def test_assumes_dims_like_own_name(self):
input_state = {
'air_temperature': DataArray(
np.zeros([2, 2, 4]),
dims=['x', 'y', 'z'],
attrs={'units': 'degK'},
)
}
input_properties = {
'air_temperature': {
'dims': ['x', 'y', 'z'],
'units': 'degK',
}
}
raw_arrays = get_numpy_arrays_with_properties(input_state, input_properties)
output_properties = {
'air_temperature': {
'units': 'degK/s',
}
}
return_value = restore_data_arrays_with_properties(
raw_arrays, output_properties, input_state, input_properties
)
assert isinstance(return_value, dict)
assert len(return_value.keys()) == 1
assert isinstance(return_value['air_temperature'], DataArray)
assert return_value['air_temperature'].attrs['units'] is 'degK/s'
assert np.byte_bounds(
return_value['air_temperature'].values) == np.byte_bounds(
input_state['air_temperature'].values)
assert (return_value['air_temperature'].values.base is
input_state['air_temperature'].values)
assert return_value['air_temperature'].shape == (2, 2, 4)
def _reduce_memmap_backed(a, m):
"""Pickling reduction for memmap backed arrays
a is expected to be an instance of np.ndarray (or np.memmap)
m is expected to be an instance of np.memmap on the top of the ``base``
attribute ancestry of a. ``m.base`` should be the real python mmap object.
"""
# offset that comes from the striding differences between a and m
a_start = np.byte_bounds(a)[0]
m_start = np.byte_bounds(m)[0]
offset = a_start - m_start
# offset from the backing memmap
offset += m.offset
if m.flags['F_CONTIGUOUS']:
order = 'F'
else:
# The backing memmap buffer is necessarily contiguous hence C if not
# Fortran
order = 'C'
# If array is a contiguous view, no need to pass the strides
if a.flags['F_CONTIGUOUS'] or a.flags['C_CONTIGUOUS']:
strides = None
else:
strides = a.strides
return (strided_from_memmap, (m.filename, a.dtype, m.mode, offset, order,
a.shape, strides))
def test_restores_new_dims_with_wildcard(self):
input_state = {
'air_pressure': DataArray(
np.zeros([2, 2, 4]),
dims=['x', 'y', 'z'],
attrs={'units': 'degK'},
),
}
input_properties = {
'air_pressure': {
'dims': ['*'],
'units': 'degK',
'alias': 'p'
},
}
raw_arrays = {
'q': np.zeros([16, 2])
}
output_properties = {
'q': {
'dims': ['*', 'new_dim'],
'units': 'm',
},
}
data_arrays = restore_data_arrays_with_properties(
raw_arrays, output_properties, input_state, input_properties
)
assert len(data_arrays.keys()) == 1
assert 'q' in data_arrays.keys()
assert np.all(data_arrays['q'].values.flatten() == raw_arrays['q'].flatten())
assert np.byte_bounds(
data_arrays['q'].values) == np.byte_bounds(
raw_arrays['q'])
assert data_arrays['q'].dims == ('x', 'y', 'z', 'new_dim')
assert data_arrays['q'].shape == (2, 2, 4, 2)
def _reduce_memmap_backed(a, m):
"""Pickling reduction for memmap backed arrays
a is expected to be an instance of np.ndarray (or np.memmap)
m is expected to be an instance of np.memmap on the top of the ``base``
attribute ancestry of a. ``m.base`` should be the real python mmap object.
"""
# offset that comes from the striding differences between a and m
a_start = np.byte_bounds(a)[0]
m_start = np.byte_bounds(m)[0]
offset = a_start - m_start
# offset from the backing memmap
offset += m.offset
if m.flags["F_CONTIGUOUS"]:
order = "F"
else:
# The backing memmap buffer is necessarily contiguous hence C if not
# Fortran
order = "C"
# If array is a contiguous view, no need to pass the strides
if a.flags["F_CONTIGUOUS"] or a.flags["C_CONTIGUOUS"]:
strides = None
else:
strides = a.strides
return (strided_from_memmap, (m.filename, a.dtype, m.mode, offset, order, a.shape, strides))
def test_restores_aliased_name(self):
input_state = {
'air_temperature': DataArray(
np.zeros([2, 2, 4]),
dims=['x', 'y', 'z'],
attrs={'units': 'degK'},
)
}
input_properties = {
'air_temperature': {
'dims': ['x', 'y', 'z'],
'units': 'degK',
}
}
raw_arrays = {
'p': np.zeros([2, 2, 4])
}
output_properties = {
'air_pressure': {
'dims': ['x', 'y', 'z'],
'units': 'm',
'alias': 'p',
},
}
data_arrays = restore_data_arrays_with_properties(
raw_arrays, output_properties, input_state, input_properties
)
assert len(data_arrays.keys()) == 1
assert 'air_pressure' in data_arrays.keys()
assert np.all(data_arrays['air_pressure'].values == raw_arrays['p'])
assert np.byte_bounds(data_arrays['air_pressure'].values) == np.byte_bounds(raw_arrays['p'])
def decode_lab (l, ab, T=None):
ab_flat = np.reshape(ab, (-1, ab.shape[-1]))
if not T is None: # need to test
o = ab_flat
ab_flat += 1e-15
np.log(ab_flat, ab_flat)
ab_flat /= T
np.exp(ab_flat, ab_flat)
S = np.sum(ab_flat, axis=0)
assert S.shape[0] == ab_flat.shape[0]
ab_flat /= S
assert np.byte_bounds(o) == np.byte_bounds(ab_flat)
pass
ab_small = np.reshape(np.dot(ab_flat, ab_dict), ab.shape[:3] + (2,))
_, H, W, _ = l.shape
lab_one = np.zeros((H, W, 3), dtype=np.float32)
rgb = np.zeros(l.shape[:3] + (3,), dtype=np.float32)
for i in range(l.shape[0]):
lab_one[:, :, :1] = l[i]
lab_one[:, :, 1:] = cv2.resize(ab_small[i], (W, H))
rgb[i] = cv2.cvtColor(lab_one, cv2.COLOR_LAB2BGR)
pass
rgb *=255
return rgb
def test_match_dims_like_star_z_matching_lengths(self):
set_direction_names(x=['lat'],
y=['lon'],
z=['mid_levels', 'interface_levels'])
input_state = {
'air_temperature':
DataArray(
np.zeros([2, 3, 4]),
dims=['lat', 'lon', 'interface_levels'],
attrs={'units': 'degK'},
),
'air_pressure':
DataArray(
np.zeros([2, 3, 4]),
dims=['lat', 'lon', 'interface_levels'],
attrs={'units': 'Pa'},
),
}
input_properties = {
'air_temperature': {
'dims': ['*', 'z'],
'units': 'degK',
'match_dims_like': 'air_pressure',
},
'air_pressure': {
'dims': ['*', 'z'],
'units': 'Pa',
},
}
raw_arrays = get_numpy_arrays_with_properties(input_state,
input_properties)
assert np.byte_bounds(raw_arrays['air_temperature']) == np.byte_bounds(
input_state['air_temperature'].values)
assert np.byte_bounds(raw_arrays['air_pressure']) == np.byte_bounds(
input_state['air_pressure'].values)
def get_base_slice(view):
'''Returns the 2D slice of view's parent that yields view.
Note that this function will return a 2D slice even if view's parent
is three-dimensional.'''
if view.dtype != np.uint8:
raise ValueError('Don''t know how to compute offset for types other '
'than uint8.')
if not hasattr(view, 'base') or view.base is None:
raise ValueError('`view` argument does not have `base` property.')
if len(view.base.strides) not in (2, 3):
raise ValueError('Base array must have two or three dimensions.')
# Determine the strides
base = view.base
ystride, xstride = base.strides[:2]
# Compute difference between base start and the view's end & start.
base_start, _ = np.byte_bounds(base)
view_start, view_end = np.byte_bounds(view)
diff_start = view_start - base_start
diff_end = view_end - base_start - 1
# Compute slice offsets
ystart = diff_start / ystride
xstart = (diff_start % ystride) / xstride
yend = diff_end / ystride
xend = (diff_end % ystride) / xstride
return slice(ystart, yend+1), slice(xstart, xend+1)
def _reduce_memmap_backed(a, m):
"""Pickling reduction for memmap backed arrays.
a is expected to be an instance of np.ndarray (or np.memmap)
m is expected to be an instance of np.memmap on the top of the ``base``
attribute ancestry of a. ``m.base`` should be the real python mmap object.
"""
# offset that comes from the striding differences between a and m
a_start, a_end = np.byte_bounds(a)
m_start = np.byte_bounds(m)[0]
offset = a_start - m_start
# offset from the backing memmap
offset += m.offset
if m.flags['F_CONTIGUOUS']:
order = 'F'
else:
# The backing memmap buffer is necessarily contiguous hence C if not
# Fortran
order = 'C'
if a.flags['F_CONTIGUOUS'] or a.flags['C_CONTIGUOUS']:
# If the array is a contiguous view, no need to pass the strides
strides = None
total_buffer_len = None
else:
# Compute the total number of items to map from which the strided
# view will be extracted.
strides = a.strides
total_buffer_len = (a_end - a_start) // a.itemsize
return (_strided_from_memmap, (m.filename, a.dtype, m.mode, offset, order,
a.shape, strides, total_buffer_len))
def test_match_dims_like_partly_hardcoded_dimensions_matching_lengths():
input_state = {
'air_temperature': DataArray(
np.zeros([2, 3, 4]),
dims=['lat', 'lon', 'mid_levels'],
attrs={'units': 'degK'},
),
'air_pressure': DataArray(
np.zeros([2, 3, 4]),
dims=['lat', 'lon', 'interface_levels'],
attrs={'units': 'Pa'},
),
}
input_properties = {
'air_temperature': {
'dims': ['*', 'mid_levels'],
'units': 'degK',
'match_dims_like': 'air_pressure',
},
'air_pressure': {
'dims': ['*', 'interface_levels'],
'units': 'Pa',
},
}
raw_arrays = get_numpy_arrays_with_properties(input_state, input_properties)
assert np.byte_bounds(input_state['air_temperature'].values) == np.byte_bounds(raw_arrays['air_temperature'])
assert np.byte_bounds(input_state['air_pressure'].values) == np.byte_bounds(raw_arrays['air_pressure'])
def _reduce_memmap_backed(a, m):
"""Pickling reduction for memmap backed arrays.
a is expected to be an instance of np.ndarray (or np.memmap)
m is expected to be an instance of np.memmap on the top of the ``base``
attribute ancestry of a. ``m.base`` should be the real python mmap object.
"""
# offset that comes from the striding differences between a and m
a_start, a_end = np.byte_bounds(a)
m_start = np.byte_bounds(m)[0]
offset = a_start - m_start
# offset from the backing memmap
offset += m.offset
if m.flags['F_CONTIGUOUS']:
order = 'F'
else:
# The backing memmap buffer is necessarily contiguous hence C if not
# Fortran
order = 'C'
if a.flags['F_CONTIGUOUS'] or a.flags['C_CONTIGUOUS']:
# If the array is a contiguous view, no need to pass the strides
strides = None
total_buffer_len = None
else:
# Compute the total number of items to map from which the strided
# view will be extracted.
strides = a.strides
total_buffer_len = (a_end - a_start) // a.itemsize
return (_strided_from_memmap,
(m.filename, a.dtype, m.mode, offset, order, a.shape, strides,
total_buffer_len))
def test_returns_simple_value(self):
input_state = {
'air_temperature': DataArray(
np.zeros([2, 2, 4]),
dims=['x', 'y', 'z'],
attrs={'units': 'degK'},
)
}
input_properties = {
'air_temperature': {
'dims': ['x', 'y', 'z'],
'units': 'degK',
}
}
raw_arrays = get_numpy_arrays_with_properties(input_state, input_properties)
raw_arrays = {key + '_tendency': value for key, value in raw_arrays.items()}
output_properties = {
'air_temperature_tendency': {
'dims': ['x', 'y', 'z'],
'units': 'degK/s',
}
}
return_value = restore_data_arrays_with_properties(
raw_arrays, output_properties, input_state, input_properties
)
assert isinstance(return_value, dict)
assert len(return_value.keys()) == 1
assert isinstance(return_value['air_temperature_tendency'], DataArray)
assert return_value['air_temperature_tendency'].attrs['units'] is 'degK/s'
assert np.byte_bounds(
return_value['air_temperature_tendency'].values) == np.byte_bounds(
input_state['air_temperature'].values)
assert (return_value['air_temperature_tendency'].values.base is
input_state['air_temperature'].values)
assert return_value['air_temperature_tendency'].shape == (2, 2, 4)
def ramp(img, out=None):
'''Remove change in illumination across an image
This function removes a wedge-like profile from the image
.. note::
For more detail, see: http://www.wadsworth.org/spider_doc/spider/docs/man/ra.html
:Parameters:
img : numpy.ndarray
Input image
out : numpy.ndarray
Output image
:Returns:
img : numpy.ndarray
Ramped image
'''
if out is None:
out = numpy.empty_like(img, dtype=numpy.float32)
elif out.dtype != numpy.float32: raise ValueError, "Output array must be float 32"
if numpy.byte_bounds(out) != numpy.byte_bounds(img): out[:]=img
tout = out.T if not out.flags.f_contiguous else out
if _spider_filter.ramp(tout) != 0:
raise ValueError, "Ramp filter failed"
return out
def test_get_numpy_array_3d_no_change():
array = DataArray(
np.random.randn(2, 3, 4),
dims=['x', 'y', 'z'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['x', 'y', 'z'])
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert np.all(numpy_array == array.values)
assert numpy_array.base is array.values
def find_index(base, view):
"""
Given an array that is a `view` of a `base`, find an index such that
`base[index] is view`
"""
if not isinstance(view, np.ndarray):
return "..."
itemsize = view.itemsize
# Find the start and end pointer of the arrays using the byte_bound method
offset_start = (np.byte_bounds(view)[0] - np.byte_bounds(base)[0]) // itemsize
offset_stop = (np.byte_bounds(view)[-1] - np.byte_bounds(base)[-1] - 1) // itemsize
# Calculate the start and stop indices from the offsets
index_start = np.unravel_index(offset_start, base.shape)
index_stop = np.unravel_index(base.size + offset_stop, base.shape)
# Use the strides property to find the No. of bytes to go from one element to the other
index_step = np.array(view.strides) // np.array(base.strides)
index = ""
for i in range(len(index_step)):
start = index_start[i]
stop = index_stop[i]
step = index_step[i]
if stop == start:
stop, step = None, None
else:
if stop == base.shape[i] - 1:
stop = None
else:
stop = stop
if start == 0:
start = None
if step is not None and stop is not None:
if step < 0:
start, stop = stop, start - 1
else:
start, stop = start, stop + 1
if start is not None:
index += str(start)
if stop is not None:
index += ":" + str(stop)
elif step is not None:
index += ":"
if step is not None:
index += ":" + str(step)
index += ','
index = index[:-1]
return index
def find_index(base, view):
"""
Given an array that is `view` of `bave`, find an index sich that
base[index] is view`
Assumes both base and view has the same itemsize??
"""
if not isinstance(view, np.ndarray):
return "..."
itemsize = view.itemsize
offset_start = (np.byte_bounds(view)[0] -
np.byte_bounds(base)[0]) // itemsize
# without the -1, we'd be pointing to first element not beginning to the view (exclusive). We want inclusive.
offset_end = (np.byte_bounds(view)[-1] - np.byte_bounds(base)[-1] -
1) // itemsize
index_start = np.unravel_index(offset_start, base.shape)
index_stop = np.unravel_index((offset_end + base.size) % base.size,
base.shape)
index_step = np.array(view.strides) // np.array(base.strides)
index = ""
for i in range(len(index_step)):
start = index_start[i]
stop = index_stop[i]
step = index_step[i]
if start == stop:
# Z[3:4] = '3' -> no need for stop or step
stop, step = None, None
else:
if start == 0:
start = None
if stop == base.shape[i] - 1:
stop = None
if step is not None and stop is not None:
if step > 0:
start, stop = start, stop + 1
else:
start, stop = stop, start - 1
# format the index properly
if start is not None:
index += str(start)
if stop is not None:
index += ":" + str(stop)
elif step is not None: # placeholder for "::2"
index += ":"
if step is not None:
index += ":" + str(step)
index += ","
index = index[:-1]
return index
def get_raw_index(self, i):
"""Get index into base array's raw data, given the index into this
segment
"""
if self.is_indexed:
return int(self.order[i])
if self.data.base is None:
return int(i)
data_start, data_end = np.byte_bounds(self.data)
base_start, base_end = np.byte_bounds(self.data.base)
return int(data_start - base_start + i)
def test_get_numpy_array_invalid_dimension_collected_by_asterisk():
array = DataArray(
np.random.randn(2),
dims=['sheep'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['*'])
assert numpy_array.shape == (2,)
assert np.all(numpy_array == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_get_numpy_array_asterisk_creates_new_dim():
array = DataArray(
np.random.randn(2),
dims=['x'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['x', '*'])
assert numpy_array.shape == (2, 1)
assert np.all(numpy_array[:, 0] == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_get_numpy_array_asterisk_flattens():
array = DataArray(
np.random.randn(2, 3),
dims=['y', 'z'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['*'])
assert numpy_array.shape == (6,)
assert np.all(numpy_array.reshape((2, 3)) == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_get_numpy_array_retrieves_explicit_dimensions():
array = DataArray(
np.random.randn(2, 3),
dims=['alpha', 'zeta'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['zeta', 'alpha'])
assert numpy_array.shape == (3, 2)
assert np.all(np.transpose(numpy_array, (1, 0)) == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_get_numpy_array_1d():
array = DataArray(
np.random.randn(2),
dims=['y'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['y'])
assert numpy_array.shape == (2,)
assert np.all(numpy_array == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def get_raw_index(self, i):
"""Get index into base array's raw data, given the index into this
segment
"""
if self.is_indexed:
return int(self.order[i])
if self.data.base is None:
return int(i)
data_start, data_end = np.byte_bounds(self.data)
base_start, base_end = np.byte_bounds(self.data.base)
return int(data_start - base_start + i)
def test_get_numpy_array_2d_reverse():
array = DataArray(
np.random.randn(2, 3),
dims=['y', 'z'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['z', 'y'])
assert numpy_array.shape == (3, 2)
assert np.all(np.transpose(numpy_array, (1, 0)) == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_get_numpy_array_creates_new_dim_in_front():
array = DataArray(
np.random.randn(2),
dims=['x'],
attrs={'units': ''},
)
numpy_array = get_numpy_array(array, ['y', 'x'])
assert numpy_array.shape == (1, 2)
assert np.all(numpy_array[0, :] == array.values)
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def test_restore_dimensions_starz_to_zyx_doesnt_copy():
array = DataArray(
np.random.randn(2, 3, 4),
dims=['z', 'y', 'x'],
attrs={'units': ''}
)
numpy_array = get_numpy_array(array, ['*', 'z'])
restored_array = restore_dimensions(
numpy_array, from_dims=['*', 'z'], result_like=array)
assert np.byte_bounds(restored_array.values) == np.byte_bounds(
array.values)
assert restored_array.values.base is array.values
def test_factorize_converges(self):
l = np.array([1e-12, 1e-3, 1e-12, 1e-3], np.dtype('float64'))
max_iter = 1000
max_diff = 0.1
d_name = 'factorized'
d = self.data[d_name]
f = Factorization(d, self.n_features_split, self.n_factors)
monitor = f.sfa(max_diff, max_iter, l, True)
assert (monitor.n_iter < max_iter)
assert (monitor.max_diff_factors[-1] < max_diff)
assert (monitor.max_diff_coefficients[-1] < max_diff)
self.assertEqual(np.byte_bounds(d), np.byte_bounds(f.data))
self.check_factorization_type_and_shape(f)
def test_get_numpy_array_zyx_to_starz_doesnt_copy():
array = DataArray(
np.random.randn(2, 3, 4),
dims=['z', 'y', 'x'],
attrs={'units': ''}
)
original_array = array.values
numpy_array = get_numpy_array(array, ['*', 'z'])
for i in range(2):
assert np.all(numpy_array[:, i] == array.values[i, :, :].flatten())
assert original_array is array.values
assert np.byte_bounds(numpy_array) == np.byte_bounds(array.values)
assert numpy_array.base is array.values
def offset(self):
"""The offset of the memory map in the file.
Returns
-------
offset : int
Offset of the memeory map in the file.
"""
if self._array.base is not None:
return np.byte_bounds(self._array)[0] - np.byte_bounds(
self._array.base)[0]
else:
return 0
def find_view(base, view):
"""
Given an array that is a `view` of a `base`, find an index such that
`base[index] is view`
"""
if not isinstance(view, np.ndarray):
return "..."
itemsize = view.itemsize
offset_start = (np.byte_bounds(view)[0] -
np.byte_bounds(base)[0]) // itemsize
offset_stop = (np.byte_bounds(view)[-1] - np.byte_bounds(base)[-1] -
1) // itemsize
index_start = np.unravel_index(offset_start, base.shape)
index_stop = np.unravel_index(base.size + offset_stop, base.shape)
index_step = np.array(view.strides) // np.array(base.strides)
index = ""
for i in range(len(index_step)):
start = index_start[i]
stop = index_stop[i]
step = index_step[i]
if stop == start:
stop, step = None, None
else:
if stop == base.shape[i] - 1:
stop = None
else:
stop = stop
if start == 0:
start = None
if step is not None and stop is not None:
if step < 0:
start, stop = stop, start - 1
else:
start, stop = start, stop + 1
if start is not None:
index += str(start)
if stop is not None:
index += ":" + str(stop)
elif step is not None:
index += ":"
if step is not None:
index += ":" + str(step)
index += ','
index = index[:-1]
return index
def test_restore_dimensions_removes_dummy_axes():
array = DataArray(
np.random.randn(2),
dims=['z'],
attrs={'units': ''}
)
numpy_array = get_numpy_array(array, ['x', 'y', 'z'])
restored_array = restore_dimensions(
numpy_array, from_dims=['x', 'y', 'z'], result_like=array)
assert np.all(restored_array.values == array.values)
assert len(restored_array.attrs) == 0
assert np.byte_bounds(restored_array.values) == np.byte_bounds(
array.values)
assert restored_array.values.base is array.values
def test_factorize_gets_close(self):
l2 = 0.1
l = np.array([0.01, l2, 0.02, l2], np.dtype('float64'))
max_iter = 1000
max_diff = 1e-6
d_name = 'factorized'
d = self.data[d_name]
f = Factorization(d, self.n_features_split, self.n_factors)
f.sfa(max_diff, max_iter, l)
self.assertEqual(np.byte_bounds(d), np.byte_bounds(f.data))
self.check_factorization_type_and_shape(f)
coef = f.coefficients * (1 + l2)
data_rec = np.dot(coef, f.factors).T
np.testing.assert_allclose(d, data_rec, atol=1)
def byte_bounds_offset(self):
"""Return start and end offsets of this segment's data into the
base array's data.
This ignores the byte order index. Arrays using the byte order index
will have the entire base array's raw data.
"""
if self.data.base is None:
if self.is_indexed:
basearray = self.data.np_data
else:
basearray = self.data
return 0, len(basearray)
data_start, data_end = np.byte_bounds(self.data)
base_start, base_end = np.byte_bounds(self.data.base)
return int(data_start - base_start), int(data_end - base_start)
def byte_bounds_offset(self):
"""Return start and end offsets of this segment's data into the
base array's data.
This ignores the byte order index. Arrays using the byte order index
will have the entire base array's raw data.
"""
if self.data.base is None:
if self.is_indexed:
basearray = self.data.np_data
else:
basearray = self.data
return 0, len(basearray)
data_start, data_end = np.byte_bounds(self.data)
base_start, base_end = np.byte_bounds(self.data.base)
return int(data_start - base_start), int(data_end - base_start)
def calc_lookups(self):
if self.is_indexed:
end = len(self.data.np_data)
self.data_start, self.data_end = 0, end
self.base_start, self.base_end = 0, end
base_size = end
elif self.data.base is None:
end = len(self.data)
self.data_start, self.data_end = 0, end
self.base_start, self.base_end = 0, end
base_size = end
else:
self.data_start, self.data_end = np.byte_bounds(self.data)
self.base_start, self.base_end = np.byte_bounds(self.data.base)
base_size = len(self.data.base)
self.base_length = base_size
self.data_length = len(self.data)
# Force regeneration of reverse index mapping the next time it's needed
self._reverse_index_mapping = None
def test_factorize(self):
l = np.array([0.01, 1] * len(self.n_features_split),
np.dtype('float64'))
max_iter = 10
max_diff = 1e-6
for d_name, d in self.data.items():
with (self.subTest(data_name=d_name)):
f = Factorization(d, self.n_features_split, self.n_factors)
monitor = f.sfa(max_diff, max_iter, l, True)
diff = max([
monitor.max_diff_factors[-1],
monitor.max_diff_coefficients[-1]
])
assert (monitor.n_iter < max_iter + 1)
assert (diff >= 0.0)
if (diff > max_diff):
self.assertEqual(monitor.n_iter, max_iter)
self.assertEqual(np.byte_bounds(d), np.byte_bounds(f.data))
self.check_factorization_type_and_shape(f)
def share_memory(a, b):
"""Returns the number of shared bytes between arrays `a` and `b`."""
#http://stackoverflow.com/a/11287440
def byte_offset(a):
"""Returns a 1-d array of the byte offset of every element in `a`.
Note that these will not in general be in order."""
stride_offset = np.ix_(*map(range,a.shape))
element_offset = sum(i*s for i, s in zip(stride_offset,a.strides))
element_offset = np.asarray(element_offset).ravel()
return np.concatenate([element_offset + x for x in range(a.itemsize)])
a_low, a_high = np.byte_bounds(a)
b_low, b_high = np.byte_bounds(b)
beg, end = max(a_low,b_low), min(a_high,b_high)
if end - beg > 0:
# memory overlaps
amem = a_low + byte_offset(a)
bmem = b_low + byte_offset(b)
return np.intersect1d(amem,bmem).size
else:
return 0
def unlock(arr):
arr.flags.writable = True
return byte_bounds(arr)
def lock(arr):
arr.flags.writable = False
return byte_bounds(arr)
import numpy as np from numpy import byte_bounds from numpush.shmem_views import sview, SyncNumpy x = np.arange(0,100) y = sview(x[:50]) z = sview(x[50:]) a = sview(x[2:98]) xptr = byte_bounds(x) yptr = byte_bounds(y) zptr = byte_bounds(y) aptr = byte_bounds(a) # Left aligned in memory assert byte_bounds(x)[0] == byte_bounds(y)[0] # Right aligned in memory assert byte_bounds(x)[1] == byte_bounds(z)[1] # Subset assert xptr[0] < aptr[0] < aptr[1] < xptr[1] from numpy import add s = SyncNumpy(x)
