3 d: @sdZddljZddlZddlZddlmZddl m Z m Z m Z m Z mZmZddgZd ayddlZdd lmZWnek rd aYnXd d ZddZGddde ZGdddeZGdddeZddZd ddZdefddZefddZddZdS)!z Base interfaces for dipy N)logging)traitsFile isdefinedLibraryBaseInterfaceBaseInterfaceInputSpec TraitedSpecWorkflowZCombinedWorkflowT)IntrospectiveArgumentParserFcCst S)zCheck if dipy is available.) HAVE_DIPYrr=/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/dipy/base.pyno_dipysrcCstr dStjS)zCheck dipy version.N)rdipy __version__rrrr dipy_version#src@seZdZdZdZdS)DipyBaseInterfacez0A base interface for py:mod:`dipy` computations.rN)__name__ __module__ __qualname____doc__Z_pkgrrrrr+src@sReZdZeddddZeddddZeddddZejddddZ ej d d Z d S) DipyBaseInterfaceInputSpecTzinput diffusion data)exists mandatorydesczinput b-values tablezinput b-vectors tableiz b0 threshold) usedefaultrzoutput prefix for file names)rN) rrrrin_filein_bvalin_bvecrIntb0_thresStr out_prefixrrrrr1s rc@s&eZdZdZeZddZdddZdS)DipyDiffusionInterfacez0A base interface for py:mod:`dipy` computations.cCsBtj|jj}tj|jjj}ddlm}|||}|jj|_ |S)Nr)gradient_table) npZloadtxtinputsrr TZdipy.core.gradientsr&r"Z b0_threshold)selfZbvalZbvecr&Zgtabrrr_get_gradient_table>s    z*DipyDiffusionInterface._get_gradient_tableNcCsrtjtj|jj\}}|dkr6tj|\}}||}t|jjsNtj|}n|jj}|dkrb|}|d||S)Nz.gz_)opsplitextbasenamer(rrr$abspath)r*nameextfnameZfextZfext2r$rrr _gen_filenameHs  z$DipyDiffusionInterface._gen_filename)N)rrrrr input_specr+r4rrrrr%9s r%cCstj|}dd|jjDS)zReturn optional arguments of a function. Parameters ---------- func: callable Returns ------- dict cSs&i|]\}}|jtjjk r|j|qSr)defaultinspect Parameterempty).0kvrrr fsz$get_default_args..)r7 signature parametersitems)funcr>rrrget_default_argsYs rBcCs(|j}td|k}d|kr.d|kr.tj|fSd|krHd|krHtj|fSd|krbd|krbtj|fSd|kr|d|kr|tj|fSd|krd|krtj|fSd|kr| rtj|fSd|kr|rt |fSd|krtj |fSd|krtj |fSd|krtj |fSd|krtj |fSdj|d }t|d S) z!Convert DIPY type to Traits type.optionalvariablestringintfloatboolcomplexz)Error during convert_to_traits_type({0}).zUnknown DIPY type.N)lowerrHrZListStrZListIntZ ListFloatZListBoolZ ListComplexr#rr!ZFloatZBoolComplexformatIOError) dipy_typeis_file is_mandatorymsgrrrconvert_to_traits_typems6              rRc Csi}|dk rx|D]}|d|d|d}}}td|kpBd|k}t||\} } |jtjkrt|dkr| |d|d d| d ||<q| |d | d ||<q| |d|dddd ||<qWtt||f|} | S)akCreate IN/Out interface specifications dynamically. Parameters ---------- class_name: str The future class name(e.g, (MyClassInSpec)) params: list of tuple dipy argument list BaseClass: TraitedSpec object parent class Returns ------- newclass: object new nipype interface specification class NrrfilesZout_rT)rrr)rr)rrrrUrU)rHrRrr lentypestr) class_nameparams BaseClassattrpr1rNrrOZ traits_typerPnewclassrrrcreate_interface_specss   r_cst}}|j|tt|jj}ddt|j|D}t|jt|j }ddt|j ||dD}|j |} t dj || t d} t dj ||td} fdd } d d } tt||f| | | | d }|S) aConstruct a class in order to respect nipype interface specifications. This convenient class factory convert a DIPY Workflow to a nipype interface. Parameters ---------- cls_name: string new class name dipy_flow: Workflow class type. It should be any children class of `dipy.workflows.workflow.Worflow` BaseClass: object nipype instance object Returns ------- newclass: object new nipype interface specification class cSsg|]\}}||fqSrr)r:argsvalrrr sz,dipy_to_nipype_interface..cSsg|]\}}||fqSrr)r:r`rarrrrbsNz {}InputSpec)r[z {}OutputSpeccs }|jj}|jf|dS)N)r(getrun)r*Zruntimeflowr`) dipy_flowrr_run_interfaces z0dipy_to_nipype_interface.._run_interfacecSsB|jj}|jdd}x$|jD]\}}tj||||<q"W|S)Nout_dir.)Z_outputsrcr@r-join)r*outputsrhkeyvaluesrrr _list_outputss   z/dipy_to_nipype_interface.._list_outputs)r5 output_specrgz_list_outputs:)r Z add_workflowlistrBrdrmzipZoptional_parametersrVoutput_parametersZpositional_parametersr_rLr r rWrX)Zcls_namerfr[parserreZdefault_valuesZoptional_paramsstartrrZinput_parametersr5rorgrnr^r)rfrdipy_to_nipype_interfaces2    rucsfddtjDS)aSearch for DIPY workflow class. Parameters ---------- module : object module object Returns ------- l_wkflw : list of tuple This a list of tuple containing 2 elements: Worflow name, Workflow class obj Examples -------- >>> from dipy.workflows import align # doctest: +SKIP >>> get_dipy_workflows(align) # doctest: +SKIP cs6g|].\}}tj|rt|jr|tkr||fqSr)r7isclass issubclassr SKIP_WORKFLOWS_LIST)r:mobj)modulerrrbs  z&get_dipy_workflows..)r7 getmembers)r{r)r{rget_dipy_workflowss r})F) ros.pathpathr-r7numpyr'rbaserrrrr r rxr rZdipy.workflows.baser ImportErrorrrrrr%rBrRr_rur}rrrrs,      ") H