# Copyright (c) 2017 The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import itertools
import logging
import sys
import numpy
logger = logging.getLogger(__file__)
[docs]class AbstractSized(object):
"""
Base class for slice and ID checking against size.
"""
__slots__ = (
"_size")
def __init__(self, size):
"""
:param size: Fixed length of the list
"""
self._size = max(int(round(size)), 0)
def __len__(self):
"""
Size of the list, irrespective of actual values.
:return: the initial and Fixed size of the list
"""
return self._size
@staticmethod
def _is_id_type(the_id):
"""
Check if the given ID has a type acceptable for IDs.
"""
return isinstance(the_id, int)
def _check_id_in_range(self, the_id):
if the_id < 0:
if self._is_id_type(the_id):
raise IndexError(f"The index {the_id} is out of range.")
# pragma: no cover
raise TypeError(f"Invalid argument type {type(the_id)}.")
if the_id >= self._size:
if self._is_id_type(the_id):
raise IndexError(f"The index {the_id} is out of range.")
raise TypeError(f"Invalid argument type {type(the_id)}.")
def _check_slice_in_range(self, slice_start, slice_stop):
if slice_start is None:
slice_start = 0
elif slice_start < 0:
slice_start = self._size + slice_start
if slice_start < 0:
if not self._is_id_type(slice_start):
raise TypeError(
f"Invalid argument type {type(slice_start)}.")
logger.warning(
"Specified slice start was %d while size is only %d. "
"Therefore slice will start at index 0",
slice_start - self._size, self._size)
slice_start = 0
elif slice_start >= len(self):
logger.warning(
"Specified slice start was %d while size is only %d. "
"Therefore slice will be empty",
slice_start - self._size, self._size)
return (self._size, self._size)
if slice_stop is None or slice_stop == sys.maxsize:
slice_stop = self._size
elif slice_stop < 0:
slice_stop = self._size + slice_stop
if slice_start > slice_stop:
if not self._is_id_type(slice_start):
raise TypeError(f"Invalid argument type {type(slice_start)}.")
if not self._is_id_type(slice_stop):
raise TypeError(f"Invalid argument type {type(slice_stop)}.")
logger.warning(
"Specified slice has a start %d greater than its stop %d "
"(based on size %d). Therefore slice will be empty",
slice_start, slice_stop, self._size)
return (self._size, self._size)
if slice_stop > len(self):
if not self._is_id_type(slice_stop):
raise TypeError(f"Invalid argument type {type(slice_stop)}.")
logger.warning(
"Specified slice has a start %d equal to its stop %d "
"(based on size %d). Therefore slice will be empty",
slice_start, slice_stop, self._size)
if slice_stop < 0:
logger.warning(
"Specified slice stop was %d while size is only %d. "
"Therefore slice will be empty",
slice_stop - self._size, self._size)
return (self._size, self._size)
elif slice_start > slice_stop:
logger.warning(
"Specified slice has a start %d greater than its stop %d "
"(based on size %d). Therefore slice will be empty",
slice_start, slice_stop, self._size)
return (self._size, self._size)
elif slice_start == slice_stop:
logger.warning(
"Specified slice has a start %d equal to its stop %d "
"(based on size %d). Therefore slice will be empty",
slice_start, slice_stop, self._size)
elif slice_stop > len(self):
logger.warning(
"Specified slice stop was %d while size is only %d. "
"Therefore slice will be truncated",
slice_stop, self._size)
slice_stop = self._size
return slice_start, slice_stop
def _check_mask_size(self, selector):
if len(selector) < self._size:
logger.warning(
"The boolean mask is too short. The expected length was %d "
"but the length was only %d. All the missing entries will be "
"treated as False!", self._size, len(selector))
elif len(selector) > self._size:
logger.warning(
"The boolean mask is too long. The expected length was %d "
"but the length was only %d. All the missing entries will be "
"ignored!", self._size, len(selector))
[docs] def selector_to_ids(self, selector, warn=False):
"""
Gets the list of IDs covered by this selector.
The types of selector currently supported are:
`None`:
Returns all IDs.
slice: Standard python slice.
Negative values and values larger than size are handled using
slices's `indices` method.
This could result in am empty list.
int: Handles negative values as normal.
Checks if ID is within expected range.
iterator(bool): Used as a mask.
If the length of the mask is longer or shorted than number of IDs
the result is the shorter of the two,
with the remainder of the longer ignored.
iterator(int) but not bool:
Every value checked that it is with the range 0 to size.
Negative values are *not* allowed.
Original order and duplication is respected so result may be
unordered and contain duplicates.
:param selector: Some object that identifies a range of IDs.
:param bool warn:
If True, this method will warn about problems with the selector.
:return: a (possibly sorted) list of IDs
"""
# Check selector is an iterable using pythonic try
try:
iterator = iter(selector)
except TypeError:
iterator = None
if iterator is not None:
# bool is superclass of int so if any are bools all must be
if any(isinstance(item, (bool, numpy.bool_)) for item in selector):
if all(isinstance(item, (bool, numpy.bool_))
for item in selector):
if warn:
self._check_mask_size(selector)
return list(itertools.compress(
range(self._size), selector))
raise TypeError(
"An iterable type must be all ints or all bools")
elif all(isinstance(item, (int, numpy.integer))
for item in selector):
# list converts any specific numpy types
ids = list(selector)
for _id in ids:
if _id < 0:
raise TypeError(
f"Selector includes the ID {_id} which is "
"less than zero")
if _id >= self._size:
raise TypeError(
f"Selector includes the ID {_id} which not "
f"less than the size {self._size}")
return ids
else:
raise TypeError(
"An iterable type must be all ints or all bools")
# OK lets try for None, int and slice after all
if selector is None:
if warn:
logger.warning("None selector taken as all IDs")
return range(self._size)
if isinstance(selector, slice):
(slice_start, slice_stop, step) = selector.indices(self._size)
return range(slice_start, slice_stop, step)
if isinstance(selector, int):
if selector < 0:
selector = self._size + selector
if selector < 0 or selector >= self._size:
raise TypeError(
f"Selector {selector-self._size} is unsupported "
f"for size {self._size}")
return [selector]
raise TypeError(f"Unexpected selector type {type(selector)}")