3 dg'@sdZddlZddlmZddlmZddlmZmZddl m Z m Z dd l m Z mZmZmZmZmZmZdd lmZejd ZGd d d eZGddde ZGdddeZGdddeZGdddeZGdddeZGdddeZddZdS)z*Provide a base interface to AFNI commands.N)platform)spawn)logging LooseVersion)split_filenamefname_presuffix) CommandLinetraitsCommandLineInputSpec isdefinedFile TraitedSpec PackageInfo)BibTeXznipype.interfacec@sTeZdZdZdZddddZdZedd Ze d d Z e d d Z eddZ dS)Infoz0Handle afni output type and version information.AFNIz.niiz.nii.gz)ZNIFTIrZNIFTI_GZzafni --versioncCs|jddjdd}|jdr2|jdd}n(|jdrV|jddjd d}nd St|jd d jd d }|ddkr|dd|d<t|S)zCheck and parse AFNI's version. rzVersion rZAFNI_ZDebianzDebian-~N_.rii)split startswithrreplaceversiontuple)Zraw_infoZ version_stamprr=/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/afni/base.py parse_version!s   zInfo.parse_versioncCsDy |j|Stk r>}zd|f}t||WYdd}~XnXdS)a: Get the file extension for the given output type. Parameters ---------- outputtype : {'NIFTI', 'NIFTI_GZ', 'AFNI'} String specifying the output type. Returns ------- extension : str The file extension for the output type. zInvalid AFNIOUTPUTTYPE: N)ftypesKeyError)cls outputtypeemsgrrr output_type_to_ext1s  zInfo.output_type_to_extcCsdS)z Set default output filetype. AFNI has no environment variables, Output filetypes get set in command line calls Nipype uses ``AFNI`` as default Returns ------- None rr)r$rrr r%GszInfo.outputtypecCsJtdddddj}|jjdkr$dS|jj}tjj|d}tjj||S)z Grab an image from the standard location. Could be made more fancy to allow for more relocatability z which afniTFZ allatonce)Zignore_exceptionZresource_monitorZterminal_outputrN) r runruntime returncodestdoutospathrjoin)Zimg_nameZcloutoutbasedirrrr standard_imageWs  zInfo.standard_imageN) __name__ __module__ __qualname____doc__Z_Info__outputtyper"Z version_cmd staticmethodr! classmethodr(r%r2rrrr rs    rcs"eZdZdZdfdd ZZS)AFNICommandBasea A base class to fix a linking problem in OSX and AFNI. 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Cox},title={AFNI: software for analysis and visualization of functional magnetic resonance neuroimages},journal={Computers and Biomedical research},volume={29},number={3},pages={162-173},year={1996},}implementation)entrytagsz@article{CoxHyde1997,author={R.W. Cox and J.S. Hyde},title={Software tools for analysis and visualization of fMRI data},journal={NMR in Biomedicine},volume={10},number={45},pages={171-178},year={1997},}cCs|jjS)zGet number of threads.)inputsrG)r>rrr rGszAFNICommand.num_threadscCs ||j_dS)N)rRrG)r>valuerrr rGscCs"|tjkr||_n td|dS)a4 Set the default output type for AFNI classes. This method is used to set the default output type for all afni subclasses. However, setting this will not update the output type for any existing instances. For these, assign the .inputs.outputtype. zInvalid AFNI outputtype: %sN)rr" _outputtypeAttributeError)r$r%rrr set_default_output_types z#AFNICommand.set_default_output_typec svtt|jf||jj|jdt|jdr>|jj|jd|jdkrRt j |_t |jj sj|j|j_ n|jdS)z)Instantiate an AFNI command tool wrapper.r%rGN) r<rN__init__rRZon_trait_change_output_updatehasattr_nthreads_updaterTrr%r )r>rR)r?rr rWs     zAFNICommand.__init__cCsd|jj|jjd<dS)z.Update environment with new number of threads.z%dZOMP_NUM_THREADSN)rRrGr;)r>rrr rZszAFNICommand._nthreads_updatecCs|jj|_dS)z Update the internal property with the provided input. i think? updates class private attribute based on instance input in fsl also updates ENVIRON variable....not valid in afni as it uses no environment variables N)rRr%rT)r>rrr rXszAFNICommand._output_updatecCs*t|\}}}tjj||tj|jjS)N)rr-r.r/rr(rRr%)r>rSnamer.baserrrr _overload_extensionszAFNICommand._overload_extensioncsztt|j}tddd}t|jjf|j}|rvx>|D]6}||rsz+AFNICommand._list_outputs..)rFrz +orig.BRIK) r<rN _list_outputsdictrIrRr rJr)r>outputsmetadataZ out_namesr[rext)r?rr r`s zAFNICommand._list_outputsTcCs~|sd|j}|d7}t||dkr.tj}|dkrDtj|jj}|r^|rZdj||fn|}|dkrjd}t ||d|d}|S)a Generate a filename based on the given parameters. 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(default True) Returns ------- fname : str New filename based on given parameters. z,Unable to generate filename for command %s. zbasename is not set!NrF)suffixZuse_extnewpath) cmd ValueErrorr-getcwdrr(rRr%r/r)r>basenamecwdreZ change_extrdr'fnamerrr _gen_fnames zAFNICommand._gen_fname)N)NNTN)r3r4r5r6rBZ input_specrTrZ _referencespropertyrGsetterr8rVrWrZrXr]r`rmrArr)r?r rNs$       rNc@s>eZdZejdeejjddZ ej de dddddZ dS) AFNIPythonCommandInputSpecrzAFNI output filetype)rDZpython2T)rM)rCdefaultN) r3r4r5r rHrIrr"rJr%ZEitherr py27_pathrrrr rp0srpcs0eZdZdZefddZeddZZS)AFNIPythonCommandz2A subtype of AFNI command line for Python scripts.cs&tt|j}tj|}|dk r"|S|S)zRevise the command path.N)r<rsrgrfind_executable)r>Zorig_cmdfound)r?rr rg<s  zAFNIPythonCommand.cmdcCsdj|jjS)Nz{} )formatrRrr)r>rrr _cmd_prefixCszAFNIPythonCommand._cmd_prefix)r3r4r5r6rnrgrwrArr)r?r rs9srscCstjdkrdSdS)z$Check whether AFNI is not available.NTF)rrrrrr no_afniHs rx) r6r-sysr distutilsrrrrZutils.filemaniprrr\r r r r rrrZ external.duer getLoggerZIFLOGGERrr9rBrLrNrprsrxrrrr s"  $  S