def run_around_tests():
# Code that will run before your test, for example:
session.clear_session()
# A test function will be run at this point
yield
# Code that will run after your test, for example:
session.clear_session()
def test_wrong_hash():
tempdir = pathlib.Path(tempfile.mkdtemp(prefix="test_shapeout2_session_"))
spath = tempdir / "session.so2"
# custom path to measurement
p0 = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
pp = pathlib.Path(tempdir) / "calibration_beads_47.rtdc"
shutil.copy(p0, pp)
pl = make_pipeline(paths=[pp])
session.save_session(spath, pl)
session.clear_session(pl) # clear session before opening h5 file rw
session.hash_file_partially.cache_clear() # force recomputation of hashes
# modify the file
with h5py.File(pp, mode="a") as h5:
h5.attrs["setup:medium"] = "unknown"
# opening modified file should just work if the path matches
pl2 = session.open_session(spath)
session.clear_session(pl2)
# but when the directory changes, the hash is checked
other = tempdir / "other"
other.mkdir()
pp.rename(other / pp.name)
try:
session.open_session(spath, search_paths=[other])
except session.DataFileNotFoundError as e:
assert pp in e.missing_paths
else:
assert False, "should have raised an error!"
def test_relative_paths():
tempdir = pathlib.Path(tempfile.mkdtemp(prefix="test_shapeout2_session_"))
# custom path for data
p0 = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
datadir = tempdir / "data"
datadir.mkdir()
pp = datadir / "calibration_beads_47.rtdc"
shutil.copy(p0, pp)
# custom path for session
sessiondir = tempdir / "session"
sessiondir.mkdir()
spath = sessiondir / "session.so2"
# pipeline
pl = make_pipeline(paths=[pp])
session.save_session(spath, pl)
session.clear_session(pl)
# new session directory
new_sessiondir = tempdir / "new" / "path" / "abracadabra"
new_sessiondir.mkdir(parents=True)
new_spath = new_sessiondir / spath.name
spath.rename(new_spath)
# new path directory (same relative path)
new_datadir = tempdir / "new" / "path" / "data"
new_datadir.mkdir(parents=True)
new_pp = new_datadir / pp.name
pp.rename(new_pp)
# and load it (without search_paths as arguments)
session.open_session(new_spath)
def test_save_all_polygon_filters_issue_101():
pl = make_pipeline()
# add a polygon filter
ds = pl.get_dataset(0)
pf1 = dclab.PolygonFilter(
axes=("deform", "area_um"),
points=[
[ds["deform"].min(), ds["area_um"].min()],
[ds["deform"].min(), ds["area_um"].mean()],
[ds["deform"].mean(), ds["area_um"].mean()],
],
name="Triangle of Minimum",
)
pf2_state = dclab.PolygonFilter(
axes=("deform", "area_um"),
points=[
[ds["deform"].max(), ds["area_um"].max()],
[ds["deform"].max(), ds["area_um"].mean()],
[ds["deform"].mean(), ds["area_um"].mean()],
],
name="Triangle of Maximum",
).__getstate__()
pl.filters[0].polylist.append(pf1.unique_id)
old_state = pl.__getstate__()
tempdir = pathlib.Path(tempfile.mkdtemp(prefix="test_shapeout2_session_"))
spath = tempdir / "session.so2"
session.save_session(spath, pl)
assert len(dclab.PolygonFilter.instances) == 2
session.clear_session(pl)
assert len(dclab.PolygonFilter.instances) == 0
# currently, there may only be one pipeline
session.open_session(spath, pl)
new_state = pl.__getstate__()
# This is the actual test for issue #101
assert len(dclab.PolygonFilter.instances) == 2
# This is a sanity check
assert equal_state(old_state, new_state)
# This is another sanity check
pf2_id = pf2_state["identifier"]
assert equal_state(
pf2_state,
dclab.PolygonFilter.get_instance_from_id(pf2_id).__getstate__())
def test_missing_path_in_session():
tempdir = pathlib.Path(tempfile.mkdtemp(prefix="test_shapeout2_session_"))
spath = tempdir / "session.so2"
# custom path to measurement
p0 = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
pp = tempdir / "calibration_beads_47.rtdc"
shutil.copy(p0, pp)
pl = make_pipeline(paths=[pp])
session.save_session(spath, pl)
session.clear_session(pl)
# rename the file
pc = pp.with_name("calibration_beads_47_moved.rtdc")
pp.rename(pc)
# load bad session
try:
session.open_session(spath)
except session.DataFileNotFoundError as e:
assert pp in e.missing_paths
else:
assert False, "should have raised an error!"
# try again with proper search path
pl3 = session.open_session(spath, search_paths=[pc])
session.clear_session(pl3)
# try again with a directory as search path
other = tempdir / "other"
other.mkdir()
pc.rename(other / pp.name) # must have same name as `pp`
pl4 = session.open_session(spath, search_paths=[other])
session.clear_session(pl4)