/usr/share/pyshared/neo/test/tools.py is in python-neo 0.2.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import numpy as np
import hashlib
import os
import quantities as pq
from neo import description
import neo
def assert_arrays_equal(a, b):
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)
assert (a.flatten()==b.flatten()).all(), "%s != %s" % (a, b)
def assert_arrays_almost_equal(a, b, threshold):
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(), "max(|a - b|) = %s" % (abs(a - b)).max()
def file_digest(filename):
with open(filename, 'rb') as f:
return hashlib.sha1(f.read()).hexdigest()
def assert_file_contents_equal(a, b):
def generate_error_message(a, b):
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 i, attr in enumerate(attributes):
attrname, attrtype = attr[0], attr[1]
#~ if attrname != '':
if classname not in description.classes_inheriting_quantities:
assert hasattr(ob, attrname), '%s neo obect have not %s' %( classname, attrname)
# test attributes types
attributes = necess + recomm
for i, attr in enumerate(attributes):
attrname, attrtype = attr[0], attr[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 = attr[2]
assert ob.ndim == ndim, '%s is %d dimension should be %d' %(classname, ob.ndim, ndim)
if attrtype == np.ndarray:
dt = attr[3]
assert ob.dtype.kind == dt.kind, '%s dtype.kind is %s should be %s' % (classname, ob.dtype.kind, dt.kind)
elif hasattr(ob, attrname):
if getattr(ob, attrname) is not None:
at = getattr(ob, attrname)
assert type(at) == attrtype, '%s in %s have not the good type (%s should be %s)'%(attrname, classname, type(at), attrtype )
if attrtype == pq.Quantity or attrtype == np.ndarray:
ndim = attr[2]
assert at.ndim == ndim, '%s.%s dimension is %d should be %d' % (classname, attrname, at.ndim, ndim)
if attrtype == np.ndarray:
dt = attr[3]
assert at.dtype.kind == dt.kind, '%s.%s dtype.kind is %s should be %s' % (classname, attrname, at.dtype.kind, dt.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 child in 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 is not symetric with %s.%ss' (childname, classname.lower(), 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 child in sub:
assert_neo_object_is_compliant(child)
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 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 do have %s but not %s 1'%(classname, child, classname)
continue
else:
assert hasattr(ob2, child.lower()+'s'), '%s 1 have %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 have not the same %s number'%(classname, child)
for i in range(len(getattr(ob1, child.lower()+'s'))):
assert_same_sub_schema(sub1[i], sub2[i], equal_almost = equal_almost)
# 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 %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 i, attr in enumerate(attributes):
attrname, attrtype = attr[0], attr[1]
#~ if attrname =='':
if classname in description.classes_inheriting_quantities and \
description.classes_inheriting_quantities[classname] == attrname:
# object is hinerited from Quantity (AnalogSIgnal, SpikeTrain, ...)
assert_eg(ob1.magnitude, ob2.magnitude)
assert ob1.dimensionality.string == ob2.dimensionality.string, 'Units of %s are not the same' % classname
continue
if not hasattr(ob1, attrname):
assert not hasattr(ob2, attrname), '%s 2 do have %s but not %s 1'%(classname, attrname, classname)
continue
else:
assert hasattr(ob2, attrname), '%s 1 have %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
assert_eg(mag1, mag2)
# 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:
assert_eg(getattr(ob1, attrname), getattr(ob2, attrname))
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' % (classname,attrname, type(getattr(ob1, attrname)), type(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 child in sub:
assert_sub_schema_is_lazy_loaded(child)
necess = description.classes_necessary_attributes[classname]
recomm = description.classes_recommended_attributes[classname]
attributes = necess + recomm
for i, attr in enumerate(attributes):
attrname, attrtype = attr[0], attr[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 awork arrounf for recordingChannelGroup.channel_names which is nupy.array but allowed to be loaded when lazy = True
if ob.__class__ == neo.RecordingChannelGroup: continue
ndim = attr[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 because of %s attribute' % (classname, attrname, )
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 hasattr(obj1, attr_name)
a1 = md5(getattr(obj1, attr_name)).hexdigest()
assert hasattr(obj2, attr_name)
a2 = md5(getattr(obj2, attr_name)).hexdigest()
assert a1 == a2, "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 attr in description.classes_necessary_attributes[obj_type]:
assert_attr(obj1, obj2, attr[0])
for attr in description.classes_recommended_attributes[obj_type]:
if hasattr(obj1, attr[0]) or hasattr(obj2, attr[0]):
assert_attr(obj1, obj2, attr[0])
if hasattr(obj1, "annotations"):
assert hasattr(obj2, "annotations")
for k, v in obj1.annotations:
assert hasattr(obj2.annotations, k)
assert obj2.annotations[k] == v
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