How to create arrays of missing data#
Data at any level of an Awkward Array can be “missing,” represented by None in Python.
This functionality is somewhat like NumPy’s masked arrays, but masked arrays can only declare numerical values to be missing (not, for instance, a row of a 2-dimensional array) and they represent missing data with an np.ma.masked object instead of None.
Pandas also handles missing data, but in several different ways. For floating point columns, NaN (not a number) is used to mean “missing,” and as of version 1.0, Pandas has a pd.NA object for missing data in other data types.
In Awkward Array, floating point NaN and a missing value are clearly distinct. Missing data, like all data in Awkward Arrays, are also not represented by any Python object; they are converted to and from None by ak.to_list() and ak.from_iter().
import awkward as ak
import numpy as np
From Python None#
The ak.Array constructor and ak.from_iter() interpret None as a missing value, and ak.to_list() converts them back into None.
ak.Array([1, 2, 3, None, 4, 5])
[1, 2, 3, None, 4, 5] ---------------- type: 6 * ?int64
The missing values can be deeply nested (missing integers):
ak.Array([[[[], [1, 2, None]]], [[[3]]], []])
[[[[], [1, 2, None]]], [[[3]]], []] ---------------------------------- type: 3 * var * var * var * ?int64
They can be shallow (missing lists):
ak.Array([[[[], [1, 2]]], None, [[[3]]], []])
[[[[], [1, 2]]], None, [[[3]]], []] ----------------------------------------- type: 4 * option[var * var * var * int64]
Or both:
ak.Array([[[[], [3]]], None, [[[None]]], []])
[[[[], [3]]], None, [[[None]]], []] ------------------------------------------ type: 4 * option[var * var * var * ?int64]
Records can also be missing:
ak.Array([{"x": 1, "y": 1}, None, {"x": 2, "y": 2}])
[{x: 1, y: 1},
None,
{x: 2, y: 2}]
--------------
type: 3 * ?{
x: int64,
y: int64
}Potentially missing values are represented in the type string as “?” or “option[...]” (if the nested type is a list, which needs to be bracketed for clarity).
From NumPy arrays#
Normal NumPy arrays can’t represent missing data, but masked arrays can. Here is how one is constructed in NumPy:
numpy_array = np.ma.MaskedArray([1, 2, 3, 4, 5], [False, False, True, True, False])
numpy_array
masked_array(data=[1, 2, --, --, 5],
mask=[False, False, True, True, False],
fill_value=999999)
It returns np.ma.masked objects if you try to access missing values:
numpy_array[0], numpy_array[1], numpy_array[2], numpy_array[3], numpy_array[4]
(1, 2, masked, masked, 5)
But it uses None for missing values in tolist:
numpy_array.tolist()
[1, 2, None, None, 5]
The ak.from_numpy() function converts masked arrays into Awkward Arrays with missing values, as does the ak.Array constructor.
awkward_array = ak.Array(numpy_array)
awkward_array
[1, 2, None, None, 5] ---------------- type: 5 * ?int64
The reverse, ak.to_numpy(), returns masked arrays if the Awkward Array has missing data.
ak.to_numpy(awkward_array)
masked_array(data=[1, 2, --, --, 5],
mask=[False, False, True, True, False],
fill_value=999999)
But np.asarray, the usual way of casting data as NumPy arrays, does not. (np.asarray is supposed to return a plain np.ndarray, which np.ma.masked_array is not.)
np.asarray(awkward_array)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/highlevel.py:1289, in Array.__array__(self, *args, **kwargs)
1288 with ak._errors.OperationErrorContext("numpy.asarray", arguments):
-> 1289 return ak._connect.numpy.convert_to_array(self._layout, args, kwargs)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_connect/numpy.py:37, in convert_to_array(layout, args, kwargs)
36 def convert_to_array(layout, args, kwargs):
---> 37 out = ak.operations.to_numpy(layout, allow_missing=False)
38 if args == () and kwargs == {}:
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/operations/ak_to_numpy.py:42, in to_numpy(array, allow_missing)
38 with ak._errors.OperationErrorContext(
39 "ak.to_numpy",
40 {"array": array, "allow_missing": allow_missing},
41 ):
---> 42 return _impl(array, allow_missing)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/operations/ak_to_numpy.py:54, in _impl(array, allow_missing)
52 numpy_layout = layout.to_backend(backend)
---> 54 return numpy_layout.to_backend_array(allow_missing=allow_missing)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/contents/content.py:1108, in Content.to_backend_array(self, allow_missing, backend)
1107 backend = regularize_backend(backend)
-> 1108 return self._to_backend_array(allow_missing, backend)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/contents/bytemaskedarray.py:1042, in ByteMaskedArray._to_backend_array(self, allow_missing, backend)
1041 def _to_backend_array(self, allow_missing, backend):
-> 1042 return self.to_IndexedOptionArray64()._to_backend_array(allow_missing, backend)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/contents/indexedoptionarray.py:1582, in IndexedOptionArray._to_backend_array(self, allow_missing, backend)
1581 else:
-> 1582 raise ValueError(
1583 "Content.to_nplike cannot convert 'None' values to "
1584 "np.ma.MaskedArray unless the "
1585 "'allow_missing' parameter is set to True"
1586 )
1587 else:
ValueError: Content.to_nplike cannot convert 'None' values to np.ma.MaskedArray unless the 'allow_missing' parameter is set to True
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
Cell In[12], line 1
----> 1 np.asarray(awkward_array)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/highlevel.py:1288, in Array.__array__(self, *args, **kwargs)
1286 arguments[i + 1] = arg
1287 arguments.update(kwargs)
-> 1288 with ak._errors.OperationErrorContext("numpy.asarray", arguments):
1289 return ak._connect.numpy.convert_to_array(self._layout, args, kwargs)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_errors.py:56, in ErrorContext.__exit__(self, exception_type, exception_value, traceback)
53 try:
54 # Handle caught exception
55 if exception_type is not None and self.primary() is self:
---> 56 self.handle_exception(exception_type, exception_value)
57 finally:
58 # `_kwargs` may hold cyclic references, that we really want to avoid
59 # as this can lead to large buffers remaining in memory for longer than absolutely necessary
60 # Let's just clear this, now.
61 self._kwargs.clear()
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_errors.py:71, in ErrorContext.handle_exception(self, cls, exception)
69 self.decorate_exception(cls, exception)
70 else:
---> 71 raise self.decorate_exception(cls, exception)
ValueError: Content.to_nplike cannot convert 'None' values to np.ma.MaskedArray unless the 'allow_missing' parameter is set to True
This error occurred while calling
numpy.asarray(
<Array [1, 2, None, None, 5] type='5 * ?int64'>
)
Missing rows vs missing numbers#
In Awkward Array, a missing list is a different thing from a list whose values are missing. However, ak.to_numpy() converts it for you.
missing_row = ak.Array([[1, 2, 3], None, [4, 5, 6]])
missing_row
[[1, 2, 3], None, [4, 5, 6]] ----------------------------- type: 3 * option[var * int64]
ak.to_numpy(missing_row)
masked_array(
data=[[1, 2, 3],
[--, --, --],
[4, 5, 6]],
mask=[[False, False, False],
[ True, True, True],
[False, False, False]],
fill_value=999999)
NaN is not missing#
Floating point NaN values are simply unrelated to missing values, in both Awkward Array and NumPy.
missing_with_nan = ak.Array([1.1, 2.2, np.nan, None, 3.3])
missing_with_nan
[1.1, 2.2, nan, None, 3.3] ------------------ type: 5 * ?float64
ak.to_numpy(missing_with_nan)
masked_array(data=[1.1, 2.2, nan, --, 3.3],
mask=[False, False, False, True, False],
fill_value=1e+20)
Missing values as empty lists#
Sometimes, it’s useful to think about a potentially missing value as a length-1 list if it is not missing and a length-0 list if it is. (Some languages define the option type as a kind of list.)
The Awkward functions ak.singletons() and ak.firsts() convert from “None form” to and from “lists form.”
none_form = ak.Array([1, 2, 3, None, None, 5])
none_form
[1, 2, 3, None, None, 5] ---------------- type: 6 * ?int64
lists_form = ak.singletons(none_form)
lists_form
[[1], [2], [3], [], [], [5]] --------------------- type: 6 * var * int64
ak.firsts(lists_form)
[1, 2, 3, None, None, 5] ---------------- type: 6 * ?int64
Masking instead of slicing#
The most common way of filtering data is to slice it with an array of booleans (usually the result of a calculation).
array = ak.Array([1, 2, 3, 4, 5])
array
[1, 2, 3, 4, 5] --------------- type: 5 * int64
booleans = ak.Array([True, True, False, False, True])
booleans
[True, True, False, False, True] -------------- type: 5 * bool
array[booleans]
[1, 2, 5] --------------- type: 3 * int64
The data can also be effectively filtered by replacing values with None. The following syntax does that:
array.mask[booleans]
[1, 2, None, None, 5] ---------------- type: 5 * ?int64
(Or use the ak.mask() function.)
An advantage of masking is that the length and nesting structure of the masked array is the same as the original array, so anything that broadcasts with one broadcasts with the other (so that unfiltered data can be used interchangeably with filtered data).
array + array.mask[booleans]
[2, 4, None, None, 10] ---------------- type: 5 * ?int64
whereas
array + array[booleans]
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/highlevel.py:1362, in Array.__array_ufunc__(self, ufunc, method, *inputs, **kwargs)
1361 with ak._errors.OperationErrorContext(name, arguments):
-> 1362 return ak._connect.numpy.array_ufunc(ufunc, method, inputs, kwargs)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_connect/numpy.py:321, in array_ufunc(ufunc, method, inputs, kwargs)
320 else:
--> 321 out = ak._broadcasting.broadcast_and_apply(
322 inputs, action, behavior, allow_records=False, function_name=ufunc.__name__
323 )
324 assert isinstance(out, tuple) and len(out) == 1
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_broadcasting.py:1098, in broadcast_and_apply(inputs, action, behavior, depth_context, lateral_context, allow_records, left_broadcast, right_broadcast, numpy_to_regular, regular_to_jagged, function_name, broadcast_parameters_rule)
1097 isscalar = []
-> 1098 out = apply_step(
1099 backend,
1100 broadcast_pack(inputs, isscalar),
1101 action,
1102 0,
1103 depth_context,
1104 lateral_context,
1105 behavior,
1106 {
1107 "allow_records": allow_records,
1108 "left_broadcast": left_broadcast,
1109 "right_broadcast": right_broadcast,
1110 "numpy_to_regular": numpy_to_regular,
1111 "regular_to_jagged": regular_to_jagged,
1112 "function_name": function_name,
1113 "broadcast_parameters_rule": broadcast_parameters_rule,
1114 },
1115 )
1116 assert isinstance(out, tuple)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_broadcasting.py:1077, in apply_step(backend, inputs, action, depth, depth_context, lateral_context, behavior, options)
1076 elif result is None:
-> 1077 return continuation()
1078 else:
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_broadcasting.py:1050, in apply_step.<locals>.continuation()
1049 elif any(x.is_list for x in contents):
-> 1050 return broadcast_any_list()
1052 # Any RecordArrays?
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_broadcasting.py:571, in apply_step.<locals>.broadcast_any_list()
570 else:
--> 571 raise ValueError(
572 "cannot broadcast RegularArray of size "
573 "{} with RegularArray of size {} {}".format(
574 x.size, dim_size, in_function(options)
575 )
576 )
577 else:
ValueError: cannot broadcast RegularArray of size 3 with RegularArray of size 5 in add
The above exception was the direct cause of the following exception:
ValueError Traceback (most recent call last)
Cell In[25], line 1
----> 1 array + array[booleans]
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/numpy/lib/mixins.py:21, in _binary_method.<locals>.func(self, other)
19 if _disables_array_ufunc(other):
20 return NotImplemented
---> 21 return ufunc(self, other)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/highlevel.py:1361, in Array.__array_ufunc__(self, ufunc, method, *inputs, **kwargs)
1359 arguments[i] = arg
1360 arguments.update(kwargs)
-> 1361 with ak._errors.OperationErrorContext(name, arguments):
1362 return ak._connect.numpy.array_ufunc(ufunc, method, inputs, kwargs)
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_errors.py:56, in ErrorContext.__exit__(self, exception_type, exception_value, traceback)
53 try:
54 # Handle caught exception
55 if exception_type is not None and self.primary() is self:
---> 56 self.handle_exception(exception_type, exception_value)
57 finally:
58 # `_kwargs` may hold cyclic references, that we really want to avoid
59 # as this can lead to large buffers remaining in memory for longer than absolutely necessary
60 # Let's just clear this, now.
61 self._kwargs.clear()
File ~/micromamba-root/envs/awkward-docs/lib/python3.10/site-packages/awkward/_errors.py:71, in ErrorContext.handle_exception(self, cls, exception)
69 self.decorate_exception(cls, exception)
70 else:
---> 71 raise self.decorate_exception(cls, exception)
ValueError: cannot broadcast RegularArray of size 3 with RegularArray of size 5 in add
This error occurred while calling
numpy.add.__call__(
<Array [1, 2, 3, 4, 5] type='5 * int64'>
<Array [1, 2, 5] type='3 * int64'>
)
With ArrayBuilder#
ak.ArrayBuilder is described in more detail in this tutorial, but you can add missing values to an array using the null method or appending None.
(This is what ak.from_iter() uses internally to accumulate data.)
builder = ak.ArrayBuilder()
builder.append(1)
builder.append(2)
builder.null()
builder.append(None)
builder.append(3)
array = builder.snapshot()
array
[1, 2, None, None, 3] ---------------- type: 5 * ?int64
In Numba#
Functions that Numba Just-In-Time (JIT) compiles can use ak.ArrayBuilder or construct a boolean array for ak.mask().
(ak.ArrayBuilder can’t be constructed or converted to an array using snapshot inside a JIT-compiled function, but can be outside the compiled context.)
import numba as nb
@nb.jit
def example(builder):
builder.append(1)
builder.append(2)
builder.null()
builder.append(None)
builder.append(3)
return builder
builder = example(ak.ArrayBuilder())
array = builder.snapshot()
array
/tmp/ipykernel_8866/3685422949.py:2: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def example(builder):
[1, 2, None, None, 3] ---------------- type: 5 * ?int64
@nb.jit
def faster_example():
data = np.empty(5, np.int64)
mask = np.empty(5, np.bool_)
data[0] = 1
mask[0] = True
data[1] = 2
mask[1] = True
mask[2] = False
mask[3] = False
data[4] = 5
mask[4] = True
return data, mask
data, mask = faster_example()
array = ak.Array(data).mask[mask]
array
/tmp/ipykernel_8866/2461453671.py:2: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def faster_example():
[1, 2, None, None, 5] ---------------- type: 5 * ?int64