3 dh@sdZddlZddlmZmZmZmZddlmZddlm Z ej Z ej de d Gd d d eZ Gd d d eZGdddeZdS)a Nipype interface for seg_FillLesions. The fusion module provides higher-level interfaces to some of the operations that can be performed with the seg_FillLesions command-line program. Examples -------- See the docstrings of the individual classes for examples. N) TraitedSpecFiletraitsCommandLineInputSpec)NiftySegCommand)get_custom_pathalways)categoryc@seZdZdZeddddddZeddddd dZed gd d d ddZdZe j eddZ dZe j eddZ dZe j eddZdZe j eddZdZe j eddZdZe j eddZdZeeddZdZe jed dZe jd!d"dZe jd#d$dZd%Ze jed&dZe jd'd(dZd)S)*FillLesionsInputSpeczInput Spec for FillLesions.z-i %sTzInput image to fill lesionsr)argstrexists mandatorydescpositionz-l %sz Lesion maskrin_filez%s_lesions_filled.nii.gzz/The output filename of the fill lesions resultsz-o %s)Z name_sourceZ name_templaterr rz5Dilate the mask times (in voxels, by default 0)z-dil %d)rr zPPercentage of minimum number of voxels between patches (by default 0.5).z -match %fzJMinimum percentage of valid voxels in target patch (by default 0).z -search %fzJSmoothing by (in minimal 6-neighbourhood voxels (by default 0.1)).z-smo %fz>Search regions size respect biggest patch size (by default 4).z-size %dz2Patch cardinality weighting factor (by default 2).z-cwf %fz/Give a binary mask with the valid search areas.z-mask %saGuizard et al. (FIN 2015) method, it doesn't include the multiresolution/hierarchical inpainting part, this part needs to be done with some external software such as reg_tools and reg_resample from NiftyReg. By default it uses the method presented in Prados et al. (Neuroimage 2016).z-otherz-Uses 2D patches in the Z axis, by default 3D.z-2Dz,Save all intermidium files (by default OFF).z-debugzMSet output (char, short, int, uchar, ushort, uint, float, double).z-odt %szVerbose (by default OFF).z-vN)__name__ __module__ __qualname____doc__rrZ lesion_maskout_filerrZIntZ in_dilationZFloatmatchsearchZsmoothsizeZcwfZbin_maskZBoolotherZuse_2ddebugStringZ out_datatypeverboser r D/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/niftyseg/lesions.pyr sL   r c@seZdZdZeddZdS)FillLesionsOutputSpeczOutput Spec for FillLesions.zOutput segmentation)rN)rrrrrrr r r r!r"dsr"c@s$eZdZdZedddZeZeZ dS) FillLesionsaIInterface for executable seg_FillLesions from NiftySeg platform. Fill all the masked lesions with WM intensity average. `Source code `_ | `Documentation `_ Examples -------- >>> from nipype.interfaces import niftyseg >>> node = niftyseg.FillLesions() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.lesion_mask = 'im2.nii' >>> node.cmdline 'seg_FillLesions -i im1.nii -l im2.nii -o im1_lesions_filled.nii.gz' Zseg_FillLesionsZ NIFTYSEGDIR)Zenv_dirN) rrrrr Z_cmdr Z input_specr"Z output_specr r r r!r#js r#)rwarningsbaserrrrrZ niftyreg.baser warnfilterwarnings UserWarningr r"r#r r r r! s  L