def test_required_input_data_missing_one(self):
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em", "-m",
"emd_1305.map"
]
with self.assertRaises(AssertionError):
cm.parse_args()
def setUp(self):
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map"
]
args = cm.parse_args()
self.tbl_test, self.transformations_test_tbl = cm.rearrange_matrix_tbl(
args)
def test_print_voxel_size(self):
"""Test when 'v' given, print the voxel_size of the .em data"""
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"-v"
]
args = cm.parse_args()
self.assertEqual(args.voxel_size, 1)
def test_data_is_compressed(self):
"""Test when '-c' or '--compress' given, its 'action' is true*. """
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"--compress"
]
args = cm.parse_args()
self.assertEqual(args.compress, 1)
def test_print_origin(self):
"""Test when '-s' given, print the origin of the .em data"""
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"-s"
]
args = cm.parse_args()
self.assertEqual(args.map_start, 1)
def test_print_map_start(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map", "-o", "rm_c.txt", "-c", "-s"
]
args = cm.parse_args()
cm.create_output_motl(args)
self.assertTrue(
"nxstart: 0\nnystart: 0\nnzstart: 0" in captured_output.getvalue())
os.remove("rm_c.txt")
def test_motl_files_assigned_correctly(self):
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map"
]
args = cm.parse_args()
self.assertTrue(os.path.exists(f"{args.motl_files[0]}"))
self.assertTrue(os.path.exists(f"{args.motl_files[1]}"))
self.assertTrue(os.path.exists(f"{args.tomogram_map_file}"))
self.assertEqual(args.compress, 0)
self.assertEqual(args.map_start, 0)
self.assertEqual(args.voxel_size, 0)
def test_output_name_specified_c(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map", "-o", "rm_c.txt", "-c"
]
args = cm.parse_args()
cm.create_output_motl(args)
self.assertTrue(os.path.exists("rm_c.txt"))
self.assertTrue("is compressed" in captured_output.getvalue())
os.remove("rm_c.txt")
def test_print_map_start(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"--output", "rm_nc_2.txt", "-s"
]
args = cm.parse_args()
cm.create_output_tbl(args)
self.assertTrue("nxstart: -162\nnystart: -162\nnzstart: -162" in
captured_output.getvalue())
os.remove("rm_nc_2.txt")
def test_print_voxel_size(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"--output", "rm_3.txt", "-v"
]
args = cm.parse_args()
cm.create_output_tbl(args)
self.assertTrue("voxel_size in x, y, z: (5.43, 5.43, 5.43)" in
captured_output.getvalue())
os.remove("rm_3.txt")
def test_output_name_specified_c(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map",
"--output", "rm_c.txt", "-c"
]
args = cm.parse_args()
cm.create_output_tbl(args)
self.assertTrue(os.path.exists("rm_c.txt"))
self.assertTrue("is compressed" in captured_output.getvalue())
os.remove("rm_c.txt")
def test_print_voxel_size(self):
captured_output = io.StringIO()
sys.stdout = captured_output
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map", "-o", "rm_c.txt", "-c",
"-s", "-v"
]
args = cm.parse_args()
cm.create_output_motl(args)
self.assertTrue("voxel_size in x, y, z: (7.12, 7.12, 7.12)" in
captured_output.getvalue())
os.remove("rm_c.txt")
def test_check_output_data(self):
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map"
]
args = cm.parse_args()
cm.create_output_motl(args)
with open("output_nc.txt",
"r") as text: # output_nc.txt created in the last step
data = text.readlines()
for each in data:
if re.match("^Data", each):
string_first_10 = each.replace("Data:\t", "")[0:10]
self.assertEqual('wLHtOYrHeD', string_first_10)
os.remove("output_nc.txt")
def test_dynamo_files_assigned_correctly(self):
"""test that the file with {args.data}.em, {args.data}.tbl and {args.map_file} exist"""
sys.argv = [
"something", "-dynamo", "emd_1305_averaged.em",
"emd_1305_averaged.tbl", "--tomogram-map-file", "emd_1305.map"
]
args = cm.parse_args()
self.assertTrue(os.path.exists(f"{args.dynamo_files[0]}"))
self.assertTrue(os.path.exists(f"{args.dynamo_files[1]}"))
# print(f"{args.dynamo_files}")
self.assertTrue(os.path.exists(f"{args.tomogram_map_file}"))
self.assertEqual(args.compress, 0)
self.assertEqual(args.map_start, 0)
self.assertEqual(args.voxel_size, 0)
def test_motl_half_box(self):
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map"
]
args = cm.parse_args()
motl, observes = cm.rearrange_matrix_motl(args)
observed = observes[0]
motl_object = cm.Data("tests/motl_1_1t.csv")
motl_row = cm.MotlRow(motl_object.col_data[0], (1.78, 1.78, 1.78))
expect_translation = motl_row.transformation
half_box_m = np.array([[0, 0, 0, 80 * 1.78], [0, 0, 0, 80 * 1.78],
[0, 0, 0, 80 * 1.78]])
# expect = expect_translation - half_box_m
expect = expect_translation
self.assertTrue(np.allclose(observed, expect))
def test_compressed(self):
sys.argv = [
"something", "-motl", "emd_3465.map", "tests/motl_1_1t.csv",
"--tomogram-map-file", "emd_3464.map", "-c"
]
args = cm.parse_args()
cm.create_output_motl(args)
self.assertTrue(os.path.exists("output_c.txt"))
with open("output_c.txt", "r") as text:
data = text.readlines()
for each in data:
if re.match("^Data", each):
string_first_10 = each.replace("Data:\t", "")[0:10]
print(string_first_10)
self.assertEqual("eJwUm/cj1e", string_first_10)
os.remove("output_c.txt")
def test_required_input_data(self):
sys.argv = ["something", "--tomogram_file", "emd_1305.map"]
with self.assertRaises(AssertionError):
cm.parse_args()
