3 dk@shdZddlZddlmZmZmZmZddlmZmZm Z ddl m Z Gd d d e Z Gd d d eZ Gd ddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdd d eZGd!d"d"e ZGd#d$d$eZGd%d&d&eZGd'd(d(e ZGd)d*d*eZGd+d,d,eZdS)-zThe regutils module provides classes for interfacing with the `niftyreg `_ utility command line tools. The interfaces were written to work with niftyreg version 1.5.10 N) TraitedSpecFiletraits isdefined)get_custom_pathNiftyRegCommandNiftyRegCommandInputSpec)split_filenamec@seZdZdZedddddZedddddZeddd d Zej d d d d*dddZ edgddd+ddZ ej dddddddZ ej dddZejdd dZejd!d"d#Zd$Zejd%ed#Zd&Zej d'dd(ed#Zd)S),RegResampleInputSpeczInput Spec for RegResample.Tz The input reference/target imagez-ref %s)existsdescargstr mandatoryzThe input floating/source imagez-flo %szThe input transformation filez -trans %s)rrrresZblankz-%srzType of output)rposition usedefaultrflo_filez%srz,The output filename of the transformed image) name_source name_templaterrrNNLINCUBSINCzInterpolation typez -inter %d)rrz Padding valuez-pad %fzResample Tensor Mapz-tensor z-voffzTurn off verbose output)rrzNPerform the resampling in two steps to resample an image to a lower resolutionz-psfzQMinimise the matrix metric (0) or the determinant (1) when estimating the PSF [0]rz -psf_alg %dN)__name__ __module__ __qualname____doc__rref_filer trans_filerEnumtypeout_file inter_valFloatZpad_valBoolZ tensor_flagZverbosity_off_flagrZpsf_flagZpsf_algr*r*E/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/niftyreg/regutils.pyr sF r c@seZdZdZeddZdS)RegResampleOutputSpeczOutput Spec for RegResample.z,The output filename of the transformed image)rN)rrr r!rr&r*r*r*r+r,Psr,cs:eZdZdZedZeZeZ fddZ dddZ Z S) RegResampleaInterface for executable reg_resample from NiftyReg platform. Tool to resample floating image in the space of a defined reference image given a transformation parametrisation generated by reg_aladin, reg_f3d or reg_transform `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegResample() >>> node.inputs.ref_file = 'im1.nii' >>> node.inputs.flo_file = 'im2.nii' >>> node.inputs.trans_file = 'warpfield.nii' >>> node.inputs.inter_val = 'LIN' >>> node.inputs.omp_core_val = 4 >>> node.cmdline 'reg_resample -flo im2.nii -inter 1 -omp 4 -ref im1.nii -trans warpfield.nii -res im2_res.nii.gz' Z reg_resamplecs<|dkr$ddddd}|j||Stt|j|||SdS)Nr'rrr )rrrr)rsuperr- _format_arg)selfnamespecvaluer') __class__r*r+r0sszRegResample._format_argNcCs,t|\}}}|jj}tjj|dj||S)Nz{0}_{1}.nii.gz)r inputsr%ospathjoinformat)r1r4r2r8base_suffixr*r*r+_overload_extensionzszRegResample._overload_extension)N) rrr r!r_cmdr input_specr, output_specr0r> __classcell__r*r*)r5r+r-Vs  r-c @s^eZdZdZdZededdZedddddZej d d d dd dddZ edgdddddZ dS)RegJacobianInputSpeczInput Spec for RegJacobian.zBReference/target file (required if specifying CPP transformations.Tz-ref %s)rrrz"The input non-rigid transformationz -trans %s)rrrrZjacZjacLZjacMz-%srzType of jacobian outcome)rrrrr#z%sz)The output jacobian determinant file namer)rrrrrNrr) rrr r!rrr"r#rr$r%r&r*r*r*r+rCs,rCc@seZdZdZeddZdS)RegJacobianOutputSpeczOutput Spec for RegJacobian.zThe output file)rN)rrr r!rr&r*r*r*r+rDsrDc@s*eZdZdZedZeZeZ dddZ dS) RegJacobianaMInterface for executable reg_resample from NiftyReg platform. Tool to generate Jacobian determinant maps from transformation parametrisation generated by reg_f3d `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegJacobian() >>> node.inputs.ref_file = 'im1.nii' >>> node.inputs.trans_file = 'warpfield.nii' >>> node.inputs.omp_core_val = 4 >>> node.cmdline 'reg_jacobian -omp 4 -ref im1.nii -trans warpfield.nii -jac warpfield_jac.nii.gz' Z reg_jacobianNcCs,t|\}}}|jj}tjj|dj||S)Nz{0}_{1}.nii.gz)r r6r%r7r8r9r:)r1r4r2r8r;r<r=r*r*r+r>szRegJacobian._overload_extension)N) rrr r!rr?rCr@rDrAr>r*r*r*r+rEs rEc@sleZdZdZedddddZedgddd d Zejd d d Z ejddd Z eddddZ dZ ej e ddZejddd ZeddddZejej edddddZejej edddddZejej edddd dZejej edddd!dZejd"d#dZd$Z ejej ej ej e d%dZejej ej ej d&d'dZd(Z ejej ej ej e d)dZejd*d+d,d-d.d/dZd0S)1RegToolsInputSpeczInput Spec for RegTools.TzThe input image file pathz-in %s)rrrrin_filez%s_tools.nii.gzzThe output file namez-out %s)rrrrz-isozMake output image isotropic)rrz-nosclzSet scale, slope to 0 and 1z&Values outside the mask are set to NaNz-nan %s)rrrz1Binarise the input image with the given thresholdz-thr %f)rrz-binzBinarise the input imagez'Compute the mean RMS between the imagesz-rms %s)rz"Divide the input by image or valuez-div %sz$Multiply the input by image or valuez-mul %szAdd to the input image or valuez-add %sz-sub %sz%Downsample the image by a factor of 2z-downz2Smooth the input image using a cubic spline kernelz-smoS %f %f %fz(Change the resolution of the input imagez-chgres %f %f %fz.Smooth the input image using a Gaussian kernelz-smoG %f %f %frrrrz5Interpolation order to use to warp the floating imagez -interp %dN)rrr r!rrGr&rr)Ziso_flagZ noscl_flagZ mask_filerr(Zthr_valZbin_flagZrms_valZEitherZdiv_valZmul_valZadd_valZsub_valZ down_flagTupleZ smo_s_valZ chg_res_valZ smo_g_valr$r'r*r*r*r+rFst   rFc@seZdZdZedddZdS)RegToolsOutputSpeczOutput Spec for RegTools.zThe output fileT)rrN)rrr r!rr&r*r*r*r+rI0srIcs4eZdZdZedZeZeZ dZ fddZ Z S)RegToolsavInterface for executable reg_tools from NiftyReg platform. Tool delivering various actions related to registration such as resampling the input image to a chosen resolution or remove the nan and inf in the input image by a specified value. `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegTools() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.mul_val = 4 >>> node.inputs.omp_core_val = 4 >>> node.cmdline 'reg_tools -in im1.nii -mul 4.0 -omp 4 -out im1_tools.nii.gz' Z reg_toolsZ_toolscs<|dkr$ddddd}|j||Stt|j|||SdS)Nr'rrr r.)rrrr)rr/rJr0)r1r2r3r4r')r5r*r+r0QszRegTools._format_arg) rrr r!rr?rFr@rIrA_suffixr0rBr*r*)r5r+rJ6s rJc @s eZdZdZejedddddddd d d d gd dZdZejedddddddd d d d gedZ dZeddddd d d gd gedZ dZedddddd d gd gedZ dZedddddd d gd gedZ dZedddddd d gd gedZ dZejeddd!ddddgedZedddddZd S)"RegAverageInputSpeczInput Spec for RegAverage.T)existrz-avg %s avg_lts_files avg_ref_filedemean1_ref_filedemean2_ref_filedemean3_ref_file warp_filesz*Averaging of images/affine transformations)rrsepxorrz(Robust average of affine transformationsz -avg_lts %s avg_fileszAll input images are resampled into the space of and averaged. A cubic spline interpolation scheme is used for resamplingz -avg_tran %s)rrrVrequiresrzZAverage images and demean average image that have affine transformations to a common spacez -demean1 %sz]Average images and demean average image that have non-rigid transformations to a common spacez -demean2 %szhAverage images and demean average image that have linear and non-rigid transformations to a common spacez -demean3 %szMtransformation files and floating image pairs/triplets to the reference spacez%srzOutput file name)genfilerrrNr)rrr r!rListrrWrrOrPrQrRrSrTr&r*r*r*r+rLYsrLc@seZdZdZeddZdS)RegAverageOutputSpeczOutput Spec for RegAverage.zOutput file name)rN)rrr r!rr&r*r*r*r+r[sr[csHeZdZdZedZeZeZ dZ ddZ ddZ e fdd ZZS) RegAverageajInterface for executable reg_average from NiftyReg platform. Compute average matrix or image from a list of matrices or image. The tool can be use to resample images given input transformation parametrisation as well as to demean transformations in Euclidean or log-Euclidean space. This interface is different than the others in the way that the options will be written in a command file that is given as a parameter. `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegAverage() >>> one_file = 'im1.nii' >>> two_file = 'im2.nii' >>> three_file = 'im3.nii' >>> node.inputs.avg_files = [one_file, two_file, three_file] >>> node.cmdline # doctest: +ELLIPSIS 'reg_average --cmd_file .../reg_average_cmd' Z reg_averageZavg_outcCsr|dkrnt|jjr$|j|jddSt|jjr^t|jjd\}}}|d kr^|j|j|dS|j|jddSdS) Nr&z.txt)extr.nii.nii.gz.hdr.img.img.gz)r^r_r`rarb)rr6rO _gen_fnamerKrWr )r1r2r<Z_extr*r*r+ _gen_filenames  zRegAverage._gen_filenamecCs8|jj}t|jjr&|jj|d<n|jd|d<|S)Nr&)rAgetrr6r&rd)r1outputsr*r*r+ _list_outputss   zRegAverage._list_outputsc sLtt|j}tjjtjd}t|d}|j|WdQRXd|j |fS)z2Rewrite the cmdline to write options in text_file.reg_average_cmdwNz%s --cmd_file %s) r/r\cmdliner7r8r9getcwdopenwritecmd)r1argvrhf)r5r*r+rj s   zRegAverage.cmdline)rrr r!rr?rLr@r[rArKrdrgpropertyrjrBr*r*)r5r+r\s  r\c@s~eZdZdZedddddZedddd d gd Zedd ddddddddddddg dZ eddd?d!ddddddddddg d"gd#Z edd$d@d!d%Z d&Z edd'dAe ddddddddddg d(gd#Z d&Z edd$dBe dgd)Zedd*dCd+ddddddddddg dZejedd,edd,d-d.dDddddddddddg d/Zedd0dEd1ddddddddddg dZd2ZejejejejejejejejejejejejejedFd3ddddddddddg d4Zd5Z edd6dGe ddddddddddg dZd7Z ejedd,edd,edd,d8dHe ddddddddddg d4ZeddId$d9d:Zd;S)JRegTransformInputSpeczInput Spec for RegTransform.Tz The input reference/target imagez-ref %sr)rrrrz'The input second reference/target imagez-ref2 %sr ref1_file)rrrrrXz-def %srz-Compute deformation field from transformation disp_input flow_input comp_inputupd_s_form_input inv_aff_input inv_nrr_input half_inputmake_aff_inputaff_2_rig_inputflirt_2_nr_input)rrrrrVz-disp %sz.Compute displacement field from transformation def_inputz-flow %sz"Compute flow field from spline SVFz-comp %sr zcompose two transformations comp_input2)rrrrrVrXz%s)rrrrz-Update s-form using the affine transformationz -updSform %supd_s_form_input2)rrrrrXz -invAff %szInvert an affine transformation)rz"Invert a non-linear transformationz -invNrr %s %s)rrrrVz-half %sz$Half way to the input transformationz,-makeAff %f %f %f %f %f %f %f %f %f %f %f %fz$Make an affine transformation matrix)rrrrVz6Extract the rigid component from affine transformationz -aff2rig %szGConvert a FLIRT affine transformation to niftyreg affine transformationz-flirtAff2NR %s %s %sztransformation file to write)rYrrrNrrrrrrrrrrrrr)rrr r!rrsZ ref2_filer~rtrurvrrrwrrxrrHryrzZ argstr_tmpr(r{r|r}r&r*r*r*r+rrs            rrc@seZdZdZeddZdS)RegTransformOutputSpeczOutput Spec for RegTransform.z*Output File (transformation in any format))rN)rrr r!rr&r*r*r*r+rsrc@s<eZdZdZedZeZeZ dZ ddZ ddZ dd Z d S) RegTransformaKInterface for executable reg_transform from NiftyReg platform. Tools to convert transformation parametrisation from one type to another as well as to compose, inverse or half transformations. `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegTransform() >>> node.inputs.def_input = 'warpfield.nii' >>> node.inputs.omp_core_val = 4 >>> node.cmdline # doctest: +ELLIPSIS 'reg_transform -omp 4 -def warpfield.nii .../warpfield_trans.nii.gz' Z reg_transformZ_transc Cs|jj|jj|jj|jj|jj|jj|jj|jj|jj |jj |jj |jj g }g}xH|D]@}t |rV|j|t|\}}}|dks|dks|dkrV|SqVWt|r|dSdS)Nz.niiz.nii.gzz.hdrr)r6r~rtrurvrrwrxryrzr{r|r}rappendr len)r1r6entriesentryr<r]r*r*r+ _find_input:s,   zRegTransform._find_inputcCs|dkrt|jjr(|jd|jddSt|jjrt|jjrt|jj\}}}t|jj\}}}|d kst|d kr|j||jddS|j||j|dSt|jjr|j|jjd |jddS|j }t|\}}}|d kr|j||j|dS|j||jddSdS)Nr&Zmatrixz.txt)r=r].nii.nii.gz.hdr.img.img.gzr)rrrrr)rrrrr)rrrrr) rr6r{rcrKrvrr r}r)r1r2r<Zbn1Zext1Zext2Z input_to_user]r*r*r+rdTs.     zRegTransform._gen_filenamecCs8|jj}t|jjr&|jj|d<n|jd|d<|S)Nr&)rArerr6r&rd)r1rfr*r*r+rgus   zRegTransform._list_outputsN)rrr r!rr?rrr@rrArKrrdrgr*r*r*r+r"s!rc @sZeZdZdZedddddZedddddZejdd d d dd d dZ edgddddZ dS)RegMeasureInputSpeczInput Spec for RegMeasure.Tz The input reference/target imagez-ref %s)rrrrzThe input floating/source imagez-flo %sZnccZlnccZnmiZssdz-%sz Measure of similarity to compute)rrrrz%sz-out %sz+The output text file containing the measure)rrrrN) rrr r!rr"rrr$ measure_typer&r*r*r*r+rs0rc@seZdZdZeddZdS)RegMeasureOutputSpeczOutput Spec for RegMeasure.z+The output text file containing the measure)rN)rrr r!rr&r*r*r*r+rsrc@s*eZdZdZedZeZeZ dddZ dS) RegMeasureaAInterface for executable reg_measure from NiftyReg platform. Given two input images, compute the specified measure(s) of similarity `Source code `_ Examples -------- >>> from nipype.interfaces import niftyreg >>> node = niftyreg.RegMeasure() >>> node.inputs.ref_file = 'im1.nii' >>> node.inputs.flo_file = 'im2.nii' >>> node.inputs.measure_type = 'lncc' >>> node.inputs.omp_core_val = 4 >>> node.cmdline 'reg_measure -flo im2.nii -lncc -omp 4 -out im2_lncc.txt -ref im1.nii' Z reg_measureNcCs,t|\}}}|jj}tjj|dj||S)Nz {0}_{1}.txt)r r6rr7r8r9r:)r1r4r2r8r;r<r=r*r*r+r>szRegMeasure._overload_extension)N) rrr r!rr?rr@rrAr>r*r*r*r+rs r)r!r7r;rrrrrr r Zutils.filemanipr r r,r-rCrDrErFrIrJrLr[r\rrrrrrrr*r*r*r+s0 @*l#w? ^"