def test_merge_config():
# test data
_, path_in, path_out = setup_test_data(medium_index=1.30,
pxsize=1.12e-6,
method="image",
model="projection",
refraction_increment=1.1)
# profile
_, path_profile = tempfile.mkstemp(prefix="drymass_test_config_",
suffix=".cfg")
cfg = config.ConfigFile(path=path_profile)
cfg.path.write_text("[meta]\n" + "medium index = 1.31\n" +
"pixel size um = None\n" + "[sphere]\n" +
"method = image\n" + "model = rytov\n")
cfg2 = config.ConfigFile(path=path_out)
assert cfg2["sphere"]["refraction increment"] == 1.1, "for test case"
assert cfg2["meta"]["pixel size um"] == 1.12, "for test case"
# apply profile (merge with original configuration)
dialog.main(path=path_in, profile=path_profile)
# Sanity checks in case DryMass defaults changed
assert cfg["sphere"]["refraction increment"] != 1.1, "for test case"
assert cfg["meta"]["pixel size um"] != 1.12, "for test case"
# The following three are all valid by just copying cfg to path_out
assert cfg2["meta"]["medium index"] == 1.31
assert cfg2["sphere"]["method"] == "image"
assert cfg2["sphere"]["model"] == "rytov"
# This one is only valid when the configs are merged
assert cfg2["sphere"]["refraction increment"] == 1.1
# This one is only valid when Nones in profile do not override path_out
assert cfg2["meta"]["pixel size um"] == 1.12
def test_update():
path1 = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg1 = config.ConfigFile(path=path1)
path2 = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg2 = config.ConfigFile(path=path2)
cfg1.path.write_text("[sphere]\nrefraction increment = 1.1\n")
assert cfg2["sphere"]["refraction increment"] == .18, "defaults"
cfg2.update(cfg1)
assert cfg2["sphere"]["refraction increment"] == 1.1
def test_compat_081():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
# initialize config
cfg.set_value("meta", "medium index", 1.3365)
filepath = cfg.path
# simulate old behavior
data = filepath.open().read()
data = data.replace("medium index = 1.3365", "medium index = nan")
filepath.write_text(data)
# check fix
cfg2 = config.ConfigFile(path=path)
assert cfg2["meta"]["medium index"] is None
def test_compat_013():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
# initialize config
cfg.set_value("bg", "phase profile", "tilt")
cfg.set_value("bg", "amplitude profile", "tilt")
filepath = cfg.path
# simulate old behavior
data = filepath.open().read()
data = data.replace(" profile = tilt\n", " profile = ramp\n")
filepath.write_text(data)
# check fix
cfg2 = config.ConfigFile(path=path)
assert cfg2["bg"]["phase profile"] == "tilt"
assert cfg2["bg"]["amplitude profile"] == "tilt"
def setup_test_data(radius_px=30, size=200, pxsize=1e-6, medium_index=1.335,
wavelength=550e-9, num=1):
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
cx = 80
cy = 120
r = np.sqrt((x - cx)**2 + (y - cy)**2)
pha = (r < radius_px) * 1.3
amp = .5 + np.roll(pha, 10) / pha.max()
qpi = qpimage.QPImage(data=(pha, amp),
which_data="phase,amplitude",
meta_data={"pixel size": pxsize,
"medium index": medium_index,
"wavelength": wavelength})
path_in = tempfile.mktemp(suffix=".h5", prefix="drymass_test_cli_sphere")
path_in = pathlib.Path(path_in)
with qpimage.QPSeries(h5file=path_in, h5mode="w", identifier="tt") as qps:
for ii in range(num):
qps.add_qpimage(qpi, identifier="image_{}".format(ii))
# add drymass configuration file
path_out = path_in.with_name(path_in.name + dialog.OUTPUT_SUFFIX)
path_out.mkdir()
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=pxsize*1e6)
cfg.set_value(section="meta", key="wavelength nm", value=wavelength*1e9)
cfg.set_value(section="meta", key="medium index", value=medium_index)
cfg.set_value(section="specimen", key="size um",
value=radius_px*2*pxsize*1e6)
cfg.set_value(section="sphere", key="method", value="edge")
cfg.set_value(section="sphere", key="model", value="projection")
return qpi, path_in, path_out
def test_exclude_roi_bad():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# bad image
cfg.set_value(section="roi", key="ignore data", value="3")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad roi
cfg.set_value(section="roi", key="ignore data", value="1.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad image and roi
cfg.set_value(section="roi", key="ignore data", value="4.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
def test_exclude_roi():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# remove first image
cfg.set_value(section="roi", key="ignore data", value="1.1")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove second image
cfg.set_value(section="roi", key="ignore data", value="2")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove all
cfg.set_value(section="roi", key="ignore data", value=["1", "2"])
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 0
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_write_complete():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
cfg.path.write_text("[bg]\nenabled = True\n")
# This triggers a completion of the configuration section [bg]
assert cfg["bg"]["phase profile"] == "tilt"
def test_use_meta_data_from_experiment():
tmp_path = pathlib.Path(tempfile.mkdtemp())
# create test dataset
radius_px = 30
size = 200
pxsize = 1e-6
wavelength = 512e-9
medium_index = 1.33123
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
cx = 80
cy = 120
r = np.sqrt((x - cx)**2 + (y - cy)**2)
pha = (r < radius_px) * 1.3
amp = .5 + np.roll(pha, 10) / pha.max()
qpi_path = tmp_path / "test.h5"
with qpimage.QPImage(data=(pha, amp),
which_data="phase,amplitude",
h5file=qpi_path,
meta_data={
"pixel size": pxsize,
"wavelength": wavelength,
"medium index": medium_index
}):
pass
# this must run without any user input required
pin, pout = dialog.main(
path=qpi_path,
req_meta=["pixel size um", "wavelength nm", "medium index"],
)
assert str(pin) == str(qpi_path.resolve())
cfg = config.ConfigFile(path=pout)
assert cfg["meta"]["medium index"] == medium_index
assert cfg["meta"]["pixel size um"] == pxsize * 1e6
assert cfg["meta"]["wavelength nm"] == wavelength * 1e9
def test_force_roi():
qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=1)
cfg.set_value(section="roi", key="force", value=((10, 160), (24, 178)))
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert qps[0].shape == (150, 154)
assert np.allclose(qpi.pha[10:160, 24:178], qps[0].pha)
assert np.all(qps[0].pha == qps[1].pha)
def test_dtype():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
cfg["specimen"] = {"size um": 11.3}
assert np.allclose(cfg["specimen"]["size um"], 11.3)
cfg.set_value(section="bg", key="amplitude border px", value=6.3)
assert isinstance(cfg["bg"]["amplitude border px"], int)
assert np.allclose(cfg["bg"]["amplitude border px"], 6)
def test_compat_015():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
# initialize config
cfg.set_value("roi", "dist border px", 3)
cfg.set_value("roi", "exclude overlap px", 5)
cfg.set_value("roi", "pad border px", 7)
filepath = cfg.path
# simulate old behavior
data = filepath.open().read()
data = data.replace("dist border px = ", "dist border = ")
data = data.replace("exclude overlap px = ", "exclude overlap = ")
data = data.replace("pad border px = ", "pad border = ")
filepath.write_text(data)
# check fix
cfg2 = config.ConfigFile(path=path)
assert cfg2["roi"]["dist border px"] == 3
assert cfg2["roi"]["exclude overlap px"] == 5
assert cfg2["roi"]["pad border px"] == 7
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_invalid_2():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
cfg.path.write_text("[bg]\nenabled = bad value\n")
try:
cfg["bg"]
except ValueError:
pass
else:
assert False, "invalid value should not work (bool expected)"
finally:
cfg.path.write_text("")
def setup_config(pxsize=1e-6, medium_index=1.335, wavelength=550e-9):
_, path = tempfile.mkstemp(prefix="drymass_test_config_", suffix=".cfg")
cfg = config.ConfigFile(path=path)
cfg.set_value("bg", "phase profile", "tilt")
cfg.set_value("bg", "amplitude profile", "tilt")
cfg.set_value("roi", "dist border px", 3)
cfg.set_value("roi", "exclude overlap px", 5)
cfg.set_value("roi", "pad border px", 7)
cfg.set_value(section="meta", key="pixel size um", value=pxsize * 1e6)
cfg.set_value(section="meta", key="wavelength nm", value=wavelength * 1e9)
cfg.set_value(section="meta", key="medium index", value=medium_index)
return cfg.path
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)
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_reuse():
_, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=1)
h5data = cli_extract_roi(path=path_in, ret_data=True)
time = h5data.stat().st_mtime
# Do the same thing
cli_extract_roi(path=path_in, ret_data=True)
assert time == h5data.stat().st_mtime
# Change something
cfg.set_value(section="meta", key="pixel size um", value=1.01)
cli_extract_roi(path=path_in, ret_data=True)
assert time != h5data.stat().st_mtime
def test_invalid_1():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
try:
cfg["invalid section"]
except ValueError:
pass
else:
assert False, "invalid section should not work"
try:
cfg["invalid section"] = {"key": "value"}
except ValueError:
pass
else:
assert False, "invalid section should not work"
try:
cfg.set_value("invalid section", "key", "value")
except ValueError:
pass
else:
assert False, "invalid section should not work"
try:
cfg.set_value("bg", "invalid key", "value")
except ValueError:
pass
else:
assert False, "invalid key should not work"
try:
cfg.set_value("bg", "enabled", "invalid value")
except ValueError:
pass
else:
assert False, "invalid value should not work (bool expected)"
def test_basic():
path = tempfile.mkdtemp(prefix="drymass_test_config_")
cfg = config.ConfigFile(path=path)
assert isinstance(cfg["bg"], dict)
