def main(args):
args = utils.splitArgs(args)
args.macenko.I_0 = numpy.array(args.macenko.I_0)
utils.create_dask_client(args.dask)
sample = utils.sample_pixels(args.sample)
stain_matrix = rgb_separate_stains_macenko_pca(sample.T,
**vars(args.macenko))
with open(args.returnParameterFile, 'w') as f:
for i, stain in enumerate(stain_matrix.T):
f.write('stainColor_{} = {}\n'.format(i + 1,
','.join(map(str, stain))))
def test_splitArgs(self):
args = Namespace(
a=1,
b_a=2,
b_b=3,
b_c_a=4,
c_a=5,
)
split = cli_utils.splitArgs(args)
self.assertEqual(
split,
Namespace(
a=1,
b=Namespace(
a=2,
b=3,
c_a=4,
),
c=Namespace(a=5, ),
))
def main(args):
args = utils.splitArgs(args)
args.snmf.I_0 = numpy.array(args.snmf.I_0)
print(">> Starting Dask cluster and sampling pixels")
utils.create_dask_client(args.dask)
sample = utils.sample_pixels(args.sample)
# Create stain matrix
print('>> Creating stain matrix')
args.snmf.w_init = utils.get_stain_matrix(args.stains, 2)
print args.snmf.w_init
# Perform color deconvolution
print('>> Performing color deconvolution')
w_est = htk_cdeconv.rgb_separate_stains_xu_snmf(sample.T, **vars(args.snmf))
w_est = htk_cdeconv.complement_stain_matrix(w_est)
with open(args.returnParameterFile, 'w') as f:
for i, stain in enumerate(w_est.T):
f.write('stainColor_{} = {}\n'.format(i+1, ','.join(map(str, stain))))