/usr/lib/python2.7/dist-packages/neo/test/tools.py is in python-neo 0.3.3-2.
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'''
Tools for use with neo tests.
'''
import hashlib
import os
import numpy as np
import quantities as pq
import neo
from neo import description
def assert_arrays_equal(a, b):
'''
Check if two arrays have the same shape and contents
'''
assert isinstance(a, np.ndarray), "a is a %s" % type(a)
assert isinstance(b, np.ndarray), "b is a %s" % type(b)
assert a.shape == b.shape, "%s != %s" % (a, b)
#assert a.dtype == b.dtype, "%s and %s not same dtype %s %s" % (a, b,
# a.dtype,
# b.dtype)
try:
assert (a.flatten() == b.flatten()).all(), "%s != %s" % (a, b)
except (AttributeError, ValueError):
try:
ar = np.array(a)
br = np.array(b)
assert (ar.flatten() == br.flatten()).all(), "%s != %s" % (ar, br)
except (AttributeError, ValueError):
assert np.all(a.flatten() == b.flatten()), "%s != %s" % (a, b)
def assert_arrays_almost_equal(a, b, threshold):
'''
Check if two arrays have the same shape and contents that differ
by abs(a - b) <= threshold for all elements.
'''
assert isinstance(a, np.ndarray), "a is a %s" % type(a)
assert isinstance(b, np.ndarray), "b is a %s" % type(b)
assert a.shape == b.shape, "%s != %s" % (a, b)
#assert a.dtype == b.dtype, "%s and %b not same dtype %s %s" % (a, b,
# a.dtype,
# b.dtype)
if a.dtype.kind in ['f', 'c', 'i']:
assert (abs(a - b) < threshold).all(), \
"abs(%s - %s) max(|a - b|) = %s threshold:%s" % \
(a, b, (abs(a - b)).max(), threshold)
def file_digest(filename):
'''
Get the sha1 hash of the file with the given filename.
'''
with open(filename, 'rb') as fobj:
return hashlib.sha1(fobj.read()).hexdigest()
def assert_file_contents_equal(a, b):
'''
Assert that two files have the same size and hash.
'''
def generate_error_message(a, b):
'''
This creates the error message for the assertion error
'''
size_a = os.stat(a).st_size
size_b = os.stat(b).st_size
if size_a == size_b:
return "Files have the same size but different contents"
else:
return "Files have different sizes: a:%d b: %d" % (size_a, size_b)
assert file_digest(a) == file_digest(b), generate_error_message(a, b)
def assert_neo_object_is_compliant(ob):
'''
Test neo compliance of one object and sub objects
(one_to_many_relation only):
* check types and/or presence of necessary and recommended attribute.
* If attribute is Quantities or numpy.ndarray it also check ndim.
* If attribute is numpy.ndarray also check dtype.kind.
'''
assert type(ob) in description.objectlist, \
'%s is not a neo object' % (type(ob))
classname = ob.__class__.__name__
necess = description.classes_necessary_attributes[classname]
recomm = description.classes_recommended_attributes[classname]
# test presence of necessary attributes
attributes = necess
for ioattr in attributes:
attrname, attrtype = ioattr[0], ioattr[1]
#~ if attrname != '':
if classname not in description.classes_inheriting_quantities:
assert hasattr(ob, attrname), '%s neo obect does not have %s' % \
(classname, attrname)
# test attributes types
attributes = necess + recomm
for ioattr in attributes:
attrname, attrtype = ioattr[0], ioattr[1]
if (classname in description.classes_inheriting_quantities and
description.classes_inheriting_quantities[classname] ==
attrname and
(attrtype == pq.Quantity or attrtype == np.ndarray)):
# object is hinerited from Quantity (AnalogSIgnal, SpikeTrain, ...)
ndim = ioattr[2]
assert ob.ndim == ndim, \
'%s dimension is %d should be %d' % (classname, ob.ndim, ndim)
if attrtype == np.ndarray:
dtp = ioattr[3]
assert ob.dtype.kind == dtp.kind, \
'%s dtype.kind is %s should be %s' % (classname,
ob.dtype.kind,
dtp.kind)
elif hasattr(ob, attrname):
if getattr(ob, attrname) is not None:
obattr = getattr(ob, attrname)
assert issubclass(type(obattr), attrtype), \
'%s in %s is %s should be %s' % \
(attrname, classname, type(obattr), attrtype)
if attrtype == pq.Quantity or attrtype == np.ndarray:
ndim = ioattr[2]
assert obattr.ndim == ndim, \
'%s.%s dimension is %d should be %d' % \
(classname, attrname, obattr.ndim, ndim)
if attrtype == np.ndarray:
dtp = ioattr[3]
assert obattr.dtype.kind == dtp.kind, \
'%s.%s dtype.kind is %s should be %s' % \
(classname, attrname, obattr.dtype.kind, dtp.kind)
# test bijectivity : one_to_many_relationship and many_to_one_relationship
if classname in description.one_to_many_relationship:
for childname in description.one_to_many_relationship[classname]:
if not hasattr(ob, childname.lower()+'s'):
continue
sub = getattr(ob, childname.lower()+'s')
for i, child in enumerate(sub):
assert hasattr(child, classname.lower()), \
'%s should have %s attribute (2 way relationship)' % \
(childname, classname.lower())
if hasattr(child, classname.lower()):
assert getattr(child, classname.lower()) == ob, \
'%s.%s %s is not symetric with %s.%s s' % \
(childname, classname.lower(), i,
classname, childname.lower())
# recursive on one to many rel
if classname in description.one_to_many_relationship:
for childname in description.one_to_many_relationship[classname]:
if not hasattr(ob, childname.lower()+'s'):
continue
sub = getattr(ob, childname.lower()+'s')
for i, child in enumerate(sub):
try:
assert_neo_object_is_compliant(child)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s %s of %s' % (childname, i,
classname),)
raise
def assert_same_sub_schema(ob1, ob2, equal_almost=False, threshold=1e-10):
'''
Test if ob1 and ob2 has the same sub schema.
Explore all one_to_many_relationship.
Many_to_many_relationship is not tested
because of infinite recursive loops.
Arguments:
equal_almost: if False do a strict arrays_equal if
True do arrays_almost_equal
'''
assert type(ob1) == type(ob2), 'type(%s) != type(%s)' % (type(ob1),
type(ob2))
classname = ob1.__class__.__name__
if isinstance(ob1, list):
assert len(ob1) == len(ob2), \
'lens %s and %s not equal for %s and %s' % \
(len(ob1), len(ob2), ob1, ob2)
for i, (sub1, sub2) in enumerate(zip(ob1, ob2)):
try:
assert_same_sub_schema(sub1, sub2, equal_almost=equal_almost,
threshold=threshold)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('%s[%s]' % (classname, i),)
raise
return
if classname in description.one_to_many_relationship:
# test one_to_many_relationship
for child in description.one_to_many_relationship[classname]:
if not hasattr(ob1, child.lower()+'s'):
assert not hasattr(ob2, child.lower()+'s'), \
'%s 2 does have %s but not %s 1' % (classname, child,
classname)
continue
else:
assert hasattr(ob2, child.lower()+'s'), \
'%s 1 has %s but not %s 2' % (classname, child, classname)
sub1 = getattr(ob1, child.lower()+'s')
sub2 = getattr(ob2, child.lower()+'s')
assert len(sub1) == len(sub2), \
'theses two %s do not have the same %s number: %s and %s' % \
(classname, child, len(sub1), len(sub2))
for i in range(len(getattr(ob1, child.lower()+'s'))):
# previously lacking parameter
try:
assert_same_sub_schema(sub1[i], sub2[i],
equal_almost, threshold)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s[%s] of %s' % (child, i, classname),)
raise
# check if all attributes are equal
if equal_almost:
def assert_arrays_equal_and_dtype(a, b):
assert_arrays_equal(a, b)
assert a.dtype == b.dtype, \
"%s and %s not same dtype %s and %s" % (a, b, a.dtype, b.dtype)
assert_eg = assert_arrays_equal_and_dtype
else:
def assert_arrays_almost_and_dtype(a, b):
assert_arrays_almost_equal(a, b, threshold)
#assert a.dtype == b.dtype, \
#"%s and %s not same dtype %s %s" % (a, b, a.dtype, b.dtype)
assert_eg = assert_arrays_almost_and_dtype
necess = description.classes_necessary_attributes[classname]
recomm = description.classes_recommended_attributes[classname]
attributes = necess + recomm
for ioattr in attributes:
attrname, attrtype = ioattr[0], ioattr[1]
#~ if attrname =='':
if (classname in description.classes_inheriting_quantities and
description.classes_inheriting_quantities[classname] ==
attrname):
# object is hinerited from Quantity (AnalogSIgnal, SpikeTrain, ...)
try:
assert_eg(ob1.magnitude, ob2.magnitude)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s' % classname,)
raise
assert ob1.dimensionality.string == ob2.dimensionality.string, \
'Units of %s are not the same: %s and %s' % \
(classname, ob1.dimensionality.string,
ob2.dimensionality.string)
continue
if not hasattr(ob1, attrname):
assert not hasattr(ob2, attrname), \
'%s 2 does have %s but not %s 1' % (classname, attrname,
classname)
continue
else:
assert hasattr(ob2, attrname), \
'%s 1 has %s but not %s 2' % (classname, attrname, classname)
if getattr(ob1, attrname) is None:
assert getattr(ob2, attrname) is None, \
'In %s.%s %s and %s differed' % (classname, attrname,
getattr(ob1, attrname),
getattr(ob2, attrname))
continue
if getattr(ob2, attrname) is None:
assert getattr(ob1, attrname) is None, \
'In %s.%s %s and %s differed' % (classname, attrname,
getattr(ob1, attrname),
getattr(ob2, attrname))
continue
if attrtype == pq.Quantity:
# Compare magnitudes
mag1 = getattr(ob1, attrname).magnitude
mag2 = getattr(ob2, attrname).magnitude
#print "2. ob1(%s) %s:%s\n ob2(%s) %s:%s" % \
#(ob1,attrname,mag1,ob2,attrname,mag2)
try:
assert_eg(mag1, mag2)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s of %s' % (attrname, classname),)
raise
# Compare dimensionalities
dim1 = getattr(ob1, attrname).dimensionality.simplified
dim2 = getattr(ob2, attrname).dimensionality.simplified
dimstr1 = getattr(ob1, attrname).dimensionality.string
dimstr2 = getattr(ob2, attrname).dimensionality.string
assert dim1 == dim2, \
'Attribute %s of %s are not the same: %s != %s' % \
(attrname, classname, dimstr1, dimstr2)
elif attrtype == np.ndarray:
try:
assert_eg(getattr(ob1, attrname), getattr(ob2, attrname))
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s of %s' % (attrname, classname),)
raise
else:
#~ print 'yep', getattr(ob1, attrname), getattr(ob2, attrname)
assert getattr(ob1, attrname) == getattr(ob2, attrname), \
'Attribute %s.%s are not the same %s %s %s %s' % \
(classname, attrname,
type(getattr(ob1, attrname)), getattr(ob1, attrname),
type(getattr(ob2, attrname)), getattr(ob2, attrname))
def assert_sub_schema_is_lazy_loaded(ob):
'''
This is util for testing lazy load. All object must load with ndarray.size
or Quantity.size ==0
'''
classname = ob.__class__.__name__
if classname in description.one_to_many_relationship:
for childname in description.one_to_many_relationship[classname]:
if not hasattr(ob, childname.lower()+'s'):
continue
sub = getattr(ob, childname.lower()+'s')
for i, child in enumerate(sub):
try:
assert_sub_schema_is_lazy_loaded(child)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s %s of %s' % (childname, i,
classname),)
raise
necess = description.classes_necessary_attributes[classname]
recomm = description.classes_recommended_attributes[classname]
attributes = necess + recomm
for ioattr in attributes:
attrname, attrtype = ioattr[0], ioattr[1]
#~ print 'xdsd', classname, attrname
#~ if attrname == '':
if (classname in description.classes_inheriting_quantities and
description.classes_inheriting_quantities[classname] ==
attrname):
assert ob.size == 0, \
'Lazy loaded error %s.size = %s' % (classname, ob.size)
assert hasattr(ob, 'lazy_shape'), \
'Lazy loaded error, %s should have lazy_shape attribute' % \
classname
continue
if not hasattr(ob, attrname) or getattr(ob, attrname) is None:
continue
#~ print 'hjkjh'
if (attrtype == pq.Quantity or attrtype == np.ndarray):
# FIXME: it is a workaround for recordingChannelGroup.channel_names
# which is nupy.array but allowed to be loaded when lazy == True
if ob.__class__ == neo.RecordingChannelGroup:
continue
ndim = ioattr[2]
#~ print 'ndim', ndim
#~ print getattr(ob, attrname).size
if ndim >= 1:
assert getattr(ob, attrname).size == 0, \
'Lazy loaded error %s.%s.size = %s' % \
(classname, attrname, getattr(ob, attrname).size)
assert hasattr(ob, 'lazy_shape'), \
'Lazy loaded error ' +\
'%s should have lazy_shape attribute ' % classname +\
'because of %s attribute' % attrname
lazy_shape_arrays = {'SpikeTrain': 'times', 'Spike': 'waveform',
'AnalogSignal': 'signal',
'AnalogSignalArray': 'signal',
'EventArray': 'times', 'EpochArray': 'times'}
def assert_lazy_sub_schema_can_be_loaded(ob, io):
'''
This is util for testing lazy load. All object must load with ndarray.size
or Quantity.size ==0
'''
classname = ob.__class__.__name__
if classname in lazy_shape_arrays:
new_load = io.load_lazy_object(ob)
assert hasattr(ob, 'lazy_shape'), \
'Object %s was not lazy loaded' % classname
assert not hasattr(new_load, 'lazy_shape'), \
'Newly loaded object from %s was also lazy loaded' % classname
if classname in description.classes_inheriting_quantities:
assert ob.lazy_shape == new_load.shape, \
'Shape of loaded object %sis not equal to lazy shape' % \
classname
else:
assert ob.lazy_shape == \
getattr(new_load, lazy_shape_arrays[classname]).shape, \
'Shape of loaded object %s not equal to lazy shape' %\
classname
elif classname in description.one_to_many_relationship:
for childname in description.one_to_many_relationship[classname]:
if not hasattr(ob, childname.lower() + 's'):
continue
sub = getattr(ob, childname.lower() + 's')
for i, child in enumerate(sub):
try:
assert_lazy_sub_schema_can_be_loaded(child, io)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from of %s %s of %s' %
(childname, i, classname),)
raise
def assert_objects_equivalent(obj1, obj2):
'''
Compares two NEO objects by looping over the attributes and annotations
and asserting their hashes. No relationships involved.
'''
def assert_attr(obj1, obj2, attr_name):
'''
Assert a single attribute and annotation are the same
'''
assert hasattr(obj1, attr_name)
attr1 = hashlib.md5(getattr(obj1, attr_name)).hexdigest()
assert hasattr(obj2, attr_name)
attr2 = hashlib.md5(getattr(obj2, attr_name)).hexdigest()
assert attr1 == attr2, "Attribute %s for class %s is not equal." % \
(attr_name, description.name_by_class[obj1.__class__])
obj_type = description.name_by_class[obj1.__class__]
assert obj_type == description.name_by_class[obj2.__class__]
for ioattr in description.classes_necessary_attributes[obj_type]:
assert_attr(obj1, obj2, ioattr[0])
for ioattr in description.classes_recommended_attributes[obj_type]:
if hasattr(obj1, ioattr[0]) or hasattr(obj2, ioattr[0]):
assert_attr(obj1, obj2, ioattr[0])
if hasattr(obj1, "annotations"):
assert hasattr(obj2, "annotations")
for key, value in obj1.annotations:
assert hasattr(obj2.annotations, key)
assert obj2.annotations[key] == value
def assert_children_empty(obj, parent):
'''
Check that the children of a neo object are empty. Used
to check the cascade is implemented properly
'''
classname = obj.__class__.__name__
errmsg = '''%s reader with cascade=False should return
empty children''' % parent.__name__
try:
childlist = description.one_to_many_relationship[classname]
except KeyError:
childlist = []
for childname in childlist:
children = getattr(obj, childname.lower() + 's')
assert len(children) == 0, errmsg
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