# # # 0===============================0 # | PLY files reader/writer | # 0===============================0 # # # ---------------------------------------------------------------------------------------------------------------------- # # function to read/write .ply files # # ---------------------------------------------------------------------------------------------------------------------- # # Hugues THOMAS - 10/02/2017 # # ---------------------------------------------------------------------------------------------------------------------- # # Imports and global variables # \**********************************/ # # Basic libs import numpy as np import sys # Define PLY types ply_dtypes = dict( [ (b"int8", "i1"), (b"char", "i1"), (b"uint8", "u1"), (b"uchar", "u1"), (b"int16", "i2"), (b"short", "i2"), (b"uint16", "u2"), (b"ushort", "u2"), (b"int32", "i4"), (b"int", "i4"), (b"uint32", "u4"), (b"uint", "u4"), (b"float32", "f4"), (b"float", "f4"), (b"float64", "f8"), (b"double", "f8"), ] ) # Numpy reader format valid_formats = {"ascii": "", "binary_big_endian": ">", "binary_little_endian": "<"} # ---------------------------------------------------------------------------------------------------------------------- # # Functions # \***************/ # def parse_header(plyfile, ext): # Variables line = [] properties = [] num_points = None while b"end_header" not in line and line != b"": line = plyfile.readline() if b"element" in line: line = line.split() num_points = int(line[2]) elif b"property" in line: line = line.split() properties.append((line[2].decode(), ext + ply_dtypes[line[1]])) return num_points, properties def parse_mesh_header(plyfile, ext): # Variables line = [] vertex_properties = [] num_points = None num_faces = None current_element = None while b"end_header" not in line and line != b"": line = plyfile.readline() # Find point element if b"element vertex" in line: current_element = "vertex" line = line.split() num_points = int(line[2]) elif b"element face" in line: current_element = "face" line = line.split() num_faces = int(line[2]) elif b"property" in line: if current_element == "vertex": line = line.split() vertex_properties.append((line[2].decode(), ext + ply_dtypes[line[1]])) elif current_element == "vertex": if not line.startswith("property list uchar int"): raise ValueError("Unsupported faces property : " + line) return num_points, num_faces, vertex_properties def read_ply(filename, triangular_mesh=False): """ Read ".ply" files Parameters ---------- filename : string the name of the file to read. Returns ------- result : array data stored in the file Examples -------- Store data in file >>> points = np.random.rand(5, 3) >>> values = np.random.randint(2, size=10) >>> write_ply('example.ply', [points, values], ['x', 'y', 'z', 'values']) Read the file >>> data = read_ply('example.ply') >>> values = data['values'] array([0, 0, 1, 1, 0]) >>> points = np.vstack((data['x'], data['y'], data['z'])).T array([[ 0.466 0.595 0.324] [ 0.538 0.407 0.654] [ 0.850 0.018 0.988] [ 0.395 0.394 0.363] [ 0.873 0.996 0.092]]) """ with open(filename, "rb") as plyfile: # Check if the file start with ply if b"ply" not in plyfile.readline(): raise ValueError("The file does not start whith the word ply") # get binary_little/big or ascii fmt = plyfile.readline().split()[1].decode() if fmt == "ascii": raise ValueError("The file is not binary") # get extension for building the numpy dtypes ext = valid_formats[fmt] # PointCloud reader vs mesh reader if triangular_mesh: # Parse header num_points, num_faces, properties = parse_mesh_header(plyfile, ext) # Get point data vertex_data = np.fromfile(plyfile, dtype=properties, count=num_points) # Get face data face_properties = [ ("k", ext + "u1"), ("v1", ext + "i4"), ("v2", ext + "i4"), ("v3", ext + "i4"), ] faces_data = np.fromfile(plyfile, dtype=face_properties, count=num_faces) # Return vertex data and concatenated faces faces = np.vstack((faces_data["v1"], faces_data["v2"], faces_data["v3"])).T data = [vertex_data, faces] else: # Parse header num_points, properties = parse_header(plyfile, ext) # Get data data = np.fromfile(plyfile, dtype=properties, count=num_points) return data def header_properties(field_list, field_names): # List of lines to write lines = [] # First line describing element vertex lines.append("element vertex %d" % field_list[0].shape[0]) # Properties lines i = 0 for fields in field_list: for field in fields.T: lines.append("property %s %s" % (field.dtype.name, field_names[i])) i += 1 return lines def write_ply(filename, field_list, field_names, triangular_faces=None): """ Write ".ply" files Parameters ---------- filename : string the name of the file to which the data is saved. A '.ply' extension will be appended to the file name if it does no already have one. field_list : list, tuple, numpy array the fields to be saved in the ply file. Either a numpy array, a list of numpy arrays or a tuple of numpy arrays. Each 1D numpy array and each column of 2D numpy arrays are considered as one field. field_names : list the name of each fields as a list of strings. Has to be the same length as the number of fields. Examples -------- >>> points = np.random.rand(10, 3) >>> write_ply('example1.ply', points, ['x', 'y', 'z']) >>> values = np.random.randint(2, size=10) >>> write_ply('example2.ply', [points, values], ['x', 'y', 'z', 'values']) >>> colors = np.random.randint(255, size=(10,3), dtype=np.uint8) >>> field_names = ['x', 'y', 'z', 'red', 'green', 'blue', values'] >>> write_ply('example3.ply', [points, colors, values], field_names) """ # Format list input to the right form field_list = ( list(field_list) if (type(field_list) == list or type(field_list) == tuple) else list((field_list,)) ) for i, field in enumerate(field_list): if field.ndim < 2: field_list[i] = field.reshape(-1, 1) if field.ndim > 2: print("fields have more than 2 dimensions") return False # check all fields have the same number of data n_points = [field.shape[0] for field in field_list] if not np.all(np.equal(n_points, n_points[0])): print("wrong field dimensions") return False # Check if field_names and field_list have same nb of column n_fields = np.sum([field.shape[1] for field in field_list]) if n_fields != len(field_names): print("wrong number of field names") return False # Add extension if not there if not filename.endswith(".ply"): filename += ".ply" # open in text mode to write the header with open(filename, "w") as plyfile: # First magical word header = ["ply"] # Encoding format header.append("format binary_" + sys.byteorder + "_endian 1.0") # Points properties description header.extend(header_properties(field_list, field_names)) # Add faces if needded if triangular_faces is not None: header.append("element face {:d}".format(triangular_faces.shape[0])) header.append("property list uchar int vertex_indices") # End of header header.append("end_header") # Write all lines for line in header: plyfile.write("%s\n" % line) # open in binary/append to use tofile with open(filename, "ab") as plyfile: # Create a structured array i = 0 type_list = [] for fields in field_list: for field in fields.T: type_list += [(field_names[i], field.dtype.str)] i += 1 data = np.empty(field_list[0].shape[0], dtype=type_list) i = 0 for fields in field_list: for field in fields.T: data[field_names[i]] = field i += 1 data.tofile(plyfile) if triangular_faces is not None: triangular_faces = triangular_faces.astype(np.int32) type_list = [("k", "uint8")] + [(str(ind), "int32") for ind in range(3)] data = np.empty(triangular_faces.shape[0], dtype=type_list) data["k"] = np.full((triangular_faces.shape[0],), 3, dtype=np.uint8) data["0"] = triangular_faces[:, 0] data["1"] = triangular_faces[:, 1] data["2"] = triangular_faces[:, 2] data.tofile(plyfile) return True def describe_element(name, df): """Takes the columns of the dataframe and builds a ply-like description Parameters ---------- name: str df: pandas DataFrame Returns ------- element: list[str] """ property_formats = {"f": "float", "u": "uchar", "i": "int"} element = ["element " + name + " " + str(len(df))] if name == "face": element.append("property list uchar int points_indices") else: for i in range(len(df.columns)): # get first letter of dtype to infer format f = property_formats[str(df.dtypes[i])[0]] element.append("property " + f + " " + df.columns.values[i]) return element