def setUp(self):
self.runner = PyFibreRunner()
self.fibre_networks = [ProbeFibreNetwork()]
self.fibre_segments = [generate_probe_segment(FibreSegment)]
self.cell_segments = [generate_probe_segment(CellSegment)]
def setUp(self):
self.regions = generate_regions()
self.fibre_network = ProbeFibreNetwork()
self.fibres = [ProbeFibre(), ProbeFibre(), ProbeFibre()]
self.segment = ProbeSegment()
self.segments = [self.segment]
self.image, _, _, _ = generate_image()
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 test_image_data(self):
new_networks = [ProbeFibreNetwork().graph]
with self.assertTraitChanges(self.image_tab, "image_data"):
self.image_tab.networks = new_networks
self.image_tab.update_tab()
def setUp(self):
self.segment = ProbeSegment()
self.fibre = ProbeFibre()
self.fibre_network = ProbeFibreNetwork()
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.network = ProbeFibreNetwork()
self.fibres = [ProbeFibre(), ProbeFibre(), ProbeFibre()]
class TestFibreNetwork(TestCase):
def setUp(self):
self.network = ProbeFibreNetwork()
self.fibres = [ProbeFibre(), ProbeFibre(), ProbeFibre()]
def test_to_json(self):
state = self.network.to_json()
self.assertIn('fibres', state)
self.assertIn('red_graph', state)
self.assertIsNotNone(state['red_graph'])
self.assertEqual(1, len(state['fibres']))
state = self.network.to_json()
self.assertDictEqual(
state['red_graph'], {
'directed': False,
'multigraph': False,
'graph': {},
'nodes': [{
'xy': [0, 0],
'id': 0
}, {
'xy': [2, 3],
'id': 1
}],
'links': [{
'r': 3.605551275463989,
'source': 0,
'target': 1
}]
})
def test_from_json(self):
self.network.red_graph = self.network.generate_red_graph()
self.network.fibres = self.fibres
status = self.network.to_json()
new_network = FibreNetwork.from_json(status)
status = new_network.to_json()
self.assertDictEqual(
status['red_graph'], {
'directed': False,
'multigraph': False,
'graph': {},
'nodes': [{
'xy': [0, 0],
'id': 0
}, {
'xy': [2, 3],
'id': 1
}],
'links': [{
'r': 3.605551275463989,
'source': 0,
'target': 1
}]
})
self.assertEqual(3, len(new_network.fibres))
self.assertListEqual([2, 3, 4, 5], new_network.fibres[0].node_list)
def test_fibres(self):
fibres = self.network.generate_fibres()
self.assertEqual(1, len(fibres))
self.assertListEqual([0, 1, 2, 3], fibres[0].node_list)
self.network.fibres = fibres
status = self.network.to_json()
self.assertEqual(1, len(status["fibres"]))
def test_generate_database(self):
self.network.red_graph = self.network.generate_red_graph()
self.network.fibres = self.fibres
database = self.network.generate_database()
self.assertEqual(8, len(database))
self.assertIn('Fibre Angle SDI', database)
for metric in FIBRE_METRICS:
self.assertIn(f'Mean Fibre {metric}', database)
for metric in NETWORK_METRICS:
self.assertIn(f'Fibre Network {metric}', database)
def setUp(self):
self.fibre_mask = np.where(np.sum(test_fibre_mask, axis=0), 1, 0)
self.multi_image = ProbeSHGPLTransImage()
self.fibre_networks = [ProbeFibreNetwork()]
def setUp(self):
(self.image, labels, self.binary, _) = generate_image()
self.segments = regionprops(labels)
self.fibre_network = ProbeFibreNetwork()