3 XdN[@sdZddlZddlmZmZddlmZmZmZmZm Z ddl m Z Gd d d eZ Gd d d eZ Gd ddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdd d eZdS)!z ANTS Apply Transforms interface N) ANTSCommandANTSCommandInputSpec) TraitedSpecFiletraits isdefinedInputMultiObject)split_filenamec@seZdZejdddddddZedddd d Zejd ddd d Z eddgddZ ej dddgdZ ej dddZ ej dddZej dddZeeddddddd Zejejd!d"Zd#S)$*WarpTimeSeriesImageMultiTransformInputSpecr z%dTzimage dimension (3 or 4)r)argstr usedefaultdescpositionz%szFimage to apply transformation to (generally a coregistered functional))r mandatorycopyfilerZ_wtsimtzAPostfix that is prepended to all output files (default = _wtsimt))rrrz-R %s tightest_boxz0reference image space that you wish to warp INTO)rxorrz--tightest-bounding-boxzFcomputes tightest bounding box (overrided by reference_image if given)reference_image)rrrz--reslice-by-headerzxUses orientation matrix and origin encoded in reference image file header. Not typically used with additional transforms)rrz--use-NNz"Use nearest neighbor interpolationz --use-Bsplinez$Use 3rd order B-Spline interpolation)existsz$transformation file(s) to be appliedF)rrrra+List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word "affine" included in their filenames.)rN)__name__ __module__ __qualname__rEnum dimensionr input_imageStr out_postfixrBoolrreslice_by_header use_nearest use_bspliner transformation_seriesListInt invert_affiner)r)S/var/www/html/virt/lib/python3.6/site-packages/nipype/interfaces/ants/resampling.pyr sH   r c@seZdZedddZdS)+WarpTimeSeriesImageMultiTransformOutputSpecTz Warped image)rrN)rrrr output_imager)r)r)r*r+Ksr+csFeZdZdZdZeZeZfddZ ddZ dgffdd Z Z S) !WarpTimeSeriesImageMultiTransforma+Warps a time-series from one space to another Examples -------- >>> from nipype.interfaces.ants import WarpTimeSeriesImageMultiTransform >>> wtsimt = WarpTimeSeriesImageMultiTransform() >>> wtsimt.inputs.input_image = 'resting.nii' >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz' >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt'] >>> wtsimt.cmdline 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt' >>> wtsimt = WarpTimeSeriesImageMultiTransform() >>> wtsimt.inputs.input_image = 'resting.nii' >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz' >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt'] >>> wtsimt.inputs.invert_affine = [1] # # this will invert the 1st Affine file: ants_Affine.txt >>> wtsimt.cmdline 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz -i ants_Affine.txt' c s|dkr.ttjj|jj\}}}|||S|dkrg}d}g} xR|D]J} d| krt|jjr|d7}||jjkr|dg7}| j||| g7}qHWt|jjrt |jjt | } | rt ddj |St t |j|||S) Nr r%rZAffinerz-izqReview invert_affine, not all indexes from invert_affine were used, check the description for the full definition )r ospathabspathinputsrr r(appendset Exceptionsjoinsuperr- _format_arg) selfoptspecval_nameextseriesaffine_counter affine_inverttransformationdiff_inv) __class__r)r*r8ls,        z-WarpTimeSeriesImageMultiTransform._format_argcCsP|jj}ttjj|jj\}}}tjjtj dj||jj |f|d<|S)Nr,) _outputsgetr r/r0r1r2rr6getcwdr )r9outputsr=r>r?r)r)r* _list_outputss   z/WarpTimeSeriesImageMultiTransform._list_outputsrcs0tt|j|ddgd}d|jkr,|j||S)Nrr)correct_return_codesz100 % complete)r7r-_run_interfacestdoutZraise_exception)r9ZruntimerL)rEr)r*rMs    z0WarpTimeSeriesImageMultiTransform._run_interface) rrr__doc___cmdr input_specr+ output_specr8rKrM __classcell__r)r))rEr*r-Os r-c@seZdZejdddddddZeddd dd Zedd dd dd gdZeddd ddgdZ eddgddZ ej dddgdZ ej dddZ ej dddZej d d!dZeedd"dd#dd(d$Zejejd%d&Zd'S)) WarpImageMultiTransformInputSpecr rz%dTzimage dimension (2 or 3)r)rrrrz%szFimage to apply transformation to (generally a coregistered functional))rrrrFzname of the output warped imager )genfile hash_filesrrrrZ_wimtz?Postfix that is prepended to all output files (default = _wimt)r,)rrVrrz-R %srz0reference image space that you wish to warp INTO)rrrz--tightest-bounding-boxzFcomputes tightest bounding box (overrided by reference_image if given)r)rrrz--reslice-by-headerzxUses orientation matrix and origin encoded in reference image file header. Not typically used with additional transforms)rrz--use-NNz"Use nearest neighbor interpolationz --use-BSplinez$Use 3rd order B-Spline interpolation)rz$transformation file(s) to be applied)rrrra+List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word "affine" included in their filenames.)rN)rrrrrrrrr,r rr!rr"r#r$r r%r&r'r(r)r)r)r*rTsX     rTc@seZdZedddZdS)!WarpImageMultiTransformOutputSpecTz Warped image)rrN)rrrrr,r)r)r)r*rXsrXcs<eZdZdZdZeZeZddZ fddZ ddZ Z S)WarpImageMultiTransformaWarps an image from one space to another Examples -------- >>> from nipype.interfaces.ants import WarpImageMultiTransform >>> wimt = WarpImageMultiTransform() >>> wimt.inputs.input_image = 'structural.nii' >>> wimt.inputs.reference_image = 'ants_deformed.nii.gz' >>> wimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt'] >>> wimt.cmdline 'WarpImageMultiTransform 3 structural.nii structural_wimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt' >>> wimt = WarpImageMultiTransform() >>> wimt.inputs.input_image = 'diffusion_weighted.nii' >>> wimt.inputs.reference_image = 'functional.nii' >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', 'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt'] >>> wimt.inputs.invert_affine = [1] # this will invert the 1st Affine file: 'func2anat_coreg_Affine.txt' >>> wimt.cmdline 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii -i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt' cCs:|dkr6ttjj|jj\}}}dj||jj|fSdS)Nr,rF)r r/r0r1r2rr6r )r9r>r=r?r)r)r* _gen_filenamesz%WarpImageMultiTransform._gen_filenamec s|dkrg}d}g}xV|D]N}d|jkr^t|jjr^|d7}||jjkr^|dg7}|j|||g7}qWt|jjrt|jjt|}|rtddj|Stt |j |||S)Nr%rZaffinerz-izqReview invert_affine, not all indexes from invert_affine were used, check the description for the full definitionr.) lowerr r2r(r3r4r5r6r7rYr8) r9r:r;r<r@rArBrCrD)rEr)r*r8 s&       z#WarpImageMultiTransform._format_argcCsH|jj}t|jjr.tjj|jj|d<ntjj|jd|d<|S)Nr,) rGrHr r2r,r/r0r1rZ)r9rJr)r)r*rK's   z%WarpImageMultiTransform._list_outputs) rrrrOrPrTrQrXrRrZr8rKrSr)r))rEr*rYs rYc @seZdZejddddddZejddddd d dZed d d d dZej ddd ddZ ej dd ddZ edd dd dZ ejddddddddd d!d d" Z ejejejejejejZeejed d#d$d!d d%d&ZeejZejd'd(d d"Zejdd)gd*d+Zejd,dd d-d.Zd/S)0ApplyTransformsInputSpecrr rz--dimensionality %dzThis option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image.)rrrrz--input-image-type %dz[Option specifying the input image type of scalar (default), vector, tensor, or time series.z --input %sTzFimage to apply transformation to (generally a coregistered functional))rrrrz --output %szoutput file nameF)rrrUrVZ_transz?Postfix that is appended to all output files (default = _trans))rrz--reference-image %sz0reference image space that you wish to warp INTOZLinearZNearestNeighborZCosineWindowedSincZWelchWindowedSincZHammingWindowedSincZLanczosWindowedSinc MultiLabelGaussianBSplinez%s)rr)ridentityzstransform files: will be applied in reverse order. For example, the last specified transform will be applied first.)rrrgz--default-value %gr,z;output a composite warp file instead of a transformed image)requiresrz --float %dz-Use float instead of double for computations.)r default_valuerrN)rrrrrrZinput_image_typerrrr,r r interpolationZEitherTupler'ZFloatinterpolation_parametersr transformsr!invert_transform_flagsrbprint_out_composite_warp_filefloatr)r)r)r*r\2sz  r\c@seZdZedddZdS)ApplyTransformsOutputSpecTz Warped image)rrN)rrrrr,r)r)r)r*rjsrjcsLeZdZdZdZeZeZddZ ddZ ddZ fd d Z d d Z ZS) ApplyTransformsa ApplyTransforms, applied to an input image, transforms it according to a reference image and a transform (or a set of transforms). Examples -------- >>> from nipype.interfaces.ants import ApplyTransforms >>> at = ApplyTransforms() >>> at.inputs.input_image = 'moving1.nii' >>> at.inputs.reference_image = 'fixed1.nii' >>> at.inputs.transforms = 'identity' >>> at.cmdline 'antsApplyTransforms --default-value 0 --float 0 --input moving1.nii --interpolation Linear --output moving1_trans.nii --reference-image fixed1.nii --transform identity' >>> at = ApplyTransforms() >>> at.inputs.dimension = 3 >>> at.inputs.input_image = 'moving1.nii' >>> at.inputs.reference_image = 'fixed1.nii' >>> at.inputs.output_image = 'deformed_moving1.nii' >>> at.inputs.interpolation = 'Linear' >>> at.inputs.default_value = 0 >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat'] >>> at.inputs.invert_transform_flags = [False, True] >>> at.cmdline 'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii --transform ants_Warp.nii.gz --transform [ trans.mat, 1 ]' >>> at1 = ApplyTransforms() >>> at1.inputs.dimension = 3 >>> at1.inputs.input_image = 'moving1.nii' >>> at1.inputs.reference_image = 'fixed1.nii' >>> at1.inputs.output_image = 'deformed_moving1.nii' >>> at1.inputs.interpolation = 'BSpline' >>> at1.inputs.interpolation_parameters = (5,) >>> at1.inputs.default_value = 0 >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat'] >>> at1.inputs.invert_transform_flags = [False, False] >>> at1.cmdline 'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii --transform ants_Warp.nii.gz --transform trans.mat' Identity transforms may be used as part of a chain: >>> at2 = ApplyTransforms() >>> at2.inputs.dimension = 3 >>> at2.inputs.input_image = 'moving1.nii' >>> at2.inputs.reference_image = 'fixed1.nii' >>> at2.inputs.output_image = 'deformed_moving1.nii' >>> at2.inputs.interpolation = 'BSpline' >>> at2.inputs.interpolation_parameters = (5,) >>> at2.inputs.default_value = 0 >>> at2.inputs.transforms = ['identity', 'ants_Warp.nii.gz', 'trans.mat'] >>> at2.cmdline 'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii --transform identity --transform ants_Warp.nii.gz --transform trans.mat' ZantsApplyTransformscCsB|dkr>|jj}t|s:t|jj\}}}||jj|}|SdS)Nr,)r2r,r r rr )r9r>outputr=r?r)r)r*rZszApplyTransforms._gen_filenamecCsg}|jj}t|s(dgt|jj}nt|jjt|krDtdxBt|jj|D]0\}}|rt|jd|dqT|jd|qTWdj|S)NFzcERROR: The invert_transform_flags list must have the same number of entries as the transforms list.z--transform [ z, 1 ]z --transform r.) r2rgr lenrf ValueErrorzipr3r6)r9retvalZ invert_flagsZ transforminvertr)r)r*_get_transform_filenamessz(ApplyTransforms._get_transform_filenamescCs8t|jjr&d|jdt|jjfSd|jdSdS)Nz--output [ %s, %d ]r,z --output %s)r r2rhrZint)r9r)r)r*_get_output_warped_filenames  z+ApplyTransforms._get_output_warped_filenamecs|dkr|jS|dkr |jS|dkrp|jjd krdt|jjrdd|jjdjd d |jjDfSd |jjStt|j |||S) Nr,rfrcr_r]r^z--interpolation %s[ %s ]z, cSsg|] }t|qSr))str).0paramr)r)r* sz/ApplyTransforms._format_arg..z--interpolation %s)r_r]r^) rtrrr2rcr rer6r7rkr8)r9r:r;r<)rEr)r*r8s   zApplyTransforms._format_argcCs&|jj}tjj|jd|d<|S)Nr,)rGrHr/r0r1rZ)r9rJr)r)r*rK s zApplyTransforms._list_outputs)rrrrOrPr\rQrjrRrZrrrtr8rKrSr)r))rEr*rks=  rkc@speZdZejddddddZeddd dd Zejd d d gdddZ ej eddddddZ ej ej ddZ dS) ApplyTransformsToPointsInputSpecrr rz--dimensionality %dzThis option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image.)rrz --input %sTaCurrently, the only input supported is a csv file with columns including x,y (2D), x,y,z (3D) or x,y,z,t,label (4D) column headers. The points should be defined in physical space. If in doubt how to convert coordinates from your files to the space required by antsApplyTransformsToPoints try creating/drawing a simple label volume with only one voxel set to 1 and all others set to 0. Write down the voxel coordinates. Then use ImageMaths LabelStats to find out what coordinates for this voxel antsApplyTransformsToPoints is expecting.)rrrrz --output %szName of the output CSV file input_fileFz%s_transformed.csv)rrZ name_sourcerVZ name_template)rz%sz-transforms that will be applied to the points)rrrz1list indicating if a transform should be reversed)rN)rrrrrrrrzr output_filer&rfr!rgr)r)r)r*rys0 ryc@seZdZedddZdS)!ApplyTransformsToPointsOutputSpecTz%csv file with transformed coordinates)rrN)rrrrr{r)r)r)r*r|?sr|cs4eZdZdZdZeZeZddZ fddZ Z S)ApplyTransformsToPointsaApplyTransformsToPoints, applied to an CSV file, transforms coordinates using provided transform (or a set of transforms). Examples -------- >>> from nipype.interfaces.ants import ApplyTransforms >>> at = ApplyTransformsToPoints() >>> at.inputs.dimension = 3 >>> at.inputs.input_file = 'moving.csv' >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz'] >>> at.inputs.invert_transform_flags = [False, False] >>> at.cmdline 'antsApplyTransformsToPoints --dimensionality 3 --input moving.csv --output moving_transformed.csv --transform [ trans.mat, 0 ] --transform [ ants_Warp.nii.gz, 0 ]' ZantsApplyTransformsToPointscCsg}xtt|jjD]x}t|jjrxt|jjt|jjkrn|jj|rNdnd}|jd|jj||fqtdq|jd|jj|qWdj|S)Nrrz--transform [ %s, %d ]z_ERROR: The useInverse list must have the same number of entries as the transformsFileName list.z--transform %sr.) rangermr2rfr rgr3 Exceptionr6)r9rpiiZ invert_coder)r)r*rr[s   z0ApplyTransformsToPoints._get_transform_filenamescs$|dkr|jStt|j|||S)Nrf)rrr7r}r8)r9r:r;r<)rEr)r*r8rsz#ApplyTransformsToPoints._format_arg) rrrrOrPryrQr|rRrrr8rSr)r))rEr*r}Cs r})rOr/baserrrrrr r Zutils.filemanipr r r+r-rTrXrYr\rjrkryr|r}r)r)r)r*s" @KIKX/