test_suite.system_tests.frame

65 """TestCase class for the functional tests of the frame order theories.""" 66

67 - def __init__(self, methodName='runTest'):

68 """Skip the tests if scipy is not installed. 69 70 @keyword methodName: The name of the test. 71 @type methodName: str 72 """ 73 74 # Missing module. 75 if not dep_check.scipy_module: 76 # Store in the status object. 77 status.skipped_tests.append([methodName, 'Scipy', 'system']) 78 79 # Execute the base class method. 80 super(Frame_order, self).__init__(methodName)

81 82

83 - def setUp(self):

84 """Set up for all the functional tests.""" 85 86 # Create the data pipe. 87 self.interpreter.pipe.create('test', 'frame order')

88 89

90 - def mesg_opt_debug(self):

91 """Method for returning a string to help debug the minimisation. 92 93 @return: The debugging string. 94 @rtype: str 95 """ 96 97 # Initialise the string. 98 string = 'Optimisation failure.\n\n' 99 100 # Create the string. 101 string = string + "%-18s%-25s\n" % ("System: ", SYSTEM) 102 string = string + "%-18s%-25s\n" % ("Release: ", RELEASE) 103 string = string + "%-18s%-25s\n" % ("Version: ", VERSION) 104 string = string + "%-18s%-25s\n" % ("Win32 version: ", (WIN32_VER[0] + " " + WIN32_VER[1] + " " + WIN32_VER[2] + " " + WIN32_VER[3])) 105 string = string + "%-18s%-25s\n" % ("Distribution: ", (DIST[0] + " " + DIST[1] + " " + DIST[2])) 106 string = string + "%-18s%-25s\n" % ("Architecture: ", (ARCH[0] + " " + ARCH[1])) 107 string = string + "%-18s%-25s\n" % ("Machine: ", MACH) 108 string = string + "%-18s%-25s\n" % ("Processor: ", PROC) 109 string = string + "%-18s%-25s\n" % ("Python version: ", PY_VER) 110 string = string + "%-18s%-25s\n" % ("Numpy version: ", NUMPY_VER) 111 string = string + "%-18s%-25s\n" % ("Libc version: ", (LIBC_VER[0] + " " + LIBC_VER[1])) 112 113 114 # Minimisation info. 115 string = string + "\n%-15s %30.17g\n" % ('ave_pos_alpha:', cdp.ave_pos_alpha) 116 string = string + "%-15s %30.17g\n" % ('ave_pos_beta:', cdp.ave_pos_beta) 117 string = string + "%-15s %30.17g\n" % ('ave_pos_gamma:', cdp.ave_pos_gamma) 118 string = string + "%-15s %30.17g\n" % ('chi2:', cdp.chi2) 119 string = string + "%-15s %30i\n" % ('iter:', cdp.iter) 120 string = string + "%-15s %30i\n" % ('f_count:', cdp.f_count) 121 string = string + "%-15s %30i\n" % ('g_count:', cdp.g_count) 122 string = string + "%-15s %30i\n" % ('h_count:', cdp.h_count) 123 string = string + "%-15s %30s\n" % ('warning:', cdp.warning) 124 125 # Return the string. 126 return string

127 128

129 - def space_probe(self, ref_chi2=None, params=None, delta=3.0 / 360.0 * 2.0 * pi):

130 """Probe the space around the supposed minimum.""" 131 132 # No function intros. 133 self.interpreter.intro_off() 134 135 # Check the minimum. 136 self.interpreter.calc() 137 print("%-20s %10.5f" % ("chi2 minimum", cdp.chi2)) 138 self.assertAlmostEqual(cdp.chi2, ref_chi2) 139 140 # Test around the minimum using small deviations. 141 for param in params: 142 print("\n\nParam: %s" % param) 143 print("%-20s %10.5f" % ("chi2 orig", ref_chi2)) 144 145 # Get the current value. 146 curr = getattr(cdp, param) 147 148 # Deviate upwards. 149 setattr(cdp, param, curr+delta) 150 self.interpreter.calc() 151 print("%-20s %10.5f" % ("chi2 up", cdp.chi2)) 152 self.assert_(cdp.chi2 > ref_chi2) 153 154 # Deviate downwards. 155 setattr(cdp, param, curr-delta) 156 self.interpreter.calc() 157 print("%-20s %10.5f" % ("chi2 down", cdp.chi2)) 158 self.assert_(cdp.chi2 > ref_chi2) 159 160 # Reset. 161 setattr(cdp, param, curr)

162 163

164 - def test_cam_free_rotor(self):

165 """Test the free rotor frame order model of CaM.""" 166 167 # Execute the script. 168 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'free_rotor.py') 169 170 # Check the average structure CoM matches that of the original position (the average structure is not defined along the rotation axis). 171 for i in range(3): 172 self.assertAlmostEqual(ds['ave pos'].CoM[i], ds['orig pos'].CoM[i], 0) 173 174 # The rotation axis. 175 self.interpreter.pipe.switch('frame order') 176 spherical_vect = zeros(3, float64) 177 spherical_vect[0] = 1.0 178 spherical_vect[1] = cdp.axis_theta 179 spherical_vect[2] = cdp.axis_phi 180 cart_vect = zeros(3, float64) 181 spherical_to_cartesian(spherical_vect, cart_vect) 182 183 # The original rotation axis. 184 pivot = array([ 37.254, 0.5, 16.7465]) 185 com = array([ 26.83678091, -12.37906417, 28.34154128]) 186 axis = pivot - com 187 axis = axis / norm(axis) 188 189 # The dot product. 190 angle = acos(dot(cart_vect, axis)) 191 192 # Check the angle. 193 if angle > 3 and angle < 4: 194 self.assertAlmostEqual(angle, pi, 1) 195 else: 196 self.assertAlmostEqual(angle, 0.0, 1)

197 198

199 - def test_cam_free_rotor2(self):

200 """Test the second free rotor frame order model of CaM.""" 201 202 # Execute the script. 203 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'free_rotor2.py') 204 205 # The base data. 206 pivot = array([ 37.254, 0.5, 16.7465]) 207 com = array([ 26.83678091, -12.37906417, 28.34154128]) 208 pivot_com_axis = com - pivot 209 rot_axis = array([ 0.62649633, 0.77455282, -0.08700742]) 210 211 # The average position CoM. 212 ave_pivot_com_axis = ds['ave pos'].CoM - pivot 213 214 # The projection of the CoMs onto the rotation axis. 215 orig_proj = dot(pivot_com_axis, rot_axis) 216 ave_proj = dot(ave_pivot_com_axis, rot_axis) 217 218 # Check that the projections are equal. 219 self.assertAlmostEqual(orig_proj, ave_proj, 0) 220 221 # The rotation axis. 222 self.interpreter.pipe.switch('frame order') 223 spherical_vect = zeros(3, float64) 224 spherical_vect[0] = 1.0 225 spherical_vect[1] = cdp.axis_theta 226 spherical_vect[2] = cdp.axis_phi 227 cart_vect = zeros(3, float64) 228 spherical_to_cartesian(spherical_vect, cart_vect) 229 print("\nReal rotation axis: %s" % repr(rot_axis)) 230 print("Fitted rotation axis: %s" % repr(cart_vect)) 231 232 # The dot product. 233 angle = acos(dot(cart_vect, rot_axis)) 234 if angle > pi/2: 235 angle = acos(dot(cart_vect, -rot_axis)) 236 237 # Check the angle. 238 self.assertAlmostEqual(angle, 0.0, 2)

239 240

241 - def test_cam_iso_cone_free_rotor(self):

242 """Test the isotropic cone, free rotor frame order model of CaM.""" 243 244 # Execute the script. 245 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'iso_cone_free_rotor.py') 246 247 # Check the average structure CoM matches that of the original position (the average structure is not defined along the rotation axis). 248 for i in range(3): 249 self.assertAlmostEqual(ds['ave pos'].CoM[i], ds['orig pos'].CoM[i], 0) 250 251 # Switch to the correct data pipe. 252 self.interpreter.pipe.switch('frame order') 253 254 # The base data. 255 pivot = array([ 37.254, 0.5, 16.7465]) 256 com = array([ 26.83678091, -12.37906417, 28.34154128]) 257 pivot_com_axis = com - pivot 258 rot_axis = pivot_com_axis / norm(pivot_com_axis) 259 260 # The average position checks. 261 ave_pivot_com_axis = ds['ave pos'].CoM - pivot 262 263 # The projection of the CoMs onto the rotation axis. 264 orig_proj = dot(pivot_com_axis, rot_axis) 265 ave_proj = dot(ave_pivot_com_axis, rot_axis) 266 print("\nReal projection of the central axis to the pivot-CoM: %s" % repr(orig_proj)) 267 print("Fitted projection of the central axis to the pivot-CoM: %s" % repr(ave_proj)) 268 269 # Check that the projections are equal. 270 self.assertAlmostEqual(orig_proj, ave_proj, 1) 271 272 # The rotation axis. 273 self.interpreter.pipe.switch('frame order') 274 spherical_vect = zeros(3, float64) 275 spherical_vect[0] = 1.0 276 spherical_vect[1] = cdp.axis_theta 277 spherical_vect[2] = cdp.axis_phi 278 axis = zeros(3, float64) 279 spherical_to_cartesian(spherical_vect, axis) 280 print("\nReal rotation axis: %s" % repr(rot_axis)) 281 print("Fitted rotation axis: %s" % repr(axis)) 282 283 # Check the angle between the real and fitted rotation axes. 284 angle = acos(dot(axis, rot_axis)) 285 if angle > pi/2: 286 angle = acos(dot(axis, -rot_axis)) 287 self.assertAlmostEqual(angle, 0.0, 2) 288 289 # Check the cone angle of 40 deg. 290 self.assertAlmostEqual(cdp.cone_theta * 2.0, 40.0 / 360.0 * 2.0 * pi, 1)

291 292

293 - def test_cam_iso_cone_free_rotor2(self):

294 """Test the second isotropic cone, free rotor frame order model of CaM.""" 295 296 # Execute the script. 297 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'iso_cone_free_rotor2.py') 298 299 # Switch to the correct data pipe. 300 self.interpreter.pipe.switch('frame order') 301 302 # The base data. 303 pivot = array([ 37.254, 0.5, 16.7465]) 304 com = array([ 26.83678091, -12.37906417, 28.34154128]) 305 pivot_com_axis = com - pivot 306 rot_axis = array([-0.4043088, -0.49985692, 0.76594873]) 307 308 # The rotation axis. 309 self.interpreter.pipe.switch('frame order') 310 spherical_vect = zeros(3, float64) 311 spherical_vect[0] = 1.0 312 spherical_vect[1] = cdp.axis_theta 313 spherical_vect[2] = cdp.axis_phi 314 axis = zeros(3, float64) 315 spherical_to_cartesian(spherical_vect, axis) 316 print("\nReal rotation axis: %s" % repr(rot_axis)) 317 print("Fitted rotation axis: %s" % repr(axis)) 318 319 # Check the angle between the real and fitted rotation axes. 320 angle = acos(dot(axis, rot_axis)) 321 if angle > pi/2: 322 angle = acos(dot(axis, -rot_axis)) 323 self.assertAlmostEqual(angle, 0.0, 2) 324 325 # Check the cone angle of 40 deg. 326 self.assertAlmostEqual(cdp.cone_theta * 2.0, 40.0 / 360.0 * 2.0 * pi, 2)

327 328

329 - def test_cam_rigid(self):

330 """Test the rigid frame order model of CaM.""" 331 332 # Execute the script. 333 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rigid.py') 334 335 # Check the average structure atomic positions (to only one decimal point as the PDB file accuracy isn't great). 336 ave_pos = ds['ave pos'].structure.structural_data[0].mol[0] 337 orig_pos = ds['orig pos'].structure.structural_data[0].mol[0] 338 for i in range(len(ave_pos.atom_name)): 339 self.assertAlmostEqual(ave_pos.x[i], orig_pos.x[i], 1) 340 self.assertAlmostEqual(ave_pos.y[i], orig_pos.y[i], 1) 341 self.assertAlmostEqual(ave_pos.z[i], orig_pos.z[i], 1)

342 343

344 - def test_cam_rotor(self):

345 """Test the rotor frame order model of CaM.""" 346 347 # Execute the script. 348 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rotor.py') 349 350 # Switch to the correct data pipe. 351 self.interpreter.pipe.switch('frame order') 352 353 # The base data. 354 pivot = array([ 37.254, 0.5, 16.7465]) 355 com = array([ 26.83678091, -12.37906417, 28.34154128]) 356 pivot_com_axis = com - pivot 357 rot_axis = pivot_com_axis / norm(pivot_com_axis) 358 359 # The average position checks. 360 real_pos = array([[-0.31334613, -0.88922808, -0.33329811], 361 [ 0.93737972, -0.23341205, -0.2585306 ], 362 [ 0.15209688, -0.39343645, 0.90668313]], float64) 363 ave_pos = zeros((3, 3), float64) 364 euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta, cdp.ave_pos_gamma, ave_pos) 365 print("\nReal domain position:\n%s" % repr(real_pos)) 366 print("Fitted domain position:\n%s" % repr(ave_pos)) 367 for i in range(3): 368 for j in range(3): 369 self.assertAlmostEqual(ave_pos[i, j], real_pos[i, j], 3) 370 371 # The axis system. 372 axis = zeros(3, float64) 373 spherical_to_cartesian(array([1, cdp.axis_theta, cdp.axis_phi]), axis) 374 print("\nReal rotation axis: %s" % repr(rot_axis)) 375 print("Fitted rotation axis: %s" % repr(axis)) 376 377 # Check the angle between the real and fitted rotation axes. 378 angle = acos(dot(axis, rot_axis)) 379 if angle > pi/2: 380 angle = acos(dot(axis, -rot_axis)) 381 self.assertAlmostEqual(angle, 0.0, 2) 382 383 # Check the cone angle of 60 deg. 384 self.assertAlmostEqual(cdp.cone_sigma_max * 2.0, 60.0 / 360.0 * 2.0 * pi, 1)

385 386

387 - def test_cam_rotor2(self):

388 """Test the second rotor frame order model of CaM.""" 389 390 # Execute the script. 391 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rotor2.py') 392 393 # Switch to the correct data pipe. 394 self.interpreter.pipe.switch('frame order') 395 396 # The base data. 397 pivot = array([ 37.254, 0.5, 16.7465]) 398 com = array([ 26.83678091, -12.37906417, 28.34154128]) 399 pivot_com_axis = com - pivot 400 rot_axis = array([ 0.40416535, 0.49967956, 0.76614014]) 401 402 # The average position checks. 403 real_pos = array([[-0.31334613, -0.88922808, -0.33329811], 404 [ 0.93737972, -0.23341205, -0.2585306 ], 405 [ 0.15209688, -0.39343645, 0.90668313]], float64) 406 ave_pos = zeros((3, 3), float64) 407 euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta, cdp.ave_pos_gamma, ave_pos) 408 print("\nReal domain position:\n%s" % repr(real_pos)) 409 print("Fitted domain position:\n%s" % repr(ave_pos)) 410 for i in range(3): 411 for j in range(3): 412 self.assertAlmostEqual(ave_pos[i, j], real_pos[i, j], 1) 413 414 # The axis system. 415 axis = zeros(3, float64) 416 spherical_to_cartesian(array([1, cdp.axis_theta, cdp.axis_phi]), axis) 417 print("\nReal rotation axis: %s" % repr(rot_axis)) 418 print("Fitted rotation axis: %s" % repr(axis)) 419 420 # Check the angle between the real and fitted rotation axes. 421 angle = acos(dot(axis, rot_axis)) 422 if angle > pi/2: 423 angle = acos(dot(axis, -rot_axis)) 424 self.assertAlmostEqual(angle, 0.0, 2) 425 426 # Check the cone angle of 60 deg. 427 self.assertAlmostEqual(cdp.cone_sigma_max * 2.0, 60.0 / 360.0 * 2.0 * pi, 1)

428 429

430 - def test_model_free_rotor(self):

431 """Test the free rotor frame order model.""" 432 433 # Execute the script. 434 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'free_rotor.py') 435 436 # Check the calculated chi2 value. 437 self.assertAlmostEqual(ds.chi2, 0.0216067401326)

438 439

440 - def test_model_free_rotor_eigenframe(self):

441 """Test the free rotor frame order model in the eigenframe.""" 442 443 # Execute the script. 444 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'free_rotor_eigenframe.py') 445 446 # Check the calculated chi2 value. 447 self.assertAlmostEqual(ds.chi2, 0.00673210578744)

448 449

450 - def test_model_iso_cone(self):

451 """Test the isotropic cone frame order model.""" 452 453 # Execute the script. 454 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'iso_cone.py') 455 456 # The reference chi2 values. 457 chi2_ref = [] 458 chi2_ref.append(0.131890484593) 459 chi2_ref.append(0.0539383731611) 460 chi2_ref.append(0.0135056297016) 461 chi2_ref.append(0.0163432453475) 462 chi2_ref.append(0.0775570503917) 463 chi2_ref.append(0.0535055367493) 464 chi2_ref.append(0.0994746492483) 465 chi2_ref.append(0.174830826376) 466 chi2_ref.append(0.193036744906) 467 chi2_ref.append(0.181480810794) 468 chi2_ref.append(0.215863920824) 469 chi2_ref.append(0.170088692559) 470 chi2_ref.append(0.152634493383) 471 chi2_ref.append(0.168711907446) 472 chi2_ref.append(0.168405354086) 473 chi2_ref.append(0.247439860108) 474 chi2_ref.append(0.143487410228) 475 chi2_ref.append(0.148318989268) 476 477 # Check the calculated chi2 values. 478 for i in range(18): 479 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

480 481

482 - def test_model_iso_cone_free_rotor(self):

483 """Test the free rotor isotropic cone frame order model.""" 484 485 # Execute the script. 486 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'iso_cone_free_rotor.py') 487 488 # The reference chi2 values. 489 chi2_ref = [] 490 chi2_ref.append(0.0177292447567 ) 491 chi2_ref.append(0.0187585146766 ) 492 chi2_ref.append(0.0440519894909 ) 493 chi2_ref.append(0.0225223798489 ) 494 chi2_ref.append(0.0239979046491 ) 495 chi2_ref.append(0.0161048633259 ) 496 chi2_ref.append(0.0267310958091 ) 497 chi2_ref.append(0.0219820914478 ) 498 chi2_ref.append(0.0194880630576 ) 499 chi2_ref.append(0.0348242343833 ) 500 chi2_ref.append(0.0401631858563 ) 501 chi2_ref.append(0.0327461783858 ) 502 chi2_ref.append(0.0391082177884 ) 503 chi2_ref.append(0.0467056691507 ) 504 chi2_ref.append(0.0407175857557 ) 505 chi2_ref.append(0.0441514158832 ) 506 chi2_ref.append(0.042078718831 ) 507 chi2_ref.append(0.0403856796359 ) 508 509 # Check the calculated chi2 values. 510 for i in range(18): 511 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

512 513

514 - def test_model_iso_cone_free_rotor_eigenframe(self):

515 """Test the free rotor isotropic cone frame order model in the eigenframe.""" 516 517 # Execute the script. 518 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'iso_cone_free_rotor_eigenframe.py') 519 520 # The reference chi2 values. 521 chi2_ref = [] 522 chi2_ref.append(0.115175446978 ) 523 chi2_ref.append(0.156911214374 ) 524 chi2_ref.append(0.209198723492 ) 525 chi2_ref.append(0.155297079942 ) 526 chi2_ref.append(0.0684780584219) 527 chi2_ref.append(0.0781922435531) 528 chi2_ref.append(0.103777394815 ) 529 chi2_ref.append(0.173740596864 ) 530 chi2_ref.append(0.199867814969 ) 531 chi2_ref.append(0.297587241555 ) 532 chi2_ref.append(0.308539214325 ) 533 chi2_ref.append(0.2543934866 ) 534 chi2_ref.append(0.168985365277 ) 535 chi2_ref.append(0.190780393086 ) 536 chi2_ref.append(0.186482798104 ) 537 chi2_ref.append(0.153839910288 ) 538 chi2_ref.append(0.160863854198 ) 539 chi2_ref.append(0.157029368992 ) 540 541 # Check the calculated chi2 values. 542 for i in range(18): 543 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

544 545

546 - def test_model_pseudo_ellipse(self):

547 """Test the pseudo-ellipse frame order model.""" 548 549 # Execute the script. 550 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'pseudo_ellipse.py') 551 552 # The reference chi2 values. 553 chi2_ref = [] 554 chi2_ref.append(0.0208490007203) 555 chi2_ref.append(0.00958146486076) 556 chi2_ref.append(0.0405488536626) 557 chi2_ref.append(0.0370142845551) 558 chi2_ref.append(0.0204537537661) 559 chi2_ref.append(0.0186122056988) 560 chi2_ref.append(0.0177783016875) 561 chi2_ref.append(0.0311747995923) 562 chi2_ref.append(0.0225532898175) 563 chi2_ref.append(0.0212562065194) 564 chi2_ref.append(0.018939663528) 565 chi2_ref.append(0.0224686987165) 566 chi2_ref.append(0.0201247095045) 567 chi2_ref.append(0.0215343817478) 568 chi2_ref.append(0.016509302331) 569 chi2_ref.append(0.0101988814638) 570 chi2_ref.append(0.00989431182393) 571 chi2_ref.append(0.0123400971524) 572 573 # Check the calculated chi2 values. 574 for i in range(18): 575 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

576 577

578 - def test_model_pseudo_ellipse_free_rotor(self):

579 """Test the free rotor pseudo-elliptic cone frame order model.""" 580 581 # Execute the script. 582 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'pseudo_ellipse_free_rotor.py') 583 584 # The reference chi2 values. 585 chi2_ref = [[], []] 586 chi2_ref[0].append(0.0493245760341) 587 chi2_ref[0].append(0.0322727678945) 588 chi2_ref[0].append(0.0399505883966) 589 chi2_ref[0].append(0.0122539315721) 590 chi2_ref[0].append(0.0263840505182) 591 chi2_ref[0].append(0.0324871952484) 592 chi2_ref[0].append(0.0247369735031) 593 chi2_ref[0].append(0.0231896861006) 594 chi2_ref[0].append(0.0285947802273) 595 chi2_ref[0].append(0.0345542627808) 596 chi2_ref[0].append(0.0289869422491) 597 chi2_ref[0].append(0.0243038470127) 598 chi2_ref[0].append(0.0226686034191) 599 chi2_ref[0].append(0.0215714556045) 600 chi2_ref[0].append(0.0173836730495) 601 chi2_ref[0].append(0.0182530810025) 602 chi2_ref[0].append(0.0212669211551) 603 chi2_ref[0].append(0.0194359136977) 604 605 chi2_ref[1].append(0.0205287391277) 606 chi2_ref[1].append(0.0246463829816) 607 chi2_ref[1].append(0.0590186061204) 608 chi2_ref[1].append(0.0441193978727) 609 chi2_ref[1].append(0.0424299319779) 610 chi2_ref[1].append(0.032589994611) 611 chi2_ref[1].append(0.0523532207508) 612 chi2_ref[1].append(0.0488535879384) 613 chi2_ref[1].append(0.0424063218455) 614 chi2_ref[1].append(0.0553525984677) 615 chi2_ref[1].append(0.0495587286781) 616 chi2_ref[1].append(0.0446625345909) 617 chi2_ref[1].append(0.0470718361239) 618 chi2_ref[1].append(0.0493615476721) 619 chi2_ref[1].append(0.0492208206006) 620 chi2_ref[1].append(0.0429966323771) 621 chi2_ref[1].append(0.0442849187057) 622 chi2_ref[1].append(0.0436756306414) 623 624 # Check the calculated chi2 values. 625 for j in range(2): 626 for i in range(18): 627 self.assertAlmostEqual(ds.chi2[j][i], chi2_ref[j][i])

628 629

630 - def test_model_pseudo_ellipse_torsionless(self):

631 """Test the pseudo-ellipse frame order model.""" 632 633 # Execute the script. 634 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'pseudo_ellipse_torsionless.py') 635 636 # The reference chi2 values. 637 chi2_ref = [] 638 chi2_ref.append(0.340228489225) 639 chi2_ref.append(0.260847963487) 640 chi2_ref.append(0.250610744982) 641 chi2_ref.append(0.228947619476) 642 chi2_ref.append(0.251996758815) 643 chi2_ref.append(0.238724080817) 644 chi2_ref.append(0.182383602599) 645 chi2_ref.append(0.172830852017) 646 chi2_ref.append(0.159757813028) 647 chi2_ref.append(0.173833227524) 648 chi2_ref.append(0.156168102428) 649 chi2_ref.append(0.171406869781) 650 chi2_ref.append(0.202653838515) 651 chi2_ref.append(0.198919351788) 652 chi2_ref.append(0.169463187543) 653 chi2_ref.append(0.156867571611) 654 chi2_ref.append(0.146139931983) 655 chi2_ref.append(0.13307108095 ) 656 657 # Check the calculated chi2 values. 658 for i in range(18): 659 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

660 661

662 - def test_model_rotor(self):

663 """Test the rotor frame order model.""" 664 665 # Execute the script. 666 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'rotor.py') 667 668 # The reference chi2 values. 669 chi2_ref = [] 670 chi2_ref.append(0.00410277546707 ) 671 chi2_ref.append(0.00112443204411 ) 672 chi2_ref.append(0.00759196190331 ) 673 chi2_ref.append(0.0956596925692 ) 674 chi2_ref.append(0.223717470059 ) 675 chi2_ref.append(0.136723330704 ) 676 chi2_ref.append(0.0588253217034 ) 677 chi2_ref.append(0.0774693384156 ) 678 chi2_ref.append(0.0855477856492 ) 679 chi2_ref.append(0.198089516589 ) 680 chi2_ref.append(0.227537351664 ) 681 chi2_ref.append(0.202005777915 ) 682 chi2_ref.append(0.192550395736 ) 683 chi2_ref.append(0.126007906472 ) 684 chi2_ref.append(0.124053264662 ) 685 chi2_ref.append(0.18203965973 ) 686 chi2_ref.append(0.191062017006 ) 687 chi2_ref.append(0.13580013153 ) 688 689 # Check the calculated chi2 values. 690 for i in range(18): 691 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

692 693

694 - def test_model_rotor_eigenframe(self):

695 """Test the rotor frame order model in the eigenframe.""" 696 697 # Execute the script. 698 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'model_calcs'+sep+'rotor_eigenframe.py') 699 700 # The reference chi2 values. 701 chi2_ref = [] 702 chi2_ref.append(0.00308229284128) 703 chi2_ref.append(0.0117874014708 ) 704 chi2_ref.append(0.0016108171487 ) 705 chi2_ref.append(0.00532862954549) 706 chi2_ref.append(0.097784753109 ) 707 chi2_ref.append(0.157147901966 ) 708 chi2_ref.append(0.182397051711 ) 709 chi2_ref.append(0.338977916543 ) 710 chi2_ref.append(0.208516866654 ) 711 chi2_ref.append(0.137660115226 ) 712 chi2_ref.append(0.0580816149373 ) 713 chi2_ref.append(0.0476543367845 ) 714 chi2_ref.append(0.0360689584006 ) 715 chi2_ref.append(0.0118024492136 ) 716 chi2_ref.append(0.0824307041139 ) 717 chi2_ref.append(0.0920614159956 ) 718 chi2_ref.append(0.0936464288916 ) 719 chi2_ref.append(0.0823025718101 ) 720 721 # Check the calculated chi2 values. 722 for i in range(18): 723 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

724 725

726 - def test_opendx_map(self):

727 """Test the mapping of the Euler angle parameters for OpenDx viewing.""" 728 729 # Execute the script. 730 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opendx_euler_angle_map.py')

731 732

733 - def test_opt_rigid_no_rot(self):

734 """Test the 'rigid' model for unrotated tensors with no motion.""" 735 736 # Execute the script. 737 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opt_rigid_no_rot.py') 738 739 # Get the debugging message. 740 self.mesg = self.mesg_opt_debug() 741 742 # Test the values. 743 self.assertEqual(cdp.iter, 92, msg=self.mesg) 744 self.assertEqual(cdp.chi2, 0.0, msg=self.mesg) 745 self.assertEqual(cdp.ave_pos_alpha, 0.0, msg=self.mesg) 746 self.assertEqual(cdp.ave_pos_beta, 0.0, msg=self.mesg) 747 self.assertEqual(cdp.ave_pos_gamma, 0.0, msg=self.mesg)

748 749

750 - def test_opt_rigid_rand_rot(self):

751 """Test the 'rigid' model for randomly rotated tensors with no motion.""" 752 753 # Execute the script. 754 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opt_rigid_rand_rot.py') 755 756 # Get the debugging message. 757 self.mesg = self.mesg_opt_debug() 758 759 # Test the values. 760 self.assertAlmostEqual(cdp.chi2, 3.085356555118994e-26, msg=self.mesg) 761 self.assertAlmostEqual(cdp.ave_pos_alpha, 5.0700283197712777, msg=self.mesg) 762 self.assertAlmostEqual(cdp.ave_pos_beta, 2.5615753919522359, msg=self.mesg) 763 self.assertAlmostEqual(cdp.ave_pos_gamma, 0.64895449611163691, msg=self.mesg)

764 765

766 - def test_parametric_restriction_iso_cone_to_iso_cone_free_rotor(self):

767 """Parametric restriction of the isotropic cone to the free rotor isotropic cone frame order model.""" 768 769 # Execute the script. 770 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'parametric_restriction'+sep+'iso_cone_to_iso_cone_free_rotor.py') 771 772 # The reference chi2 values. 773 chi2_ref = [] 774 chi2_ref.append(0.0177292447567 ) 775 chi2_ref.append(0.0187585146766 ) 776 chi2_ref.append(0.0440519894909 ) 777 chi2_ref.append(0.0225223798489 ) 778 chi2_ref.append(0.0239979046491 ) 779 chi2_ref.append(0.0161048633259 ) 780 chi2_ref.append(0.0267310958091 ) 781 chi2_ref.append(0.0219820914478 ) 782 chi2_ref.append(0.0194880630576 ) 783 chi2_ref.append(0.0348242343833 ) 784 chi2_ref.append(0.0401631858563 ) 785 chi2_ref.append(0.0327461783858 ) 786 chi2_ref.append(0.0391082177884 ) 787 chi2_ref.append(0.0467056691507 ) 788 chi2_ref.append(0.0407175857557 ) 789 chi2_ref.append(0.0441514158832 ) 790 chi2_ref.append(0.042078718831 ) 791 chi2_ref.append(0.0403856796359 ) 792 793 # Check the calculated chi2 values. 794 for i in range(18): 795 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

796 797

798 - def test_parametric_restriction_pseudo_ellipse_to_iso_cone(self):

799 """Parametric restriction of the pseudo-ellipse to the isotropic cone frame order model.""" 800 801 # Execute the script. 802 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'parametric_restriction'+sep+'pseudo_ellipse_to_iso_cone.py') 803 804 # The reference chi2 values. 805 chi2_ref = [] 806 chi2_ref.append(0.131890484593) 807 chi2_ref.append(0.0539383731611) 808 chi2_ref.append(0.0135056297016) 809 chi2_ref.append(0.0163432453475) 810 chi2_ref.append(0.0775570503917) 811 chi2_ref.append(0.0535055367493) 812 chi2_ref.append(0.0994746492483) 813 chi2_ref.append(0.174830826376) 814 chi2_ref.append(0.193036744906) 815 chi2_ref.append(0.181480810794) 816 chi2_ref.append(0.215863920824) 817 chi2_ref.append(0.170088692559) 818 chi2_ref.append(0.152634493383) 819 chi2_ref.append(0.168711907446) 820 chi2_ref.append(0.168405354086) 821 chi2_ref.append(0.247439860108) 822 chi2_ref.append(0.143487410228) 823 chi2_ref.append(0.148318989268) 824 825 # Check the calculated chi2 values. 826 for i in range(18): 827 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

828 829

830 - def test_parametric_restriction_pseudo_ellipse_to_iso_cone_free_rotor(self):

831 """Parametric restriction of the pseudo-ellipse to the free rotor isotropic cone frame order model.""" 832 833 # Execute the script. 834 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'parametric_restriction'+sep+'pseudo_ellipse_to_iso_cone_free_rotor.py') 835 836 # The reference chi2 values. 837 chi2_ref = [] 838 chi2_ref.append(0.0177292447567 ) 839 chi2_ref.append(0.0187585146766 ) 840 chi2_ref.append(0.0440519894909 ) 841 chi2_ref.append(0.0225223798489 ) 842 chi2_ref.append(0.0239979046491 ) 843 chi2_ref.append(0.0161048633259 ) 844 chi2_ref.append(0.0267310958091 ) 845 chi2_ref.append(0.0219820914478 ) 846 chi2_ref.append(0.0194880630576 ) 847 chi2_ref.append(0.0348242343833 ) 848 chi2_ref.append(0.0401631858563 ) 849 chi2_ref.append(0.0327461783858 ) 850 chi2_ref.append(0.0391082177884 ) 851 chi2_ref.append(0.0467056691507 ) 852 chi2_ref.append(0.0407175857557 ) 853 chi2_ref.append(0.0441514158832 ) 854 chi2_ref.append(0.042078718831 ) 855 chi2_ref.append(0.0403856796359 ) 856 857 # Check the calculated chi2 values. 858 for i in range(18): 859 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

860 861

862 - def test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone(self):

863 """Parametric restriction of the pseudo-ellipse to the isotropic cone frame order model.""" 864 865 # Execute the script. 866 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'parametric_restriction'+sep+'pseudo_ellipse_free_rotor_to_iso_cone.py') 867 868 # The reference chi2 values. 869 chi2_ref = [] 870 chi2_ref.append(16957.4964577) 871 chi2_ref.append(15727.13869) 872 chi2_ref.append(13903.0982799) 873 chi2_ref.append(11719.9390681) 874 chi2_ref.append(9488.44060873) 875 chi2_ref.append(7425.57820642) 876 chi2_ref.append(5713.6467735) 877 chi2_ref.append(4393.3273949) 878 chi2_ref.append(3452.97770868) 879 chi2_ref.append(2771.90973598) 880 chi2_ref.append(2247.44444894) 881 chi2_ref.append(1788.58977266) 882 chi2_ref.append(1348.38250916) 883 chi2_ref.append(921.060703519) 884 chi2_ref.append(539.03217075) 885 chi2_ref.append(244.341444558) 886 chi2_ref.append(58.4566671195) 887 chi2_ref.append(0.148318989268) 888 889 # Check the calculated chi2 values. 890 for i in range(18): 891 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

892 893

894 - def test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone_free_rotor(self):

895 """Parametric restriction of the free rotor pseudo-ellipse to the free rotor isotropic cone frame order model.""" 896 897 # Execute the script. 898 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'parametric_restriction'+sep+'pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py') 899 900 # The reference chi2 values. 901 chi2_ref = [] 902 chi2_ref.append(0.0177292447567 ) 903 chi2_ref.append(0.0187585146766 ) 904 chi2_ref.append(0.0440519894909 ) 905 chi2_ref.append(0.0225223798489 ) 906 chi2_ref.append(0.0239979046491 ) 907 chi2_ref.append(0.0161048633259 ) 908 chi2_ref.append(0.0267310958091 ) 909 chi2_ref.append(0.0219820914478 ) 910 chi2_ref.append(0.0194880630576 ) 911 chi2_ref.append(0.0348242343833 ) 912 chi2_ref.append(0.0401631858563 ) 913 chi2_ref.append(0.0327461783858 ) 914 chi2_ref.append(0.0391082177884 ) 915 chi2_ref.append(0.0467056691507 ) 916 chi2_ref.append(0.0407175857557 ) 917 chi2_ref.append(0.0441514158832 ) 918 chi2_ref.append(0.042078718831 ) 919 chi2_ref.append(0.0403856796359 ) 920 921 # Check the calculated chi2 values. 922 for i in range(18): 923 self.assertAlmostEqual(ds.chi2[i], chi2_ref[i])

924 925

926 - def test_pseudo_ellipse(self):

927 """Test the pseudo-ellipse target function.""" 928 929 # Execute the script. 930 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'pseudo_ellipse.py') 931 932 # The reference chi2 value. 933 chi2 = 0.015865464136741975 934 935 # Check the surrounding space. 936 self.space_probe(ref_chi2=chi2, params=['ave_pos_alpha', 'ave_pos_beta', 'ave_pos_gamma', 'eigen_alpha', 'eigen_beta', 'eigen_gamma', 'cone_theta_x', 'cone_theta_y', 'cone_sigma_max'])

937 938

939 - def test_pseudo_ellipse_torsionless(self):

940 """Test the torsionless pseudo-ellipse target function.""" 941 942 # Execute the script. 943 self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'pseudo_ellipse_torsionless.py') 944 945 # The reference chi2 value. 946 chi2 = 2.8393866813588198 947 948 # Check the surrounding space. 949 self.space_probe(ref_chi2=chi2, params=['ave_pos_alpha', 'ave_pos_beta', 'ave_pos_gamma', 'eigen_alpha', 'eigen_beta', 'eigen_gamma', 'cone_theta_x', 'cone_theta_y'])

Source Code for Module test_suite.system_tests.frame_order