3 dS@sdZddlZddlmZddlmZddlZddlm Z ddl m Z dd l mZmZmZmZmZmZmZmZmZdd lmZdd lmZdd lmZmZmZd Ze j dZ!ddZ"ddZ#ddZ$d"ddZ%GdddeZ&ddZ'GdddeZ(GdddeZ)Gd d!d!eZ*dS)#aThe spm module provides basic functions for interfacing with SPM tools. In order to use the standalone MCR version of spm, you need to ensure that the following commands are executed at the beginning of your script:: from nipype.interfaces import spm matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script' spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True) you can test by calling:: spm.SPMCommand().version N)deepcopy)load)logging)spm_docs) BaseInterfacetraits isdefinedInputMultiPathBaseInterfaceInputSpec Directory Undefined ImageFile PackageInfo)NoDefaultSpecified) MatlabCommand)dueDoiBibTeXZrestructuredtextznipype.interfacecCsTt|trt|dSt|}|j}t|dksHt|dkrL|ddkrLdSdSdS)z(Checks if input functional files are 3d.rrTFN) isinstancelist func_is_3drshapelen)in_fileimgrrW|d|_|d|_|d|_||_||_|S)a4 Returns the path to the SPM directory in the Matlab path If path not found, returns None. Parameters ---------- matlab_cmd: str Sets the default matlab command. If None, the value of the environment variable SPMMCRCMD will be used if set and use_mcr is True or the environment variable FORCE_SPMMCR is set. If one of FORCE_SPMMCR or SPMMCRCMD is not set, the existence of the environment variable MATLABCMD is checked and its value is used as the matlab command if possible. If none of the above was successful, the fallback value of 'matlab -nodesktop -nosplash' will be used. paths : str Add paths to matlab session use_mcr : bool Whether to use the MATLAB Common Runtime. In this case, the matlab_cmd is expected to be a valid MCR call. Returns ------- spm_path : string representing path to SPM directory returns None of path not found FORCE_SPMMCR SPMMCRCMDZ MATLABCMDzmatlab -nodesktop -nosplash)r<r8releasez8matlab command or path has changed. recomputing version.F)r5resource_monitorTz if isempty(which('spm')), throw(MException('SPMCheck:NotFound','SPM not in matlab path')); end; spm_path = spm('dir'); [name, version] = spm('ver'); fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version); exit; z%sN|:r?r8r<)osenvirongetenvr;r3r9_command_pathsloggerdebugrinputsmfiler6r nodesktopnosplashsingle_comp_threaduses_mcrscriptrunIOError RuntimeErrorsdZ _strip_headerruntimestdoutsplit) r4r5r6r7mlabouteZout_dictpartkeyvalrrr r2sV           z Info.getinfo)NNN)NNN)NNN)NNN)__name__ __module__ __qualname____doc__r3r;rFrGr9 classmethodr8r:r<r2rrrr r1s   r1cCs"dtjkstjdkrdSdSdS)zChecks if SPM is NOT installed used with pytest.mark.skipif decorator to skip tests that will fail if spm is not installedZNIPYPE_NO_MATLABNTF)rCrDr1r:rrrr no_spmsrcc@sTeZdZejddZeeddZej ddddZ ej ddZ ej dddd d Z d S) SPMCommandInputSpeczmatlab command to use)desczPaths to add to matlabpathTzRun m-code using m-file)re usedefaultzRun m-code using SPM MCR8z(Generate SPM8 and higher compatible jobs)Zmin_verrfreN) r^r_r`r Strr5r r r6BoolrKr7 use_v8structrrrr rds  rdcseZdZdZeZdgZdZdZdZ dZ dZ e dddgd gZ fd d Zed)d d ZddZddZeddZeddZeddZddZddZddZddZffd d!Zd"d#Zd*d%d&Zd+d'd(ZZS), SPMCommandzExtends `BaseInterface` class to implement SPM specific interfaces. WARNING: Pseudo prototype class, meant to be subclassed fieldZbasetypebasenameNz@book{FrackowiakFristonFrithDolanMazziotta1997,author={R.S.J. Frackowiak, K.J. Friston, C.D. Frith, R.J. Dolan, and J.C. 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In order to create an appropriate SPM job structure, a Python dict storing the job needs to be modified so that each dict embedded in dict needs to be enclosed as a list element. Examples -------- >>> a = SPMCommand()._reformat_dict_for_savemat(dict(a=1, ... b=dict(c=2, d=3))) >>> a == [{'a': 1, 'b': [{'c': 2, 'd': 3}]}] True zRequires dict inputN)rrrr_reformat_dict_for_savemat TypeErrorprint)rwcontentsZnewdictr\rrrr rs  z%SPMCommand._reformat_dict_for_savematc Csrd}|dkr|St|trxxXt|D]L\}}|jdrPd|dd|df}nd||df}||j||7}q$W|St|trx4t|jD]$\}}d||f}||j||7}qW|St|tjr6|j tj t kr|r|d|7}n|d 7}xt|D]\}}t|tjr*||jd|d 7}nt|trg} x,|D]$} | t| t t fsZd nd g7} q@Wd j | j} |dj| |7}n0t|t t fr|dj|7}n|dt |7}qW|d7}njxht|D]\\}}xP|j jD]D} |rd||d| f}nd|d| f}||j||| 7}qWqW|St|t t frZ|d||f7}|S|d|t |f7}|S)afRecursive function to generate spm job specification as a string Parameters ---------- prefix : string A string that needs to get contents : dict A non-tuple Python structure containing spm job information gets converted to an appropriate sequence of matlab commands. rN)z%s,%d)rz%s(%d)z%s.%sz %s = {... z{... )prefixrz{}z'{}'z, z [{}];... z '{}';... z%s;... z}; z %s(%d).%sz(%d).%sz %s = '%s'; z %s = %s; r)rrr&endswith _generate_jobrrr#Zndarrayr"r%strbytesjoinformatr) rwrrZ jobstringr/rZ newprefixr\r]Z items_formatelZ val_formatrlrrr rs\       "   zSPMCommand._generate_jobc Cs tj}d}|jjjrt|jjrL|jjrL||jd|j|j f|d7}nL|j dkrx||jd |j|j f|d7}n ||jd |j|j f|d7}nVddl m }d|j|j |j |digigi}|tj j|d|j ||d|j 7}|d7}|jjr |d7}|dk r||7}|S)agGenerates a mfile to build job structure Parameters ---------- contents : list a list of dicts generated by _parse_inputs in each subclass cwd : string default os.getcwd() Returns ------- mscript : string contents of a script called by matlab a %% Generated by nipype.interfaces.spm if isempty(which('spm')), throw(MException('SPMCheck:NotFound', 'SPM not in matlab path')); end [name, version] = spm('ver'); fprintf('SPM version: %s Release: %s\n',name, version); fprintf('SPM path: %s\n', which('spm')); spm('Defaults','fMRI'); if strcmp(name, 'SPM8') || strcmp(name(1:5), 'SPM12'), spm_jobman('initcfg'); spm_get_defaults('cmdline', 1); end zjobs{1}.spm.%s.%srstsmoothpreprocpreproc8 fmri_specfmri_estfactorial_designdefszjobs{1}.%s{1}.%s(1)zjobs{1}.%s{1}.%s{1})savematjobsz pyjobs_%s.matzload pyjobs_%s; z+ spm_jobman('run', jobs); z| if strcmp(name, 'SPM8') || strcmp(name(1:5), 'SPM12'), close('all', 'force'); end; N)rrrrrrrr)rCgetcwdrXrJrKr rjrrrZscipy.iorZreformat_dict_for_savematr8rr7)rwrZ postscriptcwdZmscriptrZjobdefrrr rsF    zSPMCommand._make_matlab_command)NNN)rN)N) r^r_r`rardZ input_specZ_additional_metadatarrryrGrzrZ _referencesrsrbr}rurtpropertyr:rrrvrrrrrrr __classcell__rr)rxr rks8        Brkcs(eZdZdZeddffdd ZZS) ImageFileSPMz1Defines a trait whose value must be a NIfTI file.Fc s*tt|jf||ddgd|d|dS)zCreate an ImageFileSPM trait.Znifti1Znifti2F)rexiststypesZallow_compressedresolveN)rrrrs)rwrrrr)rxrr rsls zImageFileSPM.__init__)r^r_r`rarrsrrr)rxr risr)FF)+rarCcopyrZnibabelrnumpyr#rrutilsrrTbaserr r r r r rrrZbase.traits_extensionrZmatlabrZ external.duerrrZ __docformat__ getLoggerrHrr!r,r0r1rcrdrkrrrrr s.    ,    'z  V