Difference between revisions of "CTSC Slicer XNE"
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− | ''''' 7b1. | + | ''''' 7b1. Just a Subject ID is selected; Filters are updated''''' |
* Subject: $SubjectID | * Subject: $SubjectID | ||
* Experiments: { All for $SubjectID } | * Experiments: { All for $SubjectID } | ||
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− | ''''' 7b2. OR, an Experiment ID is selected; Filters are updated''''' | + | ''''' 7b2. OR, just an Experiment ID is selected; Filters are updated''''' |
* Subject: { All for $ExperimentID } | * Subject: { All for $ExperimentID } | ||
* Experiments: $ExperimentID | * Experiments: $ExperimentID | ||
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* Subject: $SubjectIDs | * Subject: $SubjectIDs | ||
* Experiments: $ExperimentID | * Experiments: $ExperimentID |
Revision as of 17:48, 4 August 2009
Home < CTSC Slicer XNEContents
- 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. Example Query XNAT for All Scans for Selected Experiment
- 1.1.10 9. User Selects One Scan and Clicks Download
- 1.1.11 10. 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
- 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
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}
- Experiments: { All ExperimentIDs }
- Imaging Sessions: { }
- Scans: { }
- Reconstructions: { }
- Assessors: { }
- Non-imaging Assessments: { }
- Imaging Sessions: { }
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 }
- Imaging Sessions: { 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: { Allfor $ExperimentID }
- Reconstructions: { All for $ExperimentID }
- Assessors: { All for $ExperimentID }
- Non-imaging Assessments: { All for $ExperimentID }
- Imaging Sessions: { 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 }
- Imaging Sessions: { 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 }
- Imaging Sessions: $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.