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TEST: test_tck and test_trk conversion to pytest #874

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Feb 4, 2020
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TEST: test_tck and test_trk conversion to pytest #874

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TEST: test_trk to pytest
robbisg Feb 4, 2020
3a2b0d1
TEST: test_tck to pytest
robbisg Feb 4, 2020
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58 changes: 31 additions & 27 deletions nibabel/streamlines/tests/test_tck.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,17 +14,15 @@
from .. import tck as tck_module
from ..tck import TckFile

import pytest; pytestmark = pytest.mark.skip()

from nose.tools import assert_equal, assert_raises, assert_true
import pytest
from numpy.testing import assert_array_equal
from nibabel.testing import data_path, clear_and_catch_warnings
from ...testing_pytest import data_path, clear_and_catch_warnings
from .test_tractogram import assert_tractogram_equal

DATA = {}


def setup():
def setup_module():
global DATA

DATA['empty_tck_fname'] = pjoin(data_path, "empty.tck")
Expand Down Expand Up @@ -71,8 +69,8 @@ def test_load_matlab_nan_file(self):
for lazy_load in [False, True]:
tck = TckFile.load(DATA['matlab_nan_tck_fname'], lazy_load=lazy_load)
streamlines = list(tck.tractogram.streamlines)
assert_equal(len(streamlines), 1)
assert_equal(streamlines[0].shape, (108, 3))
assert len(streamlines) == 1
assert streamlines[0].shape == (108, 3)

def test_writeable_data(self):
data = DATA['simple_tractogram']
Expand All @@ -82,53 +80,57 @@ def test_writeable_data(self):
for actual, expected_tgi in zip(tck.streamlines, data):
assert_array_equal(actual, expected_tgi.streamline)
# Test we can write to arrays
assert_true(actual.flags.writeable)
assert actual.flags.writeable
actual[0, 0] = 99

def test_load_simple_file_in_big_endian(self):
for lazy_load in [False, True]:
tck = TckFile.load(DATA['simple_tck_big_endian_fname'],
lazy_load=lazy_load)
assert_tractogram_equal(tck.tractogram, DATA['simple_tractogram'])
assert_equal(tck.header['datatype'], 'Float32BE')
assert tck.header['datatype'] == 'Float32BE'

def test_load_file_with_wrong_information(self):
tck_file = open(DATA['simple_tck_fname'], 'rb').read()

# Simulate a TCK file where `datatype` has not the right endianness.
new_tck_file = tck_file.replace(asbytes("Float32LE"),
asbytes("Float32BE"))
assert_raises(DataError, TckFile.load, BytesIO(new_tck_file))

with pytest.raises(DataError):
TckFile.load(BytesIO(new_tck_file))

# Simulate a TCK file with unsupported `datatype`.
new_tck_file = tck_file.replace(asbytes("Float32LE"),
asbytes("int32"))
assert_raises(HeaderError, TckFile.load, BytesIO(new_tck_file))
with pytest.raises(HeaderError):
TckFile.load(BytesIO(new_tck_file))

# Simulate a TCK file with no `datatype` field.
new_tck_file = tck_file.replace(b"datatype: Float32LE\n", b"")
# Need to adjust data offset.
new_tck_file = new_tck_file.replace(b"file: . 67\n", b"file: . 47\n")
with clear_and_catch_warnings(record=True, modules=[tck_module]) as w:
tck = TckFile.load(BytesIO(new_tck_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("Missing 'datatype'" in str(w[0].message))
assert len(w) == 1
assert issubclass(w[0].category, HeaderWarning)
assert "Missing 'datatype'" in str(w[0].message)
assert_array_equal(tck.header['datatype'], "Float32LE")

# Simulate a TCK file with no `file` field.
new_tck_file = tck_file.replace(b"\nfile: . 67", b"")
with clear_and_catch_warnings(record=True, modules=[tck_module]) as w:
tck = TckFile.load(BytesIO(new_tck_file))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("Missing 'file'" in str(w[0].message))
assert len(w) == 1
assert issubclass(w[0].category, HeaderWarning)
assert "Missing 'file'" in str(w[0].message)
assert_array_equal(tck.header['file'], ". 56")

# Simulate a TCK file with `file` field pointing to another file.
new_tck_file = tck_file.replace(b"file: . 67\n",
b"file: dummy.mat 75\n")
assert_raises(HeaderError, TckFile.load, BytesIO(new_tck_file))
with pytest.raises(HeaderError):
TckFile.load(BytesIO(new_tck_file))

# Simulate a TCK file which is missing a streamline delimiter.
eos = TckFile.FIBER_DELIMITER.tostring()
Expand All @@ -139,11 +141,13 @@ def test_load_file_with_wrong_information(self):
buffer_size = 1. / 1024**2 # 1 bytes
hdr = TckFile._read_header(BytesIO(new_tck_file))
tck_reader = TckFile._read(BytesIO(new_tck_file), hdr, buffer_size)
assert_raises(DataError, list, tck_reader)
with pytest.raises(DataError):
list(tck_reader)

# Simulate a TCK file which is missing the end-of-file delimiter.
new_tck_file = tck_file[:-len(eof)]
assert_raises(DataError, TckFile.load, BytesIO(new_tck_file))
with pytest.raises(DataError):
TckFile.load(BytesIO(new_tck_file))

def test_write_empty_file(self):
tractogram = Tractogram(affine_to_rasmm=np.eye(4))
Expand All @@ -160,8 +164,7 @@ def test_write_empty_file(self):
assert_tractogram_equal(new_tck.tractogram, new_tck_orig.tractogram)

tck_file.seek(0, os.SEEK_SET)
assert_equal(tck_file.read(),
open(DATA['empty_tck_fname'], 'rb').read())
assert tck_file.read() == open(DATA['empty_tck_fname'], 'rb').read()

def test_write_simple_file(self):
tractogram = Tractogram(DATA['streamlines'],
Expand All @@ -179,17 +182,18 @@ def test_write_simple_file(self):
assert_tractogram_equal(new_tck.tractogram, new_tck_orig.tractogram)

tck_file.seek(0, os.SEEK_SET)
assert_equal(tck_file.read(),
open(DATA['simple_tck_fname'], 'rb').read())
assert tck_file.read() == open(DATA['simple_tck_fname'], 'rb').read()

# TCK file containing not well formatted entries in its header.
tck_file = BytesIO()
tck = TckFile(tractogram)
tck.header['new_entry'] = 'value\n' # \n not allowed
assert_raises(HeaderError, tck.save, tck_file)
with pytest.raises(HeaderError):
tck.save(tck_file)

tck.header['new_entry'] = 'val:ue' # : not allowed
assert_raises(HeaderError, tck.save, tck_file)
with pytest.raises(HeaderError):
tck.save(tck_file)

def test_load_write_file(self):
for fname in [DATA['empty_tck_fname'],
Expand All @@ -204,7 +208,7 @@ def test_load_write_file(self):

# Check that the written file is the same as the one read.
tck_file.seek(0, os.SEEK_SET)
assert_equal(tck_file.read(), open(fname, 'rb').read())
assert tck_file.read() == open(fname, 'rb').read()

# Save tractogram that has an affine_to_rasmm.
for lazy_load in [False, True]:
Expand Down
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