EjdZddlZddlZddlZddlZddlZejeZ ejdk(Z 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 dmZdnZee j#Dcgc]}|d c}Zee j'Dcgc]}|do c}ZGdpdqeZGdrdseZGdtdueZGdvdweZdxZd{dyZdzZycc}wcc}w)|zPlugin 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 )rdic eZdZy) NotADicomFileN__name__ __module__ __qualname__T/root/workspace/ytshorts/venv/lib/python3.12/site-packages/imageio/plugins/_dicom.pyrgrgermrgc eZdZy)CompressedDicomNrhrlrmrnrqrqirormrqc|eZdZdZdZedZdZdZdZ dZ dZ d Z dd Z d Zd Zd ZdZdZdZdZy)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 *t|tr|_t|d_nd_|_d_d_d_d_i_ fdfdfdfd d d d d dfddd _ jy)NrbzFTz,SimpleDicomReader.__init__..DLLa0rmc(jd|S)NLryr{s rnr~z,SimpleDicomReader.__init__..rrmc2j|tdSN\ _splitValuesfloatr{s rnr~z,SimpleDicomReader.__init__..D--a=rmc2j|tdSr)rintr{s rnr~z,SimpleDicomReader.__init__..sD--ad;rmcD|jddjdSNasciiignoredecodestripr|s rnr~z,SimpleDicomReader.__init__..AHHWh7==fErmcD|jddjdSrrrs rnr~z,SimpleDicomReader.__init__..rrmcD|jddjdSrrrs rnr~z,SimpleDicomReader.__init__..rrmcD|jddjdSrrrs rnr~z,SimpleDicomReader.__init__..rrmc`|jddjdjSNzutf-8rrrrrstriprs rnr~z,SimpleDicomReader.__init__..%AHHWh7==fELLNrmc2j|tdSrrr{s rnr~z,SimpleDicomReader.__init__..rrmc`|jddjdjSrrrs rnr~z,SimpleDicomReader.__init__..rrm) rVULrQr2rOr rr(r rrI) isinstancestr _filenameopen_file_pixel_data_locis_implicit_VRis_little_endian _unpackPrefix_info _converters_read)r}files` rn__init__zSimpleDicomReader.__init__s dC !DNdD)DJ-DNDJ## $  10=;EEEEN=N $ rmc|jSNrr}s rninfozSimpleDicomReader.info zzrmc|jdjd} ||vr?t|j|Dcgc]}|js||c}S||Scc}w#t$r|cYSwxYw)Nrr)rrtuplesplit ValueError)r}r|typesplittersvs rnrzSimpleDicomReader._splitValuessw HHW  # #F + 1}qwwx/@N!AGGId1gNOOAwO H s.A2A- A-A2%A2-A22 B?BcNtj|j|z|dS)Nr)structunpackr)r}fmtvalues rnrzzSimpleDicomReader._unpacks#}}T//#5u=a@@rmcHt|jjSr)iterrkeysrs rn__iter__zSimpleDicomReader.__iter__sDJJOO%&&rmcltj|d}||vr||Stj||S)Nr)object__getattribute__)r}keyrs rn __getattr__zSimpleDicomReader.__getattr__s8&&tW5 $;9 &&tS11rmcr|j}|jd|jddk7r td|j |j |j tjj|jr"|jjd|_yy)Nr!sDICMzNot a valid DICOM file.) rseekreadrg _read_header_read_data_elements_get_shape_and_samplingospathisfilerclose)r}fs rnrzSimpleDicomReader._reads JJ s 66!9  9: :    " $$& 77>>$.. ) JJ   DJ *rmc|j}|jd|jd}|jd|jd}|jr"|jd|jd}ni|jd}|dvr3|jd}|jd|jd}n!|jd|jd}|dk(r7|dk(r2|j }||f|_|j ||z||dfS|d k(r|j}n|j|}|||fS) NrxrTIr)sOBsOWsSQsUNrrsDeferred loading of pixel data)rrzrrtellrr_read_undefined_length_value) r}rgroupelementvlvrreservedherers rn_readDataElementz"SimpleDicomReader._readDataElements" JJ S!&&),,,sAFF1I.   c166!9-BB1166!9\\#qvvay1\\#qvvay1 F?w&0668D#'8D FF4"9 '#DD DZ99;r '5( (rmc|j}d}tj|jdztdtd}d}g}|s|j }|j |}t||kr;|j |t|z } || z }t||kr td|j|} | dk7rYd}|j|d | |j|| zd z|j d } | d k7rMtjd n7|j|j |z |j|d | |sd j|S)zOCopied (in compacted form) from PyDicom Copyright Darcy Mason. HHrreFz4End of file reached before sequence delimiter found.TNrsz6Expected 4 zero bytes after undefined length delimiterrm)rrpackrSequenceDelimiterTagrrlenEOFErrorfindappendrloggerwarningjoin) r} read_sizefp search_rewind bytes_to_findfound value_chunks chunk_start bytes_read new_bytesindexlengths rnrz.SimpleDicomReader._read_undefined_length_valuescZZ     %';A'>@TUV@W  '')K+J:*GGIJ$?@ i' z?Y."QOOM2E{##Jv$67 e+a/0[(NNS M12##J$?@38xx %%rmc|j}d} |j}|j\}}}|dk(r+|dk(r8|dk(r3|jdj d}n|j |ng ||jd<|d\}}n|dk(rd\}}nt|d k(rd \}}ni|d k(rd \}}n^|d k(rd\}}|jnC|d} } d| cxkrdkrnnd} d| cxkrdkrnnd} | dk(rd} | dk(rd} td| | d||_ ||_d||_y#t tjf$r tdwxYw)NrTrrrz*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_inflaterqrrr) r}rrfp_saverrrrrt extra_infos rnrzSimpleDicomReader._read_header(s JJ  M&&((,(=(=(?%wD=}D,1LL,A,G,G,O)FF7O +< &'  $/: ,N, "7 7/: ,N, "7 7/; ,N, "5 5/9 ,N, ": :/: ,N, MMO.rzA'1G/GG& '1G/GG+ ))% ++* !z+ - 0!"23W&,,' MKL L Ms A(D((%E c$|j} |j\}}}|tvrG||f}tj |d\}}|r(|j j |d}||||<d#t tjf$rYywxYw)N)NNc|Srrlrs rnr~z7SimpleDicomReader._read_data_elements..tsqrm) rrGROUPSMINIDICTgetrrrr) r}rrrrrnamer converters rnrz%SimpleDicomReader._read_data_elementsgszz (,(=(=(?%wF? '*C'||C>HD"$($4$4$8$8[$I %.u%5T &,,'   sA%A33BBcld|vr td|jrt|jdkrd}|jd}t |j d|_|jj|jd|jd d k(r|j}n(|jj|jd }|r!|jjd|_||jd<|j}|j|}d |jd<|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.dFNTrurrersBData converted to numpy array, raw data removed to preserve memory) TypeErrorrrrrrrrrrrr_pixel_data_numpy_apply_slope_and_offset)r} close_filerdatas rnget_numpy_arrayz!SimpleDicomReader.get_numpy_arrayys d "BC C   C$7#$=Jzz!! !$..$7 JJOOD003 4##A&*499; (<(|jdk(r$|j|j|jf}n/t d|j|jf}n t dd|vr1t|jdt|jdf}nd }d |vrt|jf|z}d t|t|z z|t| d z}||jd <||jd<y )zGet shape and sampling without actuall using the pixel data. In this way, the user can get an idea what's inside without having to load it. rWrerUrzCDICOM plugin only handles SamplesPerPixel > 1 if Bits Allocated = 8z=DICOM file has no SamplesPerPixel (perhaps this is a report?)rar)?rrc)rNshapesampling) rWrUr]r^rYNotImplementedErrorrrraabsrcrr)r}rrs rnrz)SimpleDicomReader._get_shape_and_samplings t #(;(;a(?##a'((''IILL ++TYY D $ &##a'%%* 00$))T\\IE-(  4<</R  T !T..q12E$:K:KA:N4OOHH T !D--.08;HSZ#h-788SZKM;RR$ 7!) :rmcd|vr td|jtk7}dd|j|jfz} t j |}t j|j|j}|r|jd|j|jd}|S#t$r&td|j|jfzwxYw)z'Return a NumPy array of the pixel data.rr z%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 rnrz#SimpleDicomReader._pixel_data_numpys d "BC C--1EE  d.. /   "   88J/LmmDNNL9>>@  LL ckk4::g./ # <!9!94;M;MNO  s B66/C%cd\}}d\}}d|vrd}|j}d|vrd}|j}t||k7st||k7rd}|st|t|}}|r|jtj tj fvrnm|r!|jtj }nJ|jj|jj}}t|||z|z||z|zg}t|||z|z||z|zg}d}|dkrat| |g}|dkrtj}n|d krtj}ny|d krtj}nctj }nR|d krtj}n<|d krtj}n&|d krtj}ntj }||jk7r|j|}||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. )rerrr`Tr_Nrr!ilrXil)r`r_rrrfloat32float64astypeminitemmaxint8int16int32) r}rslopeoffset needFloatsneedApplySlopeOffsetminReqmaxReqrs rnrz)SimpleDicomReader._apply_slope_and_offsets  v+7( ( T !#' %%E  %#' **F u: #f+"7JJF 6E zzbjj"**55{{2::."&!2DHHJOO4Effunv&=v~PV?VWXffunv&=v~PV?VWXA: 6'6!23F} "% "% " " } "% "% " " DJJ&;;u-D EMD FND rmcddl}ddlm}|jj }|j ||j }|||_y)Nr)BytesIO)zlibior8rr decompress MAX_WBITS)r}r9r8zippedunzippeds rnrzSimpleDicomReader._inflate:s@ "??6DNN?;X& rmN)r!)rirjrk__doc__rpropertyrrrzrrrrrrrrrrrrrlrmrnrsrsmsp"H#JA'2 )8)&V=4~$%N.*`&P@D'rmrsceZdZdZdZdZdZdZedZ edZ edZ ed Z ed Z d Zd Zd ZdZdZy) 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|_||_yr)_entries_suidr_progressIndicator)r}suidprogressIndicators rnrzDicomSeries.__init__Ss!   "3rmc,t|jSr)rrDrs rn__len__zDicomSeries.__len__\s4==!!rmc,t|jSr)rrDrs rnrzDicomSeries.__iter___sDMM""rmc |j|Sr)rD)r}rs rn __getitem__zDicomSeries.__getitem__bs}}U##rmc|jSr)rErs rnrGzDicomSeries.suiderrmc |jdS)z#The shape of the data (nz, ny, nx).rrrs rnrzDicomSeries.shapeiszz'""rmc |jdS)z8The sampling (voxel distances) of the data (dz, dy, dx).rrrs rnrzDicomSeries.samplingnszz*%%rmc|jS)z~A dictionary containing the information as present in the first dicomfile of this serie. None if there are no entries.rrs rnrzDicomSeries.infosszzrmc|j}|sdt|zSg}d|vr|jd|dz|jrB|jDcgc] }t |}}|jdj |d|vr|jd|dzdzd|vr|jd|dzdzdj |Scc}w) zA description of the dicom series. Used fields are PatientName, shape of the data, SeriesDescription, and ImageComments. z DicomSeries containing %i imagesrHrr|r%' ImageComments )rrrrrr)r}rfieldsdtmps rn descriptionzDicomSeries.descriptionys yy5D A A D MM"tM22 3 ::#'::.a3q6.C. MM#((3- ( $ & MM#%8 99C? @ d " MM#_ 55; <xx/sCcftt|j}dt||fzS)Nz")hexidupperr)r}adrs rn__repr__zDicomSeries.__repr__s,"T(m!!#3s4y#6FFFrmcrt|dk(r tdt|dk(r|djS|j t d|dj}t j |j|j}||d<|jjddt|tdt|D]6}||j||<|jj|dz8|jjddl}|j|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.reNz,Cannot return volume if series not finished.)rz loading datar)rrrrrrzerosrrrFstartrange set_progressfinishgccollect)r}slicevolzrfs rnrzDicomSeries.get_numpy_arrays t9>@A A Y!^7**, , 99 MN NQ'')hhtzz5A %%nb#d)Dq#d)$ 8A!W,,.CF  # # 0 0Q 7 8 &&(   rmc:|jj|yr)rDr)r}dcms rn_appendzDicomSeries._appends S!rmc>|jjdy)NcV|jt|dr|jdfSdfS)NrCrT)r6hasattrrC)ks rnr~z#DicomSeries._sort..s;  q"89**1-  rmr)rDsortrs rn_sortzDicomSeries._sorts   rmcP|j}t|dk(ryt|dk(r|dj|_y|d}d}|j|j f}|jddd}t t|D]}||}t|jd}t|jd} |t|| z z }|j|j f} |jddd} || k7r td|| k7r|jjd|}|t|dz z } |djj|_t|fjd z|jd <| f|jdz|jd<y) 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 rNregrrTz$Dimensions of slices does not match.zWarn: sampling does not match.r)rDrrrr]r^rcrrCrrrFwriter ) r}rds1 distance_sum dimensionsrrds2pos1pos2 dimensions2 sampling2 distance_means rn_finishzDicomSeries._finishs MM q6Q;  Vq[1DJ d XXs{{* 88J'+3q6] EE(C11!45D11!45D Ct , ,L((CKK/K,Ra0I[( !GHH9$''--.NOC+ 2%A 3 qTYY^^%  #1vi#((7*;; 7"/!1CHHZ4H!H :rmN)rirjrkr?rrJrrMr@rGrrrrYr_rrmrtrrlrmrnrBrBLs 4"#$##&&   8G D"  ?IrmrBc2tj|D]}tjj||}tjj |r t ||Otjj |so|j|y)z-List all files in the directory, recursively.N)rlistdirrrisdir list_filesrr)filesrr,s rnrr sd 4 ww||D$' 77==  ud # WW^^D ! LL  rmctjj|jr |j}n^tjj |jr*tjj |j}n t dg}t||i}d}|jddt||D]j}|dz }|j||jdr+ t|} |j"} | |vrt'| ||| <|| j)|lt+|j-}|j/d t1|D cgc]} | c} D]} t3| ||g} t5t|D]*} || j7| j9|| ,|j;d t| z| S#t$rY2t$r%} |jt!| Yd} ~ Zd} ~ wwxYw#t$$rYnwxYwcc} w#t$r$}|jt!|Yd}~d}~wwxYw) 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.Os affrmrrzFound %i correct series.)rrrfilenamerdirnamerrrbrrdcountrsrg Exceptionrvrr.AttributeErrorrBrmlistvaluesrsreversedsplitSerieIfRequiredrcrrre)requestrH readPixelDatarrseriesrrrlwhyrGserieseries_ierrs rnprocess_directoryrs9 ww}}W%%& (( )www//0WXX EudF E-wE C"  &&u- >>* %  #H-C ((D v &t->?F4Lt S!-"8&--/ "F KK$K%f5U556?UF,=>? G 3v;   1I    NN6!9 %7#g,FG NO     # #CH -      6   # #CH -  sN1 G+= H'' H7#'H<+ H$7H$?HH$' H43H4< I)I$$I)c|j|j}|d}d|vry|gg}d}tdt|D]}||}t |j d} t |j d} t | | z } |r| d|zkDr|jgd}n*|r&| d|zkDr|jd|jz| }|d j||}t|dkDr||j|} g} |D]0}t|j|}||_| j|2t| D]}|j| ||j|yy) 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. rrCNrerTg@g?zWarning: missing file after %rr)rtrDrcrrrCrrrvrrrBrGrinsertremove)rrrHrrwL2distancerrzr{r|newDistr series2insertnewSeries rnrrfs KKM A A$CS( %BHq#a&!hS--a01S--a01dTk" #.0 IIbMHGcHn4!''4s}}DH 2 c16 2w{ LL   +A"5::/@AH !H    * + !/ 'H MM!X & ' erm)F)r?sysrrloggingnumpyr getLoggerrir byteorderrrItemTagItemDelimiterTagrsetrrrVRSrrgrrqrrsrBrrr)rvals00rnrs&    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 #'   0c!f 0 1 X__. /c3q6 /0 I  l \'\'~~I&~IBL^<K1 /s 5 E& E+