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import pandas as pd
import numpy as np
from numpy.testing import assert_array_equal
from pynwb import NWBFile, NWBHDF5IO, TimeSeries
from pynwb.core import ScratchData
from pynwb.testing import NWBH5IOMixin, TestCase
class TestScratchDataIO(NWBH5IOMixin, TestCase):
def setUpContainer(self):
""" Return the test ScratchData to read/write """
return ScratchData(name='foo', data=[1, 2, 3, 4], description='test scratch')
def addContainer(self, nwbfile):
""" Add the test ScratchData to the given NWBFile """
nwbfile.add_scratch(self.container)
def getContainer(self, nwbfile):
""" Return the test ScratchData from the given NWBFile """
return nwbfile.get_scratch('foo', convert=False)
def roundtrip_scratch(self, data, case, **kwargs):
self.filename = 'test_scratch_%s.nwb' % case
description = 'a file to test writing and reading a scratch data of type %s' % case
identifier = 'TEST_scratch_%s' % case
nwbfile = NWBFile(session_description=description,
identifier=identifier,
session_start_time=self.start_time,
file_create_date=self.create_date)
nwbfile.add_scratch(data, name='foo', **kwargs)
self.writer = NWBHDF5IO(self.filename, mode='w')
self.writer.write(nwbfile)
self.writer.close()
self.reader = NWBHDF5IO(self.filename, mode='r')
self.read_nwbfile = self.reader.read()
return self.read_nwbfile.get_scratch('foo')
def test_scratch_convert_int(self):
data = 2
ret = self.roundtrip_scratch(data, 'int', description='test scratch')
self.assertEqual(data, ret)
self.validate()
def test_scratch_convert_list(self):
data = [1, 2, 3, 4]
ret = self.roundtrip_scratch(data, 'list', description='test scratch')
assert_array_equal(data, ret)
self.validate()
def test_scratch_convert_ndarray(self):
data = np.array([1, 2, 3, 4])
ret = self.roundtrip_scratch(data, 'ndarray', description='test scratch')
assert_array_equal(data, ret)
self.validate()
def test_scratch_convert_DataFrame_table_desc(self):
"""Test round trip convert of DataFrame with a table description"""
data = pd.DataFrame(data={'col1': [1, 2, 3, 4], 'col2': ['a', 'b', 'c', 'd']})
self.roundtrip_scratch(data, 'DataFrame', description='my_table')
ret = self.read_nwbfile.get_scratch('foo', convert=False)
ret_df = ret.to_dataframe()
self.assertEqual(ret.description, 'my_table')
assert_array_equal(data.values, ret_df.values)
assert_array_equal(data.index.values, ret_df.index.values)
self.validate()
def test_scratch_container(self):
data = TimeSeries(
name='test_ts',
data=[1, 2, 3, 4, 5],
unit='unit',
timestamps=[1.1, 1.2, 1.3, 1.4, 1.5]
)
nwbfile = NWBFile(
session_description='test',
identifier='test',
session_start_time=self.start_time,
file_create_date=self.create_date
)
nwbfile.add_scratch(data)
self.writer = NWBHDF5IO(self.filename, mode='w')
self.writer.write(nwbfile)
self.writer.close()
self.reader = NWBHDF5IO(self.filename, mode='r')
self.read_nwbfile = self.reader.read()
ret = self.read_nwbfile.get_scratch('test_ts')
self.assertContainerEqual(data, ret)
self.validate()
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