def _cli(ctx, label_image, intensities, output):
print('Assigning targets to cells...')
ctx.obj = dict(component=TargetAssignment,
output=output,
intensity_table=IntensityTable.load(intensities),
label_image=imread(label_image))
def _cli(ctx, input, output, codebook):
ctx.obj = dict(
component=Decoder,
input=input,
output=output,
intensities=IntensityTable.load(input),
codebook=Codebook.from_json(codebook),
)
def test_run_pipline(self):
tempdir = exec.stages(self.stages, self.subdirs, keep_data=True)
intensities = IntensityTable.load(
os.path.join(tempdir, "results", self.spots_file))
self.verify_results(intensities)
if os.getenv("TEST_KEEP_DATA") is None:
shutil.rmtree(tempdir)
def _cli(ctx, input, output, codebook):
"""assign genes to spots"""
ctx.obj = dict(
component=Decoder,
input=input,
output=output,
intensities=IntensityTable.load(input),
codebook=codebook,
)
