | cur2=cur2->next; | |
| 56 | } | |
| 57 | } | |
| 58 | cur1 = cur1->next; | |
| 59 | } | |
| 60 | } | |
| 61 | // END Point Position data & Bonds | |
| 8c1bb1 | 62 | cur = cur->next; |
| SP | 63 | } |
| 64 | ||
| 65 | xmlFreeDoc(doc); | |
| 66 | fprintf(stderr,"Restoration completed\n"); | |
| 67 | exit(0); | |
| 3c772b | 68 | vesicle_free(vesicle); |
| 8c1bb1 | 69 | return TS_SUCCESS; |
| SP | 70 | } |
| 71 | ||
| 8fa1c0 | 72 | |
| SP | 73 | |
| 74 | /* this is a parser of additional data in xml */ | |
| 8c1bb1 | 75 | ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){ |
| SP | 76 | fprintf(stderr,"Parsing trisurf tag\n"); |
| 487968 | 77 | xmlNodePtr child; |
| SP | 78 | |
| 79 | #ifdef COMPRESS | |
| 8c1bb1 | 80 | /* base64decode */ |
| SP | 81 | size_t cLen; |
| 82 | /*size_t tLen; | |
| 83 | const unsigned char test[]="Test"; | |
| 84 | char *cTest=base64_encode(test, 4,&tLen); | |
| 85 | unsigned char *cuTest=base64_decode((char *)cTest,tLen,&tLen); | |
| 86 | cuTest[tLen]=0; | |
| 87 | fprintf(stderr,"%s\n",cuTest); | |
| 88 | */ | |
| 89 | xmlChar *b64=xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); | |
| 90 | unsigned char *compressed=base64_decode((char *)b64,strlen((char *)b64)-1,&cLen); | |
| 91 | /* uncompress */ | |
| 92 | unsigned char *subtree=(unsigned char *)malloc(512000*sizeof(unsigned char)); /* TODO: again, the uncompressed string must not exceed this */ | |
| 93 | z_stream infstream; | |
| 94 | infstream.zalloc = Z_NULL; | |
| 95 | infstream.zfree = Z_NULL; | |
| 96 | infstream.opaque = Z_NULL; | |
| 97 | infstream.avail_in = (ts_uint)cLen; // size of input | |
| 98 | infstream.next_in = compressed; // input char array | |
| 99 | infstream.avail_out = (ts_uint)512000; // size of output | |
| 100 | infstream.next_out = subtree; // output char array | |
| 101 | ||
| 102 | // the actual DE-compression work. | |
| 103 | inflateInit(&infstream); | |
| 104 | inflate(&infstream, Z_NO_FLUSH); | |
| 105 | inflateEnd(&infstream); | |
| 106 | fprintf(stderr,"%lu\n",cLen); | |
| 107 | subtree[infstream.total_out]='\0'; //zero terminate string | |
| 108 | fprintf(stderr,"%s\n",subtree); | |
| 109 | ||
| 110 | free(subtree); | |
| 487968 | 111 | #endif |
| 8c1bb1 | 112 | /*parse xml subtree */ |
| SP | 113 | xmlChar *nvtx, *npoly, *nfono; |
| 114 | nvtx = xmlGetProp(cur, (xmlChar *)"nvtx"); | |
| 115 | npoly=xmlGetProp(cur, (xmlChar *)"npoly"); | |
| 116 | nfono=xmlGetProp(cur, (xmlChar *)"nfono"); | |
| 117 | fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx)); | |
| 118 | ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),10,10,10,0.1); | |
| 119 | //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle); | |
| 120 | xmlFree(nvtx); | |
| 121 | xmlFree(npoly); | |
| 122 | xmlFree(nfono); | |
| 487968 | 123 | |
| SP | 124 | child = cur->xmlChildrenNode; |
| 125 | while (child != NULL) { | |
| 126 | if ((!xmlStrcmp(child->name, (const xmlChar *)"vtxn"))){ | |
| 127 | parseTrisurfVtxn(vesicle->vlist, doc, child); | |
| 128 | } | |
| a011d2 | 129 | if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){ |
| SP | 130 | parseTrisurfTria(vesicle, doc, child); |
| 131 | } | |
| 132 | if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){ | |
| 133 | parseTrisurfTristar(vesicle, doc, child); | |
| 134 | } | |
| 135 | ||
| 487968 | 136 | child = child->next; |
| SP | 137 | } |
| 138 | ||
| 139 | ||
| 140 | ||
| 8c1bb1 | 141 | return vesicle; |
| SP | 142 | } |
| 487968 | 143 | |
| a011d2 | 144 | |
| SP | 145 | |
| 146 | /* Low level tags parsers */ | |
| 147 | ||
| 148 | ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){ | |
| 487968 | 149 | |
| SP | 150 | xmlChar *chari; |
| 151 | xmlChar *neighs; | |
| 152 | char *n; | |
| 153 | char *token; | |
| 154 | ts_uint neighi; | |
| 155 | ts_uint i; | |
| 156 | chari = xmlGetProp(cur, (xmlChar *)"idx"); | |
| 157 | i=atoi((char *)chari); | |
| 158 | xmlFree(chari); | |
| 159 | ts_vertex *vtx=vlist->vtx[i]; | |
| 160 | neighs = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); | |
| 161 | //fprintf(stderr,"Found neigh for vtx %u that seems to have index %u with neighs=%s\n",i,vtx->idx,neighs); | |
| 162 | ||
| 163 | n=(char *)neighs; | |
| 164 | token=strtok(n," "); | |
| 165 | while(token!=NULL){ | |
| 166 | neighi=atoi(token); | |
| 167 | //fprintf(stderr,"%u", neighi); | |
| 168 | vtx_add_neighbour(vtx,vlist->vtx[neighi]); | |
| 169 | token=strtok(NULL," "); | |
| 170 | } | |
| 171 | xmlFree(neighs); | |
| 172 | return TS_SUCCESS; | |
| 173 | } | |
| 174 | ||
| a011d2 | 175 | ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){ |
| SP | 176 | xmlChar *triangles; |
| 177 | char *tria; | |
| 178 | char *vtx[3]; | |
| 179 | ||
| 180 | ts_uint i; | |
| 181 | triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); | |
| 182 | tria=(char *)triangles; | |
| 183 | for(i=0;i<3;i++) vtx[i]=strtok(tria," "); | |
| 184 | while(vtx[2]!=NULL){ | |
| 185 | triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]); | |
| 186 | for(i=0;i<3;i++) vtx[i]=strtok(NULL," "); | |
| 187 | } | |
| 188 | ||
| 189 | xmlFree(triangles); | |
| 190 | return TS_SUCCESS; | |
| 191 | } | |
| 192 | ||
| 193 | ||
| 194 | ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){ | |
| 195 | ||
| 196 | xmlChar *chari; | |
| 197 | xmlChar *tristar; | |
| 198 | char *t; | |
| 199 | char *token; | |
| 200 | ts_uint neighi; | |
| 201 | ts_uint i; | |
| 202 | chari = xmlGetProp(cur, (xmlChar *)"idx"); | |
| 203 | i=atoi((char *)chari); | |
| 204 | xmlFree(chari); | |
| 205 | ts_vertex *vtx=vesicle->vlist->vtx[i]; | |
| 206 | tristar = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); | |
| 207 | // fprintf(stderr,"Found tristar for vtx %u that seems to have index %u with tristar=%s\n",i,vtx->idx,tristar); | |
| 208 | ||
| 209 | t=(char *)tristar; | |
| 210 | token=strtok(t," "); | |
| 211 | while(token!=NULL){ | |
| 212 | neighi=atoi(token); | |
| 213 | //fprintf(stderr,"%u", neighi); | |
| 214 | vertex_add_tristar(vtx,vesicle->tlist->tria[neighi]); | |
| 215 | token=strtok(NULL," "); | |
| 216 | } | |
| 217 | xmlFree(tristar); | |
| 218 | return TS_SUCCESS; | |
| 219 | } | |
| 220 | ||
| 8fa1c0 | 221 | |
| SP | 222 | /* this is a parser of vertex positions and bonds from main xml data */ |
| 223 | ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){ | |
| 224 | xmlNodePtr child = cur->xmlChildrenNode; | |
| 225 | xmlChar *points; | |
| 226 | char *pts; | |
| 227 | int i, idx; | |
| 228 | char *token[3]; | |
| 229 | while (child != NULL) { | |
| 230 | if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){ | |
| 231 | points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1); | |
| 232 | pts=(char *)points; | |
| 233 | for(i=0;i<3;i++) token[i]=strtok(pts," "); | |
| 234 | idx=0; | |
| 235 | while(token[0]!=NULL){ | |
| 236 | vesicle->vlist->vtx[idx]->x=atof(token[0]); | |
| 237 | vesicle->vlist->vtx[idx]->y=atof(token[1]); | |
| 238 | vesicle->vlist->vtx[idx]->z=atof(token[2]); | |
| 239 | for(i=0;i<3;i++) token[i]=strtok(NULL," "); | |
| 240 | idx++; | |
| 241 | } | |
| 242 | xmlFree(points); | |
| 243 | } | |
| 244 | child=child->next; | |
| 245 | } | |
| 246 | return TS_SUCCESS; | |
| 247 | } | |
| 248 | ||
| 249 | ||
