def test__recordingchannelgroup__cascade(self):
obj_type = 'RecordingChannelGroup'
cascade = True
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, RecordingChannelGroup))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.recordingchannels), 1)
rchan = res.recordingchannels[0]
self.assertEqual(rchan.annotations, self.annotations)
self.assertEqual(len(res.units), 1)
unit = res.units[0]
self.assertEqual(unit.annotations, self.annotations)
self.assertEqual(len(res.analogsignalarrays), 1)
self.assertEqual(res.analogsignalarrays[0].annotations,
self.annotations)
self.assertEqual(len(rchan.analogsignals), 1)
self.assertEqual(len(rchan.irregularlysampledsignals), 1)
self.assertEqual(rchan.analogsignals[0].annotations,
self.annotations)
self.assertEqual(rchan.irregularlysampledsignals[0].annotations,
self.annotations)
self.assertEqual(len(unit.spiketrains), 1)
self.assertEqual(len(unit.spikes), 1)
self.assertEqual(unit.spiketrains[0].annotations,
self.annotations)
self.assertEqual(unit.spikes[0].annotations,
self.annotations)
def test__analogsignalarray__cascade(self):
obj_type = 'AnalogSignalArray'
cascade = True
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, AnalogSignalArray))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
def test__event__cascade(self):
obj_type = 'Event'
cascade = True
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Event))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
def test__spike__nocascade(self):
obj_type = 'Spike'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Spike))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
def test__epocharray__nocascade(self):
obj_type = 'EpochArray'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, EpochArray))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
def test__irregularlysampledsignal__nocascade(self):
obj_type = 'IrregularlySampledSignal'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, IrregularlySampledSignal))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
def test_property_change(self):
""" Make sure all attributes are saved properly after the change,
including quantities, units, types etc."""
iom = NeoHdf5IO(filename=self.test_file)
for obj_type in objectnames:
obj = fake_neo(obj_type, cascade=False)
iom.save(obj)
self.assertTrue(hasattr(obj, "hdf5_path"))
replica = iom.get(obj.hdf5_path, cascade=False)
assert_objects_equivalent(obj, replica)
def test__unit__nocascade(self):
obj_type = 'Unit'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Unit))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.spiketrains), 0)
self.assertEqual(len(res.spikes), 0)
def test__recordingchannel__nocascade(self):
obj_type = 'RecordingChannel'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, RecordingChannel))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.analogsignals), 0)
self.assertEqual(len(res.irregularlysampledsignals), 0)
def test__block__nocascade(self):
obj_type = 'Block'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Block))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.segments), 0)
self.assertEqual(len(res.recordingchannelgroups), 0)
def test__recordingchannelgroup__nocascade(self):
obj_type = 'RecordingChannelGroup'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, RecordingChannelGroup))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.recordingchannels), 0)
self.assertEqual(len(res.units), 0)
self.assertEqual(len(res.analogsignalarrays), 0)
def test_attr_changes(self):
""" gets an object, changes its attributes, saves it, then compares how
good the changes were saved. """
iom = NeoHdf5IO(filename=self.test_file)
for obj_type in objectnames:
obj = fake_neo(obj_type=obj_type, cascade=False)
iom.save(obj)
orig_obj = iom.get(obj.hdf5_path)
for attr in obj._all_attrs:
if hasattr(orig_obj, attr[0]):
setattr(obj, attr[0], get_fake_value(*attr))
iom.save(orig_obj)
test_obj = iom.get(orig_obj.hdf5_path)
assert_objects_equivalent(orig_obj, test_obj)
def test_create(self):
"""
Create test file with signals, segments, blocks etc.
"""
iom = NeoHdf5IO(filename=self.test_file)
b1 = fake_neo() # creating a structure
iom.save(b1) # saving
# must be assigned after save
self.assertTrue(hasattr(b1, "hdf5_path"))
iom.close()
iom.connect(filename=self.test_file)
b2 = iom.get(b1.hdf5_path) # new object
assert_neo_object_is_compliant(b2)
assert_same_sub_schema(b1, b2)
def test_attr_changes(self):
""" gets an object, changes its attributes, saves it, then compares how
good the changes were saved. """
iom = NeoHdf5IO(filename=self.test_file)
for obj_type in class_by_name.keys():
obj = fake_neo(obj_type=obj_type, cascade=False)
iom.save(obj)
orig_obj = iom.get(obj.hdf5_path)
attrs = (classes_necessary_attributes[obj_type] +
classes_recommended_attributes[obj_type])
for attr in attrs:
if hasattr(orig_obj, attr[0]):
setattr(obj, attr[0], get_fake_value(*attr))
iom.save(orig_obj)
test_obj = iom.get(orig_obj.hdf5_path)
assert_objects_equivalent(orig_obj, test_obj)
def test__segment__nocascade(self):
obj_type = 'Segment'
cascade = False
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Segment))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.analogsignalarrays), 0)
self.assertEqual(len(res.analogsignals), 0)
self.assertEqual(len(res.irregularlysampledsignals), 0)
self.assertEqual(len(res.spiketrains), 0)
self.assertEqual(len(res.spikes), 0)
self.assertEqual(len(res.events), 0)
self.assertEqual(len(res.epochs), 0)
self.assertEqual(len(res.eventarrays), 0)
self.assertEqual(len(res.epocharrays), 0)
def test_relations(self):
"""
make sure the change in relationships is saved properly in the file,
including correct M2M, no redundancy etc. RC -> RCG not tested.
"""
def assert_children(self, obj, replica):
obj_type = obj.__name__
self.assertEqual(md5(str(obj)).hexdigest(),
md5(str(replica)).hexdigest())
for container in getattr(obj, '_child_containers', []):
ch1 = getattr(obj, container)
ch2 = getattr(replica, container)
self.assertEqual(len(ch1), len(ch2))
for i, v in enumerate(ch1):
self.assert_children(ch1[i], ch2[i])
iom = NeoHdf5IO(filename=self.test_file)
for obj_type in objectnames:
obj = fake_neo(obj_type, cascade=True)
iom.save(obj)
self.assertTrue(hasattr(obj, "hdf5_path"))
replica = iom.get(obj.hdf5_path, cascade=True)
self.assert_children(obj, replica)
def generate_diagram(filename, rect_pos, rect_width, figsize):
rw = rect_width
fig = pyplot.figure(figsize=figsize)
ax = fig.add_axes([0, 0, 1, 1])
all_h = {}
objs = {}
for name in rect_pos:
objs[name] = fake_neo(name)
all_h[name] = get_rect_height(name, objs[name])
# draw connections
color = ['c', 'm', 'y']
alpha = [1., 1., 0.3]
for name, pos in rect_pos.items():
obj = objs[name]
relationships = [getattr(obj, '_single_child_objects', []),
getattr(obj, '_multi_child_objects', []),
getattr(obj, '_child_properties', [])]
for r in range(3):
for ch_name in relationships[r]:
x1, y1 = calc_coordinates(rect_pos[ch_name], all_h[ch_name])
x2, y2 = calc_coordinates(pos, all_h[name])
if r in [0, 2]:
x2 += rect_width
connectionstyle = "arc3,rad=-0.2"
elif y2 >= y1:
connectionstyle = "arc3,rad=0.7"
else:
connectionstyle = "arc3,rad=-0.7"
annotate(ax=ax, coord1=(x1, y1), coord2=(x2, y2),
connectionstyle=connectionstyle,
color=color[r], alpha=alpha[r])
# draw boxes
for name, pos in rect_pos.items():
htotal = all_h[name]
obj = objs[name]
allrelationship = (getattr(obj, '_child_containers', []) +
getattr(obj, '_multi_parent_containers', []))
rect = Rectangle(pos, rect_width, htotal,
facecolor='w', edgecolor='k', linewidth=2.)
ax.add_patch(rect)
# title green
pos2 = pos[0], pos[1]+htotal - line_heigth*1.5
rect = Rectangle(pos2, rect_width, line_heigth*1.5,
facecolor='g', edgecolor='k', alpha=.5, linewidth=2.)
ax.add_patch(rect)
# single relationship
relationship = getattr(obj, '_single_child_objects', [])
pos2 = pos[1] + htotal - line_heigth*(1.5+len(relationship))
rect_height = len(relationship)*line_heigth
rect = Rectangle((pos[0], pos2), rect_width, rect_height,
facecolor='c', edgecolor='k', alpha=.5)
ax.add_patch(rect)
# multi relationship
relationship = (getattr(obj, '_multi_child_objects', []) +
getattr(obj, '_multi_parent_containers', []))
pos2 = (pos[1]+htotal - line_heigth*(1.5+len(relationship)) -
rect_height)
rect_height = len(relationship)*line_heigth
rect = Rectangle((pos[0], pos2), rect_width, rect_height,
facecolor='m', edgecolor='k', alpha=.5)
ax.add_patch(rect)
# necessary attr
pos2 = (pos[1]+htotal -
line_heigth*(1.5+len(allrelationship) +
len(obj._necessary_attrs)))
rect = Rectangle((pos[0], pos2), rect_width,
line_heigth*len(obj._necessary_attrs),
facecolor='r', edgecolor='k', alpha=.5)
ax.add_patch(rect)
# name
if hasattr(obj, '_quantity_attr'):
post = '* '
else:
post = ''
ax.text(pos[0]+rect_width/2., pos[1]+htotal - line_heigth*1.5/2.,
name+post,
horizontalalignment='center', verticalalignment='center',
fontsize=fontsize+2,
fontproperties=FontProperties(weight='bold'),
)
#relationship
for i, relat in enumerate(allrelationship):
ax.text(pos[0]+left_text_shift, pos[1]+htotal - line_heigth*(i+2),
relat+': list',
horizontalalignment='left', verticalalignment='center',
fontsize=fontsize,
)
# attributes
for i, attr in enumerate(obj._all_attrs):
attrname, attrtype = attr[0], attr[1]
t1 = attrname
if (hasattr(obj, '_quantity_attr') and
obj._quantity_attr == attrname):
t1 = attrname+'(object itself)'
else:
t1 = attrname
if attrtype == pq.Quantity:
if attr[2] == 0:
t2 = 'Quantity scalar'
else:
t2 = 'Quantity %dD' % attr[2]
elif attrtype == np.ndarray:
t2 = "np.ndarray %dD dt='%s'" % (attr[2], attr[3].kind)
elif attrtype == datetime:
t2 = 'datetime'
else:
t2 = attrtype.__name__
t = t1+' : '+t2
ax.text(pos[0]+left_text_shift,
pos[1]+htotal - line_heigth*(i+len(allrelationship)+2),
t,
horizontalalignment='left', verticalalignment='center',
fontsize=fontsize,
)
xlim, ylim = figsize
ax.set_xlim(0, xlim)
ax.set_ylim(0, ylim)
ax.set_xticks([])
ax.set_yticks([])
fig.savefig(filename, dpi=dpi)
def generate_diagram(filename, rect_pos, rect_width, figsize):
rw = rect_width
fig = pyplot.figure(figsize=figsize)
ax = fig.add_axes([0, 0, 1, 1])
all_h = {}
objs = {}
for name in rect_pos:
objs[name] = fake_neo(name)
all_h[name] = get_rect_height(name, objs[name])
# draw connections
color = ['c', 'm', 'y']
alpha = [1., 1., 0.3]
for name, pos in rect_pos.items():
obj = objs[name]
relationships = [
getattr(obj, '_single_child_objects', []),
getattr(obj, '_multi_child_objects', []),
getattr(obj, '_child_properties', [])
]
for r in range(3):
for ch_name in relationships[r]:
x1, y1 = calc_coordinates(rect_pos[ch_name], all_h[ch_name])
x2, y2 = calc_coordinates(pos, all_h[name])
if r in [0, 2]:
x2 += rect_width
connectionstyle = "arc3,rad=-0.2"
elif y2 >= y1:
connectionstyle = "arc3,rad=0.7"
else:
connectionstyle = "arc3,rad=-0.7"
annotate(ax=ax,
coord1=(x1, y1),
coord2=(x2, y2),
connectionstyle=connectionstyle,
color=color[r],
alpha=alpha[r])
# draw boxes
for name, pos in rect_pos.items():
htotal = all_h[name]
obj = objs[name]
allrelationship = (getattr(obj, '_child_containers', []) +
getattr(obj, '_multi_parent_containers', []))
rect = Rectangle(pos,
rect_width,
htotal,
facecolor='w',
edgecolor='k',
linewidth=2.)
ax.add_patch(rect)
# title green
pos2 = pos[0], pos[1] + htotal - line_heigth * 1.5
rect = Rectangle(pos2,
rect_width,
line_heigth * 1.5,
facecolor='g',
edgecolor='k',
alpha=.5,
linewidth=2.)
ax.add_patch(rect)
# single relationship
relationship = getattr(obj, '_single_child_objects', [])
pos2 = pos[1] + htotal - line_heigth * (1.5 + len(relationship))
rect_height = len(relationship) * line_heigth
rect = Rectangle((pos[0], pos2),
rect_width,
rect_height,
facecolor='c',
edgecolor='k',
alpha=.5)
ax.add_patch(rect)
# multi relationship
relationship = (getattr(obj, '_multi_child_objects', []) +
getattr(obj, '_multi_parent_containers', []))
pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship)) -
rect_height)
rect_height = len(relationship) * line_heigth
rect = Rectangle((pos[0], pos2),
rect_width,
rect_height,
facecolor='m',
edgecolor='k',
alpha=.5)
ax.add_patch(rect)
# necessary attr
pos2 = (pos[1] + htotal - line_heigth *
(1.5 + len(allrelationship) + len(obj._necessary_attrs)))
rect = Rectangle((pos[0], pos2),
rect_width,
line_heigth * len(obj._necessary_attrs),
facecolor='r',
edgecolor='k',
alpha=.5)
ax.add_patch(rect)
# name
if hasattr(obj, '_quantity_attr'):
post = '* '
else:
post = ''
ax.text(
pos[0] + rect_width / 2.,
pos[1] + htotal - line_heigth * 1.5 / 2.,
name + post,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize + 2,
fontproperties=FontProperties(weight='bold'),
)
#relationship
for i, relat in enumerate(allrelationship):
ax.text(
pos[0] + left_text_shift,
pos[1] + htotal - line_heigth * (i + 2),
relat + ': list',
horizontalalignment='left',
verticalalignment='center',
fontsize=fontsize,
)
# attributes
for i, attr in enumerate(obj._all_attrs):
attrname, attrtype = attr[0], attr[1]
t1 = attrname
if (hasattr(obj, '_quantity_attr')
and obj._quantity_attr == attrname):
t1 = attrname + '(object itself)'
else:
t1 = attrname
if attrtype == pq.Quantity:
if attr[2] == 0:
t2 = 'Quantity scalar'
else:
t2 = 'Quantity %dD' % attr[2]
elif attrtype == np.ndarray:
t2 = "np.ndarray %dD dt='%s'" % (attr[2], attr[3].kind)
elif attrtype == datetime:
t2 = 'datetime'
else:
t2 = attrtype.__name__
t = t1 + ' : ' + t2
ax.text(
pos[0] + left_text_shift,
pos[1] + htotal - line_heigth * (i + len(allrelationship) + 2),
t,
horizontalalignment='left',
verticalalignment='center',
fontsize=fontsize,
)
xlim, ylim = figsize
ax.set_xlim(0, xlim)
ax.set_ylim(0, ylim)
ax.set_xticks([])
ax.set_yticks([])
fig.savefig(filename, dpi=dpi)
def test__block__cascade(self):
obj_type = 'Block'
cascade = True
res = fake_neo(obj_type=obj_type, cascade=cascade)
self.assertTrue(isinstance(res, Block))
assert_neo_object_is_compliant(res)
self.assertEqual(res.annotations, self.annotations)
self.assertEqual(len(res.segments), 1)
seg = res.segments[0]
self.assertEqual(seg.annotations, self.annotations)
self.assertEqual(len(res.recordingchannelgroups), 1)
rcg = res.recordingchannelgroups[0]
self.assertEqual(rcg.annotations, self.annotations)
self.assertEqual(len(seg.analogsignalarrays), 1)
self.assertEqual(len(seg.analogsignals), 1)
self.assertEqual(len(seg.irregularlysampledsignals), 1)
self.assertEqual(len(seg.spiketrains), 1)
self.assertEqual(len(seg.spikes), 1)
self.assertEqual(len(seg.events), 1)
self.assertEqual(len(seg.epochs), 1)
self.assertEqual(len(seg.eventarrays), 1)
self.assertEqual(len(seg.epocharrays), 1)
self.assertEqual(seg.analogsignalarrays[0].annotations,
self.annotations)
self.assertEqual(seg.analogsignals[0].annotations,
self.annotations)
self.assertEqual(seg.irregularlysampledsignals[0].annotations,
self.annotations)
self.assertEqual(seg.spiketrains[0].annotations,
self.annotations)
self.assertEqual(seg.spikes[0].annotations,
self.annotations)
self.assertEqual(seg.events[0].annotations,
self.annotations)
self.assertEqual(seg.epochs[0].annotations,
self.annotations)
self.assertEqual(seg.eventarrays[0].annotations,
self.annotations)
self.assertEqual(seg.epocharrays[0].annotations,
self.annotations)
self.assertEqual(len(rcg.recordingchannels), 1)
rchan = rcg.recordingchannels[0]
self.assertEqual(rchan.annotations, self.annotations)
self.assertEqual(len(rcg.units), 1)
unit = rcg.units[0]
self.assertEqual(unit.annotations, self.annotations)
self.assertEqual(len(rcg.analogsignalarrays), 1)
self.assertEqual(rcg.analogsignalarrays[0].annotations,
self.annotations)
self.assertEqual(len(rchan.analogsignals), 1)
self.assertEqual(len(rchan.irregularlysampledsignals), 1)
self.assertEqual(rchan.analogsignals[0].annotations,
self.annotations)
self.assertEqual(rchan.irregularlysampledsignals[0].annotations,
self.annotations)
self.assertEqual(len(unit.spiketrains), 1)
self.assertEqual(len(unit.spikes), 1)
self.assertEqual(unit.spiketrains[0].annotations,
self.annotations)
self.assertEqual(unit.spikes[0].annotations,
self.annotations)
