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_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)
def test_run(self):
testcommand_new = (
MPI_PATH + " -np " + str(NUM_PROC) + " " +
path.join(ABSOLUTE_BIN_PATH, "sp_isac2.py") + " 'bdb:" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_Particles#stack'") + " '" + self.new_output_folder +
"' " + " --radius=145" + " --CTF")
testcommand_old = (
MPI_PATH + " -np " + str(NUM_PROC) + " " +
path.join(ABSOLUTE_OLDBIN_PATH, "sp_isac2.py") + " 'bdb:" +
path.join(ABSOLUTE_PATH_TO_SPHIRE_DEMO_RESULTS_FOLDER_NEW,
"03_Particles#stack'") + " '" + self.old_output_folder +
"' " + " --radius=145" + " --CTF")
subprocess.run(args=[testcommand_new], shell=True, capture_output=True)
subprocess.run(args=[testcommand_old], shell=True, capture_output=True)
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(
allclose(old_value.get_2dview(),
new_value.get_2dview(),
atol=TOLERANCE))
self.assertTrue(
allclose(new_value.get_2dview().flatten().tolist()[0:100], [
0.020844653248786926, 0.022487156093120575,
0.02208145707845688, 0.018550248816609383,
0.018665246665477753, 0.019494876265525818,
0.02418450079858303, 0.027667080983519554, 0.02900763787329197,
0.025944046676158905, 0.031390730291604996,
0.027120821177959442, 0.00910606887191534,
-0.0004518263158388436, 0.009620467200875282,
0.025462428107857704, 0.02613203041255474,
0.026837026700377464, 0.019651882350444794,
-0.0013422714546322823, -0.004115818999707699,
0.03214756399393082, 0.03178049996495247, 0.011443180963397026,
0.025857364758849144, 0.026638126000761986,
0.03655451536178589, 0.05426323413848877, 0.06268023699522018,
0.03984970971941948, 0.013704168610274792,
0.008193270303308964, 0.005416750907897949,
-0.012422064319252968, -0.012422808445990086,
0.014235804788768291, 0.024870628491044044,
-0.005099047441035509, -0.009270750917494297,
0.015586614608764648, -0.0036001892294734716,
-0.02533501200377941, -0.004470369778573513,
0.02382775768637657, 0.05031612142920494, 0.04690878838300705,
0.02393484115600586, 0.027014095336198807,
0.039149295538663864, 0.03573647513985634, 0.02213861420750618,
0.032027628272771835, 0.03532850742340088, 0.03128813952207565,
0.01826963573694229, 0.028490642085671425,
0.046303264796733856, 0.01782909594476223,
-0.00606165686622262, -0.016502195969223976,
-0.005856842268258333, 0.019041359424591064,
0.02800695225596428, 0.026184026151895523,
0.023107700049877167, 0.02628708817064762,
0.022019468247890472, 0.019245078787207603,
0.020709989592432976, 0.021585211157798767,
0.02417927235364914, 0.021674703806638718, 0.0199696384370327,
0.021289950236678123, 0.020935336127877235,
0.021501578390598297, 0.022525610402226448,
0.02044103667140007, 0.01824958808720112, 0.023783020675182343,
0.025899477303028107, 0.023173417896032333, 0.0289889145642519,
0.03435958921909332, 0.03157936781644821, 0.03505755960941315,
0.04005855321884155, 0.034827277064323425,
0.022344911471009254, 0.008706190623342991,
0.01249337662011385, 0.019858719781041145,
0.021026115864515305, 0.029216332361102104,
0.010308701545000076, -0.01953706704080105,
-0.012493203394114971, 0.022878523916006088,
0.022390954196453094, 0.0009752019541338086
],
atol=TOLERANCE))
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()