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def test_with_files(self, application_parse):
assert is_recursive_subnamespace(Namespace(application=Namespace(files=["img_1.mnc"]),
mbm=Namespace(lsq12=Namespace(max_pairs=20))),
application_parse)
def test_with_files(self, application_parse):
assert is_recursive_subnamespace(Namespace(application=Namespace(files=["img_1.mnc"]),
mbm=Namespace(lsq12=Namespace(max_pairs=20))),
application_parse)
def test_deeper_nesting(self, four_mbm_parse):
assert is_recursive_subnamespace(Namespace(first_two=Namespace(mbm1=Namespace(lsq12=Namespace(max_pairs=22)),
mbm2=Namespace(lsq12=Namespace(max_pairs=23))),
last_two=Namespace(mbm1=Namespace(lsq12=Namespace(max_pairs=24)),
mbm2=Namespace(lsq12=Namespace(max_pairs=25)))),
four_mbm_parse)
def test_with_files(self, application_parse):
def mock_options(self, public=False):
return Namespace(
appname='skygear-test',
cloud_asset_host='http://mock-cloud-asset.dev',
cloud_asset_token='mock-cloud-asset-token',
cloud_asset_public_prefix='http://mock-cloud-asset.dev/public',
cloud_asset_private_prefix='http://mock-cloud-asset.dev/private',
asset_store_public=public)
def test_nested_parsing(self, two_mbm_parse):
assert is_recursive_subnamespace(Namespace(mbm1=Namespace(lsq12=Namespace(max_pairs=22)),
mbm2=Namespace(lsq12=Namespace(max_pairs=25))),
two_mbm_parse)
def test_deeper_nesting(self, four_mbm_parse):
def test_sign_public(self):
signer = CloudAssetSigner.create(Namespace(
appname='skygear-test',
cloud_asset_host='http://mock-cloud-asset.dev',
cloud_asset_token='mock-cloud-asset-token',
cloud_asset_public_prefix='http://mock-cloud-asset.dev/public',
cloud_asset_private_prefix='http://mock-cloud-asset.dev/private',
asset_store_public=True))
assert signer.sign('a good fixture') == \
'http://mock-cloud-asset.dev/public/skygear-test/a%20good%20fixture' # noqa
output_xfms = output_xfms.assign(xfm_common=xfms_common, overall_xfm_common=overall_xfms_common)
log_nlin_det_common, log_full_det_common = [dets.map(lambda d:
s.defer(mincresample_new(
img=d,
xfm=xfm_to_common.xfm,
like=common_space_model,
postfix="_common",
extra_flags=("-keep_real_range",),
interpolation=Interpolation.nearest_neighbour)))
for dets in (determinants.log_nlin_det, determinants.log_full_det)]
determinants = determinants.assign(log_nlin_det_common=log_nlin_det_common,
log_full_det_common=log_full_det_common)
output = Namespace(avg_img=lsq12_nlin_result.avg_img, xfms=output_xfms, determinants=determinants)
if options.mbm.common_space.do_common_space_registration:
output.model_common = model_common
if options.mbm.segmentation.run_maget:
output.maget_result = maget_result
return Result(stages=s, output=output)
fixed = (q.cast(current_ns.__dict__[q.namespace]) #(q.cast(**vars(current_ns.__dict__[q.namespace]))
if q.cast else current_ns.__dict__[q.namespace])
if isinstance(fixed, tuple):
fixed = fixed.replace(flags_=flags)
elif isinstance(fixed, Namespace):
setattr(fixed, "flags_", flags)
else:
raise ValueError("currently only Namespace and NamedTuple objects are supported return types from "
"parsing; got %s (a %s)" % (fixed, type(fixed)))
current_ns.__dict__[q.namespace] = fixed
# TODO current_ns or current_namespace or ns or namespace?
else:
raise TypeError("parser %s wasn't a %s (%s or %s) but a %s" %
(p, Parser, BaseParser, CompoundParser, p.__class__))
main_ns = Namespace()
go_2(parser, current_prefix="", current_ns=main_ns)
return main_ns
# maget_options.maget.maget.mask = maget_options.maget.maget.mask_only = False # already done above
# del maget_options.mbm
# again using a weird combination of vectorized and loop constructs ...
# s.defer(maget([xfm.resampled for _ix, m in first_level_results.iterrows()
# for xfm in m.build_model.xfms.rigid_xfm],
# options=maget_options,
# prefix="%s_MAGeT" % options.application.pipeline_name,
# output_dir=os.path.join(options.application.output_directory,
# options.application.pipeline_name + "_processed")))
# TODO resampling to database model ...
# TODO there should be one table containing all determinants (first level, overall, resampled first level) for each file
# and another containing some groupwise information (averages and transforms to the common average)
return Result(stages=s, output=Namespace(first_level_results=first_level_results,
resampled_determinants=resampled_determinants,
overall_determinants=overall_determinants))