Actual source code: plexply.c
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
4: /*@C
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 .med 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()`, `DMPlexCreateMedFromFile()`, `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: }