def setUp(self):
self.file_name = test_image_path
self.directory = os.path.dirname(self.file_name)
self.key = 'Stack'
self.test_dict = {
'__traits_version__':
'4.6.0',
'some_important_data': {
'__traits_version__': '4.6.0',
'value': 10
},
'_some_private_data': {
'__instance_traits__': ['yes', 'some']
},
'___': {
'__': 'a',
'foo': 'bar'
},
'list_of_dicts': [{
'__bad_key__': 'bad',
'good_key': 'good'
}, {
'also_good_key': 'good'
}]
}
self.graph = generate_probe_graph()
def setUp(self):
(self.image, self.labels, self.binary, self.stack) = generate_image()
self.network = generate_probe_graph()
self.image = np.stack([self.image] * 3, axis=-1)
self.bd_filter = ProbeKmeansFilter(n_runs=2, n_clusters=2)
def setUp(self):
(self.image, self.labels, self.binary, self.stack) = generate_image()
self.network = generate_probe_graph()
self.regions = generate_regions()
self.segments = [
ProbeSegment(region=region) for region in self.regions
]
def setUp(self):
self.image, _, _, _ = generate_image()
self.network = generate_probe_graph()
self.fibre_networks = [ProbeFibreNetwork()]
self.fibre_segments = [generate_probe_segment(FibreSegment)]
self.cell_segments = [generate_probe_segment(CellSegment)]
self.multi_image = ProbeSHGImage()
self.analyser = SHGAnalyser(multi_image=self.multi_image)
self.runner = PyFibreRunner()
def setUp(self):
self.image, _, _, _ = generate_image()
self.network = generate_probe_graph()
self.pos_2D = np.array([[1, 3], [4, 2], [1, 5]])
self.answer_d_2D = np.array([[[0, 0], [3, -1], [0, 2]],
[[-3, 1], [0, 0], [-3, 3]],
[[0, -2], [3, -3], [0, 0]]])
self.answer_r2_2D = np.array([[0, 10, 4], [10, 0, 18], [4, 18, 0]])
self.answer_cos_the = np.array([0, 0.9486833])
def setUp(self):
self.graph = generate_probe_graph()
self.graph_segment = ProbeGraphSegment()
def setUp(self):
(self.image, self.labels, self.binary, self.stack) = generate_image()
self.network = generate_probe_graph()
self.regions = generate_regions()
def setUp(self):
(self.image, self.labels, self.binary, self.stack) = generate_image()
self.network = generate_probe_graph()
self.fibre_networks = [ProbeFibreNetwork()]
self.bd_filter = ProbeKmeansFilter()
def setUp(self):
self.fibre_assignment = FibreAssigner()
self.graph = generate_probe_graph()
def setUp(self):
self.network = generate_probe_graph()
self.image = imread(test_image_path).mean(axis=-1)
def setUp(self):
self.network = generate_probe_graph()
def __init__(self, *args, **kwargs):
kwargs['graph'] = generate_probe_graph()
super().__init__(*args, **kwargs)
self.fibres = self.generate_fibres()
self.red_graph = self.generate_red_graph()
def __init__(self, *args, **kwargs):
kwargs['graph'] = generate_probe_graph()
super().__init__(*args, **kwargs)
