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: PetscCheck(matchB, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse type in PLY file header: %s", line);
96: vtype[Nvp] = 'c';
97: }
98: }
99: PetscCall(PetscStrncmp(name, "x", 16, &matchB));
100: if (matchB) xi = Nvp;
101: PetscCall(PetscStrncmp(name, "y", 16, &matchB));
102: if (matchB) yi = Nvp;
103: PetscCall(PetscStrncmp(name, "z", 16, &matchB));
104: if (matchB) zi = Nvp;
105: ++Nvp;
106: }
107: }
108: /* Read cell information */
109: PetscCall(PetscStrncmp(line, "element", PETSC_MAX_PATH_LEN, &match));
110: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
111: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
112: PetscCall(PetscStrncmp(line, "face", PETSC_MAX_PATH_LEN, &match));
113: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
114: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
115: snum = sscanf(line, "%d", &Nc);
116: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
117: PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING));
118: snum = sscanf(line, "property list %s %s %s", ntype, itype, name);
119: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
120: PetscCall(PetscStrncmp(ntype, "uint8", 1024, &match));
121: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid size type in PLY file header: %s", line);
122: PetscCall(PetscStrncmp(name, "vertex_indices", 1024, &match));
123: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid property in PLY file header: %s", line);
124: /* Header should terminate */
125: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
126: PetscCall(PetscStrncmp(line, "end_header", PETSC_MAX_PATH_LEN, &match));
127: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file: %s", line);
128: } else {
129: Nc = Nv = 0;
130: }
131: PetscCall(DMCreate(comm, dm));
132: PetscCall(DMSetType(*dm, DMPLEX));
133: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
134: PetscCall(DMSetDimension(*dm, dim));
135: PetscCall(DMSetCoordinateDim(*dm, cdim));
136: /* Read coordinates */
137: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
138: PetscCall(PetscSectionSetNumFields(coordSection, 1));
139: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
140: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
141: for (v = Nc; v < Nc + Nv; ++v) {
142: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
143: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
144: }
145: PetscCall(PetscSectionSetUp(coordSection));
146: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
147: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
148: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
149: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
150: PetscCall(VecSetBlockSize(coordinates, cdim));
151: PetscCall(VecSetType(coordinates, VECSTANDARD));
152: PetscCall(VecGetArray(coordinates, &coords));
153: if (rank == 0) {
154: float rbuf[1];
155: int ibuf[1];
157: for (v = 0; v < Nv; ++v) {
158: for (p = 0; p < Nvp; ++p) {
159: if (vtype[p] == 'f') {
160: PetscCall(PetscViewerRead(viewer, &rbuf, 1, NULL, PETSC_FLOAT));
161: if (byteSwap) PetscCall(PetscByteSwap(&rbuf, PETSC_FLOAT, 1));
162: if (p == xi) coords[v * cdim + 0] = rbuf[0];
163: else if (p == yi) coords[v * cdim + 1] = rbuf[0];
164: else if (p == zi) coords[v * cdim + 2] = rbuf[0];
165: } else if (vtype[p] == 'd') {
166: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_INT));
167: if (byteSwap) PetscCall(PetscByteSwap(&ibuf, PETSC_INT, 1));
168: } else if (vtype[p] == 'c') {
169: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
170: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid vertex property type in PLY file");
171: }
172: }
173: }
174: PetscCall(VecRestoreArray(coordinates, &coords));
175: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
176: PetscCall(VecDestroy(&coordinates));
177: /* Read topology */
178: if (rank == 0) {
179: char ibuf[1];
180: PetscInt vbuf[16], corners;
182: /* Assume same cells */
183: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
184: corners = ibuf[0];
185: for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, corners));
186: PetscCall(DMSetUp(*dm));
187: for (c = 0; c < Nc; ++c) {
188: if (c > 0) PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
189: 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);
190: PetscCall(PetscViewerRead(viewer, &vbuf, ibuf[0], NULL, PETSC_INT));
191: if (byteSwap) PetscCall(PetscByteSwap(&vbuf, PETSC_INT, ibuf[0]));
192: for (v = 0; v < ibuf[0]; ++v) vbuf[v] += Nc;
193: PetscCall(DMPlexSetCone(*dm, c, vbuf));
194: }
195: }
196: PetscCall(DMPlexSymmetrize(*dm));
197: PetscCall(DMPlexStratify(*dm));
198: PetscCall(PetscViewerDestroy(&viewer));
199: if (interpolate) {
200: DM idm;
202: PetscCall(DMPlexInterpolate(*dm, &idm));
203: PetscCall(DMDestroy(dm));
204: *dm = idm;
205: }
206: PetscFunctionReturn(PETSC_SUCCESS);
207: }