3 dh@sdZddlmZddlZddlmZddlmZddlmZm Z m Z m Z m Z dd l mZejd ZGd d d e ZGd dde ZGddde ZddZddZddZdS)aThe fsl module provides classes for interfacing with the `FSL `_ command line tools. This was written to work with FSL version 4.1.4. These are the base tools for working with FSL. Preprocessing tools are found in fsl/preprocess.py Model tools are found in fsl/model.py DTI tools are found in fsl/dti.py XXX Make this doc current! Currently these tools are supported: * BET v2.1: brain extraction * FAST v4.1: segmentation and bias correction * FLIRT v5.5: linear registration * MCFLIRT: motion correction * FNIRT v1.0: non-linear warp Examples -------- See the docstrings of the individual classes for examples. )globN)logging)fname_presuffix)traits isdefined CommandLineCommandLineInputSpec PackageInfo)BibTeXznipype.interfacec@speZdZdZdddddZejdr:ejjejddd Z e d d Z e d d Z e ddZe dddZdS)Infoa; Handle FSL ``output_type`` and version information. output type refers to the type of file fsl defaults to writing eg, NIFTI, NIFTI_GZ Examples -------- >>> from nipype.interfaces.fsl import Info >>> Info.version() # doctest: +SKIP >>> Info.output_type() # doctest: +SKIP z.niiz.imgz.nii.gzz.img.gz)NIFTIZ NIFTI_PAIRZNIFTI_GZZ NIFTI_PAIR_GZFSLDIRetcZ fslversioncCs |jdS)Nr) splitlines)Zraw_infor~sz'Info.standard_image..z*nii*)rrr Exceptionpathjoinr)Zimg_nameZfsldirr)r'rstandard_imageps zInfo.standard_image)N)__name__ __module__ __qualname____doc__rrgetenvr*r+Z version_file staticmethodr classmethodrrr,rrrrr (s    r c@s*eZdZdZejdeejj ddZ dS)FSLCommandInputSpecz Base Input Specification for all FSL Commands All command support specifying FSLOUTPUTTYPE dynamically via output_type. Example ------- fsl.ExtractRoi(tmin=42, tsize=1, output_type='NIFTI') rzFSL output type)descN) r-r.r/r0rEnumlistr rkeysrrrrrr4s r4csneZdZdZeZdZeddgdgZfddZ dd Z e d d Z e d d ZdddZdddZZS) FSLCommandzBase support for FSL commands.Nz@article{JenkinsonBeckmannBehrensWoolrichSmith2012,author={M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, and S.M. Smith},title={FSL},journal={NeuroImage},volume={62},pages={782-790},year={2012},}implementation)entrytagsc sZtt|jf||jj|jd|jdkr6tj|_t |jjsN|j|j_n|jdS)Nr) superr9__init__inputsZon_trait_change_output_update _output_typer rr)selfr?) __class__rrr>s    zFSLCommand.__init__cCs$|jj|_|jjjd|jjidS)Nr)r?rrArupdate)rBrrrr@s zFSLCommand._output_updatecCs"|tjkr||_n td|dS)a*Set the default output type for FSL classes. This method is used to set the default output type for all fSL subclasses. However, setting this will not update the output type for any existing instances. For these, assign the .inputs.output_type. zInvalid FSL output_type: %sN)r rrAAttributeError)rrrrrset_default_output_types z"FSLCommand.set_default_output_typecCstjS)N)r version)rBrrrrGszFSLCommand.versionTcCs|dkr"d|j}|d7}t||dkr2tj}|dkrHtj|jj}|rd|r`dj||f}n|}|dkrpd}t ||d|d}|S)aGenerate a filename based on the given parameters. The filename will take the form: cwd/basename. If change_ext is True, it will use the extentions specified in intputs.output_type. Parameters ---------- basename : str Filename to base the new filename on. cwd : str Path to prefix to the new filename. (default is os.getcwd()) suffix : str Suffix to add to the `basename`. (defaults is '' ) change_ext : bool Flag to change the filename extension to the FSL output type. (default True) Returns ------- fname : str New filename based on given parameters. r#z,Unable to generate filename for command %s. zbasename is not set!NF)suffixZuse_extnewpath) cmd ValueErrorrgetcwdr rr?rr+r)rBbasenamecwdrHZ change_extextrfnamerrr _gen_fnames  zFSLCommand._gen_fnamecCs|tj|jjS)N)r rr?r)rBvaluenamerrr_overload_extensionszFSLCommand._overload_extension)NNTN)N)r-r.r/r0r4Z input_specrAr Z _referencesr>r@r3rFpropertyrGrQrT __classcell__rr)rCrr9s     ,r9cCstj}|rdSdSdS)Nr)r rG)verrrr check_fslsrYcCstjdkrdSdSdS)zlChecks if FSL is NOT installed used with skipif to skip tests that will fail if FSL is not installedNTF)r rGrrrrno_fsls rZcCs&dtjko"tjjtjjtjd S)z#check if fsl_course data is presentZFSL_COURSE_DATA)rrr*isdirabspathrrrrno_fsl_course_datas r])r0rrr#rZutils.filemaniprbaserrr r r Z external.duer getLoggerrr r4r9rYrZr]rrrrs     \j