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()