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 grabs all scans for a given subject by default (the simplest workflow), but has advanced functionality that can be used to focus the search:

Initial Presentation

* Subject: { SubjectIDs}
* Experiments: { ExperimentIDs }
** Imaging Sessions: {}
*** Scans: {} 
*** Reconstructions: {}
*** Assessors: {}
** Non-imaging Assessments: {}

A Subject ID is selected; Experiments are updated

* Subject: $SubjectIDs
* Experiments:  { ExperimentIDs }
** Imaging Sessions: {}
*** Scans: {} 
*** Reconstructions: {}
*** Assessors: {}
** Non-imaging Assessments: {}

An Experiment ID is selected; Imaging Sessions & Non-imaging Assessments are updated

* Subject: $SubjectIDs
* Experiments:  $ExperimentID
** Imaging Sessions: { $SessionIDs }
*** Scans: {} 
*** Reconstructions: {}
*** Assessors: {}
** Non-imaging Assessments: { $AssessmentIDs }

A Session ID is selected; ScanIDs, etc. are updated

* Subject: $SubjectIDs
* Experiments: $ExperimentID 
** Imaging Sessions: $SessionID
*** Scans: { ScanIDs } 
*** Reconstructions: { ReconstructionIDs }
*** Assessors: { AssessorIDs }
** Non-imaging Assessments: {AssessmentIDs}

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.