3 d @sdZddlZddlmZddlmZddlmZmZm Z m Z m Z m Z m Z mZdZGd d d eZGd d d e ZGd ddeZGdddeZGdddeZGddde ZGdddeZGdddeZddZdS)a The freesurfer module provides basic functions for interfacing with freesurfer tools. Currently these tools are supported: * Dicom2Nifti: using mri_convert * Resample: using mri_convert Examples -------- See the docstrings for the individual classes for 'working' examples. N) LooseVersion)fname_presuffix) CommandLine DirectoryCommandLineInputSpec isdefinedtraits TraitedSpecFile PackageInfoZrestructuredtextc@sReZdZdZejdr*ejjejddZe ddZ e ddZ e dd Z d S) InfozFreesurfer subject directory and version information. Examples -------- >>> from nipype.interfaces.freesurfer import Info >>> Info.version() # doctest: +SKIP >>> Info.subjectsdir() # doctest: +SKIP ZFREESURFER_HOMEzbuild-stamp.txtcCs |jdS)Nr) splitlines)Zraw_inforC/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/freesurfer/base.py parse_version2szInfo.parse_versionc Cs|j}|dkrtdS|jjd}yt|ddWntk rPd}YnXd|d}|r|dd krxd |}q|d d d kr|d dd}qtdd|dDdkr|d}qtd|n(d |kr|dd}n|jjdd}t|S)zcReturn a comparable version object If no version found, use LooseVersion('0.0.0') Nz0.0.0-.rdevz 6.0.0-devrvcSsg|]}|dkrdqS)rrr).0valrrr Osz%Info.looseversion..rzUnknown version string: z-devz-vrrr)versionrrstripsplitint ValueErrorlen RuntimeError)clsverZvinfoZgithashZvstrrrr looseversion6s*     zInfo.looseversioncCs|jrtjdSdS)a&Check the global SUBJECTS_DIR Parameters ---------- subjects_dir : string The system defined subjects directory Returns ------- subject_dir : string Represents the current environment setting of SUBJECTS_DIR SUBJECTS_DIRN)rosenviron)r&rrr subjectsdir\s zInfo.subjectsdirN)__name__ __module__ __qualname____doc__r*getenvpathjoinZ version_file staticmethodr classmethodr(r,rrrrr#s     &rc@seZdZedddZdS) FSTraitedSpecTzsubjects directory)existsdescN)r-r.r/r subjects_dirrrrrr6rsr6cs^eZdZdZeZdZfddZddZe ddZ fd d Z dd dZ e ddZZS) FSCommandzaGeneral support for FreeSurfer commands. 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Nc s\tt|jf||jj|jd|js2tj|_t |jj  rP|jrP|j|j_ |jdS)Nr9) superr:__init__inputson_trait_change_subjects_dir_update _subjects_dirrr,r r9)selfr=) __class__rrr<s  zFSCommand.__init__cCs"|jjr|jjjd|jjidS)Nr))r=r9r+update)rArrrr?szFSCommand._subjects_dir_updatecCs ||_dS)N)r@)r&r9rrrset_default_subjects_dirsz"FSCommand.set_default_subjects_dirc s.d|kr|d|j_|jtt|jf|S)Nr9)r=r9r?r;r:run)rAr=)rBrrrEs z FSCommand.run_fsTcCsF|dkr"d|j}|d7}t||dkr2tj}t||||d}|S)aDefine a generic mapping for a single outfile The filename is potentially autogenerated by suffixing inputs.infile Parameters ---------- basename : string (required) filename to base the new filename on fname : string if not None, just use this fname cwd : string prefix paths with cwd, otherwise os.getcwd() suffix : string default suffix rz,Unable to generate filename for command %s. zbasename is not set!N)suffixuse_extnewpath)cmdr#r*getcwdr)rAbasenamefnamecwdrGrHmsgrrr _gen_fnames zFSCommand._gen_fnamecCstj}|tdkr|jSdS)Nz0.0.0)rr(rvstring)rAr'rrrrs zFSCommand.version)NNrFT)r-r.r/r0r6 input_specr@r<r?r5rDrErPpropertyr __classcell__rr)rBrr:vs    r:c@seZdZdZeddZdS)FSSurfaceCommandajSupport for FreeSurfer surface-related functions. 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Nc s|tt|jf||jj|jd|jsNtjj dd|_|jsNtjj dd|_t |jj  rp|jrpt |j|j_ |jdS)NrdOMP_NUM_THREADSZNSLOTS) r;rer<r=r>_num_threads_update _num_threadsr*r+r^r rdr")rAr=)rBrrr<szFSCommandOpenMP.__init__cCs&|jjr"|jjjdt|jjidS)Nrf)r=rdr+rCstr)rArrrrgsz#FSCommandOpenMP._num_threads_updatec s.d|kr|d|j_|jtt|jf|S)Nrd)r=rdrgr;rerE)rAr=)rBrrrEs zFSCommandOpenMP.run) r-r.r/r0rcrRrhr<rgrErTrr)rBrres  recCstjdkrdSdSdS)zzChecks if FreeSurfer is NOT installed used with skipif to skip tests that will fail if FreeSurfer is not installedNTF)rrrrrr no_freesurfer s rj)r0r*rrZutils.filemaniprrYrrrr r r r r Z __docformat__rr6r:rUr[rbrcrerjrrrrs  ( OA #