import json import numpy as np import pandas as pd from flatbuffers import Builder from scipy import sparse from server.common.utils.type_conversion_utils import get_encoding_dtype_of_array import server.common.fbs.NetEncoding.Column as Column import server.common.fbs.NetEncoding.Float32Array as Float32Array import server.common.fbs.NetEncoding.Float64Array as Float64Array import server.common.fbs.NetEncoding.Int32Array as Int32Array import server.common.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray import server.common.fbs.NetEncoding.Matrix as Matrix import server.common.fbs.NetEncoding.TypedArray as TypedArray import server.common.fbs.NetEncoding.Uint32Array as Uint32Array # Serialization helper def serialize_column(builder, typed_arr): """Serialize NetEncoding.Column""" (u_type, u_value) = typed_arr Column.ColumnStart(builder) Column.ColumnAddUType(builder, u_type) Column.ColumnAddU(builder, u_value) return Column.ColumnEnd(builder) # Serialization helper def serialize_matrix(builder, n_rows, n_cols, columns, col_idx): """Serialize NetEncoding.Matrix""" Matrix.MatrixStart(builder) Matrix.MatrixAddNRows(builder, n_rows) Matrix.MatrixAddNCols(builder, n_cols) Matrix.MatrixAddColumns(builder, columns) if col_idx is not None: (u_type, u_val) = col_idx Matrix.MatrixAddColIndexType(builder, u_type) Matrix.MatrixAddColIndex(builder, u_val) return Matrix.MatrixEnd(builder) # Serialization helper def serialize_typed_array(builder, source_array, encoding_info): """ Serialize any of the various typed arrays, eg, Float32Array. Specific means of serialization and type conversion are provided by type_info. """ arr = source_array (array_type, as_type) = encoding_info(source_array) if isinstance(arr, pd.Index): arr = arr.to_series() # convert to a simple ndarray if as_type == "json": as_json = arr.to_json(orient="records") arr = np.array(bytearray(as_json, "utf-8")) else: if sparse.issparse(arr): arr = arr.toarray() elif isinstance(arr, pd.Series): arr = arr.to_numpy() if arr.dtype != as_type: arr = arr.astype(as_type) # serialize the ndarray into a vector if arr.ndim == 2: if arr.shape[0] == 1: arr = arr[0] elif arr.shape[1] == 1: arr = arr.T[0] vec = builder.CreateNumpyVector(arr) # serialize the typed array table builder.StartObject(1) builder.PrependUOffsetTRelativeSlot(0, vec, 0) array_value = builder.EndObject() return (array_type, array_value) def column_encoding(arr): column_encoding_type_map = { # array protocol string: ( array_type, as_type ) np.dtype(np.float64).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.float32).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.float16).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.int8).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.int16).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.int32).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.int64).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.uint8).str: (TypedArray.TypedArray.Uint32Array, np.uint32), np.dtype(np.uint16).str: (TypedArray.TypedArray.Uint32Array, np.uint32), np.dtype(np.uint32).str: (TypedArray.TypedArray.Uint32Array, np.uint32), np.dtype(np.uint64).str: (TypedArray.TypedArray.Uint32Array, np.uint32), } column_encoding_default = (TypedArray.TypedArray.JSONEncodedArray, "json") encoding_dtype = np.dtype(get_encoding_dtype_of_array(arr)) return column_encoding_type_map.get(encoding_dtype.str, column_encoding_default) def index_encoding(arr): index_encoding_type_map = { # array protocol string: ( array_type, as_type ) np.dtype(np.int32).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.int64).str: (TypedArray.TypedArray.Int32Array, np.int32), np.dtype(np.uint32).str: (TypedArray.TypedArray.Uint32Array, np.uint32), np.dtype(np.uint64).str: (TypedArray.TypedArray.Uint32Array, np.uint32), } index_encoding_default = (TypedArray.TypedArray.JSONEncodedArray, "json") return index_encoding_type_map.get(arr.dtype.str, index_encoding_default) def guess_at_mem_needed(matrix): (n_rows, n_cols) = matrix.shape if isinstance(matrix, np.ndarray) or sparse.issparse(matrix): guess = (n_rows * n_cols * matrix.dtype.itemsize) + 1024 elif isinstance(matrix, pd.DataFrame): # XXX TODO - DataFrame type estimate guess = 1 else: guess = 1 # round up to nearest 1024 bytes guess = (guess + 0x400) & (~0x3FF) return guess def encode_matrix_fbs(matrix, row_idx=None, col_idx=None): """ Given a 2D DataFrame, ndarray or sparse equivalent, create and return a Matrix flatbuffer. :param matrix: 2D DataFrame, ndarray or sparse equivalent :param row_idx: index for row dimension, Index or ndarray :param col_idx: index for col dimension, Index or ndarray NOTE: row indices are (currently) unsupported and must be None """ if row_idx is not None: raise ValueError("row indexing not supported for FBS Matrix") if matrix.ndim != 2: raise ValueError("FBS Matrix must be 2D") (n_rows, n_cols) = matrix.shape # estimate size needed, so we don't unnecessarily realloc. builder = Builder(guess_at_mem_needed(matrix)) columns = [] for cidx in range(n_cols - 1, -1, -1): # serialize the typed array col = matrix.iloc[:, cidx] if isinstance(matrix, pd.DataFrame) else matrix[:, cidx] typed_arr = serialize_typed_array(builder, col, column_encoding) # serialize the Column union columns.append(serialize_column(builder, typed_arr)) # Serialize Matrix.columns[] Matrix.MatrixStartColumnsVector(builder, n_cols) for c in columns: builder.PrependUOffsetTRelative(c) matrix_column_vec = builder.EndVector(n_cols) # serialize the colIndex if provided cidx = None if col_idx is not None: cidx = serialize_typed_array(builder, col_idx, index_encoding) # Serialize Matrix matrix = serialize_matrix(builder, n_rows, n_cols, matrix_column_vec, cidx) builder.Finish(matrix) return builder.Output() def deserialize_typed_array(tarr): type_map = { TypedArray.TypedArray.NONE: None, TypedArray.TypedArray.Uint32Array: Uint32Array.Uint32Array, TypedArray.TypedArray.Int32Array: Int32Array.Int32Array, TypedArray.TypedArray.Float32Array: Float32Array.Float32Array, TypedArray.TypedArray.Float64Array: Float64Array.Float64Array, TypedArray.TypedArray.JSONEncodedArray: JSONEncodedArray.JSONEncodedArray, } (u_type, u) = tarr if u_type is TypedArray.TypedArray.NONE: return None TarType = type_map.get(u_type, None) if TarType is None: raise TypeError(f"FBS contains unknown data type: {u_type}") arr = TarType() arr.Init(u.Bytes, u.Pos) narr = arr.DataAsNumpy() if u_type == TypedArray.TypedArray.JSONEncodedArray: narr = json.loads(narr.tobytes().decode("utf-8")) return narr def decode_matrix_fbs(fbs): """ Given an FBS-encoded Matrix, return a Pandas DataFrame the contains the data and indices. """ matrix = Matrix.Matrix.GetRootAsMatrix(fbs, 0) n_rows = matrix.NRows() n_cols = matrix.NCols() if n_rows == 0 or n_cols == 0: return pd.DataFrame() if matrix.RowIndexType() is not TypedArray.TypedArray.NONE: raise ValueError("row indexing not supported for FBS Matrix") columns_length = matrix.ColumnsLength() columns_index = deserialize_typed_array((matrix.ColIndexType(), matrix.ColIndex())) if columns_index is None: columns_index = range(0, n_cols) # sanity checks if len(columns_index) != n_cols or columns_length != n_cols: raise ValueError("FBS column count does not match number of columns in underlying matrix") columns_data = {} columns_type = {} for col_idx in range(0, columns_length): col = matrix.Columns(col_idx) tarr = (col.UType(), col.U()) data = deserialize_typed_array(tarr) columns_data[columns_index[col_idx]] = data if len(data) != n_rows: raise ValueError("FBS column length does not match number of rows") if col.UType() is TypedArray.TypedArray.JSONEncodedArray: columns_type[columns_index[col_idx]] = "category" df = pd.DataFrame.from_dict(data=columns_data).astype(columns_type, copy=False) # more sanity checks if not df.columns.is_unique or len(df.columns) != n_cols: raise KeyError("FBS column indices are not unique") return df