Difference between revisions of "CTSC Slicer XNE"

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* XNAT queried for subjects in that project
 
* XNAT queried for subjects in that project
 
* response is checked for http error codes
 
* response is checked for http error codes
−
* xml parsed to get list of subjects
+
* xml parsed to get list of subjects  
 +
* XNAT queried for experiments in that project
 +
* response is checked for http error codes
 +
* xml parsed to get list of experiments
 
* GUI populated
 
* 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"
 
* User selects one scan and "download"
 
* Scan is loaded into Slicer
 
* Scan is loaded into Slicer
Line 76: Line 73:
 
  '''query:''' curl $XNE_Svr/REST/projects/$ProjectID/subjects?format=xml --cookie JSESSIONID=$JsessionID
 
  '''query:''' curl $XNE_Svr/REST/projects/$ProjectID/subjects?format=xml --cookie JSESSIONID=$JsessionID
 
  '''parse response''' into list of SubjectIDs
 
  '''parse response''' into list of SubjectIDs
−
  for each id in list of SubjectIDs
+
  '''query:''' curl $XNE_Svr/REST/projects/$ProjectID/experiments?format=xml --cookie JSESSIONID=$JSessionID
−
{
+
'''parse response''' and add to list of ExperimentIDs
−
  '''query:''' curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$id/experiments?format=xml --cookie JSESSIONID=$JSessionID
 
−
  '''parse response''' and add to list of ExperimentIDs
 
−
}
 
 
  update GUI
 
  update GUI
  
Line 153: Line 147:
  
  
−
  '''query:''' curl $XNE_Svr/REST/projects/$ProjectID/subjects/subjects/$SubjectID/experiments/$ExperimentID/scans/$ScanID/format=xml --cookie JSESSIONID=$JSessionID
+
=== 8. User Clicks Download ===
−
  '''parse response''' and add to list of ScanIDs
 
−
 
 
−
=== 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
+
curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources?format=xml --cookie JSESSIONID=$JSessionID
 +
  curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources/DICOM/files/format=xml --cookie JSESSIONID=$JSessionID
 +
parse response into a list of resources...
  
 
This returns a list of URIs which Slicer uses to populate a vtkMRMLVolumeArchetypeStorageNode:URI and vtkMRMLVolumeArchetypeStorageNode::URIListMembers
 
This returns a list of URIs which Slicer uses to populate a vtkMRMLVolumeArchetypeStorageNode:URI and vtkMRMLVolumeArchetypeStorageNode::URIListMembers
  
−
=== 10. Scan is Loaded into Slicer ===
+
=== 9. Scan is Loaded into Slicer ===
 
vtkMRMLVolumeArchetypeStorageNode::ReadData( vtkMRMLVolumeArchetypeStorage *node) is called, which calls vtkMRMLStorageNode::StageReadData (*node) to download data using the XNE_HttpHandler.
 
vtkMRMLVolumeArchetypeStorageNode::ReadData( vtkMRMLVolumeArchetypeStorage *node) is called, which calls vtkMRMLStorageNode::StageReadData (*node) to download data using the XNE_HttpHandler.

Revision as of 18:48, 4 August 2009

Home < 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
  • XNAT queried for experiments in that project
  • response is checked for http error codes
  • xml parsed to get list of experiments
  • GUI 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} (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: { Allfor $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

curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources?format=xml --cookie JSESSIONID=$JSessionID
curl $XNE_Svr/projects/$ProjectID/subjects/$SubjectID/experiments/$ExpID/scans/$ScanID/resources/DICOM/files/format=xml --cookie JSESSIONID=$JSessionID
parse response into a list of resources...

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.

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