Force Session modality to xnat:petmrSessionData

[dev]

Hi,

We are using Xnat 1.8.2.2 build: 4, and would like to force the session Type to PET and MR instead of only PET.

I have seen the option 'Separate PET-MR (Site Wide)' in the admin interface and in existing project settings.

But when I set the value to 'Create as PET/MR session', sessions are always MR while the Dicom Modality is (0008,0060) Modality PT.

After a quick analysis of the Xnat code, I see the session type choice is made before the creation of prearchive/prj/tmpSession/catalog.xml

Exemple of catalog.xml : 

<?xml version="1.0" encoding="UTF-8"?>

<xnat:MRSession ID="">

...

Is it possible to force the session to xnat:petmrSessionData ?

[Moore, Charlie]

Hello there,

Could you include some other information?

1. Do you have any plugins installed?
2. How are you uploading the session?

Thanks,

Charlie

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[dev]

I am indeed using a plugin to create new xnat projects with a custom name.

I 'll try to debug this method.

Here is my code :

XnatProjectdata xnatProject = XnatProjectUtils.createProject (projectId, projectTitle, "", true, true, _xnatUser);

And then :

/**

* Create an XNAT project

* @param projectId

* @param projectTitle

* @param xnatUser

*/

static public XnatProjectdata createProject (final String projectId, final String projectTitle, final String projectDescription, final boolean disableAutoarchive, final boolean setPipelines, final UserI xnatUser) {

LogUtils.logDebug (XnatProjectUtils.class.getName() + ".createProject");

LogUtils.logDebug ("projectId = " + projectId);

LogUtils.logDebug ("projectTitle = " + projectTitle);

LogUtils.logDebug ("xnatUser = " + xnatUser.getLogin ());

if (!GeneralUtils.isAdminUser (xnatUser)) {

LogUtils.logString ("User [" + xnatUser.getLogin() + "] is not an XNAT administrator.");

return null;

}

XnatProjectdata xnatProject = XnatProjectdata.getProjectByIDorAlias (projectId, xnatUser, false);

if (xnatProject != null) {

LogUtils.logDebug ("Found project assignment of " + xnatProject.getProject () + " for study ID " + projectId);

return xnatProject;

}

else {

LogUtils.logDebug ("Found no project with ID or alias [" + projectId + "]");

// for the following code, refer to org.nrg.xnat.turbine.modules.actions.AddProject

xnatProject = new XnatProjectdata (xnatUser);

try {

xnatProject.setId (projectId);

xnatProject.setSecondaryId (projectTitle);

xnatProject.setName (projectTitle);

if (!("".equals (projectDescription))) {

xnatProject.setDescription (projectDescription);

}

xnatProject.trimProjectFields ();

final PersistentWorkflowI wrk = PersistentWorkflowUtils.getOrCreateWorkflowData (null, xnatUser, XnatProjectdata.SCHEMA_ELEMENT_NAME, xnatProject.getId(), xnatProject.getId(), new EventDetails (EventUtils.CATEGORY.PROJECT_ADMIN, EventUtils.TYPE.PROCESS, EventUtils.getAddModifyAction(xnatProject.getXSIType (), true), "Project not existant", "Creating project for automation"));

final EventMetaI ci = wrk.buildEvent ();

// prepare(?) the workflow for saving (?)

PersistentWorkflowUtils.save (wrk, ci);

// "real" saving of the project (with verification of authorization but since we're considered admin here, it causes no problem)

xnatProject = BaseXnatProjectdata.createProject(xnatProject, xnatUser, false, true, ci, "protected");

final XnatProjectdata xnatProjectPostSave = new XnatProjectdata (xnatUser);

xnatProjectPostSave.setId (xnatProject.getId ());

xnatProjectPostSave.setSecondaryId (xnatProject.getSecondaryId ());

xnatProjectPostSave.setName (xnatProject.getName ());

xnatProjectPostSave.getItem ().setUser(xnatUser);

xnatProjectPostSave.initGroups ();

Groups.reloadGroupForUser (xnatUser, xnatProjectPostSave.getId() + "_" + BaseXnatProjectdata.OWNER_GROUP);

// for the main folder for saving on the disk

ArcProject arcProject = new ArcProject (xnatUser);

arcProject.setCurrentArc ("arc001");

xnatProjectPostSave.initArcProject (arcProject, xnatUser, ci);

// set project accessibility to protected

// cf https://bitbucket.org/xnatdev/xnat-web/src/master/src/main/java/org/nrg/xnat/restlet/resources/ProjectAccessibilityResource.java?at=master

Permissions.setDefaultAccessibility (xnatProject.getId (), "protected", true, xnatUser, ci);

// complete(?) the workflow

PersistentWorkflowUtils.complete (wrk, ci);

// trigger event that a new project was created

final NrgEventService eventService = XDAT.getContextService ().getBean (NrgEventService.class);

eventService.triggerEvent (new XftItemEvent (XnatProjectdata.SCHEMA_ELEMENT_NAME, xnatProjectPostSave.getId (), XftItemEvent.UPDATE));

LogUtils.logString ("Project [" + projectId + "] created.");

//addProjectAdminOwner (projectId, xnatUser);

// set autoarchive to false

// NOTE : does not work above ie before the project is created

if (disableAutoarchive) {

setProjectPrearchivecode (projectId, 0, xnatUser);

}

if (setPipelines) {

final Map<String, Boolean> projectPipelines = XnatProjectUtils.getProjectPipelinesFromConfig (xnatUser);

addProjectPipelines (projectId, projectPipelines, xnatUser);

}

return xnatProject;

}

catch (Exception e) {

LogUtils.logException(e);

return null;

}

}

}

[dev]

I found the code I was looking for.

The session type (MR, PET, PETMR) seems to be detected using StudyInstanceUID and Modality.

The variable sessionBeanFactories contains 3 factories :

- XnatPetMrImageSessionDataBeanFactory (empty when I debug)

- SOPMapXnatImageSessionDataBeanFactory (24 row when I debug). Ex: 1.2.840.10008.5.1.4.1.1.2.1 -> {Class@2300} "class org.nrg.xdat.bean.XnatCtsessiondataBean"

- ModalityMapXnatImageSessionDataBeanFactory (17 rows). Ex: PT -> {Class@3480} "class org.nrg.xdat.bean.XnatPetsessiondataBean"

From what I understand, Xnat will instanciate the session type if SOPInstanceUid or Modality matches with the first factory.

In /org/nrg/dcm/xnat/DICOMSessionBuilder.java :

public XnatImagesessiondataBean call() throws IOException,NoUniqueSessionException,SQLException {

log.info("Building session for {}", studyInstanceUID);

final PrintWriterLogger sessionLog = new PrintWriterLogger(new File(fileSetDir, "dcmtoxnat.log"));

final List<XnatImagesessiondataBeanFactory> sessionBeanFactories = makeSessionBeanFactories(sessionLog);

try {

final XnatImagesessiondataBean session = makeSessionBean(sessionBeanFactories, studyInstanceUID);

}

[...]

}

[dev]

And factories are defined using .properties files :

private static final String LEAD_SCAN_TYPE_R = "/lead-scan-types.txt";
private static final String LEAD_SESSION_TYPE_R = "/lead-session-types.txt";
private static final String LEAD_MODALITY_R = "/lead-modalities.txt";
private static final String SOP_TO_SCAN_TYPE_R = "/series-scans.properties";
private static final String SOP_TO_SESSION_TYPE_R = "/study-sessions.properties";
private static final String MODALITY_TO_SESSION_TYPE_R = "/modality-sessions.properties";
private static final String PRIMARY_SOP_UID_R = "/primary-sops.txt";
private static final String UNKNOWN_UID_NAME = "Unknown UID Name:";