Actual source code: plexply.c
petsc-3.10.5 2019-03-28
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      1: #define PETSCDM_DLL
      2:  #include <petsc/private/dmpleximpl.h>

      4: /*@C
      5:   DMPlexCreatePLYFromFile - Create a DMPlex mesh from a PLY file.

      7: + comm        - The MPI communicator
      8: . filename    - Name of the .med file
      9: - interpolate - Create faces and edges in the mesh

     11:   Output Parameter:
     12: . dm  - The DM object representing the mesh

     14:   Note: https://en.wikipedia.org/wiki/PLY_(file_format)

     16:   Level: beginner

     18: .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
     19: @*/
     20: PetscErrorCode DMPlexCreatePLYFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
     21: {
     22:   PetscViewer     viewer;
     23:   Vec             coordinates;
     24:   PetscSection    coordSection;
     25:   PetscScalar    *coords;
     26:   char            line[PETSC_MAX_PATH_LEN], ntype[16], itype[16], name[1024], vtype[16];
     27:   PetscBool       match, byteSwap = PETSC_FALSE;
     28:   PetscInt        dim = 2, cdim = 3, Nvp = 0, coordSize, xi = -1, yi = -1, zi = -1, v, c, p;
     29:   PetscMPIInt     rank;
     30:   int             snum, Nv, Nc;
     31:   PetscErrorCode  ierr;

     34:   MPI_Comm_rank(comm, &rank);
     35:   PetscViewerCreate(comm, &viewer);
     36:   PetscViewerSetType(viewer, PETSCVIEWERBINARY);
     37:   PetscViewerFileSetMode(viewer, FILE_MODE_READ);
     38:   PetscViewerFileSetName(viewer, filename);
     39:   if (!rank) {
     40:     PetscBool isAscii, isBinaryBig, isBinaryLittle;

     42:     /* Check for PLY file */
     43:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     44:     PetscStrncmp(line, "ply", PETSC_MAX_PATH_LEN, &match);
     45:     if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file");
     46:     /* Check PLY format */
     47:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     48:     PetscStrncmp(line, "format", PETSC_MAX_PATH_LEN, &match);
     49:     if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file");
     50:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     51:     PetscStrncmp(line, "ascii", PETSC_MAX_PATH_LEN, &isAscii);
     52:     PetscStrncmp(line, "binary_big_endian", PETSC_MAX_PATH_LEN, &isBinaryBig);
     53:     PetscStrncmp(line, "binary_little_endian", PETSC_MAX_PATH_LEN, &isBinaryLittle);
     54:     if (isAscii) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "PLY ascii format not yet supported");
     55:     else if (isBinaryLittle) byteSwap = PETSC_TRUE;
     56:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     57:     PetscStrncmp(line, "1.0", PETSC_MAX_PATH_LEN, &match);
     58:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid version of PLY file, %s", line);
     59:     /* Ignore comments */
     60:     match = PETSC_TRUE;
     61:     while (match) {
     62:       char buf = '\0';
     63:       PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     64:       PetscStrncmp(line, "comment", PETSC_MAX_PATH_LEN, &match);
     65:       if (match) while (buf != '\n') {PetscViewerRead(viewer, &buf, 1, NULL, PETSC_CHAR);}
     66:     }
     67:     /* Read vertex information */
     68:     PetscStrncmp(line, "element", PETSC_MAX_PATH_LEN, &match);
     69:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
     70:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     71:     PetscStrncmp(line, "vertex", PETSC_MAX_PATH_LEN, &match);
     72:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
     73:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     74:     snum = sscanf(line, "%d", &Nv);
     75:     if (snum != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
     76:     match = PETSC_TRUE;
     77:     while (match) {
     78:       PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
     79:       PetscStrncmp(line, "property", PETSC_MAX_PATH_LEN, &match);
     80:       if (match) {
     81:         PetscBool matchB;

     83:         PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);
     84:         if (Nvp >= 16) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot handle more than 16 property statements in PLY file header: %s", line);
     85:         snum = sscanf(line, "%s %s", ntype, name);
     86:         if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
     87:         PetscStrncmp(ntype, "float32", 16, &matchB);
     88:         if (matchB) {
     89:           vtype[Nvp] = 'f';
     90:         } else {
     91:           PetscStrncmp(ntype, "int32", 16, &matchB);
     92:           if (matchB) {
     93:             vtype[Nvp] = 'd';
     94:           } else {
     95:             PetscStrncmp(ntype, "uint8", 16, &matchB);
     96:             if (matchB) {
     97:               vtype[Nvp] = 'c';
     98:             } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse type in PLY file header: %s", line);
     99:           }
    100:         }
    101:         PetscStrncmp(name, "x", 16, &matchB);
    102:         if (matchB) {xi = Nvp;}
    103:         PetscStrncmp(name, "y", 16, &matchB);
    104:         if (matchB) {yi = Nvp;}
    105:         PetscStrncmp(name, "z", 16, &matchB);
    106:         if (matchB) {zi = Nvp;}
    107:         ++Nvp;
    108:       }
    109:     }
    110:     /* Read cell information */
    111:     PetscStrncmp(line, "element", PETSC_MAX_PATH_LEN, &match);
    112:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
    113:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
    114:     PetscStrncmp(line, "face", PETSC_MAX_PATH_LEN, &match);
    115:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
    116:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
    117:     snum = sscanf(line, "%d", &Nc);
    118:     if (snum != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
    119:     PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING);
    120:     snum = sscanf(line, "property list %s %s %s", ntype, itype, name);
    121:     if (snum != 3) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
    122:     PetscStrncmp(ntype, "uint8", 1024, &match);
    123:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid size type in PLY file header: %s", line);
    124:     PetscStrncmp(name, "vertex_indices", 1024, &match);
    125:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid property in PLY file header: %s", line);
    126:     /* Header should terminate */
    127:     PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);
    128:     PetscStrncmp(line, "end_header", PETSC_MAX_PATH_LEN, &match);
    129:     if (!match) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file: %s", line);
    130:   } else {
    131:     Nc = Nv = 0;
    132:   }
    133:   DMCreate(comm, dm);
    134:   DMSetType(*dm, DMPLEX);
    135:   DMPlexSetChart(*dm, 0, Nc+Nv);
    136:   DMSetDimension(*dm, dim);
    137:   DMSetCoordinateDim(*dm, cdim);
    138:   /* Read coordinates */
    139:   DMGetCoordinateSection(*dm, &coordSection);
    140:   PetscSectionSetNumFields(coordSection, 1);
    141:   PetscSectionSetFieldComponents(coordSection, 0, cdim);
    142:   PetscSectionSetChart(coordSection, Nc, Nc + Nv);
    143:   for (v = Nc; v < Nc+Nv; ++v) {
    144:     PetscSectionSetDof(coordSection, v, cdim);
    145:     PetscSectionSetFieldDof(coordSection, v, 0, cdim);
    146:   }
    147:   PetscSectionSetUp(coordSection);
    148:   PetscSectionGetStorageSize(coordSection, &coordSize);
    149:   VecCreate(PETSC_COMM_SELF, &coordinates);
    150:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    151:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    152:   VecSetBlockSize(coordinates, cdim);
    153:   VecSetType(coordinates, VECSTANDARD);
    154:   VecGetArray(coordinates, &coords);
    155:   if (!rank) {
    156:     float rbuf[1];
    157:     int   ibuf[1];

    159:     for (v = 0; v < Nv; ++v) {
    160:       for (p = 0; p < Nvp; ++p) {
    161:         if (vtype[p] == 'f') {
    162:           PetscViewerRead(viewer, &rbuf, 1, NULL, PETSC_FLOAT);
    163:           if (byteSwap) PetscByteSwap(&rbuf, PETSC_FLOAT, 1);
    164:           if      (p == xi) coords[v*cdim+0] = rbuf[0];
    165:           else if (p == yi) coords[v*cdim+1] = rbuf[0];
    166:           else if (p == zi) coords[v*cdim+2] = rbuf[0];
    167:         } else if (vtype[p] == 'd') {
    168:           PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_INT);
    169:           if (byteSwap) PetscByteSwap(&ibuf, PETSC_INT, 1);
    170:         } else if (vtype[p] == 'c') {
    171:           PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR);
    172:         } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid vertex property type in PLY file");
    173:       }
    174:     }
    175:   }
    176:   VecRestoreArray(coordinates, &coords);
    177:   DMSetCoordinatesLocal(*dm, coordinates);
    178:   VecDestroy(&coordinates);
    179:   /* Read topology */
    180:   if (!rank) {
    181:     char     ibuf[1];
    182:     PetscInt vbuf[16], corners;

    184:     /* Assume same cells */
    185:     PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR);
    186:     corners = ibuf[0];
    187:     for (c = 0; c < Nc; ++c) {DMPlexSetConeSize(*dm, c, corners);}
    188:     DMSetUp(*dm);
    189:     for (c = 0; c < Nc; ++c) {
    190:       if (c > 0) {
    191:         PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR);
    192:       }
    193:       if (ibuf[0] != corners) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "All cells must have the same number of vertices in PLY file: %D != %D", ibuf[0], corners);
    194:       PetscViewerRead(viewer, &vbuf, ibuf[0], NULL, PETSC_INT);
    195:       if (byteSwap) PetscByteSwap(&vbuf, PETSC_INT, ibuf[0]);
    196:       for (v = 0; v < ibuf[0]; ++v) vbuf[v] += Nc;
    197:       DMPlexSetCone(*dm, c, vbuf);
    198:     }
    199:   }
    200:   DMPlexSymmetrize(*dm);
    201:   DMPlexStratify(*dm);
    202:   PetscViewerDestroy(&viewer);
    203:   if (interpolate) {
    204:     DM idm;

    206:     DMPlexInterpolate(*dm, &idm);
    207:     DMDestroy(dm);
    208:     *dm  = idm;
    209:   }
    210:   return(0);
    211: }