3 d/@sdZddlZddlmZmZmZmZmZmZddl m Z ddl m Z dd d d d d ddddddddddddddddgZ GdddeZGd d!d!eZGd"d#d#eZdS)$zRPETPVC is a toolbox for partial volume correction in positron emission tomography.N) TraitedSpecCommandLineInputSpec CommandLineFile isdefinedtraits)fname_presuffix)BibTeXZGTMZIYzIY+RLzIY+VCZLABBEz LABBE+MTCz LABBE+MTC+RLz LABBE+MTC+VCz LABBE+RBVz LABBE+RBV+RLz LABBE+RBV+VCZMGzMG+RLzMG+VCZMTCzMTC+RLzMTC+VCZRBVzRBV+RLzRBV+VCZRLVCc@seZdZedddddZedddddZed ddd dZeje dd d d Z ej ddddZ ej ddddZ ej ddddZejdddddZejdddddZejdddddZej dddd dZej d!d"dd#dZd$S)%PETPVCInputSpeczPET image fileTz-i %s)descexists mandatoryargstrz Output fileFz-o %s)rZgenfileZ hash_filesrzMask image filez-m %sz-p %saDesired PVC method: * Geometric transfer matrix -- ``GTM`` * Labbe approach -- ``LABBE`` * Richardson-Lucy -- ``RL`` * Van-Cittert -- ``VC`` * Region-based voxel-wise correction -- ``RBV`` * RBV with Labbe -- ``LABBE+RBV`` * RBV with Van-Cittert -- ``RBV+VC`` * RBV with Richardson-Lucy -- ``RBV+RL`` * RBV with Labbe and Van-Cittert -- ``LABBE+RBV+VC`` * RBV with Labbe and Richardson-Lucy -- ``LABBE+RBV+RL`` * Multi-target correction -- ``MTC`` * MTC with Labbe -- ``LABBE+MTC`` * MTC with Van-Cittert -- ``MTC+VC`` * MTC with Richardson-Lucy -- ``MTC+RL`` * MTC with Labbe and Van-Cittert -- ``LABBE+MTC+VC`` * MTC with Labbe and Richardson-Lucy -- ``LABBE+MTC+RL`` * Iterative Yang -- ``IY`` * Iterative Yang with Van-Cittert -- ``IY+VC`` * Iterative Yang with Richardson-Lucy -- ``IY+RL`` * Muller Gartner -- ``MG`` * Muller Gartner with Van-Cittert -- ``MG+VC`` * Muller Gartner with Richardson-Lucy -- ``MG+RL`` )rrrz1The full-width at half maximum in mm along x-axisz-x %.4f)rrrz1The full-width at half maximum in mm along y-axisz-y %.4fz1The full-width at half maximum in mm along z-axisz-z %.4fzPrints debug informationz-d)r usedefault default_valuerzNumber of iterations z-n %d)rrrrz"Number of deconvolution iterationsz-k %dz Alpha valueg?z-a %.4fzStopping criteriong{Gz?z-s %.4fN)__name__ __module__ __qualname__rin_fileout_fileZ mask_filerEnum pvc_methodspvcZFloatZfwhm_xZfwhm_yZfwhm_zZBooldebugZIntZn_iterZn_deconvalphaZ stop_critrr:/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/petpvc.pyr ,sJr c@seZdZeddZdS)PETPVCOutputSpecz Output file)rN)rrrrrrrrr r!xsr!c@sJeZdZdZeZeZdZe dddgdgZ ddZ dd d Z ddZ d S)PETPVCaUse PETPVC for partial volume correction of PET images. PETPVC ([1]_, [2]_) is a software from the Nuclear Medicine Department of the UCL University Hospital, London, UK. Examples -------- >>> from ..testing import example_data >>> #TODO get data for PETPVC >>> pvc = PETPVC() >>> pvc.inputs.in_file = 'pet.nii.gz' >>> pvc.inputs.mask_file = 'tissues.nii.gz' >>> pvc.inputs.out_file = 'pet_pvc_rbv.nii.gz' >>> pvc.inputs.pvc = 'RBV' >>> pvc.inputs.fwhm_x = 2.0 >>> pvc.inputs.fwhm_y = 2.0 >>> pvc.inputs.fwhm_z = 2.0 >>> outs = pvc.run() #doctest: +SKIP References ---------- .. [1] K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton, "A review of partial volume correction techniques for emission tomography and their applications in neurology, cardiology and oncology," Phys. Med. Biol., vol. 57, no. 21, p. R119, 2012. .. [2] https://github.com/UCL/PETPVC Zpetpvca@article{0031-9155-61-22-7975,author={Benjamin A Thomas and Vesna Cuplov and Alexandre Bousse and Adriana Mendes and Kris Thielemans and Brian F Hutton and Kjell Erlandsson},title={PETPVC: a toolbox for performing partial volume correction techniques in positron emission tomography},journal={Physics in Medicine and Biology},volume={61},number={22},pages={7975},url={http://stacks.iop.org/0031-9155/61/i=22/a=7975},doi={https://doi.org/10.1088/0031-9155/61/22/7975},year={2016},}z*PETPVC software implementation publicationimplementation)entry descriptiontagscCsd|jj}|jj|d<t|dsL|jjj}|j|jjdj |d|d<t j j |d|d<|S)Nrz_{}_pvc)suffix) output_specgetinputsrrrlower _gen_fnamerformatospathabspath)selfoutputs method_namerrr _list_outputss    zPETPVC._list_outputsNT.nii.gzcCsn|dkr"d|j}|d7}t||dkr2tj}|rN|rJdj||f}n|}|dkrZd}t||d|d}|S)aGenerate a filename based on the given parameters. The filename will take the form: cwd/basename. If change_ext is True, it will use the extentions specified in intputs.output_type. Parameters ---------- basename : str Filename to base the new filename on. cwd : str Path to prefix to the new filename. (default is os.getcwd()) suffix : str Suffix to add to the `basename`. (defaults is '' ) change_ext : bool Flag to change the filename extension to the given `ext`. (Default is False) Returns ------- fname : str New filename based on given parameters. z,Unable to generate filename for command %s. zbasename is not set!NF)r'Zuse_extnewpath)cmd ValueErrorr.getcwdjoinr )r1basenamecwdr'Z change_extextmsgfnamerrr r,s zPETPVC._gen_fnamecCs|dkr|jdSdS)Nr)r4)r1namerrr _gen_filenames zPETPVC._gen_filename)NNTr5)rrr__doc__r Z input_specr!r(Z_cmdr Z _referencesr4r,rBrrrr r"|s  *r")rCr.baserrrrrrZutils.filemanipr Z external.duer rr r!r"rrrr s:   L