def analyze(dir, gui):
"""Analyze an experiment"""
from pharedox import experiment
exp = experiment.Experiment(Path(dir))
if gui:
from pharedox.gui.gui import App
app = App(exp_=exp)
app.run()
else:
exp.full_pipeline()
def test_full_experiment_run_paired_single_timepoint(self, shared_datadir):
exp = experiment.Experiment(shared_datadir / "experiments" /
"2017_02_22-HD233_SAY47")
exp.full_pipeline()
def test_experiment_doesnt_loads_masks_if_they_dont_exist(
self, mock_segment_pharynxes, shared_datadir):
exp = experiment.Experiment(shared_datadir / "experiments" /
"2017_02_22-HD233_SAY47")
exp.segment_pharynxes()
mock_segment_pharynxes.assert_called()
self.experiment.images, r_min=0.9, r_max=1.9, i_max=1500,
),
name="R (population-normalized)",
)
for wvl in self.experiment.images.wavelength.values:
self.viewer.add_image(
self.experiment.images.sel(wavelength=wvl),
name=wvl,
visible=False,
)
if self.experiment.seg_images is not None:
self.viewer.add_labels(
self.experiment.seg_images, name="masks",
)
if __name__ == "__main__":
logging.basicConfig(
format="%(asctime)s %(levelname)s:%(message)s",
level=logging.INFO,
datefmt="%I:%M:%S",
)
exp_dir = sys.argv[1]
exp = experiment.Experiment(Path(exp_dir))
app = App(exp_=exp)
app.run()