Actual source code: plexply.c

      1: #include <petsc/private/dmpleximpl.h>

      3: /*@
      4:   DMPlexCreatePLYFromFile - Create a `DMPLEX` mesh from a PLY <https://en.wikipedia.org/wiki/PLY_(file_format)> file.

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

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

     14:   Level: beginner

     16: .seealso: `DMPlexCreateFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
     17: @*/
     18: PetscErrorCode DMPlexCreatePLYFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
     19: {
     20:   PetscViewer  viewer;
     21:   Vec          coordinates;
     22:   PetscSection coordSection;
     23:   PetscScalar *coords;
     24:   char         line[PETSC_MAX_PATH_LEN], ntype[16], itype[16], name[1024], vtype[16];
     25:   PetscBool    match, byteSwap = PETSC_FALSE;
     26:   PetscInt     dim = 2, cdim = 3, Nvp = 0, coordSize, xi = -1, yi = -1, zi = -1, v, c, p;
     27:   PetscMPIInt  rank;
     28:   int          snum, Nv, Nc;

     30:   PetscFunctionBegin;
     31:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
     32:   PetscCall(PetscViewerCreate(comm, &viewer));
     33:   PetscCall(PetscViewerSetType(viewer, PETSCVIEWERBINARY));
     34:   PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
     35:   PetscCall(PetscViewerFileSetName(viewer, filename));
     36:   if (rank == 0) {
     37:     PetscBool isAscii, isBinaryBig, isBinaryLittle;

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

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

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

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

    201:     PetscCall(DMPlexInterpolate(*dm, &idm));
    202:     PetscCall(DMDestroy(dm));
    203:     *dm = idm;
    204:   }
    205:   PetscFunctionReturn(PETSC_SUCCESS);
    206: }