def setUp(self): ifg_instance = IfgList(small_ifg_file_list()) self.ifg_list, _ = get_nml(ifg_instance, nodata_value=0) self.sorted_list = sort_list(self.ifg_list.id, self.ifg_list.master_num, self.ifg_list.slave_num, self.ifg_list.nan_frac) self.matlab_sorted_list_zero_nan_frac = [(1, 1, 3, 0.0), (2, 2, 5, 0.0), (3, 3, 7, 0.0), (4, 3, 9, 0.0), (5, 4, 5, 0.0), (6, 4, 6, 0.0), (7, 4, 8, 0.0), (8, 5, 11, 0.0), (9, 5, 12, 0.0), (10, 6, 8, 0.0), (11, 6, 13, 0.0), (12, 7, 9, 0.0), (13, 7, 10, 0.0), (14, 8, 13, 0.0), (15, 9, 10, 0.0), (16, 10, 11, 0.0), (17, 11, 12, 0.0)] self.ifg_list_mst_matlab = [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 16]
def test_mst_boolean_array(self): nan_conversion = 1 for i in self.small_ifgs: if not i.is_open: i.open(readonly=False) if nan_conversion: # nan conversion happens here in networkx mst i.nodata_value = 0 i.convert_to_nans() if not i.mm_converted: i.convert_to_mm() i.write_modified_phase() mst_nx = mst.mst_boolean_array(self.small_ifgs) small_ifg_instance = IfgList(datafiles=self.small_files) ifgs = small_ifg_instance.ifgs for i in ifgs: if not i.mm_converted: i.convert_to_mm() i.write_modified_phase() ifg_instance_updated, epoch_list = \ get_nml(small_ifg_instance, nodata_value=0, nan_conversion=nan_conversion) mst_matlab = matlab_mst_bool(ifg_instance_updated) np.testing.assert_array_equal(mst_matlab, mst_nx) # close ifgs for windows for i in self.small_ifgs: i.close()
def test_mas_mat_vs_mst_mat_generator(self): ifg_instance = IfgList(datafiles=self.ifg_file_list) ifg_list, _ = get_nml(ifg_instance, nodata_value=0, nan_conversion=True) mst_mat1 = _matlab_mst(ifg_list) mst_mat2 = _matlab_mst_bool(ifg_list) np.testing.assert_array_equal(mst_mat2, mst_mat1)
def test_calculate_connect_and_ntrees_small_data(self): ifg_instance = IfgList(small_ifg_file_list()) ifg_list, _ = get_nml(ifg_instance, nodata_value=0) edges = get_sub_structure(ifg_list, np.zeros(len(ifg_list.id), dtype=bool)) mst, connected, ntrees = matlab_mst_kruskal(edges, ntrees=True) self.assertTrue(connected[0].all()) self.assertEqual(ntrees, 1) self.assertEqual(len(connected[0]), len(mst) + 1)
def setUp(self): self.matlab_n = [1, 2, 3, 3, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 9, 10, 11, 3, 5, 7, 9, 5, 6, 8, 11, 12, 8, 13, 9, 10, 13, 10, 11, 12] self.matlab_masnum = [1, 2, 3, 3, 4, 4, 4, 5, 5, 6, 6, 7, 7, 8, 9, 10, 11] self.matlab_slvnum = [3, 5, 7, 9, 5, 6, 8, 11, 12, 8, 13, 9, 10, 13, 10, 11, 12] ifg_instance = IfgList(small_ifg_file_list()) self.ifg_list, self.epoch_list = get_nml(ifg_instance, nodata_value=0)
def test_assert_is_not_tree(self): non_overlapping = [1, 2, 5, 6, 12, 13, 14, 15, 16, 17] small_files = small_ifg_file_list() datafiles = [f for i, f in enumerate(small_files) if i+1 in non_overlapping] non_overlapping_ifg_isntance = IfgList(datafiles) ifg_list, _ = get_nml(non_overlapping_ifg_isntance, nodata_value=0) edges = _get_sub_structure(ifg_list, np.zeros(len(ifg_list.id), dtype=bool)) mst, connected, ntrees = _matlab_mst_kruskal(edges, ntrees=True) self.assertEqual(connected.shape[0], 4) self.assertEqual(ntrees, 4)
def test_assert_two_trees_overlapping(self): overlapping = [3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17] small_files = small_ifg_file_list() datafiles = [f for i, f in enumerate(small_files) if i+1 in overlapping] overlapping_ifg_isntance = IfgList(datafiles) ifg_list, _ = get_nml(overlapping_ifg_isntance, nodata_value=0) edges = _get_sub_structure(ifg_list, np.zeros(len(ifg_list.id), dtype=bool)) mst, connected, ntrees = _matlab_mst_kruskal(edges, ntrees=True) self.assertEqual(connected.shape[0], 2) self.assertEqual(ntrees, 2)
def test_matlab_mst_kruskal(self): """ test that the matlab and python mst algos outputs are the same """ ifg_instance = IfgList(datafiles=self.ifg_file_list) ifg_list, _ = get_nml(ifg_instance, nodata_value=0) edges = get_sub_structure(ifg_list, np.zeros(len(ifg_list.id), dtype=bool)) ifg_list_mst_id = matlab_mst_kruskal(edges) self.assertEquals(len(self.matlab_mst_list), len(ifg_list_mst_id)) for i in ifg_list_mst_id: self.assertIn( os.path.split(ifg_list.nml[i])[-1], self.matlab_mst_list)
def test_matlab_make_mstmat_boolean_array(self): """ tests equality of boolean mst arrays of both python and matlab. """ ifg_instance = IfgList(datafiles=self.ifg_file_list) ifg_list, _ = get_nml(ifg_instance, nodata_value=0) mst_mat = _matlab_mst_bool(ifg_list, p_threshold=1) # path to csv folders from matlab output from tests.common import SML_TEST_MATLAB_MST_DIR onlyfiles = [f for f in os.listdir(SML_TEST_MATLAB_MST_DIR) if os.path.isfile(os.path.join(SML_TEST_MATLAB_MST_DIR, f))] for i, f in enumerate(onlyfiles): mst_f = np.genfromtxt(os.path.join(SML_TEST_MATLAB_MST_DIR, f), delimiter=',') for k, j in enumerate(self.ifg_file_list): if f.split('matlab_')[-1].split('.')[0] == \ os.path.split(j)[-1].split('.')[0]: np.testing.assert_array_equal(mst_f, mst_mat[k, :, :])