3 Ydr#@sddlZddlZddlZddlmZmZddlm Z m Z ddlm Z m Z m Z mZmZmZmZGdd d e ZGd d d e ZGd d d e ZGddde ZGddde ZGddde ZGddde ZGddde ZGddde ZdS)N)split_filenamefname_presuffix)NipyBaseInterface have_nipy) TraitedSpectraitsBaseInterfaceInputSpec isdefinedFileInputMultiPathOutputMultiPathc@sJeZdZeddddZedddZejddZejddZ ej d dZ d S) ComputeMaskInputSpecTz:mean EPI image, used to compute the threshold for the mask)exists mandatorydesczTreference volume used to compute the mask. If none is give, the mean volume is used.)rrz/lower fraction of the histogram to be discarded)rz/upper fraction of the histogram to be discardedz)Keep only the largest connected componentN) __name__ __module__ __qualname__r mean_volumereference_volumer FloatmMZBoolccrrS/var/www/html/virt/lib/python3.6/site-packages/nipype/interfaces/nipy/preprocess.pyrs  rc@seZdZeddZdS)ComputeMaskOutputSpecT)rN)rrrr brain_maskrrrrr'src@s$eZdZeZeZddZddZdS) ComputeMaskc Csddlm}i}xVddt|jjDD]:}t|j|}t|r*|dkr\tjt j |j }|||<q*W|f|}t |jj \}}} tjjd|| f|_t jt j|jtjtj|j|S) Nr) compute_maskcSs"g|]\}}|tjkr|qSr)r Z trait_names).0k_rrr 4sz.ComputeMask._run_interface..rrz %s_mask.%s)rr)Znipy.labs.maskr"listinputsitemsgetattrr npZ asanyarraynbloaddataobjrrospathabspath_brain_mask_pathsave Nifti1ImageZastypeZuint8niiaffine) selfruntimer"argskeyvaluer r%nameextrrr_run_interface/s"    zComputeMask._run_interfacecCs|jj}|j|d<|S)Nr )_outputsgetr2)r7outputsrrr _list_outputsHs  zComputeMask._list_outputsN) rrrr input_specr output_specr>rBrrrrr!+sr!c @seZdZeeddddddZejddgdZej ej ejej d d d d d dddddZ ej ej ej dddddgdZdS)SpaceTimeRealignerInputSpecT)rz 0.4.0.devzFile to realign)rZmin_verrz TR in seconds slice_times)rrequiresZ asc_alt_2Z asc_alt_2_1Z asc_alt_halfZasc_alt_siemensZ ascendingZ desc_alt_2Z desc_alt_halfZ descendingzActual slice acquisition times.)rr)Zmin_lenmax_lenaSingle integer or length 2 sequence If int, the axis in `images` that is the slice axis. In a 4D image, this will often be axis = 2. If a 2 sequence, then elements are ``(slice_axis, slice_direction)``, where ``slice_axis`` is the slice axis in the image as above, and ``slice_direction`` is 1 if the slices were acquired slice 0 first, slice -1 last, or -1 if acquired slice -1 first, slice 0 last. If `slice_info` is an int, assume ``slice_direction`` == 1.N)rrrrr in_filer rtrZEitherListEnumrFInt slice_inforrrrrENs(  rEc@s0eZdZeeddddZeeddddZdS)SpaceTimeRealignerOutputSpecT)rzRealigned files)rz3Motion parameter files. Angles are not euler anglesN)rrrrr out_filepar_filerrrrrOwsrOc@s0eZdZdZeZeZddgZddZ ddZ dS) SpaceTimeRealignera|Simultaneous motion and slice timing correction algorithm If slice_times is not specified, this algorithm performs spatial motion correction This interface wraps nipy's SpaceTimeRealign algorithm [Roche2011]_ or simply the SpatialRealign algorithm when timing info is not provided. Examples -------- >>> from nipype.interfaces.nipy import SpaceTimeRealigner >>> #Run spatial realignment only >>> realigner = SpaceTimeRealigner() >>> realigner.inputs.in_file = ['functional.nii'] >>> res = realigner.run() # doctest: +SKIP >>> realigner = SpaceTimeRealigner() >>> realigner.inputs.in_file = ['functional.nii'] >>> realigner.inputs.tr = 2 >>> realigner.inputs.slice_times = list(range(0, 3, 67)) >>> realigner.inputs.slice_info = 2 >>> res = realigner.run() # doctest: +SKIP References ---------- .. [Roche2011] Roche A. A four-dimensional registration algorithm with application to joint correction of motion and slice timing in fMRI. IEEE Trans Med Imaging. 2011 Aug;30(8):1546-54. DOI_. .. _DOI: https://doi.org/10.1109/TMI.2011.2131152 z slice timingzmotion correctioncs|ddlm}mfdd|jjD}t|jjsHddlm}||}n(ddl m }|||jj |jj|jj d}|j dd|j}g|_g|_xt|D]\}} |jjtjjd t|jj|d || |j||jjtjjd tjj|jj|d t|j|d } |j|} xJt| D]>\} } d dtj| j| jfD}dj|d}| j|q*W| j qW|S)Nr) save_image load_imagecsg|] }|qSrr)r#fname)rTrrr&sz5SpaceTimeRealigner._run_interface..) 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