def __getattr__(self, attr):
if attr == 'A':
if self._is_array:
warn(
np.VisibleDeprecationWarning(
"Please use `.todense()` instead"))
return self.toarray()
elif attr == 'T':
return self.transpose()
elif attr == 'H':
if self._is_array:
warn(
np.VisibleDeprecationWarning(
"Please use `.conj().T` instead"))
return self.getH()
elif attr == 'real':
return self._real()
elif attr == 'imag':
return self._imag()
elif attr == 'size':
return self.getnnz()
else:
raise AttributeError(attr + " not found")
def build_sweep_table(self, sweep_info=None, deprecation_warning=True):
if deprecation_warning:
warnings.warn(np.VisibleDeprecationWarning(
"in ipfx version 1.0.0 build_sweep_table will not be a "
"public method of EphysDataSet"
))
if sweep_info:
self.add_clamp_mode(
sweep_info, deprecation_warning=deprecation_warning
)
self.sweep_table = pd.DataFrame.from_records(sweep_info)
else:
self.sweep_table = pd.DataFrame(columns=self.COLUMN_NAMES)
def get_barcode_table(self, **barcode_kwargs):
""" A convenience method for getting barcode times and codes in a dictionary.
Notes
-----
This method is deprecated!
"""
warnings.warn(
np.VisibleDeprecationWarning(
"This function is deprecated as unecessary (and slated for removal). Instead, simply use extract_barcodes."
))
barcode_times, barcodes = self.extract_barcodes(**barcode_kwargs)
return {"codes": barcodes, "times": barcode_times}
def __init__(
self,
ontology,
validate_stim=True,
deprecation_warning=False
):
self.sweep_table = None
self.ontology = ontology
self.validate_stim = validate_stim
if deprecation_warning:
warnings.warn(np.VisibleDeprecationWarning((
"Instead of constructing {} instances "
"directly, use ipfx.data_set_utils.create_data_set"
"this will make it easier to transition to ipfx 1.0.0"
).format(type(self))))
def add_clamp_mode(self, sweep_info, deprecation_warning=True):
"""
Check if clamp mode is available and otherwise detect it
Parameters
----------
sweep_info
Returns
-------
"""
if deprecation_warning:
warnings.warn(np.VisibleDeprecationWarning(
"in ipfx version 1.0.0 add_clamp_mode will not be a "
"public method of EphysDataSet"
))
for sweep_record in sweep_info:
sweep_number = sweep_record["sweep_number"]
sweep_record[self.CLAMP_MODE] = self.get_clamp_mode(sweep_number)
def test_sparse_bond_matrix():
"""Test :func:`sparse_bond_matrix`."""
ref1 = np.load(PATH / 'sparse_bond_matrix.npy')
ref2 = ref1.astype(int)
ref3 = ref1.astype(bool)
mat1 = sparse_bond_matrix(MOL, dtype=float)
mat2 = sparse_bond_matrix(MOL, dtype=int)
mat3 = sparse_bond_matrix(MOL)
np.testing.assert_array_equal(mat1.toarray(), ref1)
np.testing.assert_array_equal(mat2.toarray(), ref2)
np.testing.assert_array_equal(mat3.toarray(), ref3)
sparse_type_tup = (bsr_matrix, coo_matrix, csr_matrix, csc_matrix,
dia_matrix, dok_matrix, lil_matrix)
with warnings.catch_warnings():
warnings.simplefilter('ignore',
category=np.VisibleDeprecationWarning())
for sparse_type in sparse_type_tup:
mat_n = sparse_bond_matrix(MOL, sparse_type=sparse_type)
np.testing.assert_array_equal(mat_n.toarray(), ref3)
assertion.assert_(sparse_bond_matrix,
MOL,
dtype='bob',
exception=TypeError)
assertion.assert_(sparse_bond_matrix,
MOL,
sparse_type='bob',
exception=TypeError)
assertion.assert_(sparse_bond_matrix,
MOL,
sparse_type=int,
exception=TypeError)
from typing import Type import numpy as np reveal_type(np.ModuleDeprecationWarning()) # E: numpy.ModuleDeprecationWarning reveal_type(np.VisibleDeprecationWarning()) # E: numpy.VisibleDeprecationWarning reveal_type(np.ComplexWarning()) # E: numpy.ComplexWarning reveal_type(np.RankWarning()) # E: numpy.RankWarning reveal_type(np.TooHardError()) # E: numpy.TooHardError reveal_type(np.AxisError(1)) # E: numpy.AxisError
from typing import Type
import numpy as np
reveal_type(np.ModuleDeprecationWarning()) # E: numpy.ModuleDeprecationWarning
reveal_type(
np.VisibleDeprecationWarning()) # E: numpy.VisibleDeprecationWarning
reveal_type(np.ComplexWarning()) # E: numpy.ComplexWarning
reveal_type(np.RankWarning()) # E: numpy.RankWarning
reveal_type(np.TooHardError()) # E: numpy.TooHardError
reveal_type(np.AxisError(1)) # E: numpy.AxisError
def nwb_data(self):
warnings.warn(np.VisibleDeprecationWarning(
"In ipfx 1.0.0 nwb_data will not be a public attribute of "
"EphysDataSet"
))
return self._nwb_data