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: }