Source code for astropy.table.np_utils

High-level operations for numpy structured arrays.

Some code and inspiration taken from numpy.lib.recfunctions.join_by().
Redistribution license restrictions apply.

import collections
from collections import OrderedDict, Counter
from import Sequence

import numpy as np

__all__ = ['TableMergeError']

[docs]class TableMergeError(ValueError): pass
def get_col_name_map(arrays, common_names, uniq_col_name='{col_name}_{table_name}', table_names=None): """ Find the column names mapping when merging the list of structured ndarrays ``arrays``. It is assumed that col names in ``common_names`` are to be merged into a single column while the rest will be uniquely represented in the output. The args ``uniq_col_name`` and ``table_names`` specify how to rename columns in case of conflicts. Returns a dict mapping each output column name to the input(s). This takes the form {outname : (col_name_0, col_name_1, ...), ... }. For key columns all of input names will be present, while for the other non-key columns the value will be (col_name_0, None, ..) or (None, col_name_1, ..) etc. """ col_name_map = collections.defaultdict(lambda: [None] * len(arrays)) col_name_list = [] if table_names is None: table_names = [str(ii + 1) for ii in range(len(arrays))] for idx, array in enumerate(arrays): table_name = table_names[idx] for name in array.dtype.names: out_name = name if name in common_names: # If name is in the list of common_names then insert into # the column name list, but just once. if name not in col_name_list: col_name_list.append(name) else: # If name is not one of the common column outputs, and it collides # with the names in one of the other arrays, then rename others = list(arrays) others.pop(idx) if any(name in other.dtype.names for other in others): out_name = uniq_col_name.format(table_name=table_name, col_name=name) col_name_list.append(out_name) col_name_map[out_name][idx] = name # Check for duplicate output column names col_name_count = Counter(col_name_list) repeated_names = [name for name, count in col_name_count.items() if count > 1] if repeated_names: raise TableMergeError('Merging column names resulted in duplicates: {}. ' 'Change uniq_col_name or table_names args to fix this.' .format(repeated_names)) # Convert col_name_map to a regular dict with tuple (immutable) values col_name_map = OrderedDict((name, col_name_map[name]) for name in col_name_list) return col_name_map def get_descrs(arrays, col_name_map): """ Find the dtypes descrs resulting from merging the list of arrays' dtypes, using the column name mapping ``col_name_map``. Return a list of descrs for the output. """ out_descrs = [] for out_name, in_names in col_name_map.items(): # List of input arrays that contribute to this output column in_cols = [arr[name] for arr, name in zip(arrays, in_names) if name is not None] # List of names of the columns that contribute to this output column. names = [name for name in in_names if name is not None] # Output dtype is the superset of all dtypes in in_arrays try: dtype = common_dtype(in_cols) except TableMergeError as tme: # Beautify the error message when we are trying to merge columns with incompatible # types by including the name of the columns that originated the error. raise TableMergeError("The '{}' columns have incompatible types: {}" .format(names[0], tme._incompat_types)) # Make sure all input shapes are the same uniq_shapes = set(col.shape[1:] for col in in_cols) if len(uniq_shapes) != 1: raise TableMergeError(f'Key columns have different shape') shape = uniq_shapes.pop() out_descrs.append((fix_column_name(out_name), dtype, shape)) return out_descrs def common_dtype(cols): """ Use numpy to find the common dtype for a list of structured ndarray columns. Only allow columns within the following fundamental numpy data types: np.bool_, np.object_, np.number, np.character, np.void """ np_types = (np.bool_, np.object_, np.number, np.character, np.void) uniq_types = set(tuple(issubclass(col.dtype.type, np_type) for np_type in np_types) for col in cols) if len(uniq_types) > 1: # Embed into the exception the actual list of incompatible types. incompat_types = [ for col in cols] tme = TableMergeError('Columns have incompatible types {}' .format(incompat_types)) tme._incompat_types = incompat_types raise tme arrs = [np.empty(1, dtype=col.dtype) for col in cols] # For string-type arrays need to explicitly fill in non-zero # values or the final arr_common = .. step is unpredictable. for arr in arrs: if arr.dtype.kind in ('S', 'U'): arr[0] = '0' * arr.itemsize arr_common = np.array([arr[0] for arr in arrs]) return arr_common.dtype.str def _check_for_sequence_of_structured_arrays(arrays): err = '`arrays` arg must be a sequence (e.g. list) of structured arrays' if not isinstance(arrays, Sequence): raise TypeError(err) for array in arrays: # Must be structured array if not isinstance(array, np.ndarray) or array.dtype.names is None: raise TypeError(err) if len(arrays) == 0: raise ValueError('`arrays` arg must include at least one array') def fix_column_name(val): """ Fixes column names so that they are compatible with Numpy on Python 2. Raises a ValueError exception if the column name contains Unicode characters, which can not reasonably be used as a column name. """ if val is not None: try: val = str(val) except UnicodeEncodeError: raise return val