3 d|B@sdZddlZddlZddlmZddlZddlZddlmZddl m Z ddl m Z m Z mZmZmZmZmZmZmZmZGd d d eZGd d d e ZGd ddeZGddde ZGddde ZGdddeZGddde ZddZdS)zKdcm2nii converts images from the proprietary scanner DICOM format to NIfTI.N)deepcopy)iglob)split_filename) CommandLineCommandLineInputSpecInputMultiPathtraits TraitedSpecOutputMultiPath isdefinedFile Directory PackageInfoc@s eZdZdZdZeddZdS)Infoz#Handle dcm2niix version informationdcm2niixcCs tjd|}|r|jdSdS)Nz version (\S+)r)researchgroups)Zraw_infomr;/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/dcm2nii.py parse_versions zInfo.parse_versionN)__name__ __module__ __qualname____doc__Z version_cmd staticmethodrrrrrrsrc@sBeZdZeedddd.dddgdZeddd/ddgd Zej dd dd d Z edd dddZ ej ddddd Z ej ddddd Z ej ddddd Zej ddddd Zej ddddd Zej ddddd Zej ddddd ZedddddZej dd dd!d Zej d"d#d$Zej d%d&gd'd(Zej dd)dd*d Zej dd+dd,d Zd-S)0Dcm2niiInputSpecT)existsz%srF source_dir)argstrpositioncopyfile mandatoryxor source_names)r r"r#r%r&z-azRemove identifying information)r" usedefaultdescz-b %sz$Load settings from specified inifile)r r"Zgenfiler)z-czCollapse input foldersz-dzDate in filenamez-ezEvents (series/acq) in filenamez-fzSource filenamez-gzGzip output (.gz)z-izID in filenamez-nz+Save as .nii - if no, create .hdr/.img pairz-o %sz5Output dir - if unspecified, source directory is usedz-pzProtocol in filenamez-rz$Reorient image to nearest orthogonal)r"r)z-s nii_outputzSPM2/Analyze not SPM5/NIfTI)r"r&r)z-vz Convert every image in directoryz-xzReorient and crop 3D imagesNr+)rrrr rr'rr!r Bool anonymize config_filecollapse_foldersdate_in_filenameevents_in_filenamesource_in_filename gzip_outputid_in_filenamer* output_dirprotocol_in_filenamereorient spm_analyzeconvert_all_parsreorient_and_croprrrrr$s^ rc@sReZdZeeddZeeddZeeddZeeddZeeddZ dS)Dcm2niiOutputSpecT)r N) rrrr rconverted_filesreoriented_filesreoriented_and_cropped_filesbvecsbvalsrrrrr;fs r;csPeZdZdZeZeZdZfddZ fddZ ddZ d d Z d d Z ZS) Dcm2niiaUses MRIcron's dcm2nii to convert dicom files Examples ======== >>> from nipype.interfaces.dcm2nii import Dcm2nii >>> converter = Dcm2nii() >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm'] >>> converter.inputs.gzip_output = True >>> converter.inputs.output_dir = '.' >>> converter.cmdline # doctest: +ELLIPSIS 'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'Zdcm2niics`|dkr6t|}|r$|jd7_n|jd7_d}|dkrL|j|dStt|j|||S)Nr-r/r0r1r2r3r4r*r6r7r8r9r:z yz nTr'r) r-r/r0r1r2r3r4r*r6r7r8r9r:)rr"superrA _format_arg)selfoptspecval) __class__rrrCs,zDcm2nii._format_argcsJd|_tt|j|}|j|j\|_|_|_|_ |_ |jrFt j d|S)NFz config.ini) _config_createdrBrA_run_interface _parse_stdoutstdout output_filesr=r>r?r@osremove)rDruntimeZ new_runtime)rHrrrJs   zDcm2nii._run_interfacecCsg}g}g}g}g}d}d}x|jdD]p} |sd} | jdrX| tdd} n| jdr| tdd} t|rtjj|d| ddkr|jt|jj r|jj } n |j d} tjj tjj | | } n | jdr*|rt |\} }}|jtjj | |d |jtjj | |d n| jd r|x||fD]6}tjj tjj|dd tjj|df|d<q@Wnhtjd | rtjd | }|jd}t|jj r|jj } n |j d} tjj | |}tjj|r|} | r| |kr*|j| | }q*| jdr,|j| tddd}q*nl| jdrtjj| tdd\} }d|}tjjtjj | |s~|jjr|jtjj | |d}q*d}q*W|||||fS)NF zSaving zGZip...rr5zNumber of diffusion directions z.bvecz.bvalzRemoved DWI from DTI scanzx%sz.*->(.*)rzReorienting as TzCropping NIfTI/Analyze image cr+r+r+r+)split startswithlenrNpathbasenamepopr inputsr5 _gen_filenameabspathjoinrappenddirnamerrrr r:)rDrLfilesr=r>r?r@skipZlast_added_filelineout_filefnamer5basefilenameextlrGrrrrKsv  $     2        zDcm2nii._parse_stdoutcCsB|jj}|j|d<|j|d<|j|d<|j|d<|j|d<|S)Nr<r=r>r?r@) output_specgetrMr=r>r?r@)rDoutputsrrr _list_outputss      zDcm2nii._list_outputsc CsJ|dkrtjS|dkrFd|_d}t|d}|jdWdQRX|SdS)Nr5r.Tz config.iniwz[BOOL] ManualNIfTIConv=0 )rNgetcwdrIopenwrite)rDnamer.frrrr\s zDcm2nii._gen_filename)rrrrr input_specr;rj_cmdrCrJrKrmr\ __classcell__rr)rHrrAns   N rAc @s`eZdZeedddd?ddddgdZeddd@dd d gd Zej d d dZ eddddddZ ej dddddZ ej ddgddZejddddddddZej dd dd!dZej dd"dd#dZej dd$dd%dZej dd&dd'dZej dd(dd)dZejdd*d+d,d-d.d/d0d1d2d3d Zej d4d5dZej d6d7dZeej d8d9dZej d:d;dZej dS)ADcm2niixInputSpecT)r z%srFzA set of filenames to be converted. 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To only convert specific files they should be in an isolated directoryr!)r"r#r$r%r)r&z2A directory containing dicom files to be convertedr')r r"r#r%r)r&z-f %sa;Output filename template (%a=antenna (coil) number, %c=comments, %d=description, %e=echo number, %f=folder name, %i=ID of patient, %j=seriesInstanceUID, %k=studyInstanceUID, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %v=vendor, %x=study ID; %z=sequence name))r"r).z-o %szOutput directory)r(r r"r)z-bzCreate a BIDS sidecar file)r"r(r)z-ba bids_formatzAnonymize BIDS)r"requiresr)yin3z-z %sz:Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]z-mz merge 2D slices from same seriesz-szSingle file modez-vzVerbose outputz-xzCrop 3D T1 acquisitionsz-tz,Text notes including private patient detailsrrR z-%dz,Gz compression level (1=fastest, 9=smallest)z-c %sz Comment stored as NIfTI aux_filez-iz'Ignore derived, localizer and 2D imagesz-n %s...zASelectively convert by series number - can be used up to 16 timesz-pz+Philips precise float (not display) scalingz-ezExport as NRRD instead of NIfTINr+r+)rrrr rr'rr!r StrZ out_filenamer5r,ry anon_bidsEnumcompress merge_imgs single_fileverbosecrop has_private compressioncomment ignore_derivZseries_numbers philips_floatto_nrrdrrrrrw s    rwc@sDeZdZeeddZeeddZeeddZeeddZdS)Dcm2niixOutputSpecT)r N) rrrr rr<r?r@bidsrrrrrvsrcs\eZdZdZeZeZdZe ddZ fddZ fddZ d d Z d d Zd dZZS)Dcm2niixaUses Chris Rorden's dcm2niix to convert dicom files Examples ======== >>> from nipype.interfaces.dcm2nii import Dcm2niix >>> converter = Dcm2niix() >>> converter.inputs.source_dir = 'dicomdir' >>> converter.inputs.compression = 5 >>> converter.inputs.output_dir = 'ds005' >>> converter.cmdline 'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir' >>> converter.run() # doctest: +SKIP In the example below, we note that the current version of dcm2niix converts any files in the directory containing the files in the list. We also do not support nested filenames with this option. **Thus all files must have a common root directory.** >>> converter = Dcm2niix() >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm'] >>> converter.inputs.compression = 5 >>> converter.inputs.output_dir = 'ds005' >>> converter.cmdline 'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n .' >>> converter.run() # doctest: +SKIP rcCstjS)N)rversion)rDrrrrszDcm2niix.versionc sddddddddd d g }||krNt|}|r<|jd 7_n|jd 7_d }|dkrp|jtjj|dpldStt|j|||S)Nryrrrrrrrrrz yz nTr'rrx)rr"rNrXr`rBrrC)rDrErFrGZbools)rHrrrCs&zDcm2niix._format_argcs*tt|j|dd}|j|j|j|S)Nrr)Zcorrect_return_codes)rr)rBrrJ _parse_filesrKrL)rDrP)rHrrrJs  zDcm2niix._run_interfacecCsNg}xD|jdD]6}|jdrttjd|jd}|jtjj |qW|S)NrQzConvert z\S+/\S+r) rUrVstrrrgroupr_rNrXr])rDrL filenamesrcrerrrrKs  zDcm2niix._parse_stdoutc Csggggf\}}}}ddddg}|jjr8|dddg7}n |dd g7}x|D]}xt||D]}|jds|jd s|jds|jdr|j|qZ|jdr|j|qZ|jdr|j|qZ|jds|jdrZ|j|qZWqJW||_||_||_||_dS) Nz.bvalz.bvecz.jsonz.txtz.nrrdz.nhdrz.raw.gzz.niiz.nii.gzz.gz) r[r search_filesendswithr_rMr?r@r) rDroutfilesr@r?routtypesrgflrrrrs,            zDcm2niix._parse_filescCs8|jj}|j|d<|j|d<|j|d<|j|d<|S)Nr<r?r@r)rjrkrMr?r@r)rDrlrrrrms      zDcm2niix._list_outputs)rrrrrwrtrrjrupropertyrrCrJrKrrmrvrr)rHrr}s   rcstjjfdd|DS)Nc3s |]}ttj|VqdS)N)rglobescape).0Zouttype)prefixrr szsearch_files..)itchain from_iterable)rrr)rrrsr)rrNrcopyr itertoolsrrrZutils.filemaniprrfrrr r r r r rrrrrr;rArwrrrrrrrs"   0 Bjt