CTSC Slicer XNE

UXP & functionality planning for Slicer's XNE client

Workflow & Implementation approaches

All Workflow Steps:

• Select XNAT Enterprise server
• Authentication dialog presented
• Dialog input is processed
• XNAT queried for projects
• response is checked for http error codes
• xml parsed to get list of projects
• GUI populated
• One project selected
• XNAT queried for subjects in that project
• response is checked for http error codes
• xml parsed to get list of subjects
• GUI populated
• One subject and filters selected to narrow search
• User selects "search" for all scans
• XNAT queried for appropriate scans
• response is checked for http error codes
• xml is parsed to get list of scans
• GUI is populated
• User selects one scan and "download"
• Scan is loaded into Slicer

Each step is detailed below.

1. Select XNAT Enterprise Server

This sets the current URI handler to be the XNE_HttpHandler for subsequent REST-based client calls to XNE web services.

2. Authentication Dialog Presented

• Enter user name and password

3. Process Dialog Input

• Save the username (XNE_UserName) and password (XNE_Password)
• Authenticate and create a session:

curl -d POST $XNE_Svr/REST/JSESSION -u $XNE_UserName:$XNE_Password

4. Query XNAT for Projects Available to User

• XNAT queried for appropriate projects

curl $XNE_Srv/REST/projects?format=xml --cookie JSESSIONID=$sessionID

• response is checked for http error codes
  • if error is found, report to user
  • else xml is parsed to get list of scans

6. Query XNAT for Subjects in Selected Project

• XNAT queried for appropriate subjects

curl $XNE_Svr/REST/projects/$projectID/subjects?format=xml --cookie JSESSIONID=$sessionID

• response is checked for http error codes
  • if error is found, report to user
  • else xml is parsed to get list of scans

7. User Selects One Subject, Configures Filters to Narrow Search & Selects Search

Presents a search that only requires SubjectID or ExperimentID to be selected in order to populate the list of scans, but each additional selection (corresponding to the basic XNE data model) can be used to focus the search:

7a. Initial Presentation

• Subject: { All SubjectIDs} (eventually a checkbox for "include shared subjects")
• Experiments: { All ExperimentIDs } (eventually a checkbox for "include shared experiments")
  • Imaging Sessions: { }
    • Scans: { }
    • Reconstructions: { }
    • Assessors: { }
  • Non-imaging Assessments: { }

query: curl $XNE_Svr/REST/projects/$ProjectID/subjects?format=xml --cookie JSESSIONID=$sessionID
parse response into list of SubjectIDs
for each id in list of SubjectIDs
{
 query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$id/experiments?format=xml --cookie JSESSIONID=$SessionID
 parse response and add to list of ExperimentIDs
}
update GUI

7b1. Just a Subject ID is selected; Filters are updated

• Subject: $SubjectID
• Experiments: { All for $SubjectID }
  • Imaging Sessions: { All for $SubjectID }
    • Scans: { Allfor $SubjectID }
    • Reconstructions: { All for $SubjectID }
    • Assessors: { All for $SubjectID }
  • Non-imaging Assessments: { All for $SubjectID }

7b2. OR, just an Experiment ID is selected; Filters are updated

• Subject: { All for $ExperimentID }
• Experiments: $ExperimentID
  • Imaging Sessions: { All for $ExperimentID }
    • Scans: { All for $ExperimentID }
    • Reconstructions: { All for $ExperimentID }
    • Assessors: { All for $ExperimentID }
  • Non-imaging Assessments: { All for $ExperimentID }

7c. Both SubjectID && Experiment ID have been selected; Filters are updated

• Subject: $SubjectIDs
• Experiments: $ExperimentID
  • Imaging Sessions: { All for $SubjectID && $ExperimentID }
    • Scans: { All for $SubjectID && $ExperimentID }
    • Reconstructions: { All for $SubjectID && $ExperimentID }
    • Assessors: { All for $SubjectID && $ExperimentID }
  • Non-imaging Assessments: { All for $SubjectID && $ExperimentID }

7d. A Session ID is selected; Filters are updated

• Subject: $SubjectIDs
• Experiments: $ExperimentID
  • Imaging Sessions: $SessionID
    • Scans: { Focused ScanIDs }
    • Reconstructions: { Focused ReconstructionIDs }
    • Assessors: { Focused AssessorIDs }
  • Non-imaging Assessments: { All for $SubjectID && $ExperimentID && $SessionID }

8. Example Query XNAT for All Scans for Selected Experiment

• XNAT queried for appropriate scans

curl $XNE_Svr/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans?format=xml --cookie JSESSION=$sessionID

• response is checked for http error codes
  • if error is found, report to user
  • else xml is parsed to get list of scans

9. User Selects One Scan and Clicks Download

curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources/DICOM/files

This returns a list of URIs which Slicer uses to populate a vtkMRMLVolumeArchetypeStorageNode:URI and vtkMRMLVolumeArchetypeStorageNode::URIListMembers

10. Scan is Loaded into Slicer

vtkMRMLVolumeArchetypeStorageNode::ReadData( vtkMRMLVolumeArchetypeStorage *node) is called, which calls vtkMRMLStorageNode::StageReadData (*node) to download data using the XNE_HttpHandler.