def test_convert_with_profile():
cfgpath = setup_config(pxsize=1.34e-6,
medium_index=1.346,
wavelength=554.2e-9)
_, path_in, path_out = setup_test_data()
argsadd = argparse.Namespace(subparser_name="add",
name="test_8440_prof_convert",
path=cfgpath)
profile.cli_profile(args=argsadd)
try:
# perform conversion
h5data = cli_convert(path=path_in,
ret_data=True,
profile="test_8440_prof_convert")
cfg = config.ConfigFile(path_out)
assert np.allclose(cfg["meta"]["medium index"], 1.346)
assert np.allclose(cfg["meta"]["pixel size um"], 1.34)
assert np.allclose(cfg["meta"]["wavelength nm"], 554.2)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.allclose(qps[0]["medium index"], 1.346)
assert np.allclose(qps[0]["pixel size"], 1.34e-6)
assert np.allclose(qps[0]["wavelength"], 554.2e-9)
except BaseException:
raise
finally:
# cleanup
argsrem = argparse.Namespace(subparser_name="remove",
name="test_8440_prof_convert")
profile.cli_profile(args=argsrem)
def test_extract_meta_data():
"""qpformat can automatically transfer the metadata from
QPSeries files to the dataset which DryMass makes use of.
"""
_qpi, path_in, path_out = setup_test_data(pxsize=1.3e-6,
medium_index=1.345,
wavelength=555e-9,
num=2,
write_config=False)
cli_convert(path=path_in)
cfg = config.ConfigFile(path_out)
assert cfg["meta"]["medium index"] == 1.345
assert cfg["meta"]["pixel size um"] == 1.3
assert cfg["meta"]["wavelength nm"] == 555
def test_base():
qpi, path_in, path_out = setup_test_data(num=2)
h5data = cli_convert(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.allclose(qpi.pha, qps[0].pha)
assert np.allclose(qpi.amp, qps[0].amp)
def test_bg_corr_index():
_qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="bg", key="phase data", value=1)
cfg.set_value(section="bg", key="amplitude data", value=1)
h5data = cli_convert(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.all(qps[0].pha == 0)
assert np.all(qps[0].amp == 1)
def test_bg_corr_file_relative():
_bgqpi, bg_path_in, bg_path_out = setup_test_data(num=1)
_qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="bg",
key="phase data",
value=str(bg_path_in.relative_to(path_in.parent)))
cfg.set_value(section="bg",
key="amplitude data",
value=str(bg_path_in.relative_to(path_in.parent)))
h5data = cli_convert(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.all(qps[0].pha == 0)
assert np.all(qps[0].amp == 1)