3 d^@sdZddlZddlmZddlmZmZmZmZmZm Z m Z m Z m Z ddl mZddlmZejd ZGd d d eZGd d d eZGdddeZGdddeZGdddeZGddde ZdS)zVConvert3D is a command-line tool for converting 3D images between common file formats.N)glob) CommandLineInputSpectraits TraitedSpecFileSEMLikeCommandLineInputMultiPathOutputMultiPath CommandLine isdefined)split_filename)loggingZ interfacec@s^eZdZeddddZeddddZeddddZejej ed d d d d Z ej dddZ dS)C3dAffineToolInputSpecTz-ref %sr)existsargstrpositionz-src %sr z%sFzExport ITK transform.z-oitk %s)Z hash_filesdescrrz-fsl2ras)rrN) __name__ __module__ __qualname__rZreference_fileZ source_fileZtransform_filerEitherBool itk_transformZfsl2rasrr6/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/c3.pyrsrc@seZdZeddZdS)C3dAffineToolOutputSpecT)rN)rrrrrrrrrr &sr c@s$eZdZdZeZeZdZddiZ dS) C3dAffineToolaConverts fsl-style Affine registration into ANTS compatible itk format Example ======= >>> from nipype.interfaces.c3 import C3dAffineTool >>> c3 = C3dAffineTool() >>> c3.inputs.source_file = 'cmatrix.mat' >>> c3.inputs.itk_transform = 'affine.txt' >>> c3.inputs.fsl2ras = True >>> c3.cmdline 'c3d_affine_tool -src cmatrix.mat -fsl2ras -oitk affine.txt' Zc3d_affine_toolrz affine.txtN) rrr__doc__r input_specr output_spec_cmdZ_outputs_filenamesrrrrr!*s  r!c @seZdZeedddddZeddd0dgd d Zeed d gd1d dZej ddddddddddd Z ej ej ej dddZej ej ej dddZej ddd d!d"d#d$dZejd%d&dZejd'd(dZejddd)d*d+d,Zejddd-d.Zd/S)2 C3dInputSpecrz%sTz1Input file (wildcard and multiple are supported).)rr mandatoryrFz-o %s out_filesz'Output file of last image on the stack.)rrrxorrz-oo %sout_filezWrite all images on the convert3d stack as multiple files. Supports both list of output files or a pattern for the output filenames (using %d substituion).)rr)rrfloatcharZucharshortZushortintZuintdoublez-type %sznSpecifies the pixel type for the output image. By default, images are written in floating point (float) format)rrz -scale %szZMultiplies the intensity of each voxel in the last image on the stack by the given factor.z -shift %sz'Adds the given constant to every voxel.ZLinearZNearestNeighborZCubicZSincZGaussianz-interpolation %szVSpecifies the interpolation used with -resample and other commands. Default is Linear.z -resample %saResamples the image, keeping the bounding box the same, but changing the number of voxels in the image. The dimensions can be specified as a percentage, for example to double the number of voxels in each direction. The -interpolation flag affects how sampling is performed.z -smooth %szvApplies Gaussian smoothing to the image. The parameter vector specifies the standard deviation of the Gaussian kernel.z-mcrrz)Enable reading of multi-component images.) usedefaultrrrzAChanges command to support 4D file operations (default is false).)r0rNr1)rrrr rin_filer*r(rEnumZpix_typerZIntZFloatZscaleshiftZinterpStrZresampleZsmoothrZmulticomp_splitis_4drrrrr&@s~r&c@seZdZeeddZdS) C3dOutputSpecF)rN)rrrr rr(rrrrr7sr7csPeZdZdZeZeZdZfddZ ddZ fddZ d d Z d d Z ZS) C3daF Convert3d is a command-line tool for converting 3D (or 4D) images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling. The tool can also be used to obtain information about image files. More information on Convert3d can be found at: https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md Example ======= >>> from nipype.interfaces.c3 import C3d >>> c3 = C3d() >>> c3.inputs.in_file = "T1.nii" >>> c3.inputs.pix_type = "short" >>> c3.inputs.out_file = "T1.img" >>> c3.cmdline 'c3d T1.nii -type short -o T1.img' >>> c3.inputs.is_4d = True >>> c3.inputs.in_file = "epi.nii" >>> c3.inputs.out_file = "epi.img" >>> c3.cmdline 'c4d epi.nii -type short -o epi.img' c3dc s6tt|jf||jj|jd|jjr2|jdS)Nr6)superr8__init__inputsZon_trait_change_is_4dr6)selfr<) __class__rrr;sz C3d.__init__cCs|jjr dnd|_dS)NZc4dr9)r<r6r%)r>rrrr=sz C3d._is_4dcsD|j}t|jj r*t|jj r*|jtt|j|}||_|S)N) r%r r<r*r( _gen_outfiler:r8_run_interface)r>Zruntimecmd)r?rrrAs zC3d._run_interfacecCs|t|jjdks d|jjdkr(tdt|jjd\}}}|d||j_tjjtjj |jjrnt dt j ddS)Nr*rzCMultiple in_files found - specify either `out_file` or `out_files`.Z _generatedz2File already found - to overwrite, use `out_file`.zGenerating `out_file`.) lenr<r2AttributeErrorrr*ospathrabspathIOErrorifloggerinfo)r>_fnextrrrr@s zC3d._gen_outfilecCs|jj}t|jjr,tjj|jj|d<t|jjr|t |jjdkrbt tjj|jjd}ndd|jjD}||d<|S)Nr(rrcSs,g|]$}tjjtjj|rtjj|qSr)rFrGrrH).0frrr sz%C3d._list_outputs..) r$getr r<r*rFrGrHr(rDr)r>outputsZ _out_filesrrr _list_outputss    zC3d._list_outputs)rrrr"r&r#r7r$r%r;r=rAr@rT __classcell__rr)r?rr8s   r8)r"rFrbaserrrrrr r r r Zutils.filemaniprr getLoggerrJrr r!r&r7r8rrrrs ,   c