1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 4 /*@ 5 DMPlexCreatePLYFromFile - Create a `DMPLEX` mesh from a PLY <https://en.wikipedia.org/wiki/PLY_(file_format)> file. 6 7 Input Parameters: 8 + comm - The MPI communicator 9 . filename - Name of the .ply file 10 - interpolate - Create faces and edges in the mesh 11 12 Output Parameter: 13 . dm - The `DMPLEX` object representing the mesh 14 15 Level: beginner 16 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; 30 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; 39 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; 81 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]; 157 158 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; 182 183 /* 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; 202 203 PetscCall(DMPlexInterpolate(*dm, &idm)); 204 PetscCall(DMDestroy(dm)); 205 *dm = idm; 206 } 207 PetscFunctionReturn(PETSC_SUCCESS); 208 } 209