def test_parser_get_spectrum(data_path, parse_lib):
parser = ImzMLParser(data_path, parse_lib=parse_lib)
for px in range(parser.n_pixels):
mz_x, mz_y = parser.get_spectrum(px)
assert len(mz_x) == len(mz_y)
assert len(mz_x) > 0
assert len(mz_y) > 0
def test_parser_init_paths(data_path, parse_lib):
parser = ImzMLParser(data_path, parse_lib=parse_lib)
assert len(parser.coordinates) == 9
assert parser.n_pixels == 9
mz_x, mz_y = parser.get_spectrum(0)
assert len(mz_x) == len(mz_y)
assert len(mz_x) > 0
assert len(mz_y) > 0
mz_x, mz_y = parser.get_spectrum(4)
assert len(mz_x) == len(mz_y)
assert len(mz_x) == 8399
assert len(mz_y) == 8399
assert np.all(mz_x > 100.0)
assert np.all(mz_x < 800.0)
assert np.all(mz_y >= 0.0)
assert np.all(mz_y < 3.0)
def test_parser_iter(data_path, parse_lib):
parser = ImzMLParser(data_path, parse_lib=parse_lib)
count = 0
for px, (mz_x, mz_y) in enumerate(parser):
_mz_x, _mz_y = parser.get_spectrum(px)
assert len(mz_x) == len(mz_y)
assert len(mz_x) == len(_mz_x)
assert len(mz_y) == len(_mz_y)
assert_equal(_mz_x, mz_x)
assert_equal(_mz_y, mz_y)
count += 1
assert count == parser.n_pixels
def test_portable_get_spectrum(imzml_path, ibd_path, parse_lib):
# get normal parser
parser = ImzMLParser(imzml_path, parse_lib=parse_lib)
# get detached parser and get handle of the portable reader
detached_parser = ImzMLParser(imzml_path, parse_lib=parse_lib)
portable_reader = detached_parser.portable_spectrum_reader()
# pickle and unpickle to ensure it survives for its intended use case
portable_reader = pickle.loads(pickle.dumps(portable_reader))
for idx in range(parser.n_pixels):
mz_x, mz_y = parser.get_spectrum(idx)
_mz_x2, _mz_y2 = portable_reader.get_spectrum(idx)
assert np.all(mz_x == _mz_x2)
assert np.all(mz_y == _mz_y2)
