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 file.
7: + comm - The MPI communicator
8: . filename - Name of the .med file
9: - interpolate - Create faces and edges in the mesh
11: Output Parameter:
12: . dm - The DM object representing the mesh
14: Note: https://en.wikipedia.org/wiki/PLY_(file_format)
16: Level: beginner
18: .seealso: `DMPlexCreateFromFile()`, `DMPlexCreateMedFromFile()`, `DMPlexCreateGmsh()`, `DMPlexCreate()`
19: @*/
20: PetscErrorCode DMPlexCreatePLYFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
21: {
22: PetscViewer viewer;
23: Vec coordinates;
24: PetscSection coordSection;
25: PetscScalar *coords;
26: char line[PETSC_MAX_PATH_LEN], ntype[16], itype[16], name[1024], vtype[16];
27: PetscBool match, byteSwap = PETSC_FALSE;
28: PetscInt dim = 2, cdim = 3, Nvp = 0, coordSize, xi = -1, yi = -1, zi = -1, v, c, p;
29: PetscMPIInt rank;
30: int snum, Nv, Nc;
32: PetscFunctionBegin;
33: PetscCallMPI(MPI_Comm_rank(comm, &rank));
34: PetscCall(PetscViewerCreate(comm, &viewer));
35: PetscCall(PetscViewerSetType(viewer, PETSCVIEWERBINARY));
36: PetscCall(PetscViewerFileSetMode(viewer, FILE_MODE_READ));
37: PetscCall(PetscViewerFileSetName(viewer, filename));
38: if (rank == 0) {
39: PetscBool isAscii, isBinaryBig, isBinaryLittle;
41: /* Check for PLY file */
42: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
43: PetscCall(PetscStrncmp(line, "ply", PETSC_MAX_PATH_LEN, &match));
44: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file");
45: /* Check PLY format */
46: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
47: PetscCall(PetscStrncmp(line, "format", PETSC_MAX_PATH_LEN, &match));
48: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file");
49: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
50: PetscCall(PetscStrncmp(line, "ascii", PETSC_MAX_PATH_LEN, &isAscii));
51: PetscCall(PetscStrncmp(line, "binary_big_endian", PETSC_MAX_PATH_LEN, &isBinaryBig));
52: PetscCall(PetscStrncmp(line, "binary_little_endian", PETSC_MAX_PATH_LEN, &isBinaryLittle));
53: PetscCheck(!isAscii, PETSC_COMM_SELF, PETSC_ERR_SUP, "PLY ascii format not yet supported");
54: if (isBinaryLittle) byteSwap = PETSC_TRUE;
55: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
56: PetscCall(PetscStrncmp(line, "1.0", PETSC_MAX_PATH_LEN, &match));
57: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid version of PLY file, %s", line);
58: /* Ignore comments */
59: match = PETSC_TRUE;
60: while (match) {
61: char buf = '\0';
62: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
63: PetscCall(PetscStrncmp(line, "comment", PETSC_MAX_PATH_LEN, &match));
64: if (match)
65: while (buf != '\n') PetscCall(PetscViewerRead(viewer, &buf, 1, NULL, PETSC_CHAR));
66: }
67: /* Read vertex information */
68: PetscCall(PetscStrncmp(line, "element", PETSC_MAX_PATH_LEN, &match));
69: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
70: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
71: PetscCall(PetscStrncmp(line, "vertex", PETSC_MAX_PATH_LEN, &match));
72: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
73: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
74: snum = sscanf(line, "%d", &Nv);
75: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
76: match = PETSC_TRUE;
77: while (match) {
78: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
79: PetscCall(PetscStrncmp(line, "property", PETSC_MAX_PATH_LEN, &match));
80: if (match) {
81: PetscBool matchB;
83: PetscCall(PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING));
84: PetscCheck(Nvp < 16, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot handle more than 16 property statements in PLY file header: %s", line);
85: snum = sscanf(line, "%s %s", ntype, name);
86: PetscCheck(snum == 2, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
87: PetscCall(PetscStrncmp(ntype, "float32", 16, &matchB));
88: if (matchB) {
89: vtype[Nvp] = 'f';
90: } else {
91: PetscCall(PetscStrncmp(ntype, "int32", 16, &matchB));
92: if (matchB) {
93: vtype[Nvp] = 'd';
94: } else {
95: PetscCall(PetscStrncmp(ntype, "uint8", 16, &matchB));
96: if (matchB) {
97: vtype[Nvp] = 'c';
98: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse type in PLY file header: %s", line);
99: }
100: }
101: PetscCall(PetscStrncmp(name, "x", 16, &matchB));
102: if (matchB) xi = Nvp;
103: PetscCall(PetscStrncmp(name, "y", 16, &matchB));
104: if (matchB) yi = Nvp;
105: PetscCall(PetscStrncmp(name, "z", 16, &matchB));
106: if (matchB) zi = Nvp;
107: ++Nvp;
108: }
109: }
110: /* Read cell information */
111: PetscCall(PetscStrncmp(line, "element", 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: PetscCall(PetscStrncmp(line, "face", PETSC_MAX_PATH_LEN, &match));
115: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
116: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
117: snum = sscanf(line, "%d", &Nc);
118: PetscCheck(snum == 1, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
119: PetscCall(PetscViewerRead(viewer, line, 5, NULL, PETSC_STRING));
120: snum = sscanf(line, "property list %s %s %s", ntype, itype, name);
121: PetscCheck(snum == 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse PLY file header: %s", line);
122: PetscCall(PetscStrncmp(ntype, "uint8", 1024, &match));
123: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid size type in PLY file header: %s", line);
124: PetscCall(PetscStrncmp(name, "vertex_indices", 1024, &match));
125: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid property in PLY file header: %s", line);
126: /* Header should terminate */
127: PetscCall(PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING));
128: PetscCall(PetscStrncmp(line, "end_header", PETSC_MAX_PATH_LEN, &match));
129: PetscCheck(match, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid PLY file: %s", line);
130: } else {
131: Nc = Nv = 0;
132: }
133: PetscCall(DMCreate(comm, dm));
134: PetscCall(DMSetType(*dm, DMPLEX));
135: PetscCall(DMPlexSetChart(*dm, 0, Nc + Nv));
136: PetscCall(DMSetDimension(*dm, dim));
137: PetscCall(DMSetCoordinateDim(*dm, cdim));
138: /* Read coordinates */
139: PetscCall(DMGetCoordinateSection(*dm, &coordSection));
140: PetscCall(PetscSectionSetNumFields(coordSection, 1));
141: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, cdim));
142: PetscCall(PetscSectionSetChart(coordSection, Nc, Nc + Nv));
143: for (v = Nc; v < Nc + Nv; ++v) {
144: PetscCall(PetscSectionSetDof(coordSection, v, cdim));
145: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, cdim));
146: }
147: PetscCall(PetscSectionSetUp(coordSection));
148: PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize));
149: PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates));
150: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
151: PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE));
152: PetscCall(VecSetBlockSize(coordinates, cdim));
153: PetscCall(VecSetType(coordinates, VECSTANDARD));
154: PetscCall(VecGetArray(coordinates, &coords));
155: if (rank == 0) {
156: float rbuf[1];
157: int ibuf[1];
159: for (v = 0; v < Nv; ++v) {
160: for (p = 0; p < Nvp; ++p) {
161: if (vtype[p] == 'f') {
162: PetscCall(PetscViewerRead(viewer, &rbuf, 1, NULL, PETSC_FLOAT));
163: if (byteSwap) PetscCall(PetscByteSwap(&rbuf, PETSC_FLOAT, 1));
164: if (p == xi) coords[v * cdim + 0] = rbuf[0];
165: else if (p == yi) coords[v * cdim + 1] = rbuf[0];
166: else if (p == zi) coords[v * cdim + 2] = rbuf[0];
167: } else if (vtype[p] == 'd') {
168: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_INT));
169: if (byteSwap) PetscCall(PetscByteSwap(&ibuf, PETSC_INT, 1));
170: } else if (vtype[p] == 'c') {
171: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
172: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid vertex property type in PLY file");
173: }
174: }
175: }
176: PetscCall(VecRestoreArray(coordinates, &coords));
177: PetscCall(DMSetCoordinatesLocal(*dm, coordinates));
178: PetscCall(VecDestroy(&coordinates));
179: /* Read topology */
180: if (rank == 0) {
181: char ibuf[1];
182: PetscInt vbuf[16], corners;
184: /* Assume same cells */
185: PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
186: corners = ibuf[0];
187: for (c = 0; c < Nc; ++c) PetscCall(DMPlexSetConeSize(*dm, c, corners));
188: PetscCall(DMSetUp(*dm));
189: for (c = 0; c < Nc; ++c) {
190: if (c > 0) PetscCall(PetscViewerRead(viewer, &ibuf, 1, NULL, PETSC_CHAR));
191: 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);
192: PetscCall(PetscViewerRead(viewer, &vbuf, ibuf[0], NULL, PETSC_INT));
193: if (byteSwap) PetscCall(PetscByteSwap(&vbuf, PETSC_INT, ibuf[0]));
194: for (v = 0; v < ibuf[0]; ++v) vbuf[v] += Nc;
195: PetscCall(DMPlexSetCone(*dm, c, vbuf));
196: }
197: }
198: PetscCall(DMPlexSymmetrize(*dm));
199: PetscCall(DMPlexStratify(*dm));
200: PetscCall(PetscViewerDestroy(&viewer));
201: if (interpolate) {
202: DM idm;
204: PetscCall(DMPlexInterpolate(*dm, &idm));
205: PetscCall(DMDestroy(dm));
206: *dm = idm;
207: }
208: PetscFunctionReturn(PETSC_SUCCESS);
209: }