AIM XNAT on ClearCanvas

This integration can make modifying AIM more easily. We want to reconstruct the origin environment when AIM was created.

This repository combines 3 github repos listed below.

1. NCIP/annotation-and-image-markup
2. ClearCanvas/ClearCanvas
3. ClearCanvas/ReferencedAssemblies

We use AimPlugin 4.5 to combine with ClearCanvas 13.2 using Visual Studio 2015.

How to compile

Since we have used submodules and symbolic links, we should clone it by a sequence of commands.

Launch a elevated command prompt (with administrator rights) and type the following commands:

git clone https://github.com/j3soon/annotation-and-image-markup.git aim-xnat-cc
cd aim-xnat-cc
git submodule update --init --recursive
cd source_cc
git config --local core.symlinks true
git reset HEAD --hard
cd ..

Open the file aim-xnat-cc\source_cc\ImageViewer\ImageViewer.sln and set ClearCanvas.Desktop.Executable as the start up project.

Now, we can compile the entire solution directly just by clicking the debug button.

The logs can bee seen in aim-xnat-cc\source_cc\Desktop\Executable\bin\Debug\logs\ClearCanvas.Workstation.log

Modifications made

1. Folder hierarchy.

   The final folder (github repo) hierarchy is shown below.

   Root dir
   │ [annotation-and-image-markup.git]
   │
   ├─ReferencedAssemblies
   │   [ReferencedAssemblies.git]
   │
   └─source_cc
       [ClearCanvas.git]
       ReferencedAssemblies (Symbolic Link) <<===>> ..\ReferencedAssemblies
   

   The hierarchy clues are from AIM's .csproj files and ClearCanvas's Readme. We use the following command to generate the symbolic link: path\to\source_cc>mklink /D ReferencedAssemblies ..\ReferencedAssemblies

2. Connect AIMPlugin4.5 to ClearCanvas

   • Add AIM plugins and their WinForms projects to your ImageViewer solution file.
   • Make Desktop.Executable project dependent on the newly added plugins.
   • Build Desktop.Executable. During an initial build, there may be errors related to visibility of some of the ClearCanvas classes. Make the classes in question public and build again.

   The steps are exactly the same as the steps mentioned in AIMPlugin4.5's readme. Note that there shouldn't be any .dll files in the same directory as ClearCanvas.Desktop.Executable.exe (Copy Local should be False), otherwise, there will be dll conflicts.

3. Additional DLLs

   After the first 2 steps, it should work now. However, in DicomViewer-13.2.19401.1661-x64's and AIM on ClearCanvas® Workstation's plugin folder, there are some dlls that aren't included by the 2 steps above. So we also add them to the plugin folder using PostBuild_dist.proj.

   • In ClearCanvas but not in compiled:

     ClearCanvas.ImageViewer.Shreds.dll
     

   • In AIM on ClearCanvas but not in compiled:

     AIMLib.dll
     AIMLib.NET.dll
     AIMLibModel.NET.dll
     AimTmplUtil1923.dll
     AimTmplUtilV1Rv23V2Rv13.dll
     TCGA.dll
     TCGA.View.WinForms.dll
     xerces-c_3_1.dll
     

4. Release mode

   When compiling in release mode, errors will occur when clicking the AIM Data Service 2.0 tab.

   It seems to be the typo in AimDataService.View.WinForms.csproj .

   <!--<PlatformTarget>x86</PlatformTarget>-->
   <PlatformTarget>AnyCPU</PlatformTarget>

Untested problems

1. x86 and x64 dll dependencies

   The x86 parts in PostBuild_dist.proj may be changed in some circumstances.

   <SharedPluginFiles Include="$(ProjectDir)..\..\..\AIMToolkit_v4.1.0_rv44\source\xercesc-3.1\x86\bin\xerces-c_3_1.dll" />
   <SharedPluginFiles Include="$(ProjectDir..\..\..\AimPlugin4.5\AIMReferences\(Configuration)\4.0\x86\AIMLib.dll" />
   <SharedPluginFiles Include="$(ProjectDir..\..\..\AimPlugin4.5\AIMReferences\(Configuration)\4.0\x86\AIMLib.NET.dll" />
   <SharedPluginFiles Include="$(ProjectDir..\..\..\AimPlugin4.5\AIMReferences\(Configuration)\4.0\x86\AIMLibModel.NET.dll" />

2. Namespace ambiguity in SegmentationSerializer and SegmentationDocumentIod.

   //Added to avoid namespace ambiguity.
   using FrameOfReferenceModuleIod =  ClearCanvas.Dicom.Iod.Modules. FrameOfReferenceModuleIod;

3. Empty implementations to make TCGA compatible in TcgaSessionManager.

   // The 4 entries below are added to implement the new ISessionManager.
   public void InvalidateSession()
   {
   }
   
   public void TerminateSession()
   {
   }
   
   public SessionStatus SessionStatus { get; }
   public eventEventHandler<SessionStatusChangedEventArgs>SessionStatusChanged;

4. Warning in log file.

   WARN  - No audit sink extensions found - Auditing will be disabled for the remainder of the session.
   

Pull requests are welcome.

Welcome to the Annotation and Image Markup Project!

Annotation and image markup is an Open Source project that provides the functionalities to propose and create a standard means of adding information and knowledge to an image in a clinical environment, so that image content can be easily and automatically searched. AIM provides a solution to the following imaging challenges:

• No agreed upon syntax for annotation and markup
• No agreed upon semantics to describe annotations
• No standard format (for example, DICOM, XML, HL7) for annotations and markup

The AIM project includes the following.

• The AIM Model captures the descriptive information for an image with user-generated graphical symbols placed on the image into a single common information source.
• The AIM Template Service is a web service application that makes it possible for you to upload (publish) and download AIM templates created using an AIM tool such as AIM Template Builder.
• The AIM Template Builder is a Java application that allows you to build templates that are compatible with the AIM Model. Templates are a set of well-defined questions and answer choices that facilitate collecting information for a study. The AIM Template Builder has replaced the AIM Template Manager.
• AIM on ClearCanvas Workstation is a reference implementation of the AIM Model. AIM on ClearCanvas Workstation demonstrat

It is written in C, C++, Visual C++, Java using XML and ClearCanvas Workstation. The goal of Annotation and Image Markup Project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community.

AIM is distributed under the BSD 3-Clause License. Please see the NOTICE and LICENSE files for details.

You will find more details about AIM in the following links:

• [Community Wiki] (https://wiki.nci.nih.gov/x/z4X3Ag)
• Issue Tracker
• [AIM - Information Model(AIM)] (https://tracker.nci.nih.gov/browse/AIM)
• [AIM - Enterprise Service(AIMES)] (https://tracker.nci.nih.gov/browse/AIMES)
• [ AIM - Workstation (AIMWS)] (https://tracker.nci.nih.gov/browse/AIMWS)
• [Code Repository] (https://github.com/NCIP/annotation-and-image-markup)
• [View Website] (http://imaging.fsm.northwestern.edu/templates/web)

Please join us in further developing and improving Annotation and Markup(AIM).