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import numpy as np
from pathlib import Path
import warnings
from pynwb import NWBHDF5IO, validate, TimeSeries
from pynwb.image import ImageSeries
from pynwb.testing import TestCase
class TestReadOldVersions(TestCase):
expected_warnings = {
''
'2.1.0_imageseries_non_external_format.nwb': [(
"ImageSeries 'test_imageseries': Format must be 'external' when external_file is specified."
)],
'2.1.0_imageseries_nonmatch_starting_frame.nwb': [(
"ImageSeries 'test_imageseries': The number of frame indices in 'starting_frame' should have the same "
"length as 'external_file'."
)],
}
expected_errors = {
'1.0.2_str_experimenter.nwb': [("root/general/experimenter (general/experimenter): incorrect shape - expected "
"an array of shape '[None]', got non-array data 'one experimenter'")],
'1.0.3_str_experimenter.nwb': [("root/general/experimenter (general/experimenter): incorrect shape - expected "
"an array of shape '[None]', got non-array data 'one experimenter'")],
'1.0.2_str_pub.nwb': [("root/general/related_publications (general/related_publications): incorrect shape "
"- expected an array of shape '[None]', got non-array data 'one publication'")],
'1.0.3_str_pub.nwb': [("root/general/related_publications (general/related_publications): incorrect shape "
"- expected an array of shape '[None]', got non-array data 'one publication'")],
'1.5.1_timeseries_no_data.nwb': [("TimeSeries/data/data (acquisition/test_timeseries/data): argument missing")],
'1.5.1_timeseries_no_unit.nwb': [("TimeSeries/data/unit (acquisition/test_timeseries/data): argument missing")],
'1.5.1_imageseries_no_data.nwb': [("ImageSeries/data/data (acquisition/test_imageseries/data): "
"argument missing")],
'1.5.1_imageseries_no_unit.nwb': [("ImageSeries/data/unit (acquisition/test_imageseries/data): "
"argument missing")],
}
def get_io(self, path):
"""Get an NWBHDF5IO object for the given path."""
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message=r"Ignoring cached namespace .*",
category=UserWarning,
)
return NWBHDF5IO(str(path), 'r')
def test_read(self):
"""Test reading and validating all NWB files in the same folder as this file.
This folder contains NWB files generated by previous versions of NWB using the script
src/pynwb/testing/make_test_files.py
"""
dir_path = Path(__file__).parent
nwb_files = dir_path.glob('*.nwb')
for f in nwb_files:
with self.subTest(file=f.name):
with warnings.catch_warnings(record=True) as warnings_on_read:
warnings.simplefilter("always")
with self.get_io(f) as io:
errors = validate(io)
io.read()
for w in warnings_on_read:
if f.name in self.expected_warnings:
if str(w.message) not in self.expected_warnings[f.name]:
pass
# will replace above with below after the test file is updated
# raise Exception("Unexpected warning: %s: %s" % (f.name, str(w.message)))
else:
pass
# will replace above with below after the test file is updated
# raise Exception("Unexpected warning: %s: %s" % (f.name, str(w.message)))
if errors:
for e in errors:
if f.name in self.expected_errors:
if str(e) not in self.expected_errors[f.name]:
warnings.warn('%s: %s' % (f.name, e))
else:
raise Exception("Unexpected validation error: %s: %s" % (f.name, e))
# TODO uncomment below when validation errors have been fixed
# raise Exception('%d validation error(s). See warnings.' % len(errors))
def test_read_timeseries_no_data(self):
"""Test that a TimeSeries written without data is read with data set to the default value."""
f = Path(__file__).parent / '1.5.1_timeseries_no_data.nwb'
with self.get_io(f) as io:
read_nwbfile = io.read()
np.testing.assert_array_equal(read_nwbfile.acquisition['test_timeseries'].data, TimeSeries.DEFAULT_DATA)
def test_read_timeseries_no_unit(self):
"""Test that an ImageSeries written without unit is read with unit set to the default value."""
f = Path(__file__).parent / '1.5.1_timeseries_no_unit.nwb'
with self.get_io(f) as io:
read_nwbfile = io.read()
self.assertEqual(read_nwbfile.acquisition['test_timeseries'].unit, TimeSeries.DEFAULT_UNIT)
def test_read_imageseries_no_data(self):
"""Test that an ImageSeries written without data is read with data set to the default value."""
f = Path(__file__).parent / '1.5.1_imageseries_no_data.nwb'
with self.get_io(f) as io:
read_nwbfile = io.read()
np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].data, ImageSeries.DEFAULT_DATA)
def test_read_imageseries_no_unit(self):
"""Test that an ImageSeries written without unit is read with unit set to the default value."""
f = Path(__file__).parent / '1.5.1_imageseries_no_unit.nwb'
with self.get_io(f) as io:
read_nwbfile = io.read()
self.assertEqual(read_nwbfile.acquisition['test_imageseries'].unit, ImageSeries.DEFAULT_UNIT)
def test_read_imageseries_non_external_format(self):
"""Test that reading an ImageSeries with an inconsistent format does not change the value."""
fbase = "2.1.0_imageseries_non_external_format.nwb"
f = Path(__file__).parent / fbase
expected_warning = self.expected_warnings[fbase][0]
with self.assertWarnsWith(UserWarning, expected_warning):
with self.get_io(f) as io:
read_nwbfile = io.read()
self.assertEqual(read_nwbfile.acquisition['test_imageseries'].format, "tiff")
def test_read_imageseries_nonmatch_starting_frame(self):
"""Test that reading an ImageSeries with an inconsistent starting_frame does not change the value."""
fbase = "2.1.0_imageseries_nonmatch_starting_frame.nwb"
f = Path(__file__).parent / fbase
expected_warning = self.expected_warnings[fbase][0]
with self.assertWarnsWith(UserWarning, expected_warning):
with self.get_io(f) as io:
read_nwbfile = io.read()
np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].starting_frame, [1, 2, 3])
def test_read_subject_no_age__reference(self):
"""Test that reading a Subject without an age__reference set with NWB schema 2.5.0 sets the value to None"""
f = Path(__file__).parent / '2.2.0_subject_no_age__reference.nwb'
with self.get_io(f) as io:
read_nwbfile = io.read()
self.assertIsNone(read_nwbfile.subject.age__reference)
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