# Licensed under a 3-clause BSD style license - see LICENSE.rst import platform import warnings import numpy as np from .index import get_index_by_names from astropy.utils.exceptions import AstropyUserWarning __all__ = ['TableGroups', 'ColumnGroups'] def table_group_by(table, keys): # index copies are unnecessary and slow down _table_group_by with table.index_mode('discard_on_copy'): return _table_group_by(table, keys) def _table_group_by(table, keys): """ Get groups for ``table`` on specified ``keys``. Parameters ---------- table : `Table` Table to group keys : str, list of str, `Table`, or Numpy array Grouping key specifier Returns ------- grouped_table : Table object with groups attr set accordingly """ from .table import Table from .serialize import represent_mixins_as_columns # Pre-convert string to tuple of strings, or Table to the underlying structured array if isinstance(keys, str): keys = (keys,) if isinstance(keys, (list, tuple)): for name in keys: if name not in table.colnames: raise ValueError(f'Table does not have key column {name!r}') if table.masked and np.any(table[name].mask): raise ValueError(f'Missing values in key column {name!r} are not allowed') # Make a column slice of the table without copying table_keys = table.__class__([table[key] for key in keys], copy=False) # If available get a pre-existing index for these columns table_index = get_index_by_names(table, keys) grouped_by_table_cols = True elif isinstance(keys, (np.ndarray, Table)): table_keys = keys if len(table_keys) != len(table): raise ValueError('Input keys array length {} does not match table length {}' .format(len(table_keys), len(table))) table_index = None grouped_by_table_cols = False else: raise TypeError('Keys input must be string, list, tuple, Table or numpy array, but got {}' .format(type(keys))) # If there is not already an available index and table_keys is a Table then ensure # that all cols (including mixins) are in a form that can sorted with the code below. if not table_index and isinstance(table_keys, Table): table_keys = represent_mixins_as_columns(table_keys) # Get the argsort index `idx_sort`, accounting for particulars try: # take advantage of index internal sort if possible if table_index is not None: idx_sort = table_index.sorted_data() else: idx_sort = table_keys.argsort(kind='mergesort') stable_sort = True except TypeError: # Some versions (likely 1.6 and earlier) of numpy don't support # 'mergesort' for all data types. MacOSX (Darwin) doesn't have a stable # sort by default, nor does Windows, while Linux does (or appears to). idx_sort = table_keys.argsort() stable_sort = platform.system() not in ('Darwin', 'Windows') # Finally do the actual sort of table_keys values table_keys = table_keys[idx_sort] # Get all keys diffs = np.concatenate(([True], table_keys[1:] != table_keys[:-1], [True])) indices = np.flatnonzero(diffs) # If the sort is not stable (preserves original table order) then sort idx_sort in # place within each group. if not stable_sort: for i0, i1 in zip(indices[:-1], indices[1:]): idx_sort[i0:i1].sort() # Make a new table and set the _groups to the appropriate TableGroups object. # Take the subset of the original keys at the indices values (group boundaries). out = table.__class__(table[idx_sort]) out_keys = table_keys[indices[:-1]] if isinstance(out_keys, Table): out_keys.meta['grouped_by_table_cols'] = grouped_by_table_cols out._groups = TableGroups(out, indices=indices, keys=out_keys) return out def column_group_by(column, keys): """ Get groups for ``column`` on specified ``keys`` Parameters ---------- column : Column object Column to group keys : Table or Numpy array of same length as col Grouping key specifier Returns ------- grouped_column : Column object with groups attr set accordingly """ from .table import Table from .serialize import represent_mixins_as_columns if isinstance(keys, Table): keys = represent_mixins_as_columns(keys) keys = keys.as_array() if not isinstance(keys, np.ndarray): raise TypeError(f'Keys input must be numpy array, but got {type(keys)}') if len(keys) != len(column): raise ValueError('Input keys array length {} does not match column length {}' .format(len(keys), len(column))) idx_sort = keys.argsort() keys = keys[idx_sort] # Get all keys diffs = np.concatenate(([True], keys[1:] != keys[:-1], [True])) indices = np.flatnonzero(diffs) # Make a new column and set the _groups to the appropriate ColumnGroups object. # Take the subset of the original keys at the indices values (group boundaries). out = column.__class__(column[idx_sort]) out._groups = ColumnGroups(out, indices=indices, keys=keys[indices[:-1]]) return out class BaseGroups: """ A class to represent groups within a table of heterogeneous data. - ``keys``: key values corresponding to each group - ``indices``: index values in parent table or column corresponding to group boundaries - ``aggregate()``: method to create new table by aggregating within groups """ @property def parent(self): return self.parent_column if isinstance(self, ColumnGroups) else self.parent_table def __iter__(self): self._iter_index = 0 return self def next(self): ii = self._iter_index if ii < len(self.indices) - 1: i0, i1 = self.indices[ii], self.indices[ii + 1] self._iter_index += 1 return self.parent[i0:i1] else: raise StopIteration __next__ = next def __getitem__(self, item): parent = self.parent if isinstance(item, (int, np.integer)): i0, i1 = self.indices[item], self.indices[item + 1] out = parent[i0:i1] out.groups._keys = parent.groups.keys[item] else: indices0, indices1 = self.indices[:-1], self.indices[1:] try: i0s, i1s = indices0[item], indices1[item] except Exception as err: raise TypeError('Index item for groups attribute must be a slice, ' 'numpy mask or int array') from err mask = np.zeros(len(parent), dtype=bool) # Is there a way to vectorize this in numpy? for i0, i1 in zip(i0s, i1s): mask[i0:i1] = True out = parent[mask] out.groups._keys = parent.groups.keys[item] out.groups._indices = np.concatenate([[0], np.cumsum(i1s - i0s)]) return out def __repr__(self): return f'<{self.__class__.__name__} indices={self.indices}>' def __len__(self): return len(self.indices) - 1 class ColumnGroups(BaseGroups): def __init__(self, parent_column, indices=None, keys=None): self.parent_column = parent_column # parent Column self.parent_table = parent_column.parent_table self._indices = indices self._keys = keys @property def indices(self): # If the parent column is in a table then use group indices from table if self.parent_table: return self.parent_table.groups.indices else: if self._indices is None: return np.array([0, len(self.parent_column)]) else: return self._indices @property def keys(self): # If the parent column is in a table then use group indices from table if self.parent_table: return self.parent_table.groups.keys else: return self._keys def aggregate(self, func): from .column import MaskedColumn i0s, i1s = self.indices[:-1], self.indices[1:] par_col = self.parent_column masked = isinstance(par_col, MaskedColumn) reduceat = hasattr(func, 'reduceat') sum_case = func is np.sum mean_case = func is np.mean try: if not masked and (reduceat or sum_case or mean_case): if mean_case: vals = np.add.reduceat(par_col, i0s) / np.diff(self.indices) else: if sum_case: func = np.add vals = func.reduceat(par_col, i0s) else: vals = np.array([func(par_col[i0: i1]) for i0, i1 in zip(i0s, i1s)]) except Exception as err: raise TypeError("Cannot aggregate column '{}' with type '{}'" .format(par_col.info.name, par_col.info.dtype)) from err out = par_col.__class__(data=vals, name=par_col.info.name, description=par_col.info.description, unit=par_col.info.unit, format=par_col.info.format, meta=par_col.info.meta) return out def filter(self, func): """ Filter groups in the Column based on evaluating function ``func`` on each group sub-table. The function which is passed to this method must accept one argument: - ``column`` : `Column` object It must then return either `True` or `False`. As an example, the following will select all column groups with only positive values:: def all_positive(column): if np.any(column < 0): return False return True Parameters ---------- func : function Filter function Returns ------- out : Column New column with the aggregated rows. """ mask = np.empty(len(self), dtype=bool) for i, group_column in enumerate(self): mask[i] = func(group_column) return self[mask] class TableGroups(BaseGroups): def __init__(self, parent_table, indices=None, keys=None): self.parent_table = parent_table # parent Table self._indices = indices self._keys = keys @property def key_colnames(self): """ Return the names of columns in the parent table that were used for grouping. """ # If the table was grouped by key columns *in* the table then treat those columns # differently in aggregation. In this case keys will be a Table with # keys.meta['grouped_by_table_cols'] == True. Keys might not be a Table so we # need to handle this. grouped_by_table_cols = getattr(self.keys, 'meta', {}).get('grouped_by_table_cols', False) return self.keys.colnames if grouped_by_table_cols else () @property def indices(self): if self._indices is None: return np.array([0, len(self.parent_table)]) else: return self._indices def aggregate(self, func): """ Aggregate each group in the Table into a single row by applying the reduction function ``func`` to group values in each column. Parameters ---------- func : function Function that reduces an array of values to a single value Returns ------- out : Table New table with the aggregated rows. """ i0s = self.indices[:-1] out_cols = [] parent_table = self.parent_table for col in parent_table.columns.values(): # For key columns just pick off first in each group since they are identical if col.info.name in self.key_colnames: new_col = col.take(i0s) else: try: new_col = col.groups.aggregate(func) except TypeError as err: warnings.warn(str(err), AstropyUserWarning) continue out_cols.append(new_col) return parent_table.__class__(out_cols, meta=parent_table.meta) def filter(self, func): """ Filter groups in the Table based on evaluating function ``func`` on each group sub-table. The function which is passed to this method must accept two arguments: - ``table`` : `Table` object - ``key_colnames`` : tuple of column names in ``table`` used as keys for grouping It must then return either `True` or `False`. As an example, the following will select all table groups with only positive values in the non-key columns:: def all_positive(table, key_colnames): colnames = [name for name in table.colnames if name not in key_colnames] for colname in colnames: if np.any(table[colname] < 0): return False return True Parameters ---------- func : function Filter function Returns ------- out : Table New table with the aggregated rows. """ mask = np.empty(len(self), dtype=bool) key_colnames = self.key_colnames for i, group_table in enumerate(self): mask[i] = func(group_table, key_colnames) return self[mask] @property def keys(self): return self._keys