def test_background_intensity(self):
wsi_path = os.path.join(
utilities.externaldata(
'data/sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-af6f-14fefbbdf7bd.svs.sha512' # noqa
))
np.random.seed(1)
# create dask client
args = {
# In Python 3 unittesting, the scheduler fails if it uses processes
'scheduler': 'multithreading', # None,
'num_workers': -1,
'num_threads_per_worker': 1,
}
args = collections.namedtuple('Parameters', args.keys())(**args)
cli_utils.create_dask_client(args)
# compute background intensity
I_0 = htk_cn.background_intensity(wsi_path,
sample_approximate_total=5000)
np.testing.assert_allclose(I_0, [242, 244, 241], atol=1)
def test_background_intensity(self):
wsi_path = os.path.join(
TEST_DATA_DIR,
'sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-af6f-14fefbbdf7bd.svs' # noqa
)
np.random.seed(1)
I_0 = htk_cn.background_intensity(wsi_path,
sample_approximate_total=5000)
np.testing.assert_allclose(I_0, [242, 244, 241], atol=1)
def main(args):
other_args = set(['returnParameterFile', 'scheduler'])
kwargs = {k: v for k, v in vars(args).items() if k not in other_args}
# Allow (some) default parameters to work. Assume certain values
# are not valid.
for k in 'sample_fraction', 'sample_approximate_total':
if kwargs[k] == -1:
del kwargs[k]
utils.create_dask_client(args)
I_0 = background_intensity(**kwargs)
with open(args.returnParameterFile, 'w') as f:
f.write('BackgroundIntensity = ' + ','.join(map(str, I_0)) + '\n')
def test_background_intensity(self):
wsi_path = os.path.join(
TEST_DATA_DIR,
'sample_svs_image.TCGA-DU-6399-01A-01-TS1.e8eb65de-d63e-42db-af6f-14fefbbdf7bd.svs' # noqa
)
np.random.seed(1)
# create dask client
args = {
'scheduler': None,
'num_workers': -1,
'num_threads_per_worker': 1,
}
args = collections.namedtuple('Parameters', args.keys())(**args)
cli_utils.create_dask_client(args)
# compute background intensity
I_0 = htk_cn.background_intensity(wsi_path,
sample_approximate_total=5000)
np.testing.assert_allclose(I_0, [242, 244, 241], atol=1)