Actual source code: plexply.c

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

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

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

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

     15:   Level: beginner

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

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

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

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

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

    183:     /* Assume same cells */
    184:     PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
    185:     corners = ibuf[0];
    186:     for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, corners));
    187:     PetscCall(DMSetUp(*dm));
    188:     for (c = 0; c < Nc; ++c) {
    189:       if (c > 0) PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
    190:       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);
    191:       PetscCall(PetscViewerRead(viewer, &vbuf, ibuf[0], NULL, PETSC_INT));
    192:       if (byteSwap) PetscCall(PetscByteSwap(&vbuf, PETSC_INT, ibuf[0]));
    193:       for (v = 0; v < ibuf[0]; ++v) vbuf[v] += Nc;
    194:       PetscCall(DMPlexSetCone(*dm, c, vbuf));
    195:     }
    196:   }
    197:   PetscCall(DMPlexSymmetrize(*dm));
    198:   PetscCall(DMPlexStratify(*dm));
    199:   PetscCall(PetscViewerDestroy(&viewer));
    200:   if (interpolate) {
    201:     DM idm;

    203:     PetscCall(DMPlexInterpolate(*dm, &idm));
    204:     PetscCall(DMDestroy(dm));
    205:     *dm = idm;
    206:   }
    207:   PetscFunctionReturn(PETSC_SUCCESS);
    208: }