3 d6@shdZddlZddlZddlZddlmZmZmZm Z m Z m Z m Z m Z mZmZmZmZddlmZmZddlmZmZmZGdd d eZGd d d eeZGd d d eZddZGdddeZGdddeZGdddeZGdddeeZ GdddeZ!GdddeZ"GdddeZ#GdddeZ$Gd d!d!eZ%Gd"d#d#eZ&Gd$d%d%eZ'dS)&zf # changing to temporary directories >>> tmp = getfixture('tmpdir') >>> old = tmp.chdir() N) traits TraitedSpecDynamicTraitedSpecFile Undefined isdefinedOutputMultiPathInputMultiPath BaseInterfaceBaseInterfaceInputSpecStrSimpleInterface)IOBase add_traits) ensure_listcopyfilesplit_filenamecs:eZdZdZeZeZd fdd ZddZdd Z Z S) IdentityInterfaceaBasic interface class generates identity mappings Examples -------- >>> from nipype.interfaces.utility import IdentityInterface >>> ii = IdentityInterface(fields=['a', 'b'], mandatory_inputs=False) >>> ii.inputs.a >>> ii.inputs.a = 'foo' >>> out = ii._outputs() >>> out.a >>> out = ii.run() >>> out.outputs.a 'foo' >>> ii2 = IdentityInterface(fields=['a', 'b'], mandatory_inputs=True) >>> ii2.inputs.a = 'foo' >>> out = ii2.run() # doctest: +SKIP ValueError: IdentityInterface requires a value for input 'b' because it was listed in 'fields' Interface IdentityInterface failed to run. NTc sttt|jf||dks | r(tdx |D]}||kr.td|q.W||_||_t|j||jjf|dS)Nz2Identity Interface fields must be a non-empty listz1Identity Interface input is not in the fields: %s) superr__init__ ValueError_fields_mandatory_inputsrinputs trait_set)selffieldsZmandatory_inputsrZin_field) __class__@/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/utility/base.pyr<s  zIdentityInterface.__init__cCs t||jS)N)rr)rbaser r r!_add_output_traitsNsz$IdentityInterface._add_output_traitscCs|jrH|jrHx:|jD]0}t|j|}t|sd|jj|f}t|qW|jj }x*|jD] }t|j|}t|r\|||<q\W|S)Nz%s requires a value for input '%s' because it was listed in 'fields'. You can turn off mandatory inputs checking by passing mandatory_inputs = False to the constructor.) rrgetattrrrr__name__r_outputsget)rkeyvaluemsgoutputsvalr r r! _list_outputsQs        zIdentityInterface._list_outputs)NT) r% __module__ __qualname____doc__r input_spec output_specrr#r- __classcell__r r )rr!rs rc@s>eZdZejdddddZejddddZejddddZd S) MergeInputSpecvstackZhstackTzRdirection in which to merge, hstack requires same number of elements in each input) usedefaultdescFz5append to outlist instead of extending in vstack modez%ravel inputs when no_flatten is FalseN) r%r.r/rEnumaxisBool no_flatten ravel_inputsr r r r!r4fsr4c@seZdZejddZdS)MergeOutputSpecz Merged output)r7N)r%r.r/rListoutr r r r!r=wsr=cCsLt|ts|Sg}x4|D],}t|}t|tr:|j|q|j|qW|S)N) isinstancelist_ravelextendappend)Zin_valZ flat_listr,Z raveled_valr r r!rB{s    rBcs2eZdZdZeZeZdfdd ZddZ Z S)MergeaNBasic interface class to merge inputs into a single list ``Merge(1)`` will merge a list of lists Examples -------- >>> from nipype.interfaces.utility import Merge >>> mi = Merge(3) >>> mi.inputs.in1 = 1 >>> mi.inputs.in2 = [2, 5] >>> mi.inputs.in3 = 3 >>> out = mi.run() >>> out.outputs.out [1, 2, 5, 3] >>> merge = Merge(1) >>> merge.inputs.in1 = [1, [2, 5], 3] >>> out = merge.run() >>> out.outputs.out [1, [2, 5], 3] >>> merge = Merge(1) >>> merge.inputs.in1 = [1, [2, 5], 3] >>> merge.inputs.ravel_inputs = True >>> out = merge.run() >>> out.outputs.out [1, 2, 5, 3] >>> merge = Merge(1) >>> merge.inputs.in1 = [1, [2, 5], 3] >>> merge.inputs.no_flatten = True >>> out = merge.run() >>> out.outputs.out [[1, [2, 5], 3]] rc sHtt|jf|||_|dkr4ddt|D}ng}t|j|dS)NcSsg|]}d|dqS)zin%drFr ).0ir r r! sz"Merge.__init__..)rrEr _numinputsrangerr)rZ numinputsrZ input_names)rr r!rs zMerge.__init__csjj}g}jdkr|SfddfddtjD}jjdkrxt|D]>}t|trjj r|j jj rt |n|qT|j |qTWn,dd|Dfddtt d D}||d <|S) NrFcstjd|dS)Nzin%drF)r$r)idx)rr r!sz%Merge._list_outputs..cs g|]}t|r|qSr )r)rGrL)getvalr r!rIsz'Merge._list_outputs..r5cSsg|] }t|qSr )r)rGr,r r r!rIscsg|]fddDqS)csg|] }|qSr r )rGr,)rHr r!rIsz2Merge._list_outputs...r )rG)lists)rHr!rIsrr?)r&r'rJrKrr9r@rAr;rCr<rBrDlen)rr+r?valuesr)r )rNrOrr!r-s     zMerge._list_outputs)r) r%r.r/r0r4r1r=r2rr-r3r r )rr!rEs $ rEc@sLeZdZeddddZejddZedddZ eddZ ejd dd d Z d S) RenameInputSpecTzfile to rename)exists mandatoryr7z?Keep in_file extension, replace non-extension component of name)r7z,Python formatting string for output template)rTr7z7Python regexp parse string to define replacement inputsFz&Use full path as input to regex parser)r6r7N) r%r.r/rin_filerr:keep_extr format_string parse_string use_fullpathr r r r!rRs rRc@seZdZedddZdS)RenameOutputSpecTz'softlink to original file with new name)rSr7N)r%r.r/rout_filer r r r!rZsrZcs:eZdZdZeZeZd fdd ZddZ ddZ Z S) RenameayChange the name of a file based on a mapped format string. To use additional inputs that will be defined at run-time, the class constructor must be called with the format template, and the fields identified will become inputs to the interface. Additionally, you may set the parse_string input, which will be run over the input filename with a regular expressions search, and will fill in additional input fields from matched groups. Fields set with inputs have precedence over fields filled in with the regexp match. Examples -------- >>> from nipype.interfaces.utility import Rename >>> rename1 = Rename() >>> rename1.inputs.in_file = os.path.join(datadir, "zstat1.nii.gz") # datadir is a directory with exemplary files, defined in conftest.py >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz" >>> res = rename1.run() # doctest: +SKIP >>> res.outputs.out_file # doctest: +SKIP 'Faces-Scenes.nii.gz" # doctest: +SKIP >>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d") >>> rename2.inputs.in_file = os.path.join(datadir, "functional.nii") >>> rename2.inputs.keep_ext = True >>> rename2.inputs.subject_id = "subj_201" >>> rename2.inputs.run = 2 >>> res = rename2.run() # doctest: +SKIP >>> res.outputs.out_file # doctest: +SKIP 'subj_201_func_run02.nii' # doctest: +SKIP >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii") >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii") >>> rename3.inputs.parse_string = r"func_(?P\w*)_.*" >>> rename3.inputs.subject_id = "subj_201" >>> rename3.inputs.run = 2 >>> res = rename3.run() # doctest: +SKIP >>> res.outputs.out_file # doctest: +SKIP 'subj_201_epi_run02.nii' # doctest: +SKIP Nc sJtt|jf||dk r@||j_tjd||_t|j|jng|_dS)Nz %\((.+?)\)) rr\rrrWrefindall fmt_fieldsr)rrWr)rr r!rs zRename.__init__cCst}t|jjrnt|jjr<|jjrAnyinlistIntsplitsr:squeezer r r r!rq=srqc@s(eZdZdZeZeZddZddZ dS)Splita!Basic interface class to split lists into multiple outputs Examples -------- >>> from nipype.interfaces.utility import Split >>> sp = Split() >>> _ = sp.inputs.trait_set(inlist=[1, 2, 3], splits=[2, 1]) >>> out = sp.run() >>> out.outputs.out1 [1, 2] cCsXi}x:tt|jjD]&}d|d}|j|tjt||<qW|jfddi||S)Nzout%drFZtrait_change_notifyF) rKrPrruZ add_traitrrrrr)rr"Zundefined_traitsrHr(r r r!r#[s  zSplit._add_output_traitscCs|jj}t|jjrt|jjt|jjkr8tddg}|j |jjt j |}xnt t|dD]Z}t j |jjtd||||dj}|jjrt|dkr|d}||d|d<qhW|S)Nz%sum of splits != num of list elementsrrF)dtypezout%d)r&r'rrrusumrPrs RuntimeErrorrCnpZcumsumrKarrayobjecttolistrv)rr+rurHr,r r r!r-ds   zSplit._list_outputsN) r%r.r/r0rqr1rr2r#r-r r r r!rwIs   rwc@s,eZdZeejdddZeejdddZdS)SelectInputSpecTzlist of values to choose from)rTr7z#0-based indices of values to chooseN) r%r.r/r rrrrsrtindexr r r r!rvsrc@seZdZeejddZdS)SelectOutputSpeczlist of selected values)r7N)r%r.r/r rrrr?r r r r!rsrc@s eZdZdZeZeZddZdS)SelectaBasic interface class to select specific elements from a list Examples -------- >>> from nipype.interfaces.utility import Select >>> sl = Select() >>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3]) >>> out = sl.run() >>> out.outputs.out 4 >>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3, 4]) >>> out = sl.run() >>> out.outputs.out [4, 5] cCs<|jj}tj|jjtdtj|jjj}||d<|S)N)rxr?) r&r'r{r|rrsr}rr~)rr+r?r r r!r-s  zSelect._list_outputsN) r%r.r/r0rr1rr2r-r r r r!rsrc@s$eZdZedddZedddZdS)AssertEqualInputSpecT)rSrTN)r%r.r/rvolume1volume2r r r r!rs rc@seZdZeZddZdS) AssertEqualcCsHddl}tj|j|jj}tj|j|jj}tj||sDtd|S)Nrz"Input images are not exactly equal) Znibabelr{Z asanyarrayloadrrrZ array_equalrz)rrnnbZdata1Zdata2r r r!rps  zAssertEqual._run_interfaceN)r%r.r/rr1rpr r r r!rsr)(r0rcr]numpyr{r"rrrrrrr r r r r riorrZutils.filemaniprrrrr4r=rBrErRrZr\rqrwrrrrrr r r r!s*8G KV -