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 mst_calculation(ifg_paths_or_instance, params):
if isinstance(ifg_paths_or_instance, list):
ifgs = pre_prepare_ifgs(ifg_paths_or_instance, params)
mst_grid = mst.mst_parallel(ifgs, params)
else:
nan_conversion = params[cf.NAN_CONVERSION]
assert isinstance(ifg_paths_or_instance, matlab_mst.IfgListPyRate)
ifgs = ifg_paths_or_instance.ifgs
for i in ifgs:
if not i.mm_converted:
i.nodata_value = params[cf.NO_DATA_VALUE]
i.convert_to_mm()
ifg_instance_updated, epoch_list = \
matlab_mst.get_nml(ifg_paths_or_instance,
nodata_value=params[cf.NO_DATA_VALUE],
nan_conversion=nan_conversion)
mst_grid = matlab_mst.matlab_mst_bool(ifg_instance_updated)
# write mst output to a file
mst_mat_binary_file = join(params[cf.OUT_DIR], 'mst_mat')
np.save(file=mst_mat_binary_file, arr=mst_grid)
for i in ifgs:
i.close()
return mst_grid
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 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 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 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_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, :, :])