Source code for openmdao.utils.array_utils

Utils for dealing with arrays.
import sys
from itertools import product
from copy import copy

import numpy as np

[docs]def evenly_distrib_idxs(num_divisions, arr_size): """ Return evenly distributed entries for the given array size. Given a number of divisions and the size of an array, chop the array up into pieces according to number of divisions, keeping the distribution of entries as even as possible. Parameters ---------- num_divisions : int Number of parts to divide the array into. arr_size : int Number of entries in the array. Returns ------- tuple a tuple of (sizes, offsets), where sizes and offsets contain values for all divisions. """ base = arr_size // num_divisions leftover = arr_size % num_divisions sizes = np.full(num_divisions, base, dtype=int) # evenly distribute the remainder across size-leftover procs, # instead of giving the whole remainder to one proc sizes[:leftover] += 1 offsets = np.zeros(num_divisions, dtype=int) offsets[1:] = np.cumsum(sizes)[:-1] return sizes, offsets
[docs]def take_nth(rank, size, seq): """ Iterate returning every nth value. Return an iterator over the sequence that returns every nth element of seq based on the given rank within a group of the given size. For example, if size = 2, a rank of 0 returns even indexed elements and a rank of 1 returns odd indexed elements. Parameters ---------- rank : int MPI rank of this process. size : int Size of the array we're taking nth entries from. seq : iter Iterator containing the values being returned. """ assert(rank < size) it = iter(seq) while True: for proc in range(size): if rank == proc: try: yield next(it) except StopIteration: return else: try: next(it) except StopIteration: return
[docs]def convert_neg(arr, dim): """ Convert any negative indices into their positive equivalent. Parameters ---------- arr : ndarray Array having negative indices converted. dim : int Dimension of the array. Returns ------- ndarray The converted array. """ arr[arr < 0] += dim return arr
[docs]def array_viz(arr, prob=None, of=None, wrt=None, stream=sys.stdout): """ Display the structure of a boolean array in a compact form. If prob, of, and wrt are supplied, print the name of the response alongside each row and print the names of the design vars, aligned with each column, at the bottom. Parameters ---------- arr : ndarray Array being visualized. prob : Problem or None Problem object. of : list of str or None Names of response variables used in derivative calculation. wrt : list of str or None Names of design variables used in derivative calculation. stream : file-like Stream where output will be written. """ if len(arr.shape) != 2: raise RuntimeError("array_viz only works for 2d arrays.") if prob is not None: if of is None: of = prob.driver._get_ordered_nl_responses() if wrt is None: wrt = list(prob.driver._designvars) if prob is None or of is None or wrt is None: for r in range(arr.shape[0]): for c in range(arr.shape[1]): if arr[r, c]: stream.write('x') else: stream.write('.') stream.write(' %d\n' % r) else: row = 0 for res in of: for r in range(row, row + prob.driver._responses[res]['size']): col = 0 for dv in wrt: for c in range(col, col + prob.driver._designvars[dv]['size']): if arr[r, c]: stream.write('x') else: stream.write('.') col = c + 1 stream.write(' %d %s\n' % (r, res)) row = r + 1 start = 0 for name in wrt: tab = ' ' * start stream.write('%s|%s\n' % (tab, name)) start += prob.driver._designvars[name]['size']
[docs]def array_connection_compatible(shape1, shape2): """ Return True if the two arrays shapes are compatible. Array shapes are compatible if the underlying data has the same size and is stored in the same contiguous order for the two shapes. Parameters ---------- shape1 : tuple of int Shape of the first array. shape2 : tuple of int Shape of the second array. Returns ------- bool True if the two shapes are compatible for connection, else False. """ ashape1 = np.asarray(shape1, dtype=int) ashape2 = np.asarray(shape2, dtype=int) size1 = size2 = # Shapes are not connection-compatible if size is different if size1 != size2: return False nz1 = np.where(ashape1 > 1)[0] nz2 = np.where(ashape2 > 1)[0] if len(nz1) > 0: fundamental_shape1 = ashape1[np.min(nz1): np.max(nz1) + 1] else: fundamental_shape1 = np.ones((1,)) if len(nz2) > 0: fundamental_shape2 = ashape2[np.min(nz2): np.max(nz2) + 1] else: fundamental_shape2 = np.ones((1,)) return np.all(fundamental_shape1 == fundamental_shape2)
[docs]def tile_sparse_jac(data, rows, cols, nrow, ncol, num_nodes): """ Assemble arrays necessary to define a COO sparse jacobian for a vectorized component. These arrays can also be passed to csc_matrix or csr_matrix to create CSC and CSR sparse matrices. Parameters ---------- data : ndarray Array of values rows : index array Array of row indices. cols : index array Array of column indices. nrow : int Number of rows in sub jacobian. ncol : int Number of columns in sub jacobian. num_nodes : int Number of vectorized copies to tile. Returns ------- ndarray, ndarray, ndarray Arrays to define a COO sparse jacobian of size num_nodes*nrow by num_nodes*ncol """ nnz = len(rows) if np.isscalar(data): data = data * np.ones(nnz) if not np.isscalar(nrow): nrow = if not np.isscalar(ncol): ncol = repeat_arr = np.repeat(np.arange(num_nodes), nnz) data = np.tile(data, num_nodes) rows = np.tile(rows, num_nodes) + repeat_arr * nrow cols = np.tile(cols, num_nodes) + repeat_arr * ncol return data, rows, cols
def _global2local_offsets(global_offsets): """ Given existing global offsets, return a copy with offsets localized to each process. Parameters ---------- global_offsets : dict Arrays of global offsets keyed by vec_name and deriv direction. Returns ------- dict Arrays of local offsets keyed by vec_name and deriv direction. """ offsets = {} for vec_name in global_offsets: offsets[vec_name] = off_vn = {} for type_ in global_offsets[vec_name]: goff = global_offsets[vec_name][type_] off_vn[type_] = goff.copy() if goff[0].size > 0: # adjust offsets to be local in each process off_vn[type_] -= goff[:, 0].reshape((goff.shape[0], 1)) return offsets
[docs]def sub2full_indices(all_names, matching_names, sizes, idx_map=()): """ Return the given indices converted into indices into the full vector. This routine is used to compute how column indices computed during coloring of a subset of the jacobian map to column indices corresponding to the full jacobian. Parameters ---------- all_names : ordered iter of str An ordered list of variable names containing all variables of the appropriate type. matching_names : set of str Subset of all_names that make up the reduced index set. sizes : ndarray of int Array of variable sizes. idx_map : dict Mapping of var name to some subset of its full indices. Returns ------- ndarray Full array indices that map to the provided subset of variables. """ global_idxs = [] start = end = 0 for name, size in zip(all_names, sizes): end += size if size > 0 and (matching_names is None or name in matching_names): if name in idx_map: global_idxs.append(np.arange(start, end)[idx_map[name]]) else: global_idxs.append(np.arange(start, end)) start = end if global_idxs: return np.hstack(global_idxs)
[docs]def get_input_idx_split(full_idxs, inputs, outputs, use_full_cols, is_total): """ Split an array of indices into vec outs + ins into two arrays of indices into outs and ins. Parameters ---------- full_idxs : ndarray Indices into the full array (which could be outs + ins or just ins) inputs : Vector Inputs vector. outputs : Vector Outputs vector. use_full_cols : bool If True, full idxs are into the full outs + ins vector. is_total : bool If True, total derivatives are being computed and wrt vector is the outputs vector. Returns ------- list of tuples Each tuple is of the form (array, idxs). """ assert len(full_idxs) > 0, "Empty index array passed to get_input_idx_split." full_idxs = np.asarray(full_idxs) if use_full_cols: out_size = outputs._data.size out_idxs = full_idxs[full_idxs < out_size] in_idxs = full_idxs[full_idxs >= out_size] if out_idxs.size > 0 and in_idxs.size > 0: return [(inputs, in_idxs - out_size), (outputs, out_idxs)] elif in_idxs.size > 0: return [(inputs, in_idxs - out_size)] else: return [(outputs, out_idxs)] elif is_total: return [(outputs, full_idxs)] else: return [(inputs, full_idxs)]
def _flatten_src_indices(src_indices, shape_in, shape_out, size_out): """ Convert src_indices into a flat, non-negative form. Parameters ---------- src_indices : ndarray Array of src_indices. Can be flat or multi-dimensional. shape_in : tuple Shape of the input variable. shape_out : tuple Shape of the output variable. size_out : int Size of the output variable. Returns ------- ndarray The flattened src_indices. """ if len(shape_out) == 1 or shape_in == src_indices.shape: return convert_neg(src_indices.flatten(), size_out) entries = [list(range(x)) for x in shape_in] cols = np.vstack([src_indices[i] for i in product(*entries)]) dimidxs = [convert_neg(cols[:, i], shape_out[i]) for i in range(cols.shape[1])] return np.ravel_multi_index(dimidxs, shape_out)
[docs]def sizes2offsets(size_array): """ For a given array of sizes, return an array of offsets. Offsets will be computed using a flattened version of size_array and then reshaped to match the shape of size_array. Parameters ---------- size_array : ndarray Array of sizes. Returns ------- ndarray Array of offsets. """ offsets = np.zeros(size_array.size, dtype=size_array.dtype) offsets[1:] = np.cumsum(size_array.flat)[:-1] return offsets.reshape(size_array.shape)
[docs]def abs_complex(x): """ Compute the absolute value of a complex-stepped vector. Rather than taking a Euclidian norm, simply negate the values that are less than zero. Parameters ---------- x : ndarray Input array. Returns ------- ndarray Complex-step absolute value of the array. """ idx_neg = np.where(x < 0) x[idx_neg] = -x[idx_neg] return x
[docs]def dv_abs_complex(x, x_deriv): """ Compute the complex-step derivative of the absolute value function and its derivative. Parameters ---------- x : ndarray Input array, used for determining which elements to negate. x_deriv : ndarray Incominng partial derivative array, may have one additional dimension. Returns ------- ndarray Absolute value applied to x. ndarray Absolute value applied to x_deriv. """ idx_neg = np.where(x < 0) # Special case when x is (1, ) and x_deriv is (1, n). if len(x_deriv.shape) == 1: if idx_neg[0].size != 0: return -x, -x_deriv x[idx_neg] = -x[idx_neg] x_deriv[idx_neg] = -x_deriv[idx_neg] return x, x_deriv