def test_error_invalid_resample_ratio(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
"test_windows_new", "--resample_ratio=3", '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
"test_windows_old", "--resample_ratio=3", '--box_size=352'
]
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')[1].split(' ')[9],
print_old.getvalue().split('\n')[1].split(' ')[9])
def test_wrong_input_micrograph_path_pattern_error(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"), "nofile", "nofile",
"nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"), "nofile",
"nofile", "nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
sp_global_def.BATCH = True
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')[3],'** Error: Input micrograph file name pattern must contain wild card (*). Please check input_micrograph_pattern argument. Run sp_window.py -h for help.')
self.assertEqual(print_new.getvalue().split('\n')[1].split(' ')[9],
print_old.getvalue().split('\n')[1].split(' ')[9])
def test_wrong_input_coordinates_path_pattern_error(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
"nofile", "nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
"nofile", "nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit):
old_stdout = sys.stdout
print_new = StringIO()
sys.stdout = print_new
fu.main()
sp_global_def.BATCH = True
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')[3],'** Error: Input coordinates file name pattern must contain wild card (*). Please check input_coordinates_pattern argument. Run sp_window.py -h for help.')
self.assertEqual(
print_new.getvalue().split('\n')[1].split('\n')[0].split(' ')[9],
print_old.getvalue().split('\n')[1].split('\n')[0].split(' ')[9])
def test_wrong_CTF_param_source_error(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "CBOX", "TcdA1-*_frames.cbox"),
"nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "CBOX", "TcdA1-*_frames.cbox"),
"nofileCCTER", 'lucaprovawindow', '--box_size=352'
]
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')[3],'** Error: Specified CTER partres file is not found. Please check input_ctf_params_source argument. Run sp_window.py -h for help.')
self.assertEqual(print_new.getvalue().split('\n')[2],
print_old.getvalue().split('\n')[2])
def test_error_files_do_not_match(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-001*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
"outfolder_new", '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-001*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
"outfolder_old", '--box_size=352'
]
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
out_parser = print_new.getvalue().split('\n')[16]
err_new = out_parser[0] + out_parser[1]
out_parser2 = print_old.getvalue().split('\n')[16]
err_old = out_parser2[0] + out_parser2[1]
# self.assertEqual(err_new,'** Error: A micrograph name TcdA1-0100_frames.mrc) in the CTER partres file does not match with input micrograph basename pattern TcdA1-001*_frames.mrc) ')
self.assertEqual(err_new, err_old)
def test_(self):
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
self.new_output_folder, '--box_size=352'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_window.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-*_frames.mrc"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"02_CRYOLO", "EMAN", "TcdA1-*_frames.box"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_partres_select.txt"),
self.old_output_folder, '--box_size=352'
]
with patch.object(sys, 'argv', testargs_new):
fu.main()
with patch.object(sys, 'argv', testargs_old):
oldfu.main()
old_data = mrcfile_open(
path.join(self.old_output_folder, self.filename)).data[0]
new_data = mrcfile_open(
path.join(self.new_output_folder, self.filename)).data[0]
self.assertTrue(array_equal(old_data, new_data))
self.assertTrue(
array_equal(new_data.flatten().tolist()[0:100], [
2.033139944076538, 2.118870258331299, 2.0796854496002197,
1.8459678888320923, 1.7696151733398438, 1.4505984783172607,
1.2712483406066895, 1.221462607383728, 0.6416369080543518,
0.5872614979743958, -0.6979288458824158, -1.0111565589904785,
-0.7067759037017822, -0.8540730476379395, -1.3486729860305786,
-1.7476952075958252, -1.3114615678787231, -0.8387683629989624,
-0.787508487701416, -0.9037533402442932, -0.663044810295105,
-0.294295996427536, -0.09013121575117111, 0.04511815309524536,
0.19695419073104858, -0.033459026366472244,
-0.3311372697353363, -0.8275147676467896, -1.0807580947875977,
-1.0741568803787231, -0.533863365650177, -0.19527646899223328,
-0.36622801423072815, -0.4379308223724365, -0.4848000705242157,
-0.49066489934921265, -0.4228202700614929, 0.41493555903434753,
0.506386935710907, 0.2449536770582199, 0.3998281955718994,
0.2207028865814209, 0.40251466631889343, 0.3158993124961853,
0.4267796576023102, 1.6939674615859985, 1.8226191997528076,
1.889028549194336, 1.858549952507019, 1.552672028541565,
1.4727593660354614, 0.594339907169342, 0.2293643206357956,
0.16122445464134216, -0.050342343747615814,
-0.2755216360092163, 0.3465840220451355, 0.2246960550546646,
0.16776084899902344, 0.22618092596530914, -0.4091913104057312,
-0.3639237880706787, -0.6263998746871948, -0.37294498085975647,
-0.7555119395256042, -0.7194178104400635, -0.8766475319862366,
-0.7931090593338013, -0.9084152579307556, -1.1437935829162598,
-1.3992165327072144, -1.2049322128295898, -1.1964422464370728,
-0.5358992218971252, -0.19423657655715942,
-0.054526664316654205, -0.26979440450668335, -1.20499849319458,
-1.6301522254943848, -1.9685299396514893, -1.4616751670837402,
-0.6779497861862183, -0.34084251523017883, 0.30665281414985657,
0.7742570638656616, 0.8332902789115906, 1.022173523902893,
1.3131401538848877, 1.2987929582595825, 1.7227187156677246,
1.8645423650741577, 1.0463528633117676, -0.2233831286430359,
-0.5092124938964844, -0.24659070372581482, 0.08108771592378616,
-0.021659117192029953, -0.19913935661315918,
-0.7791047692298889, -0.6084468960762024
]))
remove_dir(self.old_output_folder)
remove_dir(self.new_output_folder)
