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This test runs a two-stages registration process including following stages:

1) Affine

2) BSpline

That the affine stage is run in 3 resolution levels.

Moving image is a BSpline warped version of fixed image. For evalution the checker board result before and after regsitration are shown.





In [1]:



    


## Boiler plate code common to many notebooks.  See the TestFilesCommonCode.ipynb for details
from __future__ import print_function
%run TestFilesCommonCode.ipynb



    


















    






SimpleITK Version: 0.9.0.dev2042-g22c5b
Compiled: Aug 14 2014 10:17:06


















In [2]:



    


fixedImageFilename = fdata('BrainProtonDensitySliceBorder20.png')
movingImageFilename = fdata('BrainProtonDensitySliceBSplined10.png')
#movingImageFilename = fdata('ITK/Examples/RegistrationITKv3/test/Baseline/BSplineWarping1Test.png')
fixed = sitk.ReadImage(fixedImageFilename,sitk.sitkFloat32)
moving = sitk.ReadImage(movingImageFilename, sitk.sitkFloat32)
myshow3d(fixed, xslices=[], yslices=[], zslices=[], title="fixed")
myshow3d(moving, xslices=[], yslices=[], zslices=[], title="moving")



    


















    

















    
























In [3]:



    


cshow(fixed,moving)



    


















    






<bound method ResampleImageFilter.GetTransform of <SimpleITK.SimpleITK.ResampleImageFilter; proxy of <Swig Object of type 'itk::simple::ResampleImageFilter::Self *' at 0x1147f6d80> >>










    
























In [4]:



    


# Set the first stage
tx1 = sitk.AffineTransform(fixed.GetDimension())



    











In [5]:



    


ctx = sitk.Transform(tx1) # Set composite transform
                          # This composite transform is update at each stage
                          # and finally will be considered as the output of 
                          # the registration process since the InPlace is TRUE.
ctx.SetFixedParameters(ctx.GetFixedParameters()) # hack to force deep copy, as registion is done in place..
# Set the registration filter
R = sitk.ImageRegistrationMethod()
R.SetMetricAsJointHistogramMutualInformation()
R.SetOptimizerAsGradientDescent(learningRate=1.0,
                                numberOfIterations=100,
                                convergenceMinimumValue = 1e-6,
                                convergenceWindowSize = 10,
                                estimateLearningRate = R.Once,
                                maximumStepSizeInPhysicalUnits = 1.0)
R.SetOptimizerScalesFromPhysicalShift()
R.SetShrinkFactorsPerLevel([3,2,1])
R.SetSmoothingSigmasPerLevel([2,1,1])
R.SetInitialTransform(ctx)
R.SetInterpolator(sitk.sitkLinear)
R.SetMetricSamplingPercentage(0.5)
R.SetMetricSamplingStrategy(R.RANDOM)



    


















    
Out[5]:








<SimpleITK.SimpleITK.ImageRegistrationMethod; proxy of <Swig Object of type 'itk::simple::ImageRegistrationMethod *' at 0x11481f600> >

















In [6]:



    


R.RemoveAllCommands()
R.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration(R) )
affineOut = R.Execute(fixed,moving)

print("-------")
print(affineOut)
print("Optimizer stop condition: {0}".format(R.GetOptimizerStopConditionDescription()))
print(" Iteration: {0}".format(R.GetOptimizerIteration()))
print(" Metric value: {0}".format(R.GetMetricValue()))



    


















    






0 = -1.06482139024 : (0.9993462253030309, -0.0008806439299396415, -0.000812716920520217, 0.9995866232203046, -0.4237888898224726, -0.33094286632642284)
1 = -1.1249970959 : (0.9986824826968085, -0.0017153754212635073, -0.0015940212950997855, 0.9992252489402708, -0.8349581607931358, -0.6480991806657452)
2 = -1.17848527185 : (0.998210392480809, -0.002348691494188304, -0.002285352853910274, 0.9989635039573607, -1.1607582901963733, -0.934038911097159)
3 = -1.21688745348 : (0.9980761734649872, -0.0026940694085630275, -0.00278886988322814, 0.9988610564910634, -1.3575609158052238, -1.1528079995310914)
4 = -1.22990377972 : (0.9982639237682195, -0.00279084618068336, -0.0030752549065135026, 0.9989395562987327, -1.4399136466136129, -1.2911949375447969)
5 = -1.23499173404 : (0.998516472809124, -0.0028272434734203716, -0.003243261073672852, 0.9991041069685702, -1.495527390311354, -1.3830042099347315)
6 = -1.23571308739 : (0.9987865963562115, -0.0028375359114697417, -0.0033523123811505674, 0.9993073440169769, -1.5387841704976757, -1.450458056558552)
7 = -1.23655321874 : (0.9990558535230993, -0.0028281747353595004, -0.0034150582449243706, 0.9995297268597476, -1.5745983435233504, -1.500560555610391)
8 = -1.23652943409 : (0.9993194864151571, -0.002811391726348306, -0.003444812090390556, 0.9997747270446475, -1.6068727795035953, -1.5370489532047371)
9 = -1.23645255055 : (0.9995676900392187, -0.0027973665339274508, -0.0034712046398086656, 1.0000018590696906, -1.6403811722088146, -1.5720864513905428)
10 = -1.23611220301 : (0.9998102694935045, -0.002775763113821183, -0.003492402587214523, 1.0002241199707254, -1.669879015082032, -1.605075242590393)
11 = -1.23592233955 : (1.0000255663880637, -0.002762025806572856, -0.003509697699213055, 1.0004418389659817, -1.7038234799179646, -1.6363137533466394)
12 = -1.23545245609 : (1.0002372483666442, -0.002742773957380262, -0.003520013244397768, 1.0006542000809333, -1.735314165884536, -1.6651196823545817)
13 = -1.23544332613 : (1.000440016846556, -0.0027179196842880326, -0.0035308614173476887, 1.0008589528429483, -1.7629913596335707, -1.6936621208243132)
0 = -1.17219601981 : (1.0046833222240206, -0.0019035435261777153, -0.003929155459669339, 1.003204313570683, -1.9990843021743527, -2.3717219484152423)
1 = -1.13580306376 : (1.0027016490799707, -0.005255755987503559, -0.0003018140080770994, 1.0080951792035315, -3.95109345272711, -1.1044836085843428)
2 = -0.963310375819 : (1.0207635178480507, 0.006166684478156105, -0.006950391393482927, 1.0058769804184917, 1.6953191255370301, -4.0008905675449675)
3 = -0.715100713519 : (1.0158268170919371, -0.0028743736214084416, -0.0038757453977434544, 1.011905384041791, -2.6434747863784445, -2.4404924950232036)
4 = -1.02686404427 : (1.0102670454376181, -0.005533196564932336, -0.007412984570444271, 1.0076384490557997, -4.548245799662762, -4.384336048420957)
5 = -0.962404017486 : (1.0240481605562997, 0.0058365890290669326, 0.0029537608144857615, 1.0163752193853148, 0.035528138951044674, -0.782578191842735)
6 = -0.756001137679 : (1.0191309328704654, -0.0016579149357987578, -0.000560796024334172, 1.0164871551506596, -3.917895573420556, -2.475156448019455)
7 = -1.00155047971 : (1.0166645363879356, -0.0012016713399369537, -0.0052233012644862156, 1.0127392382978377, -3.898941539149906, -4.512223418884267)
8 = -1.02991128968 : (1.0149472875233652, 0.0009978636523557865, 0.0014659601599210223, 1.0177933617789587, -3.3587810712731487, -2.167988316114261)
0 = -0.985550987033 : (1.014603499582614, 0.0007461840240079051, 0.0002533339232295049, 1.0170721630214161, -3.4928416708932115, -2.688790851149103)
1 = -1.01373117078 : (1.0141361231431056, 0.0005367531420921612, -0.00046908647321873803, 1.0165434919136838, -3.6197601747022823, -3.004031543718616)
2 = -1.02983463706 : (1.0136955252793358, 0.00037825026803270996, -0.0009794220897758749, 1.016030914727364, -3.7068443485190485, -3.2151089373342105)
3 = -1.04169390344 : (1.013339179493782, 0.0002994325260843336, -0.0013143246211425148, 1.015556770059542, -3.75366227423545, -3.3526908235975648)
4 = -1.04949687668 : (1.0130366816673142, 0.0002646835637823627, -0.0015642561834431534, 1.0150799325942717, -3.7764913065895627, -3.4544026289285674)
5 = -1.05598585506 : (1.0127684121235436, 0.00024734649061878416, -0.0017790731482952358, 1.0145979407686183, -3.788674986399387, -3.540460686872105)
6 = -1.06246477667 : (1.0125202930073331, 0.0002361052495160277, -0.0019662498255209647, 1.0141253358557178, -3.795121699835497, -3.6134131974765373)
7 = -1.06671543168 : (1.0122854811010944, 0.00023327646083985633, -0.0021010715464759395, 1.0136910825314884, -3.798196005834545, -3.665604182725503)
8 = -1.07044160771 : (1.0120692310933854, 0.0002420018143017984, -0.0021931317154121077, 1.0132937521265202, -3.796750796882008, -3.7010888922795635)
9 = -1.07344186533 : (1.0118767378218096, 0.00026444718725120793, -0.0022358286460006454, 1.0129459124426432, -3.790061454333224, -3.7180095922556355)
10 = -1.07600224066 : (1.0117111035040862, 0.0003034075848847032, -0.0022333965881730384, 1.0126447751229186, -3.7782337017410073, -3.718809923686744)
11 = -1.07872181954 : (1.0115553906358783, 0.0003471864462561851, -0.002200233370663974, 1.0123771881696213, -3.764860886900759, -3.707789586554322)
12 = -1.08048956754 : (1.0114103134488623, 0.0003953507394534954, -0.0021493584957921097, 1.012131721441696, -3.7497037826448985, -3.690133946535888)
13 = -1.08278646675 : (1.0112671055665372, 0.0004394391998170347, -0.0020908899391369326, 1.011896870585595, -3.73610961623267, -3.6691448383061553)
14 = -1.08495888291 : (1.0111279025617221, 0.0004816691675849786, -0.002029298080310803, 1.011668589149825, -3.723056901180155, -3.646332455349077)
15 = -1.08653189569 : (1.0109982367519024, 0.0005271728157721302, -0.0019609431668683097, 1.0114528784323855, -3.708432203183168, -3.620538895159252)
16 = -1.08874587821 : (1.0108704794417576, 0.0005696201814689708, -0.001892689425314333, 1.0112395073623441, -3.6946660106842693, -3.594604595274264)
17 = -1.09037655736 : (1.0107465736083092, 0.0006116196815976291, -0.001827290440124144, 1.0110284064134405, -3.6807131608540877, -3.5693164722024937)
18 = -1.09212934458 : (1.0106257589040357, 0.0006509275608681616, -0.0017627928260437922, 1.0108199306243542, -3.6671129868974957, -3.5436754768509755)
19 = -1.09358907896 : (1.0105065459123856, 0.0006895459045247417, -0.001698477894907288, 1.0106130955225978, -3.6538212048987293, -3.518051118762954)
20 = -1.09532794911 : (1.0103950806776425, 0.0007284010061881244, -0.0016401120642212837, 1.0104068227851455, -3.6393747031052515, -3.4940728760842004)
21 = -1.09735952681 : (1.0102828435942128, 0.0007632016720794855, -0.0015791998305722667, 1.0102065474465967, -3.626881223814969, -3.4691468675311805)
22 = -1.09886889225 : (1.0101736224169982, 0.0007959111716403375, -0.0015214331098664506, 1.0100089500139473, -3.6150057070071107, -3.445382642731656)
23 = -1.10051387367 : (1.0100652784907092, 0.0008247942612837684, -0.0014615305615338257, 1.0098177781300541, -3.6046889576466468, -3.4204816614202187)
24 = -1.10227543919 : (1.009960421287008, 0.000854141305394737, -0.0014014873963602026, 1.00962840526342, -3.594165042213473, -3.3958792898224184)
25 = -1.10432551342 : (1.0098601418135706, 0.0008831251567019027, -0.0013474515591161789, 1.009440772693651, -3.5831900116467703, -3.3731018686515855)
26 = -1.10563798564 : (1.0097628824646887, 0.0009112187519863535, -0.0012923902659593561, 1.0092585671720111, -3.5726073043344457, -3.3497863451126353)
27 = -1.10714859768 : (1.009666915196504, 0.000935363861484168, -0.001234517300662787, 1.0090838507927777, -3.563406261594177, -3.324923665596079)
28 = -1.10866164447 : (1.0095764524223088, 0.0009603720090716294, -0.0011807619421160434, 1.0089095852524383, -3.5532112649536756, -3.301332262791078)
29 = -1.10975646061 : (1.0094900669114133, 0.0009824519922688314, -0.0011270507173137421, 1.0087425535688612, -3.5439205940220533, -3.2775854953833816)
30 = -1.1110466006 : (1.0094071701396514, 0.0010035801960676092, -0.0010803768709552468, 1.0085758945463514, -3.534806841107086, -3.2564339948594574)
31 = -1.11212457497 : (1.0093273167736951, 0.001019164026137415, -0.0010370875009040196, 1.00841302460725, -3.5273942299640155, -3.236148473440019)
32 = -1.11351223499 : (1.0092511479715829, 0.0010350148406201754, -0.0009967340621406218, 1.0082533486021497, -3.5195758137613216, -3.216766712471285)
33 = -1.11465916251 : (1.0091789397833582, 0.0010499578429859662, -0.0009578765275080618, 1.0080970212145763, -3.5118935195245915, -3.1978095684446064)
34 = -1.11569247761 : (1.0091108888068379, 0.0010649262861370228, -0.0009181203415457627, 1.007948940900301, -3.5038191275375894, -3.1781673290490255)
35 = -1.11671937657 : (1.0090495173688045, 0.0010798941901803089, -0.0008843453978717746, 1.0078028532371424, -3.4945955263530073, -3.1601227253471778)
36 = -1.11753031109 : (1.0089897927693985, 0.001091816678454856, -0.0008545424578665636, 1.0076600879953042, -3.486064666198401, -3.143334058828238)
37 = -1.11834505927 : (1.008931152093632, 0.0011002172428298163, -0.0008264319060904853, 1.0075222458805029, -3.4786380617902704, -3.126811510121316)
38 = -1.11928500746 : (1.008877578190236, 0.001108554023203648, -0.000801694172034446, 1.0073876180777135, -3.470495327343511, -3.1111838742525544)
39 = -1.12032847796 : (1.0088248392822243, 0.0011154608647186174, -0.0007811322498720746, 1.0072563432017962, -3.4628737984928764, -3.0970911783514206)
40 = -1.12132970898 : (1.0087732836673, 0.0011211404502793332, -0.0007583575625983576, 1.0071329077021745, -3.4556981151526274, -3.082100400583568)
41 = -1.1224463894 : (1.0087237469510741, 0.0011248705611062498, -0.0007403250026405327, 1.0070116119761454, -3.4489594609675263, -3.0690758467752692)
42 = -1.12327620328 : (1.0086770102874825, 0.0011283817721536489, -0.0007201636805996188, 1.0068976797247309, -3.4421122496387215, -3.0549861326110666)
43 = -1.12398659151 : (1.0086324561114446, 0.0011293930428057913, -0.0007011990937314759, 1.0067876707388106, -3.4360833889959705, -3.0410827785722905)
44 = -1.12480621886 : (1.0085908710420266, 0.0011295383556216788, -0.0006829313316562922, 1.0066818564334212, -3.4300020114017062, -3.0272217889390043)
45 = -1.12535579987 : (1.0085537944749645, 0.0011288268578695916, -0.0006693789910430166, 1.0065782934100729, -3.4237198767614565, -3.014758973438355)
46 = -1.12583131529 : (1.0085173650236325, 0.0011267162533403247, -0.0006581305224914342, 1.0064782717497305, -3.4182857744841866, -3.003461754655479)
47 = -1.12632070983 : (1.0084839197408497, 0.0011234105854597222, -0.0006471296471444194, 1.0063832261241865, -3.4130461533217518, -2.9918543563344517)
48 = -1.12701413478 : (1.0084517323980855, 0.0011196037844507303, -0.0006373889041429389, 1.0062915016918712, -3.408062900796358, -2.9808303311513398)
49 = -1.12758795882 : (1.0084224317073258, 0.0011164909983984016, -0.0006272533289949962, 1.006204033089255, -3.4028654057860073, -2.9696970339920354)
50 = -1.12798674034 : (1.008399123432636, 0.00111469227210086, -0.0006186729464159868, 1.006120533295076, -3.396736954245867, -2.9591771601118935)
51 = -1.12874789861 : (1.0083720194599606, 0.0011102569839689324, -0.0006098526015789166, 1.006042065511567, -3.3921510682428484, -2.948629336944313)
52 = -1.12924470213 : (1.0083531351473234, 0.0011086168605516633, -0.0006016358871479135, 1.0059683957862422, -3.385980388565679, -2.938218047906304)
53 = -1.12963144069 : (1.008327505547565, 0.001101083715881661, -0.0005950459721642004, 1.0058972266687407, -3.3824095976088095, -2.9281986517433007)
54 = -1.1300549325 : (1.008309633208647, 0.0010958225671934686, -0.0005867120492488811, 1.0058339289394722, -3.377217729514844, -2.917224072495087)
55 = -1.13040309535 : (1.0082889645062738, 0.0010862951984740592, -0.0005824162008949224, 1.0057707920359436, -3.3740512816841792, -2.9078664665889717)
56 = -1.13094222304 : (1.0082733185384232, 0.00107689568969158, -0.0005794675130369823, 1.0057123175848066, -3.3703848324072814, -2.8987081062935047)
57 = -1.13125928251 : (1.0082584047842342, 0.0010674776683569631, -0.0005794475700226954, 1.0056548067449709, -3.366930992324171, -2.8908935598087493)
58 = -1.13157910855 : (1.008244504002517, 0.001058016649923464, -0.0005797370990805699, 1.005599811238326, -3.3634342246705016, -2.883195655031366)
59 = -1.13197023839 : (1.0082312620459877, 0.0010481846105166474, -0.0005806078063295836, 1.0055471275744539, -3.360036537449387, -2.8757605496569765)
60 = -1.13221349954 : (1.008218969968452, 0.0010382339075716647, -0.0005821452596088955, 1.0054971088935691, -3.3566839937882564, -2.8685483479819283)
61 = -1.13276698567 : (1.0082074517072313, 0.0010281346998858125, -0.0005818260487941331, 1.0054527259150938, -3.3533543577038034, -2.8606021205308165)
62 = -1.13301501404 : (1.0081965500705288, 0.001016998381063848, -0.0005835274965666451, 1.005409718633114, -3.3502570334219173, -2.8534365191703497)
63 = -1.13323157002 : (1.0081862616120816, 0.001005939983477601, -0.0005871804997891048, 1.0053676269012837, -3.3473502933574557, -2.8472130680635486)
64 = -1.13350156309 : (1.0081768225673302, 0.0009949885523714936, -0.0005909581510539424, 1.0053277190282937, -3.344425641019781, -2.8410987297002155)
65 = -1.13374933864 : (1.0081677837802838, 0.0009839889346372889, -0.0005951459488805827, 1.005289563181011, -3.3416011012252227, -2.8352038231374084)
66 = -1.1338225573 : (1.0081596644120978, 0.0009732071567743937, -0.0005988838650325824, 1.0052538866983691, -3.338712504905382, -2.8292521597987994)
67 = -1.13405870722 : (1.0081518679965606, 0.0009622828006366109, -0.0006033116188648767, 1.0052194235765577, -3.3359953298885765, -2.823653966855128)
68 = -1.13432534043 : (1.008144686534364, 0.0009514632276042053, -0.0006082231205196465, 1.0051862983167068, -3.3332635216687225, -2.818299973317974)
69 = -1.13452192911 : (1.0081382429656256, 0.0009405823032705652, -0.000615252407203665, 1.0051539941212515, -3.330505258890169, -2.813810446279323)
70 = -1.13460109104 : (1.0081334442975842, 0.0009309122368635864, -0.0006201458841036553, 1.0051250017713775, -3.3274629923710535, -2.8086391458249413)
71 = -1.13474577499 : (1.0081278612168079, 0.0009205400085914224, -0.000625901120933527, 1.0050970118329967, -3.3250383871727447, -2.8040192241137114)
72 = -1.13482491629 : (1.0081196088925335, 0.0009090788235200564, -0.0006315715967693253, 1.0050703742696676, -3.323384058229597, -2.7994422844157345)
73 = -1.13487387154 : (1.0081161917757464, 0.0008998807899066476, -0.0006379327761178194, 1.0050445359377884, -3.3205532640959348, -2.7952301741508174)
74 = -1.13494508831 : (1.008109152860814, 0.0008889455369557061, -0.0006421252990829975, 1.0050227691436067, -3.3188780935000044, -2.790229509946336)
75 = -1.13502445087 : (1.0081105956690666, 0.0008814439550381903, -0.0006514057840356258, 1.0049995014339999, -3.3150381192001577, -2.786957879794315)
76 = -1.13512669654 : (1.0081016782817507, 0.000869126157719711, -0.0006557981106430423, 1.0049796696420519, -3.3143152208303235, -2.7821924948586)
77 = -1.13522662868 : (1.0080980682993586, 0.0008598868821980241, -0.0006657934223715799, 1.004958215076145, -3.3119784639874235, -2.7796463937553852)
78 = -1.13523461465 : (1.0080935917274445, 0.000850053163368352, -0.0006733267322488057, 1.0049396863023923, -3.310137411027122, -2.7762294185778167)
79 = -1.13525960469 : (1.0080893897908574, 0.0008405024639740907, -0.0006807647096442929, 1.0049220622303205, -3.3083247598229613, -2.7728940657926864)
80 = -1.1352792903 : (1.0080856354396772, 0.0008312301606087092, -0.0006882347802324935, 1.0049052710012596, -3.306482764814274, -2.769665880333412)
81 = -1.13532306493 : (1.0080826415958366, 0.0008224509781122986, -0.0006951072563897675, 1.004890105658332, -3.304529591209647, -2.7662703521452543)
82 = -1.13535552246 : (1.0080794944738836, 0.0008136204571204708, -0.0007025161999213225, 1.0048751402651652, -3.3027091567282936, -2.7632056881881772)
83 = -1.13553705947 : (1.0080764839707856, 0.0008048891329168497, -0.0007100025071430426, 1.004860835670534, -3.300941591977117, -2.7602595364760845)
84 = -1.1356515078 : (1.008073815288481, 0.0007965097711482614, -0.0007173276377515092, 1.0048472996212596, -3.2991412910975804, -2.7573746156262513)
85 = -1.1357058815 : (1.0080709764335316, 0.0007880643937493633, -0.0007246686798237682, 1.0048343220004754, -3.297523284875114, -2.754664820313507)
86 = -1.13579625305 : (1.0080684854561826, 0.0007799376628074716, -0.0007315645319327497, 1.004822308651584, -3.2958847527889046, -2.7519167982722283)
87 = -1.13590630781 : (1.0080660058674888, 0.0007719680524483366, -0.0007386436126537735, 1.0048106156444088, -3.2942638937578343, -2.749358176401729)
88 = -1.13592887893 : (1.0080634307569758, 0.0007640843055661675, -0.0007457784250227387, 1.0047993294743627, -3.2927101756043164, -2.7469905168334283)
89 = -1.13602709021 : (1.0080607526314125, 0.0007562507769587839, -0.0007526286518193212, 1.0047887011697432, -3.2912429339889506, -2.7446125483917014)
90 = -1.13606255886 : (1.0080583107887222, 0.0007485775246820659, -0.0007594852128925382, 1.0047785924124435, -3.2897920452945053, -2.7423192780330004)
91 = -1.13606610803 : (1.008055978312489, 0.0007410461622149799, -0.0007662995581584752, 1.0047689523955416, -3.2883806545434386, -2.7401003473405443)
92 = -1.13607018469 : (1.0080537602986819, 0.0007336484411235432, -0.000773090517998279, 1.0047597483029047, -3.2870094361668043, -2.7379617994143217)
93 = -1.13611948047 : (1.0080517495313734, 0.0007264571283569426, -0.000779778433479113, 1.0047510464961202, -3.2856338060503023, -2.7358633070462512)
94 = -1.13621633248 : (1.0080496746735346, 0.0007193457598642748, -0.0007864526929322012, 1.004742668580334, -3.284320808610672, -2.733844530104281)
95 = -1.13619997861 : (1.0080485249550173, 0.0007130077276182975, -0.0007929480121355259, 1.0047347652789929, -3.282830535833912, -2.7318580348598114)
96 = -1.13620226659 : (1.0080469710414182, 0.0007064287467312154, -0.0007994016803275321, 1.0047272416002668, -3.281570084839807, -2.7299432127210776)
97 = -1.13622954047 : (1.008045452471131, 0.000699928428431818, -0.0008059745978232396, 1.004720050148043, -3.280382549361917, -2.7281311267010646)
98 = -1.13624950741 : (1.0080435933984355, 0.0006929549000765748, -0.0008104846763179542, 1.0047165135894816, -3.279385275885602, -2.7254241019622722)
99 = -1.13636760802 : (1.0080427117423614, 0.0006871394683149913, -0.0008191414197049495, 1.0047080266979547, -3.2779896299694506, -2.724613218284918)
-------
AffineTransform (0x7fcd55f7b1a0)
  RTTI typeinfo:   itk::AffineTransform<double, 2u>
  Reference Count: 4
  Modified Time: 209559
  Debug: Off
  Object Name: 
  Observers: 
    none
  Matrix: 
    1.00804 0.000687139 
    -0.000819141 1.00471 
  Offset: [-3.27799, -2.72461]
  Center: [0, 0]
  Translation: [-3.27799, -2.72461]
  Inverse: 
    0.992021 -0.000678462 
    0.000808798 0.995313 
  Singular: 0

Optimizer stop condition: GradientDescentOptimizerv4Template: Maximum number of iterations (100) exceeded.
 Iteration: 100
 Metric value: -1.13636760802

















In [7]:



    


cshow(fixed,moving,ctx)



    


















    






<bound method ResampleImageFilter.GetTransform of <SimpleITK.SimpleITK.ResampleImageFilter; proxy of <Swig Object of type 'itk::simple::ResampleImageFilter::Self *' at 0x1147f69f0> >>










    
























In [8]:



    


# Define the second stage as BSpline transform
BSplineOrder=3
# Set fixed parameters of the BSpline transform using transform initializer
transfromDomainMeshSize=[8-BSplineOrder, 8-BSplineOrder, 8-BSplineOrder]
tx2 = sitk.BSplineTransformInitializer(fixed, transfromDomainMeshSize, BSplineOrder )



    











In [9]:



    


ctx.AddTransform(tx2)
ctx.SetFixedParameters(ctx.GetFixedParameters())
R.SetInitialTransform(ctx)
R.SetOptimizerAsLBFGSB(gradientConvergenceTolerance=1e-7,
                       maximumNumberOfIterations=1500,
                       maximumNumberOfCorrections=20,
                       maximumNumberOfFunctionEvaluations=1000,
                       costFunctionConvergenceFactor=1e+9)
R.SetShrinkFactorsPerLevel([1])
R.SetSmoothingSigmasPerLevel([0])

R.RemoveAllCommands()
R.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration_bsplineAndDisplacment(R) )
BSplineOut = R.Execute(fixed,moving)

print("-------")
print(BSplineOut)
print("Optimizer stop condition: {0}".format(R.GetOptimizerStopConditionDescription()))
print(" Iteration: {0}".format(R.GetOptimizerIteration()))
print(" Metric value: {0}".format(R.GetMetricValue()))



    


















    






0 = -1.04603917675
0 = -1.04371626548
0 = -1.04577664708
0 = -1.04607858563
0 = -1.04605206261
0 = -1.04602736535
0 = -1.04608925891
0 = -1.04605627473
0 = -1.04609962603
0 = -1.04608399823
0 = -1.04608735236
0 = -1.04609962603
0 = -1.04609962603
1 = -1.0445528398
1 = -1.05176661338
1 = -1.05176661338
2 = -1.0413135489
2 = -1.05681624198
2 = -1.05681624198
3 = -1.0372967253
3 = -1.06554470136
3 = -1.06554470136
4 = -0.987589818665
4 = -1.05621473339
4 = -1.06422939769
4 = -1.06532330849
4 = -1.06552095558
4 = -1.06556651001
4 = -1.06555914402
4 = -1.06555438331
4 = -1.06556651001
4 = -1.06555438331
4 = -1.06556651001
4 = -1.06556064375
4 = -1.06556651001
4 = -1.06556651001
4 = -1.06556651001
4 = -1.06556651001
5 = -0.904351177742
5 = -1.04646850796
5 = -1.06296139858
5 = -1.06517770164
5 = -1.06545129225
5 = -1.06555261228
5 = -1.06555438331
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06556651001
5 = -1.06568126679
5 = -1.06606724311
5 = -1.06762112666
5 = -1.06762112666
6 = -1.09120304917
6 = -1.09120304917
7 = -1.10765437199
7 = -1.10472360544
7 = -1.10472360544
8 = -1.10921506278
8 = -1.10921506278
9 = -1.11110803057
9 = -1.11110803057
10 = -1.11377391516
10 = -1.11377391516
11 = -1.11151440125
11 = -1.11297806722
11 = -1.11375131409
11 = -1.11387564473
11 = -1.1139163118
11 = -1.11380142867
11 = -1.11386527942
11 = -1.1139163118
11 = -1.11389962074
11 = -1.1139163118
11 = -1.1139163118
12 = -1.10049177343
12 = -1.11293157027
12 = -1.11363398249
12 = -1.11363901831
12 = -1.11383321215
12 = -1.11390489705
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
12 = -1.1139163118
-------
CompositeTransform (0x7fcd5603d310)
  RTTI typeinfo:   itk::CompositeTransform<double, 2u>
  Reference Count: 4
  Modified Time: 209868
  Debug: Off
  Object Name: 
  Observers: 
    none
  Transforms in queue, from begin to end:
  >>>>>>>>>
  AffineTransform (0x7fcd55cf8590)
    RTTI typeinfo:   itk::AffineTransform<double, 2u>
    Reference Count: 1
    Modified Time: 209862
    Debug: Off
    Object Name: 
    Observers: 
      none
    Matrix: 
      1.00804 0.000687139 
      -0.000819141 1.00471 
    Offset: [-3.27799, -2.72461]
    Center: [0, 0]
    Translation: [-3.27799, -2.72461]
    Inverse: 
      0.992021 -0.000678462 
      0.000808798 0.995313 
    Singular: 0
  >>>>>>>>>
  BSplineTransform (0x7fcd560d0f30)
    RTTI typeinfo:   itk::BSplineTransform<double, 2u, 3u>
    Reference Count: 3
    Modified Time: 342334
    Debug: Off
    Object Name: 
    Observers: 
      none
    CoefficientImage: [ 0x7fcd560b58e0, 0x7fcd560d7140 ]
    TransformDomainOrigin: [-0.625, -0.625]
    TransformDomainPhysicalDimensions: [221.25, 257.25]
    TransformDomainDirection: 1 0
0 1

    GridSize: [8, 8]
    GridOrigin: [-44.875, -52.075]
    GridSpacing: [44.25, 51.45]
    GridDirection: 1 0
0 1

  End of MultiTransform.
<<<<<<<<<<
  TransformsToOptimizeFlags, begin() to end(): 
    0 1 
  TransformsToOptimize in queue, from begin to end:
  >>>>>>>>>
  BSplineTransform (0x7fcd560d0f30)
    RTTI typeinfo:   itk::BSplineTransform<double, 2u, 3u>
    Reference Count: 3
    Modified Time: 342334
    Debug: Off
    Object Name: 
    Observers: 
      none
    CoefficientImage: [ 0x7fcd560b58e0, 0x7fcd560d7140 ]
    TransformDomainOrigin: [-0.625, -0.625]
    TransformDomainPhysicalDimensions: [221.25, 257.25]
    TransformDomainDirection: 1 0
0 1

    GridSize: [8, 8]
    GridOrigin: [-44.875, -52.075]
    GridSpacing: [44.25, 51.45]
    GridDirection: 1 0
0 1

  End of TransformsToOptimizeQueue.
<<<<<<<<<<
  End of CompositeTransform.
<<<<<<<<<<

Optimizer stop condition: LBFGSBOptimizerv4: Function tolerance reached after 13 iterations. The relative reduction of the cost function <= 2.22045e-07 = CostFunctionConvergenceFactor (1e+09) * machine precision (2.22045e-16).
 Iteration: 13
 Metric value: -1.1139163118

















In [10]:



    


cshow(fixed,moving,ctx)



    


















    






<bound method ResampleImageFilter.GetTransform of <SimpleITK.SimpleITK.ResampleImageFilter; proxy of <Swig Object of type 'itk::simple::ResampleImageFilter::Self *' at 0x11481f690> >>










    
























In [11]:



    


rescaled_fixed, deformed_rescaled_moving = prepare_resampled_values( fixed, moving, ctx)
ck = sitk.CheckerBoardImageFilter()

ckOutput = ck.Execute(fixed, moving,[10,10])
myshow(ckOutput, title="checkerboard result before registration",dpi=60)

ckOutput2 = ck.Execute(rescaled_fixed, deformed_rescaled_moving,[10,10])
myshow(ckOutput2, title="checkerboard result after registration",dpi=60)



    


















    






<bound method ResampleImageFilter.GetTransform of <SimpleITK.SimpleITK.ResampleImageFilter; proxy of <Swig Object of type 'itk::simple::ResampleImageFilter::Self *' at 0x106438540> >>










    

















    
























In [11]:

Content source: aghayoor/SimpleITK-Notebook-Answers

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