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test_tag.py
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test_tag.py
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# Copyright (c) 2014, German Neuroinformatics Node (G-Node)
#
# All rights reserved.
#
# Redistribution and use in section and binary forms, with or without
# modification, are permitted under the terms of the BSD License. See
# LICENSE file in the root of the Project.
from __future__ import (absolute_import, division, print_function)
import os
import unittest
import numpy as np
import nixio as nix
skip_cpp = not hasattr(nix, "core")
class TagTestBase(unittest.TestCase):
backend = None
testfilename = "tagtest.h5"
def setUp(self):
self.file = nix.File.open(self.testfilename, nix.FileMode.Overwrite,
backend=self.backend)
self.block = self.file.create_block("test block", "recordingsession")
self.my_array = self.block.create_data_array("my array", "test",
nix.DataType.Int16, (1, ))
self.my_tag = self.block.create_tag(
"my tag", "tag", [0]
)
self.my_tag.references.append(self.my_array)
self.your_array = self.block.create_data_array(
"your array", "test", nix.DataType.Int16, (1, )
)
self.your_tag = self.block.create_tag(
"your tag", "tag", [0]
)
self.your_tag.references.append(self.your_array)
def tearDown(self):
del self.file.blocks[self.block.id]
self.file.close()
os.remove(self.testfilename)
def test_tag_eq(self):
assert(self.my_tag == self.my_tag)
assert(not self.my_tag == self.your_tag)
assert(self.my_tag is not None)
def test_tag_id(self):
assert(self.my_tag.id is not None)
def test_tag_name(self):
assert(self.my_tag.name is not None)
def test_tag_type(self):
def set_none():
self.my_tag.type = None
assert(self.my_tag.type is not None)
self.assertRaises(Exception, set_none)
self.my_tag.type = "foo type"
assert(self.my_tag.type == "foo type")
def test_tag_definition(self):
assert(self.my_tag.definition is None)
self.my_tag.definition = "definition"
assert(self.my_tag.definition == "definition")
self.my_tag.definition = None
assert(self.my_tag.definition is None)
def test_tag_timestamps(self):
created_at = self.my_tag.created_at
assert(created_at > 0)
updated_at = self.my_tag.updated_at
assert(updated_at > 0)
self.my_tag.force_created_at(1403530068)
assert(self.my_tag.created_at == 1403530068)
def test_tag_units(self):
assert(self.my_tag.units == ())
self.my_tag.units = ["mV", "ms"]
assert(self.my_tag.units == ("mV", "ms"))
self.my_tag.units = []
assert(self.my_tag.units == ())
def test_tag_position(self):
assert(self.my_tag.position == (0, ))
self.my_tag.position = (1.0, 2.0, 3.0)
assert(self.my_tag.position == (1.0, 2.0, 3.0))
def test_tag_extent(self):
assert(self.my_tag.extent == ())
self.my_tag.extent = (1.0, 2.0, 3.0)
assert(self.my_tag.extent == (1.0, 2.0, 3.0))
self.my_tag.extent = []
assert(self.my_tag.extent == ())
def test_tag_references(self):
assert(len(self.my_tag.references) == 1)
self.assertRaises(TypeError,
lambda _: self.my_tag.references.append(100))
reference1 = self.block.create_data_array("reference1", "stimuli",
nix.DataType.Int16, (1, ))
reference2 = self.block.create_data_array("reference2", "stimuli",
nix.DataType.Int16, (1, ))
self.my_tag.references.append(reference1)
self.my_tag.references.append(reference2)
assert(reference1.name in self.my_tag.references)
assert(len(self.my_tag.references) == 3)
assert(reference1 in self.my_tag.references)
assert(reference2 in self.my_tag.references)
# id and name access
assert(reference1 == self.my_tag.references[reference1.name])
assert(reference1 == self.my_tag.references[reference1.id])
assert(reference2 == self.my_tag.references[reference2.name])
assert(reference2 == self.my_tag.references[reference2.id])
assert(reference1.name in self.my_tag.references)
assert(reference2.name in self.my_tag.references)
assert(reference1.id in self.my_tag.references)
assert(reference2.id in self.my_tag.references)
del self.my_tag.references[reference2]
assert(self.my_array in self.my_tag.references)
assert(reference1 in self.my_tag.references)
del self.my_tag.references[reference1]
assert(len(self.my_tag.references) == 1)
def test_tag_features(self):
assert(len(self.my_tag.features) == 0)
data_array = self.block.create_data_array("feature", "stimuli",
nix.DataType.Int16, (1, ))
feature = self.my_tag.create_feature(data_array, nix.LinkType.Untagged)
assert(len(self.my_tag.features) == 1)
assert(feature in self.my_tag.features)
assert(feature.id in self.my_tag.features)
assert("notexist" not in self.my_tag.features)
assert(feature.id == self.my_tag.features[0].id)
assert(feature.id == self.my_tag.features[-1].id)
# id and name access
assert(feature.id == self.my_tag.features[feature.id].id)
assert(feature.id == self.my_tag.features[data_array.id].id)
assert(feature.id == self.my_tag.features[data_array.name].id)
assert(data_array == self.my_tag.features[data_array.id].data)
assert(data_array == self.my_tag.features[data_array.name].data)
assert(data_array.id in self.my_tag.features)
assert(data_array.name in self.my_tag.features)
del self.my_tag.features[0]
assert(len(self.my_tag.features) == 0)
def test_tag_retrieve_data(self):
sample_iv = 1.0
ticks = [1.2, 2.3, 3.4, 4.5, 6.7]
unit = "ms"
pos = [0.0, 2.0, 3.4]
ext = [0.0, 6.0, 2.3]
units = ["none", "ms", "ms"]
data = np.random.random((2, 10, 5))
da = self.block.create_data_array("dimtest", "test",
data=data)
setdim = da.append_set_dimension()
setdim.labels = ["Label A", "Label B"]
samdim = da.append_sampled_dimension(sample_iv)
samdim.unit = unit
randim = da.append_range_dimension(ticks)
randim.unit = unit
postag = self.block.create_tag("postag", "event", pos)
postag.references.append(da)
postag.units = units
segtag = self.block.create_tag("region", "segment", pos)
segtag.references.append(da)
segtag.extent = ext
segtag.units = units
posdata = postag.retrieve_data(0)
assert(len(posdata.shape) == 3)
assert(posdata.shape == (1, 1, 1))
segdata = segtag.retrieve_data(0)
assert(len(segdata.shape) == 3)
assert(segdata.shape == (1, 7, 2))
# retrieve data by id and name
posdata = postag.retrieve_data(da.name)
assert(len(posdata.shape) == 3)
assert(posdata.shape == (1, 1, 1))
segdata = segtag.retrieve_data(da.name)
assert(len(segdata.shape) == 3)
assert(segdata.shape == (1, 7, 2))
posdata = postag.retrieve_data(da.id)
assert(len(posdata.shape) == 3)
assert(posdata.shape == (1, 1, 1))
segdata = segtag.retrieve_data(da.id)
assert(len(segdata.shape) == 3)
assert(segdata.shape == (1, 7, 2))
def test_tag_retrieve_feature_data(self):
number_feat = self.block.create_data_array("number feature", "test",
data=10.)
ramp_data = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
ramp_feat = self.block.create_data_array("ramp feature", "test",
data=np.asarray(ramp_data))
ramp_feat.label = "voltage"
ramp_feat.unit = "mV"
dim = ramp_feat.append_sampled_dimension(1.0)
dim.unit = "ms"
pos_tag = self.block.create_tag("feature test", "test", [5.0])
pos_tag.units = ["ms"]
pos_tag.create_feature(number_feat, nix.LinkType.Untagged)
pos_tag.create_feature(ramp_feat, nix.LinkType.Tagged)
pos_tag.create_feature(ramp_feat, nix.LinkType.Untagged)
assert(len(pos_tag.features) == 3)
data1 = pos_tag.retrieve_feature_data(0)
data2 = pos_tag.retrieve_feature_data(1)
data3 = pos_tag.retrieve_feature_data(2)
assert(data1.size == 1)
assert(data2.size == 1)
assert(data3.size == len(ramp_data))
# make the tag pointing to a slice
pos_tag.extent = [2.0]
data1 = pos_tag.retrieve_feature_data(0)
data2 = pos_tag.retrieve_feature_data(1)
data3 = pos_tag.retrieve_feature_data(2)
assert(data1.size == 1)
assert(data2.size == 3)
assert(data3.size == len(ramp_data))
# get by name
data1 = pos_tag.retrieve_feature_data(number_feat.name)
data2 = pos_tag.retrieve_feature_data(ramp_feat.name)
assert(data1.size == 1)
assert(data2.size == 3)
@unittest.skipIf(skip_cpp, "HDF5 backend not available.")
class TestTagCPP(TagTestBase):
backend = "hdf5"
class TestTagPy(TagTestBase):
backend = "h5py"