o
    å•ªiÒ_  ã                   @   s8  d Z 	 dd„ ZddlmZ ddlmZ ddlZddlmZ ddl	Z	ddl
mZ ddlZg d¢Zg d	¢Zg d
¢Zg d¢Zg d¢Zg d¢Zg d¢Zg d¢Zg d¢Zg d¢Zg d¢Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zd d!„ Z d-d#d$„Z!d.d&d'„Z"d(d)„ Z#d*d+„ Z$e%d,krše#ƒ Z&e& '¡ Z(e$e(ƒ dS dS )/a1  
The MIT License (MIT)

Copyright (c) 2014 VUIIS

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
c                 C   s   | |k| |k  S )N© )ÚaÚbr   r   ú^/var/www/Credit_scoring_API/venv310/lib/python3.10/site-packages/../../../bin/sessionmirror.pyÚcmp   s   r   é    )Úzip)ÚstrN)ÚcElementTree)zxnat:projectData/namezxnat:projectData/descriptionzxnat:projectData/keywords)zxnat:subjectData/groupzxnat:subjectData/srcz'xnat:subjectData/investigator/firstnamez&xnat:subjectData/investigator/lastnamezAxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/dobzAxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/yobzAxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/agezDxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/genderzHxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/handednesszAxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/seszGxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/educationzKxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/educationDesczBxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/racezGxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/ethnicityzDxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/weightzDxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/heightzMxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/gestational_agezPxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/post_menstrual_agezJxnat:subjectData/demographics[@xsi:type=xnat:demographicData]/birth_weight)úxnat:experimentData/dateúxnat:experimentData/visit_idúxnat:experimentData/timeúxnat:experimentData/noteú*xnat:experimentData/investigator/firstnameú)xnat:experimentData/investigator/lastnameú*xnat:imageSessionData/scanner/manufacturerú#xnat:imageSessionData/scanner/modelúxnat:imageSessionData/operatorú(xnat:imageSessionData/dcmAccessionNumberú"xnat:imageSessionData/dcmPatientIdú$xnat:imageSessionData/dcmPatientNameú"xnat:imageSessionData/session_typeúxnat:imageSessionData/modalityúxnat:imageSessionData/UIDzxnat:mrSessionData/coilz xnat:mrSessionData/fieldStrengthzxnat:mrSessionData/markerz xnat:mrSessionData/stabilization)úxnat:imageScanData/typeúxnat:imageScanData/UIDúxnat:imageScanData/noteúxnat:imageScanData/qualityúxnat:imageScanData/conditionú%xnat:imageScanData/series_descriptionú xnat:imageScanData/documentationúxnat:imageScanData/framesúxnat:imageScanData/startTimeú'xnat:imageScanData/scanner/manufacturerú xnat:imageScanData/scanner/model)#r   r   r   r   r   r   r   r    r!   r"   r#   zxnat:mrScanData/parameters/flipz&xnat:mrScanData/parameters/orientationzxnat:mrScanData/parameters/trzxnat:mrScanData/parameters/tiúxnat:mrScanData/parameters/tez#xnat:mrScanData/parameters/sequencez$xnat:mrScanData/parameters/imageTypez'xnat:mrScanData/parameters/scanSequencez%xnat:mrScanData/parameters/seqVariantz&xnat:mrScanData/parameters/scanOptionsz"xnat:mrScanData/parameters/acqTypez)xnat:mrScanData/parameters/pixelBandwidthz%xnat:mrScanData/parameters/voxelRes/xz%xnat:mrScanData/parameters/voxelRes/yz%xnat:mrScanData/parameters/voxelRes/zz xnat:mrScanData/parameters/fov/xz xnat:mrScanData/parameters/fov/yz#xnat:mrScanData/parameters/matrix/xz#xnat:mrScanData/parameters/matrix/yz%xnat:mrScanData/parameters/partitionszxnat:mrScanData/fieldStrengthzxnat:mrScanData/markerzxnat:mrScanData/stabilizationzxnat:mrScanData/coil)
r   r   r   r   r   r   r   r    r"   r#   )r
   r   r   r   r   r   r   r   r   r   r   r   r   r   r   zxnat:petSessionData/studyTypezxnat:petSessionData/patientIDzxnat:petSessionData/patientNamez!xnat:petSessionData/stabilizationz#xnat:petSessionData/start_time_scanz(xnat:petSessionData/start_time_injectionzxnat:petSessionData/tracer/namez$xnat:petSessionData/tracer/startTimezxnat:petSessionData/tracer/dosez+xnat:petSessionData/tracer/specificActivityz$xnat:petSessionData/tracer/totalMassz'xnat:petSessionData/tracer/intermediatez"xnat:petSessionData/tracer/isotopez,xnat:petSessionData/tracer/isotope/half-lifez(xnat:petSessionData/tracer/transmissionsz2xnat:petSessionData/tracer/transmissions_starttime)r
   r   r   r   r   r   r   r   r   r   r   r   r   r   r   )r   r   r   r   r   r   r   r    r"   r#   r!   z'xnat:petScanData/parameters/orientationz,xnat:petScanData/parameters/originalFileNamez&xnat:petScanData/parameters/systemTypez$xnat:petScanData/parameters/fileTypez)xnat:petScanData/parameters/transaxialFOVz#xnat:petScanData/parameters/acqTypez$xnat:petScanData/parameters/facilityz%xnat:petScanData/parameters/numPlanesz,xnat:petScanData/parameters/frames/numFramesz$xnat:petScanData/parameters/numGatesz+xnat:petScanData/parameters/planeSeparationz#xnat:petScanData/parameters/binSizez$xnat:petScanData/parameters/dataType)z"proc:genProcData/validation/statuszproc:genProcData/procstatuszproc:genProcData/proctypezproc:genProcData/procversionzproc:genProcData/walltimeusedzproc:genProcData/memusedc                 C   sJ   | j  |¡}ttt||ƒƒƒ}d}||v r| j  |¡||< |j  |¡ dS )z5 Copies list of attributes form source to destinationr$   r   )ÚattrsZmgetÚdictÚlistr   ÚgetZmset)Úsrc_objÚdest_objZ	attr_listZ	src_attrsZsrc_listZte_keyr   r   r   Ú
copy_attrs  s   r+   c                 C   s\   |   ¡ }ttttttttt	t
tdœ}zt| ||| ƒ W dS  ty-   td| ƒ Y dS w )z Copy attributes from src to dest)zxnat:projectDatazxnat:subjectDatazxnat:mrSessionDatazxnat:petSessionDatazxnat:ctSessionDatazxnat:mrScanDatazxnat:petScanDatazxnat:ctScanDatazxnat:scScanDatazproc:genProcDataúxnat:otherDicomScanDataz3ERROR:cannot copy attributes, unsupported datatype:N)ÚdatatypeÚ
PROJ_ATTRSÚ
SUBJ_ATTRSÚMR_EXP_ATTRSÚPET_EXP_ATTRSÚCT_EXP_ATTRSÚMR_SCAN_ATTRSÚPET_SCAN_ATTRSÚCT_SCAN_ATTRSÚSC_SCAN_ATTRSÚ
PROC_ATTRSÚOTHER_DICOM_SCAN_ATTRSr+   ÚKeyErrorÚprint)r)   r*   Zsrc_typeÚtypesr   r   r   Úcopy_attributes  s$   öÿr<   c                 C   s   t |  ¡ | ¡ ƒS )zCompare sort of items)r   Úlabel)Zitem1Zitem2r   r   r   Úsubj_compare,  s   r>   c           
      C   s"  |   ¡ }|d | }t |¡}t |¡st |¡ zat |¡du r&|  |¡ |  ¡ }| d¡}| d¡}| d¡}	|rJ|rJ|	sJ| |¡ 	|||¡ n)|rZ|sZ|	sZ| |¡ 	||¡ n|rk|rk|	rk| |¡ 	|||¡ n| |¡ 	|¡ t 
|¡ W dS  ty   td|t ¡ d f ƒ Y dS w )	zc
    Copy file from XNAT file source to XNAT resource destination,
    using local cache in betweenú/FZfile_contentZfile_formatÚ	file_tagsz&ERROR:failed to copy file:%s, error=%sr   N)r=   ÚopÚdirnameÚexistsÚosÚmakedirsr(   Ú
attributesÚfileÚputÚremoveÚ	Exceptionr:   ÚsysÚexc_info)
Zsrc_fÚdest_rÚcache_dZf_labelZloc_fZloc_dZ
f_in_attrsZ	f_contentZf_formatZf_tagsr   r   r   Ú	copy_file1  s2   






ÿÿrO   c                 C   sf   zt dƒ | j|dd}t dƒ |j|dd t |¡ W dS  ty2   t d|t ¡ d f ƒ ‚ w )	z_
    Copy a resource from XNAT source to XNAT destination using local cache
    in between
    z#INFO:Downloading resource as zip...F)Úextractz!INFO:Uploading resource as zip...TzERROR:failed to copy:%s:%sr   N)r:   r(   Zput_ziprD   rI   Ú
IndexErrorrK   rL   )Zsrc_rrM   rN   Zcache_zr   r   r   Úcopy_res_zipY  s   þrR   c                 C   s0   d}|   ¡  d¡D ]
}|d7 } |dkS |dkS )z$Check if resource contains any filesr   Úobjé   )ÚfilesÚfetchall)Z_resZf_countZf_inr   r   r   Úis_empty_resourceo  s
   rW   c                 C   s  t dƒ t |¡st |¡ |  ¡ }t |d¡}t||ƒ |  ¡ }|j	|d t
| |ƒ |  ¡  d¡D ]}| ¡ }t d| ƒ | |¡}t ||¡}	t|||	ƒ q3|  ¡ D ]}
|
 ¡ }t d| ƒ qU|  ¡  d¡D ]}| ¡ }t d| ƒ | |¡}t ||¡}t|||dd	 qid
S )z,Copy XNAT session from source to destinationz(INFO:uploading session attributes as xmlzsess.xml)ÚexperimentsrS   zINFO:Processing scan:%s...zINFO:Processing assessor:%s:...úINFO:Processing resource:%s...T©Úuse_zipN)r:   rA   rC   rD   rE   r(   ÚjoinÚ	write_xmlr-   Úcreater<   ÚscansrV   r=   ÚscanÚ	copy_scanZ	assessorsÚ	resourcesÚresourceÚcopy_res)Úsrc_sessÚdst_sessZsess_cache_dirZsess_xmlZxml_pathZ	sess_typeÚsrc_scanZ
scan_labelÚdst_scanÚscan_cache_dirZsrc_assrZ
assr_labelÚsrc_resÚ	res_labelÚdst_resÚres_cache_dirr   r   r   Úcopy_session·  s2   





÷rn   c                 C   s’   |   ¡ }|dkr
d}|j|d t| |ƒ |  ¡  d¡D ]*}| ¡ }td| ƒ | |¡}t 	||¡}|dkr>t
|||ƒ qt
|||dd qd	S )
z.Copy scan from source XNAT to destination XNATÚ r,   )r_   rS   rY   Z	SNAPSHOTSTrZ   N)r-   r^   r<   rb   rV   r=   r:   rc   rA   r\   rd   )rg   rh   ri   Z	scan_typerj   rk   rl   rm   r   r   r   ra   ã  s   

õra   Fc                 C   s$  t  |¡s
t |¡ d}t|jƒ | ¡ s| ¡  d}nt|ƒr"d}t| ƒr,tdƒ dS |r|rmztd|  ¡  ƒ t	| ||ƒ W dS  t
yl   ztd|  ¡  ƒ t	| ||ƒ W Y dS  t
yi   d}t|ƒ Y nw Y nw d}|  ¡ D ]}td	| ¡  ƒ |d
7 }t|||ƒ qstd| ƒ dS dS )z2Copy resource from source XNAT to destination XNATFTz$WARN:empty resource, nothing to copyNz#INFO:Copying resource as zip: %s...z3INFO: second attempt to copy resource as zip: %s...zEERROR:failed twice to copy resource as zip, willcopy individual filesr   zINFO:Copying file: %s...rT   z/INFO:Finished copying resource, %d files copied)rA   rC   rD   rE   r:   Z_urir^   rW   r=   rR   rJ   rU   rO   )rj   rl   rm   r[   Zis_emptyÚmsgZ
copy_countÚfr   r   r   rd   û  sL   


ÿý÷érd   Tc              
   C   s˜  t  | ¡}|r‹d|jv r|jd= d}| |¡D ]}| |¡ q| d¡D ]}| |¡  d}| |¡D ]}| |¡ q3| d¡D ]}| |¡ q@d}| |¡D ]}| |¡ qO| d¡D ]}| |¡  | d¡D ]}| |¡  | d	¡D ]}| |¡  | d
¡D ]}| |¡  z#t  dd¡ t  dd¡ t  dd¡ t  dd¡ t  |¡ |¡ W dS  tyË } zt	d 
|t|ƒ¡ƒ W Y d}~dS d}~ww )zWriting XML.ÚIDz"{http://nrg.wustl.edu/xnat}sharingz{http://nrg.wustl.edu/xnat}outz*{http://nrg.wustl.edu/xnat}imageSession_IDz%{http://nrg.wustl.edu/xnat}subject_IDz+{http://nrg.wustl.edu/xnat}image_session_IDz {http://nrg.wustl.edu/xnat}scansz${http://nrg.wustl.edu/xnat}assessorsz${http://nrg.wustl.edu/xnat}resourcesz&{http://nrg.wustl.edu/xnat}experimentsZxnatzhttp://nrg.wustl.edu/xnatÚproczhttp://nrg.wustl.edu/procZprovzhttp://www.nbirn.net/provÚfszhttp://nrg.wustl.edu/fszERROR:writing xml file: {}: {}N)ÚETZ
fromstringZattribÚfindallrI   Zregister_namespaceZElementTreeÚwriteÚIOErrorr:   Úformatr   )Zxml_strÚ	file_pathZ
clean_tagsÚrootÚtagÚchildÚerrorr   r   r   r]   I  sP   






"€ÿr]   c               	   C   s„   dd l } 	 | jd| jd}|jdddddd	 |jd
ddddd |jddddd |jdddddd |jdddddddd |S )Nr   z‡Downloads a given experiment/session from an XNAT instance and uploads it to an independent one. Only DICOM resources will be imported.)ÚdescriptionÚformatter_classz--h1z--source_configÚsource_configzSource XNAT configuration fileT)ÚdestÚhelpÚrequiredz--h2z--dest_configÚdest_configz#Destination XNAT configuration file)r‚   r„   rƒ   z-ez--experiment_idz4Which resource to download? (Entity name/identifier))r„   rƒ   z-pz--project_idÚ
project_idz&Which project to store the resource inz-vz	--verboseÚverboseÚ
store_trueFz'Display verbosal information (optional))r‚   ÚactionÚdefaultrƒ   r„   )ÚargparseÚArgumentParserÚRawTextHelpFormatterÚadd_argument)r‹   Z
arg_parserr   r   r   Úcreate_parserŠ  s6   üþþþþ
þr   c           
      C   s®   t j| jd}t j| jd}ddg}|jj| j|djd }|j 	| j
¡}| |d ¡}| ¡ s4| ¡  | |d ¡}|j 	|d ¡ |d ¡ |d ¡}|}	t||	d	ƒ d S )
N)ÚconfigZsubject_labelr=   )Úexperiment_idÚcolumnsr   ÚprojectZ
subject_IDrr   z/tmp)ÚpyxnatZ	Interfacer   r…   ÚarrayrX   r‘   ÚdataÚselectr“   r†   ÚsubjectrC   r^   Z
experimentrn   )
ÚargsÚx1Zx2r’   Úe1ÚpÚsÚere   rf   r   r   r   Úmain¥  s    
ÿÿ$rŸ   Ú__main__)F)T))Ú__doc__r   Úbuiltinsr   r   rD   Zos.pathÚpathrA   rK   Z	xml.etreer	   ru   r”   r.   r/   r0   r8   r3   r6   r1   r2   r4   r5   r7   r+   r<   r>   rO   rR   rW   rn   ra   rd   r]   r   rŸ   Ú__name__ÚparserÚ
parse_argsÚ	argumentsr   r   r   r   Ú<module>   sL   &"
(H,

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