0-PhdZddlZddlZddlZddlZddlZejeZ ej dkZ idddddd d d d d ddddddddddddddddddd d!d"d#d$d%id&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;dd?d@dAdBdCdDdEdFdGidHdIdJdKdLdMdNdOdPdQdRdSdTdUdVdWdXdYdZd[d\d]d^d_d`dadbdcdddedfdgdhdidjdkiZ dlZ dmZdnZedoe DZedpe DZGdqdreZGdsdteZGdudveZGdwdxeZdyZd}d{Zd|ZdS)~z! Plugin for reading DICOM files. Nlittle)) PixelDataOB) ) StudyDateDA)r!) SeriesDater )r")AcquisitionDater )r#) ContentDater )r0) StudyTimeTM)r1) SeriesTimer)r2)AcquisitionTimer)r3) ContentTimer)r`)ModalityCS)rp) ManufacturerLO)r)InstitutionNamer )r0)StudyDescriptionr )ri>)SeriesDescriptionr )r) SOPClassUIDUI)r)SOPInstanceUIDr()r )StudyInstanceUIDr()r )SeriesInstanceUIDr()ri) ContextUIDr()r ) SeriesNumberIS)r )AcquisitionNumberr2)r )InstanceNumberr2)r ) IsotopeNumberr2)r ) PhaseNumberr2)r r&)IntervalNumberr2)r )TimeSlotNumberr2)r r)) AngleNumberr2)r ) ItemNumberr2)r r )PatientOrientationr)r r) ImagePositionr)r r)ImagePositionPatientr)r 5)ImageOrientationr)r 7)ImageOrientationPatientr)rr) PatientNamePN)rr ) PatientIDr )rr)PatientBirthDater )r@) PatientSexr)ri) PatientAgeAS)ri ) PatientSizeDS)rr#) PatientWeightrQ)()SamplesPerPixelUS)rSr)NumberOfFramesr2)rS) BitsAllocatedrV)rSi) BitsStoredrV)rSi)HighBitrV)rSi)PixelRepresentationrV)rSr)RowsrV)rSr0)ColumnsrV)rSiR)RescaleInterceptrQ)rSiS) RescaleSloperQ)rSr) PixelSpacingrQ)r)) SliceSpacingrQ)i)rdi )rdicg|] }|d S)r).0keys V/var/www/html/test/jupyter/venv/lib/python3.11/site-packages/imageio/plugins/_dicom.py rjcs 0 0 0c!f 0 0 0cg|] }|d S)rf)rgvals rirjrjds / / /c3q6 / / /rkceZdZdS) NotADicomFileN__name__ __module__ __qualname__rfrkrirprpgDrkrpceZdZdS)CompressedDicomNrqrfrkrirwrwkrurkrwceZdZdZdZedZdZdZdZ dZ dZ d Z dd Z d Zd ZdZdZdZdZdZdS)SimpleDicomReadera@ This class provides reading of pixel data from DICOM files. It is focussed on getting the pixel data, not the meta info. To use, first create an instance of this class (giving it a file object or filename). Next use the info attribute to get a dict of the meta data. The loading of pixel data is deferred until get_numpy_array() is called. Comparison with Pydicom ----------------------- This code focusses on getting the pixel data out, which allows some shortcuts, resulting in the code being much smaller. Since the processing of data elements is much cheaper (it skips a lot of tags), this code is about 3x faster than pydicom (except for the deflated DICOM files). This class does borrow some code (and ideas) from the pydicom project, and (to the best of our knowledge) has the same limitations as pydicom with regard to the type of files that it can handle. Limitations ----------- For more advanced DICOM processing, please check out pydicom. * Only a predefined subset of data elements (meta information) is read. * This is a reader; it can not write DICOM files. * (just like pydicom) it can handle none of the compressed DICOM formats except for "Deflated Explicit VR Little Endian" (1.2.840.10008.1.2.1.99). c Ft|tr|_t|d_nd_|_d_d_d_d_i_ fdfdfdfd d d d d dfddd _ dS)NrbzFTz,SimpleDicomReader.__init__..DLLa00rkc0d|S)NLrrs rirz,SimpleDicomReader.__init__..rrkc<|tdSN\ _splitValuesfloatrs rirz,SimpleDicomReader.__init__..D--a==rkc<|tdSr)rintrs rirz,SimpleDicomReader.__init__..sD--ad;;rkcT|dddSNasciiignoredecodestriprs rirz,SimpleDicomReader.__init__.."AHHWh77==fEErkcT|dddSrrrs rirz,SimpleDicomReader.__init__..rrkcT|dddSrrrs rirz,SimpleDicomReader.__init__..rrkcT|dddSrrrs rirz,SimpleDicomReader.__init__..rrkcx|dddSNzutf-8rrrrrstriprs rirz,SimpleDicomReader.__init__...AHHWh77==fEELLNNrkc<|tdSrrrs rirz,SimpleDicomReader.__init__..rrkcx|dddSrrrs rirz,SimpleDicomReader.__init__..rrk) rVULrQr2rOr rr(r rrI) isinstancestr _filenameopen_file_pixel_data_locis_implicit_VRis_little_endian _unpackPrefix_info _converters_read)rfiles` ri__init__zSimpleDicomReader.__init__s dC  !DNdD))DJJ-DNDJ## $  10000000====;;;;EEEEEEEENN====NN  $ rkc|jSNrrs riinfozSimpleDicomReader.info zrkc|dd} ||vr.tfd||DS|S#t$r|cYSwxYw)NrrcNg|]!}||"Srf)r)rgvtypes rirjz2SimpleDicomReader._splitValues..s.NNN!AGGIINdd1ggNNNrk)rrtuplesplit ValueError)rrrsplitterss ` rirzSimpleDicomReader._splitValuess HHW   # #F + + 1}}NNNNqwwx/@/@NNNOOOtAww   HHH s1A( A(( A76A7cHtj|j|z|dS)Nr)structunpackr)rfmtvalues rirzSimpleDicomReader._unpacks!}T/#5u==a@@rkcNt|jSr)iterrkeysrs ri__iter__zSimpleDicomReader.__iter__sDJOO%%&&&rkct|d}||vr||St||S)Nr)object__getattribute__)rrhrs ri __getattr__zSimpleDicomReader.__getattr__s@&&tW55 $;;9 &&tS111rkc|j}|d|ddkrtd|||tj |j r"|j d|_dSdS)Nr!sDICMzNot a valid DICOM file.) rseekreadrp _read_header_read_data_elements_get_shape_and_samplingospathisfilerclose)rfs rirzSimpleDicomReader._reads J s 66!99   9:: :    """ $$&&& 7>>$. ) )  J     DJJJ  rkc|j}|d|d}|d|d}|jr*|d|d}n|d}|dvr?|d}|d|d}n)|d|d}|dkr@|dkr:|}||f|_|||z||dfS|d kr|}n||}|||fS) Nr~rTIr)sOBsOWsSQsUNrrsDeferred loading of pixel data)rrrrtellrr_read_undefined_length_value) rrgroupelementvlvrreservedherers ri_readDataElementz"SimpleDicomReader._readDataElements] J S!&&)),,,,sAFF1II..   2c166!99--BBB11166!99\\#qvvayy11\\#qvvayy11 F??w&006688D#'8D FF4"9   '#DD DZ99;;r '5( (rkr!cp|j}d}tj|jdztdtd}d}g}|s^|}||}t||krL||t|z } || z }t||krtd| |} | dkrpd}| |d | | || zd z|d } | d krt d nH| ||z | |d | |^d |S)zOCopied (in compacted form) from PyDicom Copyright Darcy Mason. HHrrmFz4End of file reached before sequence delimiter found.TNrsz6Expected 4 zero bytes after undefined length delimiterrk)rrpackrSequenceDelimiterTagrrlenEOFErrorfindappendrloggerwarningjoin) r read_sizefp search_rewind bytes_to_findfound value_chunks chunk_start bytes_read new_bytesindexlengths rirz.SimpleDicomReader._read_undefined_length_valuesZ    %';A'>@TUV@W    A''))K++J:**GGIJ$?@@ i' z??Y.."QOOM22E{{##Jvv$6777 e+a/000[((NNS M1222##J$?@@@3 A8xx %%%rkc|j}d} |}|\}}}|dkr5|dkr.|dkr(|dd}n||n~n)#t tjf$rtdwxYw||j d<|d\}}n|d krd\}}n|d krd \}}ny|d krd \}}nm|dkrd\}}| nM|d} } d| cxkrdkrnnd} d| cxkrdkrnnd} | dkrd} | dkrd} td| | d||_ ||_d||_dS)NTrTrrrz*End of file reached while still in header.TransferSyntaxUID)FTz1.2.840.10008.1.2.1z1.2.840.10008.1.2.2FFz1.2.840.10008.1.2)TTz1.2.840.10008.1.2.1.99z1.2.840.10008.1.2.4.50z1.2.840.10008.1.2.4.99z (JPEG)z1.2.840.10008.1.2.4.90z (JPEG 2000)z1.2.840.10008.1.2.5z (RLE)z1.2.840.10008.1.2.6.1z (RFC 2557)zHThe dicom reader can only read files with uncompressed image data - not z7. You can try using dcmtk or gdcm to convert the image.z><)rrrrrrrrerror RuntimeErrorr_inflaterwrrr) rrrfp_saverrrrrt extra_infos rirzSimpleDicomReader._read_header*s- J  M &&(((,(=(=(?(?%wD==}}D,1LL,A,A,G,G,O,O)FF7OOO &,' M M MKLL L M+< &'  $/: ,N,, "7 7 7/: ,N,, "7 7 7/; ,N,, "5 5 5/9 ,N,, ": : :/: ,N, MMOOOO.rzA'1GGGG/GGGGGG& '1GGGG/GGGGGG+ )))% +++* !/Azzz+ - 0!"23s A?B &B1c.|j} |\}}}|tvrN||f}t|d\}}|r*|j|d}||||<p#t tjf$rYdSwxYw)NT)NNc|Srrfrs rirz7SimpleDicomReader._read_data_elements..vsqrk) rrGROUPSMINIDICTgetrrrr) rrrrrrhnamer converters rirz%SimpleDicomReader._read_data_elementsisz  6(,(=(=(?(?%wF?? '*C'||C>>HD"6$($4$8$8[[$I$I %.Yu%5%5T  6&,'    DD sA1A::BBcRd|vrtd|jrt|jdkrd}|jd}t |jd|_|j|jd|jd d kr|}n%|j |jd }|r |j d|_||j d<| }| |}d |j d<|S) zsGet numpy arra for this DICOM file, with the correct shape, and pixel values scaled appropriately. r$No pixel data found in this dataset.dFNTr{rrmrsBData converted to numpy array, raw data removed to preserve memory) TypeErrorrrrrrrrrrrr_pixel_data_numpy_apply_slope_and_offset)r close_filerdatas riget_numpy_arrayz!SimpleDicomReader.get_numpy_array{s/ d " "BCC C   ,C$7$7#$=$=Jz!! !$.$77 JOOD03 4 4 4#A&*4499;; ( 1 if Bits Allocated = 8z=DICOM file has no SamplesPerPixel (perhaps this is a report?)rar)?rrc)rNshapesampling) rWrUr]r^rYNotImplementedErrorrrraabsrcrr)rrrs rirz)SimpleDicomReader._get_shape_and_samplings t # #(;a(?(?#a''('IL +TY D $ & &#a''%** 0$)T\IEE-(  4</R  T ! !T.q122E$:KA:N4O4OOHHH T ! !D-..08;HSZZ#h--788SZZKMM;RR$ 7!) :rkcd|vrtd|jtk}dd|j|jfz} t j|}n-#t$r td||j|jfzwxYwt j|j| }|r| d|j |j d}|S)z'Return a NumPy array of the pixel data.rrz%sint%d)urzYData type not understood by NumPy: format='%s', PixelRepresentation=%d, BitsAllocated=%dTr) rrsys_is_little_endianr\rYnpdtype frombufferrcopybyteswapreshaper)r need_byteswap format_str numpy_formatarrs rirz#SimpleDicomReader._pixel_data_numpys d " "BCC C-1EE  d. /  "   8J//LL   <!94;MNO  mDNL99>>@@   LL   ck4:g./ s A*A;cd\}}d\}}d|vr d}|j}d|vr d}|j}t||kst||krd}|st|t|}}|r|jtjtjfvrnp|r!|tj}nM| | }}t|||z|z||z|zg}t|||z|z||z|zg}d}|dkrXt| |g}|dkr tj }nx|d kr tj }ne|d kr tj }nRtj}nE|d kr tj }n2|d kr tj }n|d kr tj }n tj}||jkr||}||z}||z }|S)z If RescaleSlope and RescaleIntercept are present in the data, apply them. The data type of the data is changed if necessary. )rmrrr`Tr_Nrr!ilrXil)r`r_rr$r#float32float64astypeminitemmaxint8int16int32) rrslopeoffset needFloatsneedApplySlopeOffsetminReqmaxReqr$s rirz)SimpleDicomReader._apply_slope_and_offsets%  v+7( ( T ! !#' %E  % %#' *F u::  #f++"7"7J 4JJF 6E ) zbj"*555! .{{2:.."&!2!2DHHJJOO4E4Effunv&=v~PV?VWXXffunv&=v~PV?VWXXA:: 6'6!233F}} "% "% " " }} "% "% " " DJ&&;;u--D EMD FND rkcddl}ddlm}|j}|||j }|||_dS)Nr)BytesIO)zlibior>rr decompress MAX_WBITS)rr?r>zippedunzippeds rirzSimpleDicomReader._inflate<s`  ""??6DN?;;WX&& rkN)r!)rrrsrt__doc__rpropertyrrrrrrrrrrrrrrrrfrkriryryos-""H###JXAAA'''222   )))8)&)&)&)&V=4=4=4~$%%%N.*.*.*`&&&P@@@D'''''rkryceZdZdZdZdZdZdZedZ edZ edZ ed Z ed Z d Zd Zd ZdZdZdS) DicomSerieszDicomSeries This class represents a serie of dicom files (SimpleDicomReader objects) that belong together. If these are multiple files, they represent the slices of a volume (like for CT or MRI). c>g|_||_i|_||_dSr)_entries_suidr_progressIndicator)rsuidprogressIndicators rirzDicomSeries.__init__Us'   "3rkc*t|jSr)rrJrs ri__len__zDicomSeries.__len__^s4=!!!rkc*t|jSr)rrJrs rirzDicomSeries.__iter__asDM"""rkc|j|Sr)rJ)rrs ri __getitem__zDicomSeries.__getitem__ds}U##rkc|jSr)rKrs rirMzDicomSeries.suidgrrkc|jdS)z#The shape of the data (nz, ny, nx).rrrs rirzDicomSeries.shapeksz'""rkc|jdS)z8The sampling (voxel distances) of the data (dz, dy, dx).rrrs rirzDicomSeries.samplingpsz*%%rkc|jS)z~A dictionary containing the information as present in the first dicomfile of this serie. None if there are no entries.rrs rirzDicomSeries.infous zrkc|j}|sdt|zSg}d|vr|d|dz|jr9d|jD}|d|d|vr!|d|dzdzd|vr!|d|dzdzd |S) zA description of the dicom series. Used fields are PatientName, shape of the data, SeriesDescription, and ImageComments. z DicomSeries containing %i imagesrHrc,g|]}t|Srf)r)rgds rirjz+DicomSeries.description..s...a3q66...rkrr%' ImageComments )rrrrr)rrfieldstmps ri descriptionzDicomSeries.description{s y B5D A A D MM"tM22 3 3 3 : )..4:...C MM#((3-- ( ( ( $ & & MM#%8 99C? @ @ @ d " " MM#_ 55; < < <xxrkctt|}dt||fzS)Nz")hexidupperr)radrs ri__repr__zDicomSeries.__repr__s5"T((mm!!##3s4yy#6FFFrkct|dkrtdt|dkr|dS|jt d|d}t j|j|j}||d<|j ddt|tdt|D]<}||||<|j |dz=|j ddl}||S) zGet (load) the data that this DicomSeries represents, and return it as a numpy array. If this serie contains multiple images, the resulting array is 3D, otherwise it's 2D. rz!Serie does not contain any files.rmNz,Cannot return volume if series not finished.)r$z loading datar)rrrrrr#zerosrr$rLstartrange set_progressfinishgccollect)rslicevolzrms rirzDicomSeries.get_numpy_arraysC t99>>@AA A YY!^^7**,, , 9 MNN NQ''))htz555A %%nb#d))DDDq#d))$$ 8 8A!W,,..CF  # 0 0Q 7 7 7 7 &&(((    rkc:|j|dSr)rJr)rdcms ri_appendzDicomSeries._appends S!!!!!rkc>|jddS)NcN|jt|dr |jdndfS)NrCrT)r6hasattrrC)ks rirz#DicomSeries._sort..s4 q"899A*1-- rkrh)rJsortrs ri_sortzDicomSeries._sorts5   rkcj|j}t|dkrdSt|dkr|dj|_dS|d}d}|j|jf}|jddd}t t|D]}||}t|jd}t|jd} |t|| z z }|j|jf} |jddd} || krtd|| kr|j d|}|t|dz z } |dj |_t|f|jd z|jd <| f|jdz|jd<dS) a Evaluate the series of dicom files. Together they should make up a volumetric dataset. This means the files should meet certain conditions. Also some additional information has to be calculated, such as the distance between the slices. This method sets the attributes for "shape", "sampling" and "info". This method checks: * that there are no missing files * that the dimensions of all images match * that the pixel spacing of all images match rNrmgrrTz$Dimensions of slices does not match.zWarn: sampling does not match.r)rJrrrr]r^rjrrCrrrLwriter&) rrds1 distance_sum dimensionsrrds2pos1pos2 dimensions2 sampling2 distance_means ri_finishzDicomSeries._finishs M q66Q;; F VVq[[1DJ Fd Xs{* 8J'+3q66]]  EE(C1!455D1!455D Ct ,, ,L(CK/K,RaR0I[(( !GHHH9$$'--.NOOOCC%A 3 qTY^^%%  #1vvi#(7*;; 7"/!1CHZ4H!H :rkN)rrrsrtrErrPrrSrFrMrrrr`rfrrtr{rrfrkrirHrHNs5 444"""###$$$X##X#&&X&X   X 8GGG   D"""    ?I?I?I?I?IrkrHc<tj|D]}tj||}tj|rt ||Rtj|r||dS)z-List all files in the directory, recursively.N)rlistdirrrisdir list_filesrr)filesrr2s rirrs 4  w||D$'' 7==    ud # # # # W^^D ! !  LL    rkFc`tj|jr|j}nXtj|jr%tj|j}nt dg}t||i}d}|ddt||D]}|dz }| || dr2 t|}nD#t$rYOt$r,} |t!| Yd} ~ d} ~ wwxYw |j} n#t$$rYwxYw| |vrt'| ||| <|| |t+|}|d t1d |DD]} t3| ||g} t5t|D]q} || | || 9#t$r,}|t!|Yd}~jd}~wwxYw|d t| z| S) a Reads dicom files and returns a list of DicomSeries objects, which contain information about the data, and can be used to load the image or volume data. if readPixelData is True, the pixel data of all series is read. By default the loading of pixeldata is deferred until it is requested using the DicomSeries.get_pixel_array() method. In general, both methods should be equally fast. z.Qsafrkrycg|]}|Srfrf)rgseries rirjz%process_directory..Ts555U5555rkzFound %i correct series.)rrrfilenamerdirnamerrrirrkcountryrp Exceptionr}rr.AttributeErrorrHrtlistvaluesrzreversedsplitSerieIfRequiredrjrrrl)requestrN readPixelDatarrseriesrrrswhyrMrseries_ierrs riprocess_directoryrs w}}W%&&Y ( ) )Yww/00WXXX EudF E-wE CCC""  &&u--- >>* % %   #H--CC    H     # #CHH - - - HHHH  (DD    H  v  &t->??F4Lt S!!!! &--// " "F KK$$K%%%55f55566??UF,=>>>>G 3v;;    1I      NN6!9 % % % %     # #CHH - - - DDDD 7#g,,FGGG NsH4D E E"EE E EE5I J"JJcR||j}|d}d|vrdS|gg}d}tdt|D]}||}t |jd} t |jd} t | | z } |r!| d|zkr|gd}n*|r&| d|zkr|d|j z| }|d ||}t|dkr| |} g} |D]3}t|j |}||_| |4t| D]}|| |||dSdS) a Split the serie in multiple series if this is required. The choice is based on examing the image position relative to the previous image. If it differs too much, it is assumed that there is a new dataset. This can happen for example in unspitted gated CT data. rrCNrmrTg@g?zWarning: missing file after %rr)r{rJrjrrrCrrr}rrrHrMrinsertremove)rrrNrr~L2distancerrrrnewDistr series2insertnewSeries rirrhs KKMMM A A$CS(( %BHq#a&&!!hS-a011S-a011dTk""  #.00 IIbMMMHH GcHn44!''4s}DH 2 c 2ww{{ LL    + +A"5:/@AAH !H    * * * * // ' 'H MM!X & & & & e{rk)F)rEsysrrloggingnumpyr# getLoggerrrr byteorderr"r ItemTagItemDelimiterTagrsetrr rVRSrrprrwrryrHrrrrfrkrirs   8 $ $}0= )= )= * =  / =  + = )= *= /= += (= ,= /=  0!= "1#= &+'= (.)= *0+= = ,1-= .*/= 2,3= 415= 6.7= 8-9= :+;= <.== >.?= @+A= B*C= D2E= F-G= H4I= J0K= L7M= P+Q= = = R)S= T0U= V*W= X*Y= Z+[= \-]= `/a= b.c= d-e= f*g= h'i= j3k= lnm= n'o= p0q= r,s= v,w= = x,y= = B #'  0 0  0 0 0 1 1 c / /X__.. / / /00     I        l   \'\'\'\'\'\'\'\'~~I~I~I~I~I&~I~I~IBLLLL^<<<<<rk