3 Xd:.@sdZddlmZddlZddlmZddlmZmZddlmZm Z m Z m Z m Z d d l mZGd d d eZGd ddeZGdddeZGdddeZGdddeZGdddeZGdddeZdS)zANTS Legacy Interfaces These interfaces are for programs that have been deprecated by ANTs, but are preserved for backwards compatibility. )rangeN)glob) ANTSCommandANTSCommandInputSpec) TraitedSpecFiletraits isdefinedOutputMultiPath)split_filenamec @seZdZejdddddddZeddd ddd Zedd d dd d Zej dddZ ej dddZ ej ej ddddZej dddZejdddddddZejdd d!d"d#d$d%d&d'dd(d) Zejd*d+dd,d)Zej d-d.dZd/S)0antsIntroductionInputSpecr rz-d %dTzimage dimension (2 or 3)r)argstr usedefaultdescpositionz-r %sztemplate file to warp to)existsrr mandatorycopyfilez-i %szinput image to warp to templateFz-f 1z;force script to proceed even if headers may be incompatible)rrz-lz}Applies inverse warp to the template labels to estimate label positions in target space (use for template-based segmentation)z-m %sxzmaximum number of iterations (must be list of integers in the form [J,K,L...]: J = coarsest resolution iterations, K = middle resolution interations, L = fine resolution iterations)rseprz-n 1z-Applies bias field correction to moving imagePRCCMIMSQz-s %szType of similartiy metric used for registration (CC = cross correlation, MI = mutual information, PR = probability mapping, MSQ = mean square difference)GRELSYS2EXDDRIRAz-t %sa9Type of transofmration model used for registration (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential mapping, RI = purely rigid, RA = affine rigid)rrrZants_z-o %sz>Prefix that is prepended to all output files (default = ants_)z-q 1z%Perform a quality check of the resultN)__name__ __module__ __qualname__r Enum dimensionr Zreference_imageZ input_imageBoolZ force_proceedZinverse_warp_template_labelsListIntmax_iterationsbias_field_correctionsimilarity_metrictransformation_modelStr out_prefixZ quality_checkr3r3O/var/www/html/virt/lib/python3.6/site-packages/nipype/interfaces/ants/legacy.pyrst rc@sHeZdZedddZedddZedddZedddZedddZdS) antsIntroductionOutputSpecTzaffine (prefix_Affine.txt))rrzwarp field (prefix_Warp.nii)z+inverse warp field (prefix_InverseWarp.nii)z!input image (prefix_repaired.nii)z"output image (prefix_deformed.nii)N) r%r&r'r affine_transformation warp_fieldinverse_warp_field input_file output_filer3r3r3r4r5os     r5c@s$eZdZdZdZeZeZddZ dS)antsIntroductionaUses ANTS to generate matrices to warp data from one space to another. Examples -------- >>> from nipype.interfaces.ants.legacy import antsIntroduction >>> warp = antsIntroduction() >>> warp.inputs.reference_image = 'Template_6.nii' >>> warp.inputs.input_image = 'structural.nii' >>> warp.inputs.max_iterations = [30,90,20] >>> warp.cmdline 'antsIntroduction.sh -d 3 -i structural.nii -m 30x90x20 -o ants_ -r Template_6.nii -t GR' zantsIntroduction.shcCs|jj}|jj}t| s.t|rj|d krjtjjtj|jj d|d<tjjtj|jj d|d<tjjtj|jj d|d<tjjtj|jj d |d <tjjtj|jj d |d <|S)Nr#r$z Warp.nii.gzr7zInverseWarp.nii.gzr8z Affine.txtr6zrepaired.nii.gzr9zdeformed.nii.gzr:)r#r$) _outputsgetinputsr0r ospathjoingetcwdr2)selfoutputsZ transmodelr3r3r4 _list_outputss  zantsIntroduction._list_outputsN) r%r&r'__doc___cmdr input_specr5 output_specrEr3r3r3r4r;ys r;c@s eZdZdS) GenWarpFieldsN)r%r&r'r3r3r3r4rJsrJc @seZdZejddddddddZejd d dd d Zeje dd dddd6dZ ejddddddd Z ej dddZ ejddddd ZejddgddZejejdddd Zejd!d"dZejd#d$dZejd%d&d'd(d)d*dZejd+d,d-d.d/d0d1dd2d Zejd3d4Zd5S)7buildtemplateparallelInputSpecr rz-d %dTzimage dimension (2, 3 or 4)r)rrrrZ antsTMPL_z-o %szBPrefix that is prepended to all output files (default = antsTMPL_))rrr)rz(list of images to generate template fromz%s)rrrrrz-c %dz\control for parallel processing (0 = serial, 1 = use PBS, 2 = use PEXEC, 3 = use Apple XGridz-g %fz@smaller magnitude results in more cautious steps (default = .25))rrz-i %dz#iterations of template constructionz-j %dparallelizationzERequires parallelization = 2 (PEXEC). Sets number of cpu cores to use)rrequiresrz-m %srzmaximum number of iterations (must be list of integers in the form [J,K,L...]: J = coarsest resolution iterations, K = middle resolution interations, L = fine resolution iterations)rrrz-n 1z-Applies bias field correction to moving imagez-r 1zSregisters inputs before creating template (useful if no initial template available)rrrrz-s %szType of similartiy metric used for registration (CC = cross correlation, MI = mutual information, PR = probability mapping, MSQ = mean square difference)rrrr r!r"z-t %saType of transofmration model used for registration (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential mappingzeuses first volume as target of all inputs. When not used, an unbiased average image is used to start.)rN)r%r&r'r r(r)r1r2r+r in_filesrMZFloatZgradient_step_sizer,Ziteration_limit num_coresr-r*r.Zrigid_body_registrationr/r0use_first_as_targetr3r3r3r4rKs rKc@s<eZdZedddZeeddddZeeddddZdS) buildtemplateparallelOutputSpecTzfinal ANTS template)rr)rz,Templates from different stages of iteration)rz~Outputs for each input image. Includes warp field, inverse warp, Affine, original image (repaired) and warped image (deformed)N)r%r&r'r final_template_filer template_filessubject_outfilesr3r3r3r4rS s  rScs4eZdZdZdZeZeZfddZ ddZ Z S)buildtemplateparallelaGenerate a optimal average template .. warning:: This can take a VERY long time to complete Examples -------- >>> from nipype.interfaces.ants.legacy import buildtemplateparallel >>> tmpl = buildtemplateparallel() >>> tmpl.inputs.in_files = ['T1.nii', 'structural.nii'] >>> tmpl.inputs.max_iterations = [30, 90, 20] >>> tmpl.cmdline 'buildtemplateparallel.sh -d 3 -i 4 -m 30x90x20 -o antsTMPL_ -c 0 -t GR T1.nii structural.nii' zbuildtemplateparallel.shcsj|dkr$|jjdkr dt|SdS|dkrV|jjr:d}nd}|djdd |DStt|j|||S) NrQrz-j rPz-z  css|] }|VqdS)Nr3).0namer3r3r4 Qsz4buildtemplateparallel._format_arg..)r>rMstrrRrAsuperrW _format_arg)rCoptspecvalstart) __class__r3r4r_Fs  z!buildtemplateparallel._format_argc Cs(|jj}g|d<xttttjjdD]}tjjd|jj ||jj f}tj |tjjd|jj ||jj |fd|jj ||jj |f}|dj tjj|tjjd|jj |d<q.Wg|d<xX|jj D]L}t|\}}}ttjjd|jj |f}x|D]}|dj |qWqW|S) NrUz *iteration*z!%s_iteration_%d/%stemplate.nii.gzz%%s_iteration_%d/%stemplate_i%d.nii.gzz%stemplate.nii.gzrTrVz%s%s*)r<r=rlenrr?r@realpathr>r0r2renameappendrPr)rCrDitempfile_filename_baser3r3r4rETs4  z#buildtemplateparallel._list_outputs) r%r&r'rFrGrKrHrSrIr_rE __classcell__r3r3)rdr4rW/s  rW)rFbuiltinsrr?rrnrrrr r r r Zutils.filemaniprrr5r;rJrKrSrWr3r3r3r4s   ] 4o