CTSC Slicer XNE
Contents
- 1 UXP & functionality planning for Slicer's XNE client
- 1.1 Workflow & Implementation approaches
- 1.1.1 All Workflow Steps:
- 1.1.2 1. Select XNAT Enterprise Server
- 1.1.3 2. Authentication Dialog Presented
- 1.1.4 3. Process Dialog Input
- 1.1.5 4. Query XNAT for Projects Available to User
- 1.1.6 5. User Selects One Project
- 1.1.7 6. Query XNAT for Subjects in Selected Project
- 1.1.8 7. User Selects One Subject, Configures Filters to Narrow Search & Selects Search
- 1.1.9 8. User Clicks Download
- 1.1.10 9. Scan is Loaded into Slicer
- 1.1 Workflow & Implementation approaches
UXP & functionality planning for Slicer's XNE client
Workflow & Implementation approaches
All Workflow Steps:
- Select XNAT Enterprise server
- Authentication dialog presented
- XNAT login performed and session opened;
- Response is checked for error codes
- 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 and experiments in that project
- GUI populated
- User performs search for data
- User selects one scan and "download"
- Scan is loaded into Slicer
This workflow 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
5. User Selects One Project
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")
- Scans: { }
- Reconstructions: { }
- Assessors: { }
- Non-imaging Assessments: { }
query: curl $XNE_Svr/REST/projects/$ProjectID/subjects?format=xml --cookie JSESSIONID=$JsessionID parse response into list of SubjectIDs query: curl $XNE_Svr/REST/projects/$ProjectID/experiments?format=xml --cookie JSESSIONID=$JSessionID 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 }
- Scans: { All for $SubjectID }
- Reconstructions: { All for $SubjectID }
- Assessors: { All for $SubjectID }
- Non-imaging Assessments: { All for $SubjectID }
query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/$SubjectID/experiments?format=xml --cookie JSESSIONID=$JsessionID parse response into list of ExperimentIDs for each id in list of ExperimentIDs { query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$id/scans?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ScanIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$id/reconstructions?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ReconstructionIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$idD/assessors?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of AssessorIDs } update GUI
7b2. OR, just an Experiment ID is selected; Filters are updated
- Subject: { All for $ExperimentID }
- Experiments: $ExperimentID
- Scans: { All for $ExperimentID }
- Reconstructions: { All for $ExperimentID }
- Assessors: { All for $ExperimentID }
- Non-imaging Assessments: { All for $ExperimentID }
query: curl $XNE_Svr/REST/projects/$ProjectID/experiments/$ExperimentID/subjects?format=xml --cookie JSESSIONID=$JsessionID parse response into list of SubjectIDs for each id in list of SubjectIDs { query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$id/experiments/$ExperimentID/scans?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ScanIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$id/experiments/$ExperimentID/reconstructions?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ReconstructionIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$id/experiments/$ExperimentID/assessors?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of AssessorIDs } update GUI
7c. Both SubjectID && Experiment ID have been selected; Filters are updated
- Subject: $SubjectIDs
- Experiments: $ExperimentID
- Scans: { All for $SubjectID && $ExperimentID }
- Reconstructions: { Focused for $SubjectID && $ExperimentID }
- Assessors: { Focused for $SubjectID && $ExperimentID }
- Non-imaging Assessments: { Focused for $SubjectID && $ExperimentID }
query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$ExperimentID/scans?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ScanIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$ExperimentID/reconstructions?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of ReconstructionIDs query: curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$ExperimentID/assessors?format=xml --cookie JSESSIONID=$JSessionID parse response and add to list of AssessorIDs update GUI
7d. A ScanID is selected; Filters are updated
- Subject: $SubjectIDs
- Experiments: $ExperimentID
- Scans: { $ScanID }
- Reconstructions: { }
- Assessors: { }
- Non-imaging Assessments: { }
8. User Clicks Download
Questions for the XNAT Team:
- once we get this far, presume we don't know the format of the resource (DICOM, Analyze, NRRD, etc.) so we can't just use the following to retrieve a list of files:
curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources/DICOM/files/format=xml --cookie JSESSIONID=$JSessionID
What is the recommended way to download the resource?
This returns a list of URIs which Slicer uses to populate a vtkMRMLVolumeArchetypeStorageNode:URI and vtkMRMLVolumeArchetypeStorageNode::URIListMembers
9. Scan is Loaded into Slicer
vtkMRMLVolumeArchetypeStorageNode::ReadData( vtkMRMLVolumeArchetypeStorage *node) is called, which calls vtkMRMLStorageNode::StageReadData (*node) to download data using the XNE_HttpHandler.