"""
Tests for chunked adjustments.
"""
from collections import namedtuple
from itertools import chain, product
from textwrap import dedent
from unittest import TestCase
from nose_parameterized import parameterized
from numpy import (
arange,
array,
asarray,
dtype,
full,
where,
)
from six.moves import zip_longest
from toolz import curry
from catalyst.errors import WindowLengthNotPositive, WindowLengthTooLong
from catalyst.lib.adjustment import (
Datetime64Overwrite,
Datetime641DArrayOverwrite,
Float64Multiply,
Float64Overwrite,
Float641DArrayOverwrite,
Int64Overwrite,
ObjectOverwrite,
)
from catalyst.lib.adjusted_array import AdjustedArray, NOMASK
from catalyst.lib.labelarray import LabelArray
from catalyst.testing import check_arrays, parameter_space
from catalyst.utils.compat import unicode
from catalyst.utils.numpy_utils import (
coerce_to_dtype,
datetime64ns_dtype,
default_missing_value_for_dtype,
float64_dtype,
int64_dtype,
object_dtype,
)
def moving_window(array, nrows):
"""
Simple moving window generator over a 2D numpy array.
"""
count = num_windows_of_length_M_on_buffers_of_length_N(nrows, len(array))
for i in range(count):
yield array[i:i + nrows]
def num_windows_of_length_M_on_buffers_of_length_N(M, N):
"""
For a window of length M rolling over a buffer of length N,
there are (N - M) + 1 legal windows.
Example:
If my array has N=4 rows, and I want windows of length M=2, there are
3 legal windows: data[0:2], data[1:3], and data[2:4].
"""
return N - M + 1
def valid_window_lengths(underlying_buffer_length):
"""
An iterator of all legal window lengths on a buffer of a given length.
Returns values from 1 to underlying_buffer_length.
"""
return iter(range(1, underlying_buffer_length + 1))
@curry
def as_dtype(dtype, data):
"""
Curried wrapper around array.astype for when you have the dtype before you
have the data.
"""
return asarray(data).astype(dtype)
@curry
def as_labelarray(initial_dtype, missing_value, array):
"""
Curried wrapper around LabelArray, that round-trips the input data through
`initial_dtype` first.
"""
return LabelArray(
array.astype(initial_dtype),
missing_value=initial_dtype.type(missing_value),
)
bytes_dtype = dtype('S3')
unicode_dtype = dtype('U3')
AdjustmentCase = namedtuple(
'AdjustmentCase',
[
'name',
'baseline',
'window_length',
'adjustments',
'missing_value',
'perspective_offset',
'expected_result',
]
)
def _gen_unadjusted_cases(name,
make_input,
make_expected_output,
missing_value):
nrows = 6
ncols = 3
raw_data = arange(nrows * ncols).reshape(nrows, ncols)
input_array = make_input(raw_data)
expected_output_array = make_expected_output(raw_data)
for windowlen in valid_window_lengths(nrows):
num_legal_windows = num_windows_of_length_M_on_buffers_of_length_N(
windowlen, nrows
)
yield AdjustmentCase(
name="%s_length_%d" % (name, windowlen),
baseline=input_array,
window_length=windowlen,
adjustments={},
missing_value=missing_value,
perspective_offset=0,
expected_result=[
expected_output_array[offset:offset + windowlen]
for offset in range(num_legal_windows)
],
)
def _gen_multiplicative_adjustment_cases(dtype):
"""
Generate expected moving windows on a buffer with adjustments.
We proceed by constructing, at each row, the view of the array we expect in
in all windows anchored on that row.
In general, if we have an adjustment to be applied once we process the row
at index N, should see that adjustment applied to the underlying buffer for
any window containing the row at index N.
We then build all legal windows over these buffers.
"""
adjustment_type = {
float64_dtype: Float64Multiply,
}[dtype]
nrows, ncols = 6, 3
adjustments = {}
buffer_as_of = [None] * 6
baseline = buffer_as_of[0] = full((nrows, ncols), 1, dtype=dtype)
# Note that row indices are inclusive!
adjustments[1] = [
adjustment_type(0, 0, 0, 0, coerce_to_dtype(dtype, 2)),
]
buffer_as_of[1] = array([[2, 1, 1],
[1, 1, 1],
[1, 1, 1],
[1, 1, 1],
[1, 1, 1],
[1, 1, 1]], dtype=dtype)
# No adjustment at index 2.
buffer_as_of[2] = buffer_as_of[1]
adjustments[3] = [
adjustment_type(1, 2, 1, 1, coerce_to_dtype(dtype, 3)),
adjustment_type(0, 1, 0, 0, coerce_to_dtype(dtype, 4)),
]
buffer_as_of[3] = array([[8, 1, 1],
[4, 3, 1],
[1, 3, 1],
[1, 1, 1],
[1, 1, 1],
[1, 1, 1]], dtype=dtype)
adjustments[4] = [
adjustment_type(0, 3, 2, 2, coerce_to_dtype(dtype, 5))
]
buffer_as_of[4] = array([[8, 1, 5],
[4, 3, 5],
[1, 3, 5],
[1, 1, 5],
[1, 1, 1],
[1, 1, 1]], dtype=dtype)
adjustments[5] = [
adjustment_type(0, 4, 1, 1, coerce_to_dtype(dtype, 6)),
adjustment_type(2, 2, 2, 2, coerce_to_dtype(dtype, 7)),
]
buffer_as_of[5] = array([[8, 6, 5],
[4, 18, 5],
[1, 18, 35],
[1, 6, 5],
[1, 6, 1],
[1, 1, 1]], dtype=dtype)
return _gen_expectations(
baseline,
default_missing_value_for_dtype(dtype),
adjustments,
buffer_as_of,
nrows,
perspective_offsets=(0, 1),
)
def _gen_overwrite_adjustment_cases(dtype):
"""
Generate test cases for overwrite adjustments.
The algorithm used here is the same as the one used above for
multiplicative adjustments. The only difference is the semantics of how
the adjustments are expected to modify the arrays.
This is parameterized on `make_input` and `make_expected_output` functions,
which take 2-D lists of values and transform them into desired input/output
arrays. We do this so that we can easily test both vanilla numpy ndarrays
and our own LabelArray class for strings.
"""
adjustment_type = {
float64_dtype: Float64Overwrite,
datetime64ns_dtype: Datetime64Overwrite,
int64_dtype: Int64Overwrite,
bytes_dtype: ObjectOverwrite,
unicode_dtype: ObjectOverwrite,
object_dtype: ObjectOverwrite,
}[dtype]
make_expected_dtype = as_dtype(dtype)
missing_value = default_missing_value_for_dtype(datetime64ns_dtype)
if dtype == object_dtype:
# When we're testing object dtypes, we expect to have strings, but
# coerce_to_dtype(object, 3) just gives 3 as a Python integer.
def make_overwrite_value(dtype, value):
return str(value)
else:
make_overwrite_value = coerce_to_dtype
adjustments = {}
buffer_as_of = [None] * 6
baseline = make_expected_dtype([[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
buffer_as_of[0] = make_expected_dtype([[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
# Note that row indices are inclusive!
adjustments[1] = [
adjustment_type(0, 0, 0, 0, make_overwrite_value(dtype, 1)),
]
buffer_as_of[1] = make_expected_dtype([[1, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
# No adjustment at index 2.
buffer_as_of[2] = buffer_as_of[1]
adjustments[3] = [
adjustment_type(1, 2, 1, 1, make_overwrite_value(dtype, 3)),
adjustment_type(0, 1, 0, 0, make_overwrite_value(dtype, 4)),
]
buffer_as_of[3] = make_expected_dtype([[4, 2, 2],
[4, 3, 2],
[2, 3, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
adjustments[4] = [
adjustment_type(0, 3, 2, 2, make_overwrite_value(dtype, 5))
]
buffer_as_of[4] = make_expected_dtype([[4, 2, 5],
[4, 3, 5],
[2, 3, 5],
[2, 2, 5],
[2, 2, 2],
[2, 2, 2]])
adjustments[5] = [
adjustment_type(0, 4, 1, 1, make_overwrite_value(dtype, 6)),
adjustment_type(2, 2, 2, 2, make_overwrite_value(dtype, 7)),
]
buffer_as_of[5] = make_expected_dtype([[4, 6, 5],
[4, 6, 5],
[2, 6, 7],
[2, 6, 5],
[2, 6, 2],
[2, 2, 2]])
return _gen_expectations(
baseline,
missing_value,
adjustments,
buffer_as_of,
nrows=6,
perspective_offsets=(0, 1),
)
def _gen_overwrite_1d_array_adjustment_case(dtype):
"""
Generate test cases for overwrite adjustments.
The algorithm used here is the same as the one used above for
multiplicative adjustments. The only difference is the semantics of how
the adjustments are expected to modify the arrays.
This is parameterized on `make_input` and `make_expected_output` functions,
which take 1-D lists of values and transform them into desired input/output
arrays. We do this so that we can easily test both vanilla numpy ndarrays
and our own LabelArray class for strings.
"""
adjustment_type = {
float64_dtype: Float641DArrayOverwrite,
datetime64ns_dtype: Datetime641DArrayOverwrite,
}[dtype]
make_expected_dtype = as_dtype(dtype)
missing_value = default_missing_value_for_dtype(datetime64ns_dtype)
adjustments = {}
buffer_as_of = [None] * 6
baseline = make_expected_dtype([[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
buffer_as_of[0] = make_expected_dtype([[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
vals1 = [1]
# Note that row indices are inclusive!
adjustments[1] = [
adjustment_type(
0, 0, 0, 0,
array([coerce_to_dtype(dtype, val) for val in vals1])
)
]
buffer_as_of[1] = make_expected_dtype([[1, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
# No adjustment at index 2.
buffer_as_of[2] = buffer_as_of[1]
vals3 = [4, 4, 1]
adjustments[3] = [
adjustment_type(
0, 2, 0, 0,
array([coerce_to_dtype(dtype, val) for val in vals3])
)
]
buffer_as_of[3] = make_expected_dtype([[4, 2, 2],
[4, 2, 2],
[1, 2, 2],
[2, 2, 2],
[2, 2, 2],
[2, 2, 2]])
vals4 = [5] * 4
adjustments[4] = [
adjustment_type(
0, 3, 2, 2,
array([coerce_to_dtype(dtype, val) for val in vals4]))
]
buffer_as_of[4] = make_expected_dtype([[4, 2, 5],
[4, 2, 5],
[1, 2, 5],
[2, 2, 5],
[2, 2, 2],
[2, 2, 2]])
vals5 = range(1, 6)
adjustments[5] = [
adjustment_type(
0, 4, 1, 1,
array([coerce_to_dtype(dtype, val) for val in vals5])),
]
buffer_as_of[5] = make_expected_dtype([[4, 1, 5],
[4, 2, 5],
[1, 3, 5],
[2, 4, 5],
[2, 5, 2],
[2, 2, 2]])
return _gen_expectations(
baseline,
missing_value,
adjustments,
buffer_as_of,
nrows=6,
perspective_offsets=(0, 1),
)
def _gen_expectations(baseline,
missing_value,
adjustments,
buffer_as_of,
nrows,
perspective_offsets):
for windowlen, perspective_offset in product(valid_window_lengths(nrows),
perspective_offsets):
# How long is an iterator of length-N windows on this buffer?
# For example, for a window of length 3 on a buffer of length 6, there
# are four valid windows.
num_legal_windows = num_windows_of_length_M_on_buffers_of_length_N(
windowlen, nrows
)
# Build the sequence of regions in the underlying buffer we expect to
# see. For example, with a window length of 3 on a buffer of length 6,
# we expect to see:
# (buffer[0:3], buffer[1:4], buffer[2:5], buffer[3:6])
#
slices = [slice(i, i + windowlen) for i in range(num_legal_windows)]
# The sequence of perspectives we expect to take on the underlying
# data. For example, with a window length of 3 and a perspective offset
# of 1, we expect to see:
# (buffer_as_of[3], buffer_as_of[4], buffer_as_of[5], buffer_as_of[5])
#
initial_perspective = windowlen + perspective_offset - 1
perspectives = range(
initial_perspective,
initial_perspective + num_legal_windows
)
def as_of(p):
# perspective_offset can push us past the end of the underlying
# buffer/adjustments. When it does, we should always see the latest
# version of the buffer.
if p >= len(buffer_as_of):
return buffer_as_of[-1]
return buffer_as_of[p]
expected_iterator_results = [
as_of(perspective)[slice_]
for slice_, perspective in zip(slices, perspectives)
]
test_name = "dtype_{}_length_{}_perpective_offset_{}".format(
baseline.dtype,
windowlen,
perspective_offset,
)
yield AdjustmentCase(
name=test_name,
baseline=baseline,
window_length=windowlen,
adjustments=adjustments,
missing_value=missing_value,
perspective_offset=perspective_offset,
expected_result=expected_iterator_results
)
class AdjustedArrayTestCase(TestCase):
@parameterized.expand(
chain(
_gen_unadjusted_cases(
'float',
make_input=as_dtype(float64_dtype),
make_expected_output=as_dtype(float64_dtype),
missing_value=default_missing_value_for_dtype(float64_dtype),
),
_gen_unadjusted_cases(
'datetime',
make_input=as_dtype(datetime64ns_dtype),
make_expected_output=as_dtype(datetime64ns_dtype),
missing_value=default_missing_value_for_dtype(
datetime64ns_dtype
),
),
# Test passing an array of strings to AdjustedArray.
_gen_unadjusted_cases(
'bytes_ndarray',
make_input=as_dtype(bytes_dtype),
make_expected_output=as_labelarray(bytes_dtype, b''),
missing_value=b'',
),
_gen_unadjusted_cases(
'unicode_ndarray',
make_input=as_dtype(unicode_dtype),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value=u'',
),
_gen_unadjusted_cases(
'object_ndarray',
make_input=lambda a: a.astype(unicode).astype(object),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value='',
),
# Test passing a LabelArray directly to AdjustedArray.
_gen_unadjusted_cases(
'bytes_labelarray',
make_input=as_labelarray(bytes_dtype, b''),
make_expected_output=as_labelarray(bytes_dtype, b''),
missing_value=b'',
),
_gen_unadjusted_cases(
'unicode_labelarray',
make_input=as_labelarray(unicode_dtype, None),
make_expected_output=as_labelarray(unicode_dtype, None),
missing_value=u'',
),
_gen_unadjusted_cases(
'object_labelarray',
make_input=(
lambda a: LabelArray(a.astype(unicode).astype(object), u'')
),
make_expected_output=as_labelarray(unicode_dtype, ''),
missing_value='',
),
)
)
def test_no_adjustments(self,
name,
data,
lookback,
adjustments,
missing_value,
perspective_offset,
expected_output):
array = AdjustedArray(data, NOMASK, adjustments, missing_value)
for _ in range(2): # Iterate 2x ensure adjusted_arrays are re-usable.
in_out = zip(array.traverse(lookback), expected_output)
for yielded, expected_yield in in_out:
check_arrays(yielded, expected_yield)
@parameterized.expand(_gen_multiplicative_adjustment_cases(float64_dtype))
def test_multiplicative_adjustments(self,
name,
data,
lookback,
adjustments,
missing_value,
perspective_offset,
expected):
array = AdjustedArray(data, NOMASK, adjustments, missing_value)
for _ in range(2): # Iterate 2x ensure adjusted_arrays are re-usable.
window_iter = array.traverse(
lookback,
perspective_offset=perspective_offset,
)
for yielded, expected_yield in zip_longest(window_iter, expected):
check_arrays(yielded, expected_yield)
@parameterized.expand(
chain(
_gen_overwrite_adjustment_cases(int64_dtype),
_gen_overwrite_adjustment_cases(float64_dtype),
_gen_overwrite_adjustment_cases(datetime64ns_dtype),
_gen_overwrite_1d_array_adjustment_case(float64_dtype),
_gen_overwrite_1d_array_adjustment_case(datetime64ns_dtype),
# There are six cases here:
# Using np.bytes/np.unicode/object arrays as inputs.
# Passing np.bytes/np.unicode/object arrays to LabelArray,
# and using those as input.
#
# The outputs should always be LabelArrays.
_gen_unadjusted_cases(
'bytes_ndarray',
make_input=as_dtype(bytes_dtype),
make_expected_output=as_labelarray(bytes_dtype, b''),
missing_value=b'',
),
_gen_unadjusted_cases(
'unicode_ndarray',
make_input=as_dtype(unicode_dtype),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value=u'',
),
_gen_unadjusted_cases(
'object_ndarray',
make_input=lambda a: a.astype(unicode).astype(object),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value=u'',
),
_gen_unadjusted_cases(
'bytes_labelarray',
make_input=as_labelarray(bytes_dtype, b''),
make_expected_output=as_labelarray(bytes_dtype, b''),
missing_value=b'',
),
_gen_unadjusted_cases(
'unicode_labelarray',
make_input=as_labelarray(unicode_dtype, u''),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value=u'',
),
_gen_unadjusted_cases(
'object_labelarray',
make_input=(
lambda a: LabelArray(
a.astype(unicode).astype(object),
None,
)
),
make_expected_output=as_labelarray(unicode_dtype, u''),
missing_value=None,
),
)
)
def test_overwrite_adjustment_cases(self,
name,
baseline,
lookback,
adjustments,
missing_value,
perspective_offset,
expected):
array = AdjustedArray(baseline, NOMASK, adjustments, missing_value)
for _ in range(2): # Iterate 2x ensure adjusted_arrays are re-usable.
window_iter = array.traverse(
lookback,
perspective_offset=perspective_offset,
)
for yielded, expected_yield in zip_longest(window_iter, expected):
check_arrays(yielded, expected_yield)
@parameter_space(
__fail_fast=True,
dtype=[
float64_dtype,
int64_dtype,
datetime64ns_dtype,
],
missing_value=[0, 10000],
window_length=[2, 3],
)
def test_masking(self, dtype, missing_value, window_length):
missing_value = coerce_to_dtype(dtype, missing_value)
baseline_ints = arange(15).reshape(5, 3)
baseline = baseline_ints.astype(dtype)
mask = (baseline_ints % 2).astype(bool)
masked_baseline = where(mask, baseline, missing_value)
array = AdjustedArray(
baseline,
mask,
adjustments={},
missing_value=missing_value,
)
gen_expected = moving_window(masked_baseline, window_length)
gen_actual = array.traverse(window_length)
for expected, actual in zip(gen_expected, gen_actual):
check_arrays(expected, actual)
@parameter_space(
__fail_fast=True,
dtype=[bytes_dtype, unicode_dtype, object_dtype],
missing_value=["0", "-1", ""],
window_length=[2, 3],
)
def test_masking_with_strings(self, dtype, missing_value, window_length):
missing_value = coerce_to_dtype(dtype, missing_value)
baseline_ints = arange(15).reshape(5, 3)
# Coerce to string first so that coercion to object gets us an array of
# string objects.
baseline = baseline_ints.astype(str).astype(dtype)
mask = (baseline_ints % 2).astype(bool)
masked_baseline = LabelArray(baseline, missing_value=missing_value)
masked_baseline[~mask] = missing_value
array = AdjustedArray(
baseline,
mask,
adjustments={},
missing_value=missing_value,
)
gen_expected = moving_window(masked_baseline, window_length)
gen_actual = array.traverse(window_length=window_length)
for expected, actual in zip(gen_expected, gen_actual):
check_arrays(expected, actual)
def test_invalid_lookback(self):
data = arange(30, dtype=float).reshape(6, 5)
adj_array = AdjustedArray(data, NOMASK, {}, float('nan'))
with self.assertRaises(WindowLengthTooLong):
adj_array.traverse(7)
with self.assertRaises(WindowLengthNotPositive):
adj_array.traverse(0)
with self.assertRaises(WindowLengthNotPositive):
adj_array.traverse(-1)
def test_array_views_arent_writable(self):
data = arange(30, dtype=float).reshape(6, 5)
adj_array = AdjustedArray(data, NOMASK, {}, float('nan'))
for frame in adj_array.traverse(3):
with self.assertRaises(ValueError):
frame[0, 0] = 5.0
def test_bad_input(self):
msg = "Mask shape \(2L?, 3L?\) != data shape \(5L?, 5L?\)"
data = arange(25).reshape(5, 5)
bad_mask = array([[0, 1, 1], [0, 0, 1]], dtype=bool)
with self.assertRaisesRegexp(ValueError, msg):
AdjustedArray(data, bad_mask, {}, missing_value=-1)
def _test_inspect(self):
data = arange(15, dtype=float).reshape(5, 3)
adj_array = AdjustedArray(
data,
NOMASK,
{4: [Float64Multiply(2, 3, 0, 0, 4.0)]},
float('nan'),
)
expected = dedent(
"""\
Adjusted Array (float64):
Data:
array([[ 0., 1., 2.],
[ 3., 4., 5.],
[ 6., 7., 8.],
[ 9., 10., 11.],
[ 12., 13., 14.]])
Adjustments:
{4: [Float64Multiply(first_row=2, last_row=3, first_col=0, \
last_col=0, value=4.000000)]}
"""
)
got = adj_array.inspect()
self.assertEqual(expected, got)
