VRE Cancer Imaging BL RIC Workshop 22032011
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VRE Cancer Imaging BL RIC Workshop 22032011

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  • //Based on the algorithm from section 4.3 of http://www.ietf.org/rfc/rfc4122.txt public static Guid NameBasedGuid(string Group, string Element) { byte[] inputBytes = new byte[4];inputBytes[0] = Byte.Parse(Group.Substring(0, 2), System.Globalization.NumberStyles.HexNumber);inputBytes[1] = Byte.Parse(Group.Substring(2, 2), System.Globalization.NumberStyles.HexNumber);inputBytes[2] = Byte.Parse(Element.Substring(0, 2), System.Globalization.NumberStyles.HexNumber);inputBytes[3] = Byte.Parse(Element.Substring(2, 2), System.Globalization.NumberStyles.HexNumber); //Get an array of the input in byte form //byte[] inputBytes = Encoding.Default.GetBytes(input); //Prepare an array for the input bytes and the Namespace Guid byte[] concatenatedBytes = new byte[16 + inputBytes.Length]; //Copy the namespace id guid and the input sequence to a second array { //GuidNameSpaceID = new Guid("596bdb90-e5ad-4952-a904-dc47da78d260"); byte[] NamespaceIDBytes = new byte[] { 0x90,0xDB,0x6B,0x59,0xAD,0xE5,0x52,0x49,0xA9,0x04,0xDC,0x47,0xDA,0x78,0xD2,0x60 }; //GuidNameSpaceID = new Guid(NamespaceIDBytes);Array.Copy(NamespaceIDBytes, concatenatedBytes, 16);Array.Copy(inputBytes, 0, concatenatedBytes, 16, inputBytes.Length); } //Calculate the SHA1 hash of the second array - this gives us 20 bytes of which we use the first 16. SHA1CryptoServiceProvider SHAProvider = new SHA1CryptoServiceProvider(); byte[] hashBytes = SHAProvider.ComputeHash(concatenatedBytes); //Construct the guid byte[] GuidData = new byte[16]; //Copy across the first 16 bytes of the hashArray.Copy(hashBytes, GuidData, 16); //Special treatment is required for bytes 7 and 8 //In byte 7 the 4 most significant bits of the time_hi_and_version field need to be set to 1010 (small endian) //This is to set it to version 5 of the UUID as outlined in section 4.1.3. Note they are using big endian for their numbers. byte LowerMask_7 = 15; // 00001111 byte UpperBits_7 = 160; // 10100000 GuidData[7] &= LowerMask_7;GuidData[7] |= UpperBits_7; //Byte 8 has to have the two most significant bits (bits 6 and 7) of the //clock_seq_hi_and_reserved to zero and one, respectively. byte LowerMask_8 = 63; // 00111111 byte UpperBits_8 = 128; // 10000000 GuidData[8] &= LowerMask_8;GuidData[8] |= UpperBits_8;GuidhashGuid = new Guid(GuidData); return hashGuid; }

VRE Cancer Imaging BL RIC Workshop 22032011 VRE Cancer Imaging BL RIC Workshop 22032011 Presentation Transcript

  • A Virtual Research Environment for Cancer Imaging (VRE-CI)
    British Library – RIC Workshop
    22 March 2011
  • Outline
    VRE-CI Project
    Manage Image Metadata
    Using Business Connectivity Services (BCS)
    Building the VRE-CI Site Template
  • A Virtual Research Environment for Cancer Imaging (VRE-CI)
    • VRE-CIproject is funded by the Joint Information Systems Committee (JISC) to provide a framework to allow researchers and clinicians involved in Cancer Imaging to share information, images and algorithms.
    • JISC VRE frameworks phase 3.
    • 22 months 01/05/2009 – 21/02/2011.
    • Project Partner: Microsoft Research
    • Lee Dirks
    • Alex Wade
    • Roger Barga
    • Team members:
    • PI. Prof. Anne E. Trefethen
    • Co-I. Dr. Vicente Grau
    • Project Manager Dr. M. Susana Avila-Garcia.
    • Technical developers: Xin Xiong, Charles Crichton and Andrew Tsui.
  • VRE-CI
    VRE Toolkit for SP2010
  • DICOM Image Viewer
  • Manage Image Metadata
    All of the images in the document set share the common metadata
  • Manage Image Metadata
    These fields are the Managed Terms which can be modified by users
  • Manage Image Metadata
    Managed Terms is stored in the Taxonomy Term Store in the Managed Metadata Service
  • The Image Metadata can be used for...
    Filtering images
  • The Image Metadata can be used for...
    Grouping images
  • The Image Metadata can be used for...
    • Searching images
  • The Image Metadata can be used for...
    • Searching Results
  • Exposing external data using Business Connectivity Services (BCS)
    Improved Business Data Catalog (BDC) in MOSS 2007
    BCS Architecture
    Rely on External Content Types & External Lists
    Options to create BCS solution: SharePoint Designer 2010 & Visual Studio 2010
    Image Source: http://msdn.microsoft.com/en-us/magazine/ee819133.aspx
  • SharePoint Designer 2010 BCS Solution to Access Trident Registry
    Add a new External Content Type
  • Connection to Trident SQL Server
  • Create Operations on “Activity” table
  • Create Filter Parameters
  • Create External List
  • Retrieve Trident Registry Information
    Trident Workflow Information
  • Visual Studio 2010 BCS Solution to Access Remote Image Metadata
    User Case:
    Unix file storing system in ROB
    Large volume of files
    Raw data containing no or less meaningful metadata
    Using a specific folder structure to indicate the image metadata e.g. Technology, Image Acquisition Machine, Group Head, Users.
    Allow SSH to the file server
  • Folder Structure Example
    tomography
    Systems
    Inveon
    MRI47
    Data
    Data
    RM1
    RM1
    SF1
    SF1
    RM1_SF1_SF36_420
    RM1_SF1_SF36_420
    20100223_static_VCAM_tumour_M1_5hpi
    20100223180102_01
  • Image Metadata Retrieved:
    Technology: Tomography
    Image Acquisition Machines: Inveon; MRI47
    Group Head: RM1
    User: SF1
    Study NameNumber: RM1_SF1_SF36_420
    DataSet Name: 20100223_static_VCAM_tumour_M1_5hpi; 20100223180102_01
  • Solution
    Shell script to populate the image metadata XML
    Use SSH to transfer the image metadata XML to the SharePoint Server
    Apply Business Data Connectivity Services to connect SharePoint to the external image metadata XML
    Navigating and searching the image metadata within SharePoint
  • Business Data Connectivity Model template
  • Edit TypeDescriptor Xml
  • Implement ReadItem & ReadList Methods in the service class
  • New External Content Type Created in BDC Service
  • Create External List
  • ROB Image List in SharePoint
  • Aims
    A reusable site definition for SharePoint to manage cancer related DICOM files.
    Make visible the metadata from inside the DICOM files within SharePoint. Especially within Search.
    Enable areas of the DICOM files to be marked for subsequent analysis.
    To link with Trident for subsequent analysis
  • Visual Studio 2010
    The definition is built using Visual Studio
    XML, C#, SharePoint APIs, Silverlight APIs
  • Creating a new site from a site definition
  • Site provisioning
    SharePoint ‘provisions’ a new site from a site definition.
    This requires the site definition to have to perform various actions – in the right order:
    Global onet.xmlThis file defines list templates for hidden lists, list base types, a default definition configuration, and modules that apply globally to the deployment.
    SPSite scoped features defined in site definitions onet.xml, in the order they are defined in the file.The onet.xml file defined in the site definition can define navigational areas, list templates, document templates, configurations, modules, components, and server e-mail footers used in the site definition to which it corresponds.
    SPSite scoped stapled features, in quasi random order
    SPWeb scoped features defined in onet.xml, in the order they are defined in the file.
    SPWeb scoped stapled features, in quasi random order
    List instances defined in onet.xml
    Modules defined in onet.xml
    [Source: Site Configurator v2: User Guide for Developers]
    This is frustratingly easy to get wrong!
  • Site Configurator
    To help build the definition we used the SharePoint Site Configurator Feature
    http://spsiteconfigurator.codeplex.com/ (January 2011)
    This enabled simpler ‘provisioning’
  • Useful techniques: mapping folders
  • Issues with document library names
    Site Configurator does not deal correctly with spaces in document library names for provisioning. Best to avoid spaces.
    Thicket folders: folders ending in ‘_Files’ and a host of other similar names are hidden/renamed by SharePoint. See KB905231.
    This ‘feature’ directly interacts with the DeepZoom technology, which uses ‘_files’ as a suffix for a directory.
  • Including external unmanaged code
    Technically tricky: avoid if at all possible
    Map C:Program FilesCommon FilesMicrosoft SharedWeb Server Extensions14BIN and place unmanaged DLLs in it.
    Use managed code to call the unmanaged code. E.g. [DllImport("DICOM.dll")]
  • DICOM types
    DICOM has approximately 3500 field types – identified by their Tag name which has the form (Group, Element).
    We adapted the IETF RFC4122 name-based GUID algorithm (section 4.3 of http://www.ietf.org/rfc/rfc4122.txt) to map these onto SharePoint Field definitions with name based GUIDs, and generated corresponding fields within the site definition.
    An example generated field is:
    There can be issues when re-loading fields into SharePoint. It worked first time isn’t good enough! We found that the above form worked the second time as well. The key extra attribute is ‘DisplaceOnUpgrade’.
  • Things we would do differently
    Use the Silverlight client object model
    Prefer ‘Plain Old Document Libraries’ over Document Sets until they are more mature
    Separate the DICOM field definitions from the site definition during development (they take an age to load on a development VM)
    Consider recoding some of the ‘Untrusted code’ as trusted code.