def test_run_output_dir_not_existing(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
"output_dir_not_existing", 'new_output_folder'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
"output_dir_not_existing", 'old_output_folder'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => ISAC or Beautifier run output directory does not exist. Please check the directory path and restart the program.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_substack_basename_empty_string(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'NEW_OUTPUT', "--substack_basename= "
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'OLD_OUTPUT', "--substack_basename= "
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => Substack basename cannot be empty string or only white spaces.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_bdb_not_existing(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
'bdb:' + "Bad_path_toDB",
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'new_output_folder'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
'bdb:' + "Bad_path_toDB",
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'old_output_folder'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => Input BDB image stack file does not exist. Please check the file path and restart the program.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_default_ordered_class_averagesHDF_not_found(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"), "/", 'new_output_folder'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"), "/", 'new_output_folder'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => ISAC or Beautifier run output directory does not contain the default ISAC class average stack file (/ordered_class_averages.hdf). Please check the directory path or specify ISAC class average stack file, then restart the program.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_output_dir_existing(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), ' /'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), ' /'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => Output directory exists. Please change the name and restart the program.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_run_tutorial(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.new_output_folder, '--pixel_size=1.14', '--mol_mass=1400',
"--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
testargs_old = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.old_output_folder, '--pixel_size=1.14', '--mol_mass=1400',
"--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
with patch.object(sys, 'argv', testargs_new):
fu.main()
with patch.object(sys, 'argv', testargs_old):
oldfu.main()
old_value = get_im(path.join(self.old_output_folder, self.filename))
new_value = get_im(path.join(self.new_output_folder, self.filename))
self.assertTrue(
array_equal(old_value.get_3dview(), new_value.get_3dview()))
self.assertTrue(
allclose(
new_value.get_3dview().flatten().tolist()[4884850:4885000], [
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
45.657344818115234, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 45.90496063232422, 46.82423400878906,
46.874420166015625, 46.04456329345703, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
0.0
],
atol=0.1))
remove_dir(self.new_output_folder)
remove_dir(self.old_output_folder)
def test_run(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), self.new_output_folder
] #," --isac_class_avgs_path ='/home/lusnig/Downloads/LucaTest_beaut/best.hdf'"]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), self.old_output_folder
]
with patch.object(sys, 'argv', testargs_new):
fu.main()
with patch.object(sys, 'argv', testargs_old):
oldfu.main()
def test_no_molMass_and_densityThresholdError(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER",
"average_volume_001.hdf"), self.new_output_folder,
'--pixel_size=1.14', "--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
testargs_old = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER",
"average_volume_001.hdf"), self.old_output_folder,
'--pixel_size=1.14', "--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => Molecular mass [kDa] or density_threshold is required. Please set a pasitive value larger than 0.0 to --mol_mass option or --use_density_threshold option.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_run(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'angular_distribution',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"11_MERIDIEN", "final_params_028.txt"),
self.new_output_folder, '--symmetry=c5', '--pixel_size=1.14',
'--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'angular_distribution',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"11_MERIDIEN", "final_params_028.txt"),
self.old_output_folder, '--symmetry=c5', '--pixel_size=1.14',
'--box_size=352'
]
with patch.object(sys, 'argv', testargs_new):
fu.main()
with patch.object(sys, 'argv', testargs_old):
oldfu.main()
remove_dir(self.new_output_folder)
remove_dir(self.old_output_folder)
def test_invali_lowPass_filter_resolutionError(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.new_output_folder, '--mol_mass=1400', '--pixel_size=0.5',
'--fl=0.2', "--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
testargs_old = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.old_output_folder, '--mol_mass=1400', '--fl=0.2',
'--pixel_size=0.5', "--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--invert_handedness'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => Invalid low-pass filter resolution 0.2[A] for 3D volume. Please set a value larger than or equal to Nyquist resolution 1.0[A].'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_specified_ordered_class_averagesHDF_not_found(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'NEW_OUTPUT', "--isac_class_avgs_path=" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"invalidDB.hdf")
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_pipe.py"), 'isac_substack',
"bdb:" + path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_PARTICLES#stack"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"04_ISAC"), 'old_outpuT', "--isac_class_avgs_path=" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"invalidDB.hdf")
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
with self.assertRaises(SystemExit):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => The specifed ISAC class average stack file does not exist. Please check the file path and restart the program.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
def test_run_molMass_and_threashold_ignoring_values(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.new_output_folder, '--pixel_size=1.14', '--mol_mass=1400',
"--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--use_density_threshold=0.1',
'--invert_handedness'
]
testargs_old = [
path.join(ABSOLUTE_BIN_PATH, "sp_pipe.py"), 'moon_eliminator',
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"07_RVIPER", "average_volume_001.hdf"),
self.old_output_folder, '--pixel_size=1.14', '--mol_mass=1400',
"--resample_ratio=" + path.join(
ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW, "04_ISAC"),
'--box_size=352', '--use_density_threshold=0.1',
'--invert_handedness'
]
with patch.object(sys, 'argv', testargs_new):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
with patch.object(sys, 'argv', testargs_old):
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
old_value = get_im(path.join(self.old_output_folder, self.filename))
new_value = get_im(path.join(self.new_output_folder, self.filename))
self.assertTrue(
array_equal(old_value.get_3dview(), new_value.get_3dview()))
self.assertEqual(
print_new.getvalue().split('\n')[5].split("ERROR")[1],
' => You provided values for both --mol_mass and --use_density_threshold. --mol_mass is used and --use_density_threshold ignored.'
)
self.assertEqual(print_new.getvalue().split('\n')[5].split("ERROR")[1],
print_old.getvalue().split('\n')[5].split("ERROR")[1])
self.assertTrue(
allclose(
new_value.get_3dview().flatten().tolist()[4884850:4885000], [
13.436051368713379, 16.304325103759766, 19.431846618652344,
22.773143768310547, 26.281518936157227, 29.846433639526367,
33.33924865722656, 36.65176010131836, 39.61358642578125,
42.10240936279297, 44.03025436401367, 45.198368072509766,
45.6573486328125, 45.332122802734375, 44.2328987121582,
42.458248138427734, 39.976200103759766, 36.98574447631836,
33.579429626464844, 29.869462966918945, 26.018442153930664,
22.143997192382812, 18.370195388793945, 14.833773612976074,
11.611379623413086, 8.771808624267578, 6.44216775894165,
4.582822799682617, 3.266218423843384, 2.4977657794952393,
2.247335910797119, 2.614610195159912, 3.500377893447876,
4.934632301330566, 6.914317607879639, 9.367624282836914,
12.337867736816406, 15.699345588684082, 19.383285522460938,
23.31256675720215, 27.345870971679688, 31.34865379333496,
35.194488525390625, 38.70415496826172, 41.74859619140625,
44.22425842285156, 45.90496063232422, 46.82423400878906,
46.874420166015625, 46.04456329345703, 44.42490005493164,
41.9677619934082, 38.900634765625, 35.33403396606445,
31.41274642944336, 27.333709716796875, 23.237581253051758,
19.26754379272461, 15.562416076660156, 12.18584156036377,
9.18964672088623, 6.660860061645508, 4.532906532287598,
2.8384335041046143, 1.5370008945465088, 0.5794053077697754,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, 0.0,
0.1746208667755127, 0.19713549315929413,
0.16420751810073853, 0.0, 0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.0, -0.0, -0.0, -0.0,
-0.0, -0.0, -0.0, 0.0
],
atol=0.1))
remove_dir(self.new_output_folder)
remove_dir(self.old_output_folder)