def test_highest_resolution_error(self):
sp_global_def.BATCH = True
self.remove_folders()
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
self.new_output_folder, '--apix=1.0', '--f_stop=0.3'
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
self.old_output_folder, '--apix=1.0', '--f_stop=0.3'
]
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')[1].split("ERROR")[1],
' => f_stop should be in Angstrom')
self.assertEqual(print_new.getvalue().split('\n')[1].split("ERROR")[1],
print_old.getvalue().split('\n')[1].split("ERROR")[1])
self.remove_folders()
def test_too_few_params_error(self):
sp_global_def.BATCH = True
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc")
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc")
]
with patch.object(sys, 'argv', testargs_new):
with self.assertRaises(SystemExit) as cnew:
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) as cold:
print_old = StringIO()
sys.stdout = print_old
oldfu.main()
sys.stdout = old_stdout
self.assertEqual(str(cnew.exception), str(cold.exception))
self.assertEqual(str(cnew.exception), "None")
def test_cter_pap(self):
sp_global_def.BATCH = True
self.remove_folders()
testargs_new = [
path.join(ABSOLUTE_BIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
self.new_output_folder + "pap", "--selection_list=" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_micrographs_select.txt"),
"--apix=1.14", "--Cs=0", "--pap", "--f_start=40", "--f_stop=34"
]
testargs_old = [
path.join(ABSOLUTE_OLDBIN_PATH, "sp_cter.py"),
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"CorrectedSums", "corrsum_dw", "TcdA1-001*_frames.mrc"),
self.old_output_folder + "pap", "--selection_list=" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"01_CTER", "Tutorial_micrographs_select.txt"),
"--apix=1.14", "--Cs=0", "--pap", "--f_start=40", "--f_stop=34"
]
with patch.object(sys, 'argv', testargs_new):
fu.main()
sp_global_def.BATCH = True
with patch.object(sys, 'argv', testargs_old):
oldfu.main()
old_value = get_im(
path.join(self.old_output_folder + "pap", self.filename))
new_value = get_im(
path.join(self.new_output_folder + "pap", self.filename))
self.assertTrue(
array_equal(old_value.get_2dview(), new_value.get_2dview()))
self.assertTrue(
array_equal(new_value.get_2dview().flatten().tolist()[0:100], [
-151.91610717773438, -5.15772008895874, -7.199570178985596,
16.844715118408203, -86.01467895507812, 224.5313720703125,
255.96446228027344, 127.28541564941406, -107.42439270019531,
-146.97732543945312, 45.27460861206055, 134.89849853515625,
193.75506591796875, 1.6738426685333252, -291.7831726074219,
-261.452880859375, -87.77507019042969, -253.7869873046875,
-14.231243133544922, 105.49187469482422, 54.15253448486328,
202.34719848632812, -145.9459686279297, -310.8766784667969,
-168.98582458496094, -246.27511596679688, -267.9120788574219,
-83.6864013671875, 277.79608154296875, 151.8765106201172,
13.589789390563965, 11.07779312133789, -84.60417175292969,
100.78224182128906, -182.1418914794922, -1.2914609909057617,
-105.66407775878906, -8.37000560760498, 96.46575164794922,
-81.93226623535156, -29.234130859375, -128.64105224609375,
80.63739776611328, -11.062923431396484, 107.84751892089844,
-108.09345245361328, 17.696636199951172, -93.53311157226562,
67.41581726074219, 273.3633728027344, -28.720521926879883,
-34.706932067871094, -195.11680603027344, -200.7438507080078,
-46.45978546142578, -22.808040618896484, -91.24805450439453,
113.92597961425781, 115.37574005126953, -19.18140411376953,
-39.19940948486328, -80.63643646240234, 291.9253845214844,
32.61348342895508, -112.9101333618164, -130.7708282470703,
-70.37080383300781, -260.5411071777344, -163.13958740234375,
-141.8155975341797, -4.3243408203125, -79.0434341430664,
-118.28507232666016, 245.7770233154297, -86.85401153564453,
-84.1547622680664, -5.078440189361572, -53.13208770751953,
-47.206058502197266, 53.22468948364258, 75.35106658935547,
77.2694320678711, 113.52538299560547, -53.97866439819336,
1.6344045400619507, 57.784603118896484, -78.45945739746094,
-69.10759735107422, -83.55438232421875, 63.753501892089844,
75.83992767333984, -36.30785369873047, 97.44556427001953,
100.17158508300781, 57.608177185058594, -89.75988006591797,
141.65589904785156, 14.772521018981934, -143.1587371826172,
-54.35596466064453
]))
self.remove_folders()