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()