test_suite.system_tests.frame

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

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

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

80 81

82 - def setUp(self):

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

87 88

89 - def mesg_opt_debug(self):

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

126 127

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

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

161 162

163 - def test_cam_free_rotor(self):

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

196 197

198 - def test_cam_free_rotor2(self):

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

238 239

240 - def test_cam_iso_cone_free_rotor(self):

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

290 291

292 - def test_cam_iso_cone_free_rotor2(self):

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

326 327

328 - def test_cam_rigid(self):

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

341 342

343 - def test_cam_rotor(self):

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

384 385

386 - def test_cam_rotor2(self):

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

427 428

429 - def test_model_free_rotor(self):

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

437 438

439 - def test_model_free_rotor_eigenframe(self):

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

447 448

449 - def test_model_iso_cone(self):

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

479 480

481 - def test_model_iso_cone_free_rotor(self):

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

511 512

513 - def test_model_iso_cone_free_rotor_eigenframe(self):

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

543 544

545 - def test_model_pseudo_ellipse(self):

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

575 576

577 - def test_model_pseudo_ellipse_free_rotor(self):

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

627 628

629 - def test_model_pseudo_ellipse_torsionless(self):

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

659 660

661 - def test_model_rotor(self):

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

691 692

693 - def test_model_rotor_eigenframe(self):

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

723 724

725 - def test_opendx_map(self):

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

730 731

732 - def test_opt_rigid_no_rot(self):

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

747 748

749 - def test_opt_rigid_rand_rot(self):

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

763 764

765 - def test_parametric_restriction_iso_cone_to_iso_cone_free_rotor(self):

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

795 796

797 - def test_parametric_restriction_pseudo_ellipse_to_iso_cone(self):

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

827 828

829 - def test_parametric_restriction_pseudo_ellipse_to_iso_cone_free_rotor(self):

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

859 860

861 - def test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone(self):

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

891 892

893 - def test_parametric_restriction_pseudo_ellipse_free_rotor_to_iso_cone_free_rotor(self):

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

923 924

925 - def test_pseudo_ellipse(self):

926 """Test the pseudo-ellipse target function.""" 927 928 # Execute the script. 929 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'pseudo_ellipse.py') 930 931 # The reference chi2 value. 932 chi2 = 0.015865464136741975 933 934 # Check the surrounding space. 935 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'])

936 937

938 - def test_pseudo_ellipse_torsionless(self):

939 """Test the torsionless pseudo-ellipse target function.""" 940 941 # Execute the script. 942 self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'pseudo_ellipse_torsionless.py') 943 944 # The reference chi2 value. 945 chi2 = 2.8393866813588198 946 947 # Check the surrounding space. 948 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