3 d!@sdZddljZddlZddlmZddlmZddlm Z m Z m Z m Z m Z ejd ZGd d d eZGd d d e ZGddde ZGdddeZGddde ZGddde ZGdddeZGddde ZGdddeZGdddeZGddde ZGd d!d!e ZdS)"zo Interfaces to perform image registrations and to apply the resulting displacement maps to images and points. N)logging)ElastixBaseInputSpec) CommandLine TraitedSpecFiletraitsInputMultiPathznipype.interfacec@sleZdZedddddZedddddZeeddddd d Zedd d d Zedddd Z edddd Z dS)RegistrationInputSpecTz-f %sz fixed image)exists mandatoryargstrdescz-m %sz moving image)r z-p %s...z,parameter file, elastix handles 1 or more -p)rrrz -fMask %szmask for fixed image)r rrz -mMask %szmask for moving imagez-t0 %sz$parameter file for initial transformN) __name__ __module__ __qualname__r Z fixed_image moving_imager parametersZ fixed_maskZ moving_maskZinitial_transformrrH/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/elastix/registration.pyr sr c@sNeZdZeeddddZeddZeeddddZej ej dddZ d S) RegistrationOutputSpecT)r zoutput transform)rz(input moving image warped to fixed imageFz6input moving image warped to fixed image at each levelz-flag indicating if warped image was generatedN) rrrr r transform warped_file warped_filesr ListZBoolwarped_files_flagsrrrrr&s rc@s,eZdZdZdZeZeZddZ ddZ dS) Registrationa Elastix nonlinear registration interface Example ------- >>> from nipype.interfaces.elastix import Registration >>> reg = Registration() >>> reg.inputs.fixed_image = 'fixed1.nii' >>> reg.inputs.moving_image = 'moving1.nii' >>> reg.inputs.parameters = ['elastix.txt'] >>> reg.cmdline 'elastix -f fixed1.nii -m moving1.nii -threads 1 -out ./ -p elastix.txt' Zelastixc CsP|jj}tj|jj}tjd}g|d<g|d<g|d<xt|jj D]\}}i}t |dd}x\|j D]P}|j }|j d rl|rl|j|} | rl|j| jdj } | || jdj <qlWWdQRX|djtj|d |d} |d r tj|d ||d f} |dj| |dj|d qJW|ddrL|dd|d <|S)Nz^\((\w+)\s(.+)\)$rrrrz//rrzTransformParameters.%01d.txtZWriteResultImagezresult.%01d.%sZResultImageFormatrr )_outputsgetopabspathinputs output_pathrecompile enumerateropen readlinesstrip startswithsearch_castgroupappendjoin) selfoutputsout_dirregexiparamsconfigflinemvaluerrrr _list_outputsHs6      zRegistration._list_outputscCsx|jdr8|jdr8|dkr dS|dkr,dS|ddSyt|Stk rryt|Stk rl|SXYnXdS)N"z"true"Tz"false"Frr )r-endswithint ValueErrorfloat)r3valrrrr/qs zRegistration._castN) rrr__doc___cmdr input_specr output_specr>r/rrrrr2s )rc@s,eZdZedddddZedddddZdS) ApplyWarpInputSpecTz-tp %sz transform-parameter file, only 1)r rrrz-in %szinput image to deform)r rrrN)rrrr transform_filerrrrrrIsrIc@seZdZeddZdS)ApplyWarpOutputSpecz(input moving image warped to fixed image)rN)rrrr rrrrrrKsrKc@s$eZdZdZdZeZeZddZ dS) ApplyWarpa Use ``transformix`` to apply a transform on an input image. The transform is specified in the transform-parameter file. Example ------- >>> from nipype.interfaces.elastix import ApplyWarp >>> reg = ApplyWarp() >>> reg.inputs.moving_image = 'moving1.nii' >>> reg.inputs.transform_file = 'TransformParameters.0.txt' >>> reg.cmdline 'transformix -in moving1.nii -threads 1 -out ./ -tp TransformParameters.0.txt' transformixcCs.|jj}tj|jj}tj|d|d<|S)Nz result.nii.gzr)r!r"r#r$r%r&r2)r3r4r5rrrr>s zApplyWarp._list_outputsN) rrrrErFrIrGrKrHr>rrrrrLs rLc@sReZdZejddddddZejddddd Zejddd d d Zedd d dZ dS)AnalyzeWarpInputSpecallTrz-def %sz[transform all points from the input-image, which effectively generates a deformation field.) usedefaultpositionrrz-jac %sz>generate an image with the determinant of the spatial Jacobian)rPrrz -jacmat %sz@generate an image with the spatial Jacobian matrix at each voxelz-in %sz input image to deform (not used))r rrN) rrrr EnumZpointsZjacZjacmatr rrrrrrNs$rNc@s*eZdZeddZeddZeddZdS)AnalyzeWarpOutputSpeczdisplacements field)rzdet(Jacobian) mapzJacobian matrix mapN)rrrr disp_field jacdet_map jacmat_maprrrrrSs  rSc@s eZdZdZeZeZddZdS) AnalyzeWarpa Use transformix to get details from the input transform (generate the corresponding deformation field, generate the determinant of the Jacobian map or the Jacobian map itself) Example ------- >>> from nipype.interfaces.elastix import AnalyzeWarp >>> reg = AnalyzeWarp() >>> reg.inputs.transform_file = 'TransformParameters.0.txt' >>> reg.cmdline 'transformix -def all -jac all -jacmat all -threads 1 -out ./ -tp TransformParameters.0.txt' cCsN|jj}tj|jj}tj|d|d<tj|d|d<tj|d|d<|S)NzdeformationField.nii.gzrTzspatialJacobian.nii.gzrUzfullSpatialJacobian.nii.gzrV)r!r"r#r$r%r&r2)r3r4r5rrrr>s  zAnalyzeWarp._list_outputsN) rrrrErNrGrSrHr>rrrrrWsrWc@s,eZdZedddddZedddddZdS) PointsWarpInputSpecTz-def %sz.input points (accepts .vtk triangular meshes).)r rrrz-tp %sz transform-parameter file, only 1)r rrrN)rrrr points_filerJrrrrrXsrXc@seZdZeddZdS)PointsWarpOutputSpecz,input points displaced in fixed image domain)rN)rrrr rrrrrrZsrZc@s$eZdZdZdZeZeZddZ dS) PointsWarpaUse ``transformix`` to apply a transform on an input point set. The transform is specified in the transform-parameter file. Example ------- >>> from nipype.interfaces.elastix import PointsWarp >>> reg = PointsWarp() >>> reg.inputs.points_file = 'surf1.vtk' >>> reg.inputs.transform_file = 'TransformParameters.0.txt' >>> reg.cmdline 'transformix -threads 1 -out ./ -def surf1.vtk -tp TransformParameters.0.txt' rMcCsJ|jj}tj|jj}tjtj|jj\}}tj |d||d<|S)Nzoutputpoints%sr) r!r"r#r$r%r&splitextbasenamerYr2)r3r4r5fnameextrrrr>s  zPointsWarp._list_outputsN) rrrrErFrXrGrZrHr>rrrrr[s r[)rEos.pathpathr#r'rbaserrrr r r getLoggerZifloggerr rrrIrKrLrNrSrWrXrZr[rrrr s$     Q