Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval :...
-
Upload
theodora-austin -
Category
Documents
-
view
213 -
download
0
Transcript of Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval :...
![Page 1: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/1.jpg)
Medical Data Manager 1
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Dicom retrieval : overview of the DPM
• One command line to retrieve a file: lcg-cp <file in> <file out>
• The interface is a grid standard storage element interface.
• The DPM-DICOM library retrieve the file from a DICOM sever and make additional step before storing the file in a disk spool.
DICOM
server
DPM
DPM
Disks pool
Standard interface
Request a file
Retrieve
the file
DPM-DICOM
PluginDPM-DICOM
Library
Copy
the file
![Page 2: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/2.jpg)
Medical Data Manager 2
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Dicom retrieval : get the dicom file
DPM
Request a file
with the SFN DPM-DICOM
Library
DPM-DICOM
Plugin
• The PFN associates with a DICOM file is handled by the DPM-DICOM plugin.
• The plugin make a DICOM transaction with the DICOM server to retrieve the medical picture.
• By default, the MDM uses the Conquest server as DICOM server, but any DICOM server can be used
The database
assocites eachSFN with a PFN
DICOM transaction
with the DICOM protocol
![Page 3: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/3.jpg)
Medical Data Manager 3
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Dicom retrieval : Anonymization and encryption
DPM
Disks pool
Standard interface
Retrieve the file
DPM-DICOM
Library
DPM-DICOM
Plugin
Copy the final file
DICOM file
1A
1B
2 Anonymous
medical picture
• Step 1A: The DPM-DICOM uses the DCMTK library to anonymise the DICOM file
• Or Step 1B: The creaLibs convert the DICOM file to an inrimage.
• Step 2: The DPM-DICOM call Hydra to encrypt the final file• DPM-DICOM use the RFIO library to copy the file in a spool
disk. The spool disk is only a buffer for the file.
![Page 4: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/4.jpg)
Medical Data Manager 4
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Register a DICOM file
• The file must be recorded in the DICOM server:
PUSH
DICOM
Medical Data Manager(AMGA, LFC, DPM,
Hydra, DICOM server)
– A DICOM transaction can initiate the registration:
– All this step can be done by a command line:
– The file must be registered in all the components:
AMGALFC
Hydra DPM
![Page 5: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/5.jpg)
Medical Data Manager 5
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Register in Hydra
• The first registration step is a security step• The DICOM picture contains a unique identifier the SOP
identifier. The Study/Serie identifier is unique for each study/serie.
• The hydra servers generate a key for the selected cypher.
• The cyper and the key is associated to the unique DICOM numbers
analyzeStudy ID
Serie IDSop ID
Select a cypher
and generate a key
DICOM image
Hydra
servers
![Page 6: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/6.jpg)
Medical Data Manager 6
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Register in the DICOM server
• In the next step, the DPM-DICOM library records the DICOM picture in the DICOM server.
• The DPM-DICOM simulate a user call. It obtain the size of the final file.
• The size depends of :
Size of the
encrypted anonymous file
DPM-DICOM
LibraryDICOM file
1A
1B2
Anonymous
medical pictureDICOM server
The cyper and the key
The fields erased in the anonymous step
The size of the original file
The DICOM server
![Page 7: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/7.jpg)
Medical Data Manager 7
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Register references to the file
• A reference to a file is recorded in the DPM, but no copy of the file in the DPM disk pool is needed
• Directories with the Study, Sery and SOP identifier are created in the LFC
• The data erases during the anonymization step are registered in the AMGA server.
- the size of the file
- SFN and PFN- host of the disk pool- ...
- LFN and SFN
- size of the file- The metadata
of the DICOM file
DPM LFC AMGA
![Page 8: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/8.jpg)
Medical Data Manager 8
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Strong Security
• To allow one user to access a medical file and its metadata the owner of the file must set the right in all the component :
• Example :
LFC
DPM
Hydra
AMGA
![Page 9: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/9.jpg)
Medical Data Manager 9
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Fine-grained security
• The user can set the permission a group or a VO• The user can set the ACL for an individual user (based
on the DN)
Query> getattr /mdm/PATIENT/b67982a3b0e825af054741a58e750ca5cc6278e name
>> Marc-Elian Begin
Query> getattr /mdm/IMAGE/guid:0617a6bf-09ba-428c-b5f4-f674312c5aa0 nx ny SOPinsUID>> 256>> 256>> 1.2.826.0.1.3680043.2.1143..20060202124502415.63
The permission can be set for :
All the anonymous DICOM picture of a studyAll the anonymous DICOM picture of a serieAn individual anonymous DICOM pictureEach element of the metadata of a file
![Page 10: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/10.jpg)
Medical Data Manager 10
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Metadata: AMGA
• AMGA is the ARDA METADA CATALOGUE PROJECT– http://amga.web.cern.ch
• The purpose is to store the metadata of the patient and of the medical picture
AMGA is a front-end for PostgreSQL, MySQL, Oracle and SQLite database.
The user VOMS credential can be used for the authentification The protocol is a streamed ASCII protocol with SSL encryption
![Page 11: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/11.jpg)
Medical Data Manager 11
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Distributed metadata
• AMGA provides a powerfull but limited distributed schema : – Replication in AMGA follows an asynchronous, master-slave
model, and supports partial replication of the directory hierarchy.
– Slaves can replicate any sub-tree of the metadata hierarchy• The MDM needs a full autonomy of the site
– The metadata are stored and managed locally• The MDM provide a library and a client that provide multi-site
communication. This work is based on the AMGA client and used the same syntax.
- Users can send the commands to
all the servers or the selected one.- Users can dynamically add
or remove servers
AMGA AMGA AMGA AMGA
![Page 12: Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Medical Data Manager 1 Dicom retrieval : overview of the DPM One command line to retrieve a file:](https://reader035.fdocuments.us/reader035/viewer/2022062805/5697c01c1a28abf838ccfccd/html5/thumbnails/12.jpg)
Medical Data Manager 12
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Distributed Key: Hydra
• Hydra have been developped at CERN by Akos Frohner• It store key and cypher to encrypt/decrypt file.• Each pair (key,cypher) is associated to a string• The command line is: glite-eds-encrypt <string> <in file> <out file>
• It is based on the Shamir's Secret Sharing algorithm– By default the MDM used 3 servers and 2 are need to decypher– Each site could install multiple hydra servers
• Hydra allow a strong security and very reliable service
Part of
the Key
Part of
the Key
Part of
the Key
Key