3 d8 @sdZddlZddlmZmZmZmZddlmZddlm Z ej Z ej de d Gd d d eZ Gd d d eZGdddeZdS)z The fusion module provides higher-level interfaces to some of the operations that can be performed with the seg_DetectLesions command-line program. N) TraitedSpecFiletraitsCommandLineInputSpec)NiftySegCommand)get_custom_pathalways)categoryc@seZdZdZeddddddZeddddd dZed ddd d dZed gdddddZe j dddZ dZ e j e ddZ e j dddZe j dddZdZ e j e ddZdS)PatchMatchInputSpeczInput Spec for PatchMatch.z-i %sTzInput image to segmentr)argstrexists mandatorydescpositionz-m %sz0Input mask for the area where applies PatchMatchrz-db %szDatabase with the segmentationsin_filez %s_pm.nii.gzz-The output filename of the patchmatch resultsz-o %s)Z name_sourceZ name_templaterr rzPatch size, #voxelsz-size %i)rr zGConstrained search area size, number of times bigger than the patchsizez-cs %izNumber of better matchingz -match %izNumber of patchmatch executionsz-pm %iz1Number of iterations for the patchmatch algorithmz-it %iN)__name__ __module__ __qualname____doc__rrZ mask_fileZ database_fileout_filerZIntZ patch_sizerZcs_sizeZ match_numZpm_numZit_numrrG/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/niftyseg/patchmatch.pyr s@r c@seZdZdZeddZdS)PatchMatchOutputSpeczOutputSpec for PatchMatch.zOutput segmentation)rN)rrrrrrrrrrrGsrc@s(eZdZdZedddZeZeZ dZ dS) PatchMatchaInterface for executable seg_PatchMatch from NiftySeg platform. The database file is a text file and in each line we have a template file, a mask with the search region to consider and a file with the label to propagate. Input image, input mask, template images from database and masks from database must have the same 4D resolution (same number of XxYxZ voxels, modalities and/or time-points). Label files from database must have the same 3D resolution (XxYxZ voxels) than input image but can have different number of volumes than the input image allowing to propagate multiple labels in the same execution. `Source code `_ | `Documentation `_ Examples -------- >>> from nipype.interfaces import niftyseg >>> node = niftyseg.PatchMatch() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.mask_file = 'im2.nii' >>> node.inputs.database_file = 'db.xml' >>> node.cmdline 'seg_PatchMatch -i im1.nii -m im2.nii -db db.xml -o im1_pm.nii.gz' Zseg_PatchMatchZ NIFTYSEGDIR)Zenv_dirZ_pmN) rrrrr Z_cmdr Z input_specrZ output_spec_suffixrrrrrMs  r)rwarningsbaserrrrrZ niftyreg.baser warnfilterwarnings UserWarningr rrrrrrs  5