o i@sdZddlmZmZmZddlZddlZddlmZddl Z ddl Z ddl m Z ddl mZmZmZmZddlZddlmZddlmZmZdd lmZdd lmZmZmZdd lmZm Z dd l!m"Z"dd l#m$Z$m%Z%m&Z&ddl'm(Z(ddl)m*Z*m+Z+ddl,m-Z.ddl,m/Z/m0Z0m1Z1m2Z2m3Z3e 4dZ5iddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;dd?d@dAdBdCZ6dDZ7dEZ8dFZ9dGZ: IddJe;dKedPedMe=fdQdRZ?GdSdTdTedTZ@GdUdVdVe@ZAGdWdXdXZBee;BejCBZDGdYdZdZZEd[ed\eFe;dMdfd]d^ZGd[edMefd_d`ZHd[edMefdadbZId[edMefdcddZJd[edMefdedfZKd[edMefdgdhZLd[edMefdidjZMd[edMefdkdlZNd[edMefdmdnZOd[edMefdodpZPd[edMefdqdrZQd[edMefdsdtZRd[edMefdudvZSd[edMefdwdxZTd[edMefdydzZUd[edMefd{d|ZVd[edMefd}d~ZWd[edMefddZXd[edMefddZYd[edMefddZZd[edMefddZ[d[edMefddZ\d[edMefddZ]d[edMefddZ^d[edMefddZ_ideHdeIdeJdeKdeLdeMdeNd eOd"ePd$e]d&eQd(eRd*eSd,e]d.e^d0e^d2eTeUe^e_eVeWeXeYe_e^e^eZe^e[e\dZ` e.jad2e.jbde.jcde.jdde.jediZfie.jgde.jhde.jid e.jjd e.jkd e.jld e.jmd"e.jnd"e.jod"e.jpd"e.jqd"e.jrd"e.jsd$e.jtd$e.jud$e.jvd$e.jwd$ie.jxd$e.jyd$e.jzd$e.j{d$e.j|d$e.j}d$e.j~d$e.jd$e.jd$e.jd$e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&ie.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd&e.jd(e.jd*e.jd,e.jd.e.jd.e.jd0e.jde.jde.jde.jde.jde.jde.jde.jde.jde.jde.jde.jde.jde.jdiZd[edMe;fddZd[edMe;fddZdS)zDICOM File-set handling.)IteratorIterableCallableN)Path)TemporaryDirectory)OptionalUnionAnycast)default_encoding)tag_for_keyworddictionary_description) DataElement)DatasetFileMetaDataset FileDataset) DicomBytesIO DicomFileLike)dcmread) write_datasetwrite_data_elementwrite_file_meta_info) warn_and_log)TagBaseTag) generate_uidUIDExplicitVRLittleEndianImplicitVRLittleEndianMediaStorageDirectoryStoragez ^[A-Z0-9_]*$PATIENTPTSTUDYSTSERIESSEIMAGEIMzRT DOSERDzRT STRUCTURE SETRSRT PLANRPzRT TREAT RECORDRX PRESENTATIONPRWAVEFORMWVz SR DOCUMENTSRzKEY OBJECT DOCKY SPECTROSCOPYSPzRAW DATARW REGISTRATIONRGFIDUCIALFDzHANGING PROTOCOLHGEDVMSXPAIPIAIGPLMXSFSSTRASRTP) ENCAP DOC VALUE MAP STEREOMETRICPALETTEIMPLANT IMPLANT ASSY IMPLANT GROUPPLAN MEASUREMENTSURFACE SURFACE SCANTRACT ASSESSMENT RADIOTHERAPYPRIVATE7OffsetOfTheFirstDirectoryRecordOfTheRootDirectoryEntityOffsetOfTheNextDirectoryRecord+OffsetOfReferencedLowerLevelDirectoryEntity6OffsetOfTheLastDirectoryRecordOfTheRootDirectoryEntityFprefixstart alphanumericreturnc cst|dkr tdd}|s|dd}|}t|}dt|}|||krW|}d}|r;||||7}||}|s-||dddd |V|d 7}|||ks'dSdS) aYield File IDs for a File-set. Maximum number of File IDs is: * Numeric: (10 ** (8 - `prefix`)) - `start` * Alphanumeric: (35 ** (8 - `prefix`)) - `start` .. versionchanged:: 3.0 The characters used when `alphanumeric` is ``True`` have been reduced to [0-9][A-I,K-Z] Parameters ---------- prefix : str, optional The prefix to use for all filenames, default (``""``). start : int, optional The starting index to use for the suffixes, (default ``0``). i.e. if you want to start at ``'00010'`` then `start` should be ``10``. alphanumeric : bool, optional If ``False`` (default) then only generate suffixes using the characters [0-9], otherwise use [0-9][A-I,K-Z]. Yields ------ str A unique filename with 8 characters, with each incremented by 1 from the previous one (i.e. ``'00000000'``, ``'00000001'``, ``'00000002'``, and so on). z0The 'prefix' must be less than 8 characters long#0123456789ABCDEFGHIKLMNOPQRSTUVWXYZN r]>0)len ValueError) r^r_r`charsidxblengthnsuffixrqE/mnt/sdb/aimis/docanh/lib/python3.10/site-packages/pydicom/fileset.pygenerate_filenameLs& !    rspathcCsr|j}tdd|DrdSt|dkrdSd|}z |jdddWn ty.YdSwtt|r7d SdS) a{Return ``True`` if `path` is a conformant File ID. **Conformance** * :dcm:`No more than 8 components` (parts) in the path * :dcm:`No more than 8 characters per component` * :dcm:`Characters in a component must be ASCII` * :dcm:`Valid characters in a component are 0-9, A-Z and _ ` Parameters ---------- path : pathlib.Path The path to check, relative to the File-set root directory. Returns ------- bool ``True`` if `path` is conformant, ``False`` otherwise. cSsg|]}t|dkqS)re)ri).0pprqrqrr z)is_conformant_file_id..Frer]asciistrict)encodingerrorsT) partsanyrijoinencodeUnicodeEncodeErrorrematch _RE_FILE_ID)rtr}rkrqrqrris_conformant_file_ids    rc@seZdZdZdEdedBddfddZdFdd Zededfd d Z ede fd d Z de e dfde fddZde e dfddfddZedefddZdGde defddZededBfddZedHddZde e dfddfddZede fd d!Zedefd"d#Zede fd$d%Zdedfd&d'Zede fd(d)Zededfd*d+ZedId,d-Zej dJd/d-ZdKd1e dee fd2d3Z!ededfd4d5Z"d6eddfd7d8Z#ede fd9d:Z$dJd;d<Z%de&dfd=d>Z'edId?d@Z(de fdAdBZ)dLdCdDZ*dS)M RecordNodeaSRepresentation of a DICOMDIR's directory record. Attributes ---------- children : list of RecordNode The current node's child nodes (if any) instance : FileInstance or None If the current node is a leaf node, a :class:`~pydicom.fileset.FileInstance` for the corresponding SOP Instance. NrecordracCs:g|_d|_d|_||r||d|_d|_d|_dS)zCreate a new ``RecordNode``. Parameters ---------- record : pydicom.dataset.Dataset, optional A *Directory Record Sequence's* directory record. Nr)childreninstance_parent _set_record_offset _offset_next _offset_lower)selfrrqrqrr__init__s  zRecordNode.__init__leafcCsV|j}||ur |jd}|j}||vr&|jr&||}|jd}||vr&|js||_dS)a Add a leaf to the tree. Parameters ---------- leaf : pydicom.fileset.RecordNode A leaf node (i.e. one with a :class:`~pydicom.fileset.FileInstance`) to be added to the tree (if not already present). rN)rootrparent)rrnodecurrentrqrqrradds    zRecordNode.addcsfddDS)zaReturn a list of the current node's ancestors, ordered from nearest to furthest. csg|]}|ur|qSrqrq)runnrrqrrrwrxz(RecordNode.ancestors..)reverserrqrrr ancestorsszRecordNode.ancestorscCs|jrtdt|j}|jdkr||j}d}|jjs$|dd}d}|j}t|}|r=||||7}||}|s/|ddddd t|}||S) z@Return a File ID component as :class:`str` for the current node.z4The root node doesn't contribute a File ID componentrXrcNrdr]rfrgre) is_rootrj _PREFIXES record_typedepthfile_set_use_alphanumericindexri)rr^rkrprormrlrqrqrr components"     zRecordNode.componentkeycCs$t|tr|j}|dd|jDvS)z?Return ``True`` if the current node has a child matching `key`.cSsg|]}|jqSrqr)ruchildrqrqrrrwz+RecordNode.__contains__..) isinstancerrrrrrqrqrr __contains__ s zRecordNode.__contains__csVttrj|vrtfdd|jD|_|js'|js)|j|=dSdSdS)zRemove one of the current node's children and if the current node becomes childless recurse upwards and delete it from its parent. csg|] }|jkr|qSrqrruiirrqrrrwz*RecordNode.__delitem__..N)rrrKeyErrorrrrrrqrrr __delitem__s   zRecordNode.__delitem__cCstt|dS)z;Return the number of nodes to the level below the tree rootrh)rilistrrrqrqrrr$szRecordNode.depthFforce_implicitcCst}d|_||_|jdt}t|jD]-}|jdkr$|j dkr$q|dkr0| d|_ n |dkr;| d|_ t ||j||qt|S)aEncode the node's directory record. * Encodes the record as explicit VR little endian * Sets the ``RecordNode._offset_next`` and ``RecordNode._offset_lower`` attributes to the position of the start of the values of the *Offset of the Next Directory Record* and *Offset of Referenced Lower Level Directory Entity* elements. Note that the offsets are relative to the start of the current directory record. The values for the *Offset Of The Next Directory Record* and *Offset of Referenced Lower Level Directory Entity* elements are not guaranteed to be correct. Parameters ---------- force_implicit : bool, optional ``True`` to force using implicit VR encoding, which is non-conformant. Default ``False``. Returns ------- int The length of the encoded directory record. See Also -------- :meth:`~pydicom.fileset.RecordNode._update_record_offsets` TSpecificCharacterSetrirei )ris_little_endianis_implicit_VR_recordgetr sortedkeyselementgrouptellrrrrigetvalue)rrfpr{tagrqrqrr_encode_record)s zRecordNode._encode_recordcCs\d|jvr*|jd}|jdkrttt|jjS|jdkr(tttt|jjSdStd)aReturn the *Referenced File ID* as a :class:`~pathlib.Path`. Returns ------- pathlib.Path or None The *Referenced File ID* from the directory record as a :class:`pathlib.Path` or ``None`` if the element value is null. ReferencedFileIDrhNz/No 'Referenced File ID' in the directory record)rr<rr strrrAttributeError)relemrqrqrr_file_id]s   zRecordNode._file_idFileSetcC|jjSz4Return the tree's :class:`~pydicom.fileset.FileSet`.)rrrrqrqrrrrszRecordNode.file_setcCs6t|tr|j}|jD] }||jkr|Sq t|)zcReturn the current node's child using it's :attr:`~pydicom.fileset.RecordNode.key` )rrrrr)rrrrqrqrr __getitem__ws   zRecordNode.__getitem__cCs |jduS)z?Return ``True`` if the current node corresponds to an instance.N)rrrqrqrr has_instances zRecordNode.has_instancecCs|jsdS|jj|S)z:Return the index of the current node amongst its siblings.r)rrrrrqrqrrrszRecordNode.indexcCdS).leaf_summary..cSh|]}|jqSrqrrrqrqrr rz.leaf_summary..cg|] }|jkr|qSrqrrrrqrrrwrcSg|] }tt|jjr|qSrq)r FileInstancer for_additionrrqrqrrrws  cSrrq)r rr for_removalrrqrqrrrwsrz initialrhsr] addition removal: z SOP Instancez (, ))rrrrrirr)rroutindentsibsrtypesnrrrminitialresultchangespluralsummaryrqrrr leaf_summarysD      z)RecordNode.prettify..leaf_summaryrz: 1 SOP Instancez (to be added)z (to be removed)) rrrrrrextendr rrrrr)rrrrrrrlinerqrqrrprettifys, 1    zRecordNode.prettifycCs*|jsdS|jdkr dS|jj|jdS)z=Return the node before the current one (if any), or ``None``.Nrrh)rrrrrqrqrrprevious"s  zRecordNode.previousdsc stdd}dd}|r|dnd}d|d}|r&d|d|d }dg}fd d |D}|rB|d d |}t|tvrLttdtvrVttdd_|_z|j WdSt tfyx}zt|d|d}~ww)aSet the node's initial directory record dataset. The record is used as a starting point when filling the DICOMDIR's *Directory Record Sequence* and is modified as required during encoding. Parameters ---------- ds : pydicom.dataset.Dataset Set the node's initial directory record dataset, must be conformant to :dcm:`Part 3, Annex F of the DICOM Standard `. seq_item_tellNDirectoryRecordType r]zThe zdirectory record is missingzdirectory record at offset z is missingcsg|]}|vr|qSrqrqrukwrrqrrrwCrxz*RecordNode._set_record..z one or more required elements: rrz a required element) getattrrrrj _NEXT_OFFSETsetattr _LOWER_OFFSETRecordInUseFlagrrr)rroffsetrmsgkeywordsmissingrrqrrrr-s.      zRecordNode._set_recordcCstt|jjS)z.Flagsrr N)r r!r"r%__annotations__rqrqrqrrFlagss  r2xN)uuiduuid4_uuid_flags _apply_stage _stage_pathr)rrr2rqrqrrrs    zFileInstance.__init__flagcCs|dkrd|j_d|j_d|_dS|dkr3|jjr"d|j_d|_dSd|j_|jjd|j|_dS|dkrM|jjrDd|j_d|_dSd|j_d|_dSdS)a0Apply staging to the instance. Parameters ---------- flag : str The staging to apply, one of ``'+'``, ``'-'`` or ``'x'``. This will flag the instance for addition to or removal from the File-set, or to reset the staging, respectively. r3FN+Trt-)r7rr r9r_stager6)rr:rqrqrrr8s"     zFileInstance._apply_stagenamecCs$z||WdStyYdSw)aReturn ``True`` if the element with keyword or tag `name` is in one of the corresponding directory records. Parameters ---------- name : str or int The element keyword or tag to search for. Returns ------- bool ``True`` if the corresponding element is present, ``False`` otherwise. FT)r)rr>rqrqrrrs   zFileInstance.__contains__cs8|jjfdd|jD}tt|dddS)z.Return the File ID of the referenced instance.csg|] }|ur|jqSrq)rrrrqrrrwrz'FileInstance.FileID..Nrf)rrrosfspathr)r componentsrqr?rrFileIDszFileInstance.FileIDrcCr)zWReturn the :class:`~pydicom.fileset.FileSet` this instance belongs to. )rrrrqrqrrrzFileInstance.file_setcCr)z^Return ``True`` if the instance has been staged for addition to the File-set. )r7rrrqrqrrr rDzFileInstance.for_additioncCsP|jrdS|djdkr|jtjj}|jg|kStt |j|jtjjkS)zeReturn ``True`` if the instance will be moved to a new location within the File-set. Frrh) rr<rCsplitr@rtseprr r%)rfile_idrqrqrr for_moving's  zFileInstance.for_movingcCr)z_Return ``True`` if the instance has been staged for removal from the File-set. )r7r rrqrqrrr5rDzFileInstance.for_removalcsNt|}|dur!t|}|jD]}||jvr |j|jSqt|S)aeReturn the class attribute value for `name`. Parameters ---------- name : str An element keyword or a class attribute name. Returns ------- object If `name` matches a DICOM keyword and the element is present in one of the directory records then returns the corresponding element's value. Otherwise returns the class attribute's value (if present). Directory records are searched from the lowest (i.e. an IMAGE or similar record type) to the highest (PATIENT or similar). N)r rrrrrr*__getattribute__)rr>rrr,rqrrrI<s  zFileInstance.__getattribute__rcCs|t|tr|}nt|}|dkrtd}n|dkrtd}n|dkr&td}|jD]}||jvr9|j|Sq+t|)aReturn the DataElement with keyword or tag `key`. Parameters ---------- key : str or int An element keyword or tag. Returns ------- pydicom.dataelem.DataElement The DataElement corresponding to `key`, if present in one of the directory records. Directory records are searched from the lowest (i.e. an IMAGE or similar record type) to the highest (PATIENT or similar). iiiiii)rrrrrrr)rrrrrqrqrrrWs    zFileInstance.__getitem__cCs |jjdkS)z5Return ``True`` if the instance is privately defined.rX)rrrrqrqrr is_private}rzFileInstance.is_privatecCs|jp|jp|jS)zZReturn ``True`` if the instance is staged for moving, addition or removal )rrHrrrqrqrr is_stagedszFileInstance.is_stagedcCs |jr ttt|jSt|jS)zWReturn the referenced instance as a :class:`~pydicom.dataset.Dataset`. )rrr rr9rtrrqrqrrloads zFileInstance.loadcCs:|jr ttt|jSttt|jjtt|jj S)aKReturn the path to the corresponding instance as :class:`str`. Returns ------- str The absolute path to the corresponding instance. If the instance is staged for addition to the File-set this will be a path to the staged file in the temporary staging directory. ) rr@rAr rr9rrtrrrrqrqrrrts  zFileInstance.pathcC tt|jS)z6Return the *SOP Class UID* of the referenced instance.)r rReferencedSOPClassUIDInFilerrqrqrr SOPClassUIDrzFileInstance.SOPClassUIDcCrM)z9Return the *SOP Instance UID* of the referenced instance.)r rrrrqrqrrSOPInstanceUIDrzFileInstance.SOPInstanceUIDcCrM)zd?Z'e'jd@e'ddfdAd?Z'   dNde e j BdBdBededdfdCdDZ( dOdEe)dFededdfdGdHZ*dS)Prz#Representation of a DICOM File-set.NrracCsd|_t||_tiiddd|_t|jdj|jd<t|_g|_ d|_ d|_ d|_ d|_ d|_|r<||dSt|_dS)zCreate or load a File-set. Parameters ---------- ds : pydicom.dataset.Dataset, str or PathLike, optional If loading a File-set, the DICOMDIR dataset or the path to the DICOMDIR file. NF)tr;r<~^rSrt)_pathr(_treerr=rr>r_ds _instancesr_id_uid _descriptor_charsetrLrrrrrqrqrrrs&  zFileSet.__init__ ds_or_pathc st|ttjBr t|}n|}|jfdd|D}|jdvr?|jd}|jd=|j|| dt t |S|rE|dS| |}t |}t|}|}|D] }t|}||_|}qVt |}||_|j|||jd|j<|j|| d|j|jddt t |S)aStage an instance for addition to the File-set. If the instance has been staged for removal then calling :meth:`~pydicom.fileset.FileSet.add` will cancel the staging and the instance will not be removed. Parameters ---------- ds_or_path : pydicom.dataset.Dataset, str or PathLike The instance to add to the File-set, either as a :class:`~pydicom.dataset.Dataset` or the path to the instance. Returns ------- FileInstance The :class:`~pydicom.fileset.FileInstance` that was added. See Also -------- :meth:`~pydicom.fileset.FileSet.add_custom` crrqrPrrrqrrrw rzFileSet.add..r<r;rTenforce_file_format)rrr@PathLikerrPr=rYrr8r r _recordifyrrrrrWrsave_asrt) rr_r have_instancer record_genrrrrqrrrrs:          z FileSet.addrcst|ttjBr t|}n|}|jdkrtd|jfdd|D}|jdvrH|jd}|jd=|j || dt t |S|rN|dSd|j_|j|j_|j_|jj|j_t |}||_|j|||jd|j<|j || d|j|jd d t t |S) a Stage an instance for addition to the File-set using custom records. This method allows you to add a SOP instance and customize the directory records that will be used when writing the DICOMDIR file. It must be used when you require PRIVATE records and may be used instead of modifying :attr:`~pydicom.fileset.DIRECTORY_RECORDERS` with your own record definition functions when the default functions aren't suitable. The following elements will be added automatically to the supplied directory records if required and not present: * (0004,1400) *Offset of the Next Directory Record* * (0004,1410) *Record In-use Flag* * (0004,1420) *Offset of Referenced Lower-Level Directory Entity* * (0004,1500) *Referenced File ID* * (0004,1510) *Referenced SOP Class UID in File* * (0004,1511) *Referenced SOP Instance UID in File* * (0004,1512) *Referenced Transfer Syntax UID in File* If the instance has been staged for removal then calling :meth:`~pydicom.fileset.FileSet.add_custom` will cancel the staging and the instance will not be removed. Examples -------- Add a SOP Instance using a two record hierarchy of PATIENT -> PRIVATE .. code-block:: python from pydicom import Dataset, examples from pydicom.fileset import FileSet, RecordNode from pydicom.uid import generate_uid # The instance to be added ds = examples.ct # Define the leaf node (the PRIVATE record) record = Dataset() record.DirectoryRecordType = "PRIVATE" record.PrivateRecordUID = generate_uid() leaf_node = RecordNode(record) # Define the top node (the PATIENT record) record = Dataset() record.DirectoryRecordType = "PATIENT" record.PatientID = ds.PatientID record.PatientName = ds.PatientName top_node = RecordNode(record) # Set the node relationship leaf_node.parent = top_node # Add the instance to the File-set fs = FileSet() instance = fs.add_custom(ds, leaf_node) Parameters ---------- ds_or_path : pydicom.dataset.Dataset, str or PathLike The instance to add to the File-set, either as a :class:`~pydicom.dataset.Dataset` or the path to the instance. leaf : pydicom.fileset.RecordNode The leaf node for the instance, should have its ancestors nodes set correctly as well as their corresponding directory records. Should have no more than 7 ancestors due to the semantics used by :class:`~pydicom.fileset.FileSet` when creating the directory structure. Returns ------- FileInstance The :class:`~pydicom.fileset.FileInstance` that was added. See Also -------- :meth:`~pydicom.fileset.FileSet.add` rbzrThe 'leaf' node must not have more than 7 ancestors as 'FileSet' supports a maximum directory structure depth of 8crrqr`rrrqrrrwrz&FileSet.add_custom..r<r;rNTra)rrr@rcrrrjrPr=rYrr8r rrrrOrNr file_metarRrQrrWrrert)rr_rrrfrrqrrr add_custom3s:Q            zFileSet.add_customcCsg|j_g|_d|_t|_d|_t|_d|_ d|_ i|j d<i|j d<d|j d<d|j d<|j d t |j d<t|j dj|j d<dS) zClear the File-set.Nr;r<FrTrUrSrt)rWrrYrVrrXrZrr[r\r]r=cleanuprrr>rrqrqrrclears     z FileSet.clearFrtrc Csnt|}|jrt|j|krtdt|dkrd|_t|dkr%tdg}|jdD]}||j |j |j q.g}|D])}||j |t|j }|jjdddt|j||j tjj|j j_ qB|d}t|d }t|} |j| d|d Wd n1swYt||D] \}} | |j j_ q|D]} |j | qt} | j|dd | S) aCopy the File-set to a new root directory and return the copied File-set. Changes staged to the original :class:`~pydicom.fileset.FileSet` will be applied to the new File-set. The original :class:`~pydicom.fileset.FileSet` will remain staged. Parameters ---------- path : str or PathLike The root directory where the File-set is to be copied to. force_implicit : bool, optional If ``True`` force the DICOMDIR file to be encoded using *Implicit VR Little Endian* which is non-conformant to the DICOM Standard (default ``False``). Returns ------- pydicom.fileset.FileSet The copied File-set as a :class:`~pydicom.fileset.FileSet`. z3Cannot copy the File-set as the 'path' is unchanged@BTmUpydicom doesn't support writing File-sets with more than 1838265625 managed instancesr<parentsexist_okDICOMDIRwb) copy_saferN raise_orphans)rrtrjrirNotImplementedErrorr=valuesrrrWr rrCrmkdirshutilcopyfilerEr@rFropenr_write_dicomdirziprrrL) rrtrdetached_nodesrfile_idsdstprfrGrr)rqrqrrcopysB      z FileSet.copycCsnt}d|_t|_t|j_|j|j_t|j_ |j |_ d|_ d|_ d|_g|_|jr.|j|_|jr5|j|_|S)z&Return a new minimal DICOMDIR dataset.Nr)rfilenamerrhrrRrMediaStorageSOPInstanceUIDrMediaStorageSOPClassUIDID FileSetIDrYr\FileSetConsistencyFlagDirectoryRecordSequencedescriptor_file_idFileSetDescriptorFileIDdescriptor_character_set+SpecificCharacterSetOfFileSetDescriptorFiler^rqrqrr_create_dicomdirs" zFileSet._create_dicomdircCr.)zlReturn the *Specific Character Set of File-set Descriptor File* (if available) or ``None``. )r]rrqrqrrr(sz FileSet.descriptor_character_setvalcCs0||jkrdS||_|jr||j_d|jd<dS)aSet the *Specific Character Set of File-set Descriptor File*. The descriptor file itself is used for user comments related to the File-set (e.g. a README file) and is up the user to create. Parameters ---------- val : str or None The value to use for the DICOMDIR's (0004,1142) *Specific Character Set of File-set Descriptor File*. See :dcm:`C.12.1.1.2 in Part 3 of the DICOM Standard ` for defined terms. See Also -------- :attr:`~pydicom.fileset.FileSet.descriptor_file_id` set the descriptor file ID for the file that uses the character set. NTrU)r]rXrr=rrrqrqrrr/s cCr.)zDReturn the *File-set Descriptor File ID* (if available) or ``None``.)r\rrqrqrrrKr/zFileSet.descriptor_file_idcCs||jkrdS|dur n]t|trKz&t|dksJ|D]}t|ts%Jdt|kr2dks5JJqWn tyBtdwtt|j}nt|tredt|kr_dksdtdtdnt d||_|j rt|j|j _ d|j d <dS) aSet the *File-set Descriptor File ID*. The descriptor file itself is used for user comments related to the File-set (e.g. a README file) and is up the user to create. Parameters ---------- val : str, list of str or None The value to use for the DICOMDIR's (0004,1141) *File-set Descriptor File ID*. Should be the relative path to the descriptor file and has a maximum length of 8 components, with each component up to 16 characters long. Raises ------ ValueError If `val` has more than 8 items or if each item is longer than 16 characters. See Also -------- :attr:`~pydicom.fileset.FileSet.descriptor_character_set` the character set used in the descriptor file, required if an expanded or replaced character set is used. NrerzfThe 'File-set Descriptor File ID' has a maximum of 8 components, each between 0 and 16 characters longzREach 'File-set Descriptor File ID' component has a maximum length of 16 charactersz:The 'DescriptorFileID' must be a str, list of str, or NoneTrU) r\rrrirAssertionErrorrjrr} TypeErrorrXrr=)rrrrqrqrrrPsD  "   rLkwargsc s^s |jddSddttBdtdtffdd fdd |D}s-s-td |S) aTReturn matching instances in the File-set **Limitations** * Only single value matching is supported so neither ``PatientID=['1234567', '7654321']`` or ``PatientID='1234567', PatientID='7654321'`` will work (although the first example will work if the *Patient ID* is actually multi-valued). * Repeating group and private elements cannot be used when searching. Parameters ---------- load : bool, optional If ``True``, then load the SOP Instances belonging to the File-set and perform the search against their available elements. Otherwise (default) search only the elements available in the corresponding directory records (more efficient, but only a limited number of elements are available). **kwargs Search parameters, as element keyword=value (i.e. ``PatientID='1234567', StudyDescription="My study"``. Returns ------- list of pydicom.fileset.FileInstance A list of matching instances. NFrrrac slrtfdd|Drd|D]\}}z |j|ks%JWqttfy3YdSwdS)Ncsg|]}|vqSrqrqrrrqrrrwz/FileSet.find..match..TF)rLallitemsrrr)rrrr) has_elementsrLrrrrszFileSet.find..matchcs g|] }|fir|qSrqrq)rur)rrrqrrrws z FileSet.find..zNone of the records in the DICOMDIR dataset contain all the query elements, consider using the 'load' parameter to expand the search to the corresponding SOP instances)rYrrr r%r)rrLrmatchesrq)rrrLrrrfinds z FileSet.findelements instancesc Cst|tr|n|g}dd|D}dd|D}|pt|}|D](}|r(|}|D]} | |vr1q*d|| <|| j} | || vrG|| | q*q dd|D} |s^| r^td| dt|tsi||d S|S) aReturn a list of unique values for given element(s). Parameters ---------- elements : str, int or pydicom.tag.BaseTag, or list of these The keyword or tag of the element(s) to search for. instances : list of pydicom.fileset.FileInstance, optional Search within the given instances. If not used then all available instances will be searched. load : bool, optional If ``True``, then load the SOP Instances belonging to the File-set and perform the search against their available elements. Otherwise (default) search only the elements available in the corresponding directory records (more efficient, but only a limited number of elements are available). Returns ------- list of object(s), or dict of lists of object(s) * If single element was queried: A list of value(s) for the element available in the instances. * If list of elements was queried: A dict of element value pairs with lists of value(s) for the elements available in the instances. cSsi|]}|dqSrrqrurrqrqrr rz'FileSet.find_values..cSsi|]}|gqSrqrqrrqrqrrrrTcSsg|]\}}|s|qSrqrq)rurvrqrqrrrwrxz'FileSet.find_values..z4None of the records in the DICOMDIR dataset contain z], consider using the 'load' parameter to expand the search to the corresponding SOP instancesr)rriterrLrrrr) rrrrL element_list has_elementresultsiter_instancesrrrmissing_elementsrqrqrr find_valuess4      zFileSet.find_valuescCr.)z4Return the *File-set ID* (if available) or ``None``.)rZrrqrqrrr r/z FileSet.IDcCsb||jkrdS|dusdt|krdkr-ntd||_|jr&||j_d|jd<dStd)aSet the File-set ID. Parameters ---------- val : str or None The value to use for the DICOMDIR's (0004,1130) *File-set ID*. Raises ------ ValueError If `val` is greater than 16 characters long. NrrTrUz8The maximum length of the 'File-set ID' is 16 characters)rZrirXrr=rjrrqrqrrrs "cstfdddDS)z=Return ``True`` if the File-set is new or has changes staged.c3s|]}j|VqdSr)r=)rucrrqrr ,sz$FileSet.is_staged..z+-^~)r~rrqrrrrK)szFileSet.is_stagedccs|jddEdHdS)z?Yield :class:`~pydicom.fileset.FileInstance` from the File-set.N)rYrrqrqrrr.szFileSet.__iter__cCs t|jS)z/Return the number of instances in the File-set.)rirYrrqrqrr__len__2s zFileSet.__len__Tinclude_orphansrvc Cst|tr|}nt|}|jdd}|tkrtd|jj}|tkr,t d|j dzt t t |jjdd}WntyItd|jtyStd w|t t dB|d d|_t tdB|jd }|sxt}||j_||_t t dB|d d|_t t dB|d d|_|j|_||_||||g} |D]G} | jj} | dur| | qzt t |j!| jddWn ty| | t d| jj"dt t |j!| Yqw| j#rd|j$d<q| D]} |j%&| qdS)aLoad an existing File-set. Existing File-sets that do not use the same directory structure as *pydicom* will be staged to be moved to a new structure. This is because the DICOM Standard attaches no semantics to *how* the files in a File-set are to be structured so it's impossible to determine what the layout will be when changes are to be made. Parameters ---------- ds_or_path : pydicom.dataset.Dataset, str or PathLike An existing File-set's DICOMDIR, either as a :class:`~pydicom.dataset.Dataset` or the path to the DICOMDIR file as :class:`str` or pathlike. include_orphans : bool, optional If ``True`` (default) include instances referenced by orphaned directory records in the File-set. raise_orphans : bool, optional If ``True`` then raise an exception if orphaned directory records are found in the File-set (default ``False``). rNz_Unable to load the File-set as the supplied dataset is not a 'Media Storage Directory' instancez6The DICOMDIR dataset uses an invalid transfer syntax 'z8' and will be updated to use 'Explicit VR Little Endian'T)rzzfUnable to load the File-set as the 'filename' attribute for the DICOMDIR dataset is not a valid path: zyUnable to load the File-set as the DICOMDIR dataset must have a 'filename' attribute set to the path of the DICOMDIR filerrrrz?The referenced SOP Instance for the directory record at offset z does not exist: rT)'rrrrhrrrjrRrrr>rr rrresolveFileNotFoundErrorrrkrZrrrr[r\r]rrVrX_parse_recordsrrrrtrrHr=rYr ) rr_rrvr sop_classtsyntaxrtuid bad_instancesrrGrqrqrrrL6s       z FileSet.loadc sittt|jD]}tt|j}t|}||_||<q rE|tj }j |_ t |j tdrE|j tj }j |_ t |j tds2dtddffdd j jD]}|qVttttj krldS|rrtdtddj D}fd d |D}d d |D}|r|std t|d dS|D],}|j j} |j} | durqttj| } |jdkrĈ| |} n| } | | jj _qdS)aParse the records in an existing DICOMDIR. Parameters ---------- ds : pydicom.dataset.Dataset The File-set's DICOMDIR dataset. include_orphans : bool If ``True`` then include within the File-set orphaned records that contain a valid (and unique) *Referenced File ID* element. Orphaned records are those that aren't placed within the *Directory Record Sequence* hierarchy. raise_orphans : bool, optional If ``True`` then raise an exception if orphaned directory records are found in the File-set (default ``False``). Nrracst|jtd}|r*|}||_t|jtd}|r)|}||_t|jtd}|sn d|jvr3|j|=d|jvrDt||_j|j|j D]}|qGdS)Nr) rrrrrrrrYrr)r child_offsetr next_offsetrecords recurse_noderrqrrrs&     z,FileSet._parse_records..recurse_nodez0The DICOMDIR contains orphaned directory recordscSrrq)rrrqrqrrrrz)FileSet._parse_records..csg|]}|qSrqrq)ruo)rrqrrrwrz*FileSet._parse_records..cSsg|] }d|jvr|qS)r)r)rurrqrqrrrwrzThe DICOMDIR has z` orphaned directory records that reference an instance that will not be included in the File-setrX)r rrrr&rrr _FIRST_OFFSETrrWrrrrrrirrrjsetrrrrrrtrrirr) rrrrvrrr missing_setr original_valuerGrtrrqrrrrsN       zFileSet._parse_recordscCs|jdur t|jS|jS)zxReturn the absolute path to the File-set root directory as :class:`str` (if set) or ``None`` otherwise. N)rVr@rArrqrqrrrts  z FileSet.pathc cs^t|}|dkrKzt||}Wnty)}z td|d|d|d}~wwd|_d|_d|_||_d|_|j|_ |j |_ |j j |_|VdSg}t|}ddd |fD]<}zt||}Wntyy}z td|d|d|d}~wwd|_d|_d|_||_d |vr|j|_||qW|d }d|_|j|_ |j |_ |j j |_|EdHdS) a#Yield directory records for a SOP Instance. Parameters ---------- ds : pydicom.dataset.Dataset The SOP Instance to create DICOMDIR directory records for. Yields ------ ds : pydicom.dataset.Dataset A directory record for the instance, ordered from highest to lowest level. Raises ------ ValueError If unable to create the required directory records because of a missing required element or element value. r zUnable to use the default 'z' record creator: z. See DICOM PS3.3 Section F.5. Either update the instance, define your own record creation function or use 'FileSet.add_custom()' insteadNrrr"r$r)_single_level_record_typeDIRECTORY_RECORDERSrjrZrr[rrrOrNrPrrhrRrQ_four_level_record_typerr)rrrrrr leaf_typerrqrqrrrdsj     zFileSet._recordifyrcCst|tr|D]}||qdS||jvrtd|j|jdvrP|j}|j|=|jd|j=z t |j  Wn t yBYnw| d|j|dS|j|jdvrm| d||jd|j<|j|dSdS)aStage instance(s) for removal from the File-set. If the instance has been staged for addition to the File-set, calling :meth:`~pydicom.fileset.FileSet.remove` will cancel the staging and the instance will not be added. Parameters ---------- instance : pydicom.fileset.FileInstance or a list of FileInstance The instance(s) to remove from the File-set. Nz No such instance in the File-setr;r<)rrr rYrjrPr=rrrrtunlinkrr8)rritemrrqrqrrr _s,      zFileSet.removecCs\dd|jpdd|jp dd|jd|jpdd|jp dg}|jrg}|js2|dn|d |jd rA|d |jd rbt |jd d krQdnd}|t |jd d||jdrt |jdd krrdnd}|t |jdd||dd ||j j sd |S|d| dd|j Dd |S)z.Return a string representation of the FileSet.zDICOM File-setz Root directory: z(no value available)z File-set ID: z File-set UID: z Descriptor file ID: z! Descriptor file character set: zDICOMDIR creationzDICOMDIR updaterTzdirectory structure updater;rhrr]rr<rz Changes staged for write(): r z Managed instances:cSsg|]}d|qS)z rqrrqrqrrrwrz#FileSet.__str__..)rtrrrrrKrXrr=rirrWrrr)rrrrprqrqrrrs<          zFileSet.__str__cCrM)zReturn the File-set's UID.)r rr[rrqrqrrrrz FileSet.UIDrcCsD||jkrdSt|}|jsJ||_|jr||jj_d|jd<dS)zSet the File-set UID. Parameters ---------- uid : pydicom.uid.UID The UID to use as the new File-set UID. NTrU)r[ris_validrXrhrr=)rrrqrqrrrs    use_existingc s|s jdur td|rjrtd|rt|_js dSttjd}tjd}|r7|r7td|s@|jdO}tdkrId _ td krSt d jd  D]}z t|j Wn t ynYnwj|jqZ|r|st|d }t|}j||dWdn1swYj|d ddSddD} fddD} | | @fddDD]}|jd|j<|dtj|jj|jqD]?}j|j} | jjd d d|jjdvr|j} tj} n j|jj} tj} | t| t| |j tjj!|jj"_#qt|d }t|}j||dWdn 1s;wYj|d ddS)a4 Write the File-set, or changes to the File-set, to the file system. .. warning:: If modifying an existing File-set it's **strongly recommended** that you follow standard data management practices and ensure that you have an up-to-date backup of the original data. By default, for both new or existing File-sets, *pydicom* uses the following directory structure semantics when writing out changes: * For instances defined using the standard four-levels of directory records (i.e. PATIENT/STUDY/SERIES + one of the record types such as IMAGE or RT DOSE): ``PTxxxxxx/STxxxxxx/SExxxxxx/`` with a filename such as ``IMxxxxxx`` (for IMAGE), where the first two characters are dependent on the record type and ``xxxxxx`` is a numeric or alphanumeric index. * For instances defined using the standard one-level directory record (i.e. PALETTE, IMPLANT): a filename such as ``PAxxxxxx`` (for PALETTE). * For instances defined using PRIVATE directory records then the structure will be along the lines of ``P0xxxxxx/P1xxxxxx/P2xxxxxx`` for PRIVATE/PRIVATE/PRIVATE, ``PTxxxxxx/STxxxxxx/P2xxxxxx`` for PATIENT/STUDY/PRIVATE. When only changes to the DICOMDIR file are required or instances have only been removed from an existing File-set you can use the `use_existing` keyword parameter to keep the existing directory structure and only update the DICOMDIR file. Parameters ---------- path : str or PathLike, optional For new File-sets, the absolute path to the root directory where the File-set will be written. Using `path` with an existing File-set will raise :class:`ValueError`. use_existing : bool, optional If ``True`` and no instances have been added to the File-set (removals are OK), then only update the DICOMDIR file, keeping the current directory structure rather than converting everything to the semantics used by *pydicom* for File-sets (default ``False``). force_implicit : bool, optional If ``True`` force the DICOMDIR file to be encoded using *Implicit VR Little Endian* which is non-conformant to the DICOM Standard (default ``False``). Raises ------ ValueError If `use_existing` is ``True`` but instances have been staged for addition to the File-set. Nz=The path to the root directory is required for a new File-setzqThe path for an existing File-set cannot be changed, use 'FileSet.copy()' to write the File-set to a new locationrrr;zi'Fileset.write()' called with 'use_existing' but additions to the File-set's managed instances are stagedrTrlTrmrnr<rs)rrucSsh|]}t|jqSrq)rrCrrqrqrrrFrz FileSet.write..cs$h|]}|jjdvr|jjqS)r;)rPr=rrrrrqrrrGscsg|] }|jjvr|qSrq)rrr) collisionsrqrrrwKsz!FileSet.write..ro)$rtrjrrVrKr r%r=rirrwrxrrrWr rr|rr}rLrPr8rzr{rrCrrymover@rArErFrr)rrtrrr major_changerrrfoutfinrsrcfnrq)rrrrwrites;          z FileSet.writerrtcCs|j}|s|s |}t|j_d}|rt|j_d}|jjj|_|jjj|_|t}d|_ |t }d|_ | dt ||jddt ||dd|}t ||dd ||} |jD]} | | _| d7} | | |7} | jjrw| d7} q_g|_|jD]>} | j} |s| n't| } | t} d| _ | jr| jj| _ | t} d| _ | jr| jdj| t_ ttt|j| q~t ||d d|jjr|jjdj|_ |jjd j|_ | |t!||t!||| dd dSdS) aEncode and write the File-set's DICOMDIR dataset. Parameters ---------- fp : file-like The file-like to write the encoded DICOMDIR dataset to. Must have ``write()``, ``tell()`` and ``seek()`` methods. copy_safe : bool, optional If ``True`` then the function doesn't make any changes to the public parts of the current :class:`~pydicom.fileset.FileSet` instance. force_implicit : bool, optional Force encoding the DICOMDIR with 'Implicit VR Little Endian' which is non-conformant to the DICOM Standard (default ``False``). rersDICMT)enforce_standardNii rf)"rXrrrhrRrrrrr _LAST_OFFSETrrrrrWrrr!is_undefined_length_sequence_itemrrrdeepcopyrrrrr rrrseekr)rrrtrr seq_offset first_elem last_elemtell_offset_firstrrrrrrqrqrrr}gsf            zFileSet._write_dicomdirrrr)NF)TF)NFF)FF)+r r!r"r# DSPathTyperrrrrirkrr@rcr%rrrr$rr'rr rrr&dictrrrKrrrrLrrtrdr rrrrr}rqrqrqrrrs1G I=A  ? m d O'+  rrr cCsj|D]0}tttt|}t|}||vr td|d|d||jdkr(qtd|d|ddS)aCheck the dataset module for the Type 1 `keywords`. Parameters ---------- ds : pydicom.dataset.Dataset The dataset to check. keywords : list of str The DICOM keywords for Type 1 elements that are to be checked. Raises ------ KeyError If an element is not in the dataset. ValueError If the element is present but has no value. zThe instance's z 'z' element is missingrz' element cannot be emptyN)rr r&r r rjr<)rr rrr>rqrqrr_check_datasetsrcCs*t|dgt}|d|_|j|_|S)z,Return a PATIENT directory record from `ds`.rr)rrrrrrrrqrqrr_define_patients  rcCsdt|gdt}|j|_|j|_|d|_d|vr&t|dg|j|_|j|_|d|_|S)z*Return a STUDY directory record from `ds`.)rrStudyIDrrAccessionNumber) rrrrrrrrrrrqrqrr _define_studys   rcC0t|gdt}|j|_|j|_|j|_|S)z+Return a SERIES directory record from `ds`.)rrr)rrrrrrrqrqrr_define_series rcCst|dgt}|j|_|S)z+Return an IMAGE directory record from `ds`.r)rrrrrqrqrr _define_image s rcC(t|ddgt}|j|_|j|_|S)z-Return an RT DOSE directory record from `ds`.rDoseSummationType)rrrrrrqrqrr_define_rt_dose rcC@t|ddgt}|j|_|j|_|d|_|d|_|S)z6Return an RT STRUCTURE SET directory record from `ds`.rStructureSetLabelStructureSetDateStructureSetTime)rrrrrrrrrqrqrr_define_rt_structure_set$   rcCr)z-Return an RT PLAN directory record from `ds`.r RTPlanLabel RTPlanDate RTPlanTime)rrrrrrrrrqrqrr_define_rt_plan1 rrcCs6t|dgt}|j|_|d|_|d|_|S)z5Return an RT TREAT RECORD directory record from `ds`.r TreatmentDate TreatmentTime)rrrrrrrrqrqrr_define_rt_treatment_record> s   rcCst|gdt}|j|_|j|_|j|_|j|_|d|_|d|_d|vr4t|dg|j |_ d|vrBt|dg|j |_ |S)z1Return a PRESENTATION directory record from `ds`.)PresentationCreationDatePresentationCreationTimer ContentLabelContentDescriptionContentCreatorNameReferencedSeriesSequenceBlendingSequence) rrrrrrrrrrrrrqrqrr_define_presentationJ s$     rcCst|gdt}|j|_|j|_|j|_|j|_|j|_d|vr,t|dg|j|_|j|_d|vr>t|dg|j |_ |S)z0Return a SR DOCUMENT directory record from `ds`.)rCompletionFlagVerificationFlag ContentDate ContentTimeConceptNameCodeSequenceVerificationDateTimeContentSequence) rrrrrrrrrrrrqrqrr_define_sr_documenth s$   rcCsTt|gdt}|j|_|j|_|j|_|j|_d|vr(t|dg|j|_|S)z3Return a KEY OBJECT DOC directory record from `ds`.)rrrrr)rrrrrrrrrqrqrr_define_key_object_doc s  r cCs|t|gdt}|j|_|j|_|j|_|j|_d|vr(t|dg|j|_|j|_|j|_|j |_ |j |_ |j |_ |S)z2Return an SPECTROSCOPY directory record from `ds`.) ImageTyperrrNumberOfFramesRowsColumns DataPointRowsDataPointColumnsReferencedImageEvidenceSequence) rrr rrrrr r r rrrrqrqrr_define_spectroscopy s$ rcCsFt|gdt}|j|_|j|_|j|_|j|_|dg|_|S)z5Return a HANGING PROTOCOL directory record from `ds`.)HangingProtocolCreatorHangingProtocolCreationDateTime!HangingProtocolDefinitionSequenceNumberOfPriorsReferenced-HangingProtocolUserIdentificationCodeSequence)rrrrrrrrrrqrqrr_define_hanging_protocol s rcCstt|ddgt}|d|_|d|_|j|_|d|_d|vr.t|dg|j|_|d|_|j |_ |S)z/Return an ENCAP DOC directory record from `ds`.rMIMETypeOfEncapsulatedDocumentrr DocumentTitleHL7InstanceIdentifierr) rrrrrrrrrrrrqrqrr_define_encap_doc s     rcCs*t|dgt}|j|_|d|_|S)z,Return a PALETTE directory record from `ds`.rr)rrrrrrrqrqrr_define_palette s  rcCsLt|gdt}|j|_|j|_d|vr t|dg|j|_|j|_|S)z,Return a IMPLANT directory record from `ds`.) 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