DicomBrowser CLI

[Gabriele]

May I get a current non-webstart version of the DicomBrowser somewhere? Getting Java WebStart installed on all our cross-institutional nodes is proving extremely involved if not flat out effectively impossible. Thanks,

-Gabriele

[Dan]

Installers for Windows and Mac here:
http://nrg.wustl.edu/software/dicom-browser/

-Dan

[Archie, Kevin]

The official page is here:

http://nrg.wustl.edu/software/dicom-browser

I've been fixing a lot of bugs lately in preparation for a 1.5 release, and the official page hasn't always been keeping up; the most recent builds are here:

ftp://ftp.nrg.wustl.edu/pub/DicomBrowser

  - Kevin

On Sep 14, 2011, at 9:15 AM, Gabriele wrote:

May I get a current non-webstart version of the DicomBrowser somewhere? Getting Java WebStart installed on all our cross-institutional nodes is proving extremely involved if not flat out effectively impossible. Thanks,

-Gabriele

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[Gabriele]

Thanks Dan,

Saw those. Unfortunately we're all Linux on our managed nodes more or less everywhere. RHEL, CentOS, Debian/Ubuntu, etc. Was hoping there was just a DicomBrowser.jar somewhere that "just worked" like the old 1.4 one which I can't find anymore.

Best,

-Gabriele

[Archie, Kevin]

Gabriele,

Check the FTP site ftp://ftp.nrg.wustl.edu/pub/DicomBrowser -- the .tgz there unpacks into a build that will run on Linux.

  - Kevin

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[James]

Gabriele <gabriele...@gmail.com> wrote:

>May I get a current non-webstart version of the DicomBrowser somewhere?
>Getting Java WebStart installed on all our cross-institutional nodes is
>proving extremely involved if not flat out effectively impossible. Thanks,
>

>-Gabriele
>
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>You received this message because you are subscribed to the Google Groups "xnat_discussion" group.

>To view this discussion on the web visit https://groups.google.com/d/msg/xnat_discussion/-/xOXM5LxeeWIJ.

[James]

[Gabriele]

Thanks Kevin.

Thanks for the link. Installed 1.5.0b8 and when I try to send raw Seimens IMA/SR files (DICOM files in the original Syngo scanner console format) to our 1.5.2 XNAT installation I see this on the Client (in the window from which DicomBrowser was run):

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at java.lang.StringBuilder.<init>(StringBuilder.java:109)
        at org.nrg.dcm.browse.CStoreDialog$AEAddr.toString(CStoreDialog.java:118)
        at org.nrg.dcm.browse.CStoreDialog$AEHistory.toString(CStoreDialog.java:204)
        at org.nrg.dcm.browse.CStoreDialog.actionPerformed(CStoreDialog.java:466)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:253)
        at java.awt.Component.processMouseEvent(Component.java:6203)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:5968)
        at java.awt.Container.processEvent(Container.java:2105)
        at java.awt.Component.dispatchEventImpl(Component.java:4564)
        at java.awt.Container.dispatchEventImpl(Container.java:2163)
        at java.awt.Component.dispatchEvent(Component.java:4390)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4461)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4125)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4055)
        at java.awt.Container.dispatchEventImpl(Container.java:2149)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4390)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:649)
        at java.awt.EventQueue.access$000(EventQueue.java:96)
        at java.awt.EventQueue$1.run(EventQueue.java:608)
        at java.awt.EventQueue$1.run(EventQueue.java:606)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
        at java.awt.EventQueue$2.run(EventQueue.java:622)
        at java.awt.EventQueue$2.run(EventQueue.java:620)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:619)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)

While on the XNAT server, the application log contains:

2011-09-14 11:32:58,974 [XNAT_DICOM-71] ERROR org.nrg.dcm.CStoreService - C-STORE operation failed
org.nrg.action.ServerException: org.nrg.xnat.helpers.prearchive.SessionException: A record with session 11.09.05-15:26:56-DST-1.3.12.2.1107.5.2.32.35380, timestamp 20110905_181016 and project Limbo could not be found.
        at org.nrg.xnat.archive.GradualDicomImporter.call(GradualDicomImporter.java:442)
        at org.nrg.dcm.CStoreService.doCStore(CStoreService.java:216)
        at org.nrg.dcm.CStoreService.cstore(CStoreService.java:198)
        at org.dcm4che2.net.DicomServiceRegistry.process(DicomServiceRegistry.java:238)
        at org.dcm4che2.net.NetworkApplicationEntity.perform(NetworkApplicationEntity.java:1158)
        at org.dcm4che2.net.Association.onDimseRQ(Association.java:979)
        at org.dcm4che2.net.PDUDecoder.decodeDIMSE(PDUDecoder.java:530)
        at org.dcm4che2.net.Association.onPDataTF(Association.java:956)
        at org.dcm4che2.net.State$Sta6.receivedPDataTF(State.java:239)
        at org.dcm4che2.net.Association.receivedPDataTF(Association.java:952)
        at org.dcm4che2.net.PDUDecoder.nextPDU(PDUDecoder.java:231)
        at org.dcm4che2.net.Association.run(Association.java:851)
        at java.lang.Thread.run(Thread.java:662)
Caused by: org.nrg.xnat.helpers.prearchive.SessionException: A record with session 11.09.05-15:26:56-DST-1.3.12.2.1107.5.2.32.35380, timestamp 20110905_181016 and project Limbo could not be found.
        at org.nrg.xnat.helpers.prearchive.PrearcDatabase.checkUniqueRow(PrearcDatabase.java:1692)
        at org.nrg.xnat.helpers.prearchive.PrearcDatabase.checkSession(PrearcDatabase.java:1675)
        at org.nrg.xnat.helpers.prearchive.PrearcDatabase.withSession(PrearcDatabase.java:1736)
        at org.nrg.xnat.helpers.prearchive.PrearcDatabase.modifySession(PrearcDatabase.java:1741)
        at org.nrg.xnat.helpers.prearchive.PrearcDatabase.setLastModifiedTime(PrearcDatabase.java:1616)
        at org.nrg.xnat.archive.GradualDicomImporter.call(GradualDicomImporter.java:438)
        ... 12 more

One entry per file. And then application.log ends with

FOOFOOFOO

On a line all by itself (I put "FOO" as the local AE Title this time, wtin no local AE Title, there is no last line).

While the velocity.log contains:

2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 7, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 11, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 15, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 19, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 23, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 28, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 33, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 38, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 43, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 48, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 58, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 62, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 67, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 72, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 77, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 85, column 1]
2011-09-14 11:34:28,727 ["http-apr-80"-exec-42] ERROR velocity - RHS of #set statement is null. Context will not be modified. /screens/Variables.vm [line 90, column 1]
2011-09-14 11:34:28,732 ["http-apr-80"-exec-42] ERROR velocity - Left side ($data.getSession().getAttribute("user").getUsername()) of '==' operation has null value. If a reference, it may not be in the context. Operation not possible. navigations//NoMenuTop.vm [line 9, column 76]

When I try to send the same files using dcmtk's storescu command, I get an identical application.log error for the first file, and it quits:

% storescu -v -aec CBSCENTRAL cbscentral.xxxx.xxxx.xxxxxx.xxxxxxxx.xxx 4444 *
Requesting Association
Association Accepted (Max Send PDV: 16372)
--------------------------
Sending file: 110905_HTT01310.MR.INVESTIGATORS_BUCKNER.0001.0001.2011.09.06.09.10.44.125000.244971595.IMA
Transfer: LittleEndianExplicit -> LittleEndianExplicit
Store SCU RQ: MsgID 1, (MR)
XMIT:.....................................
C-Store RSP: MsgID: 1 [Status=Refused: OutOfResources]
  AffectedSOPClassUID: =MRImageStorage
  AffectedSOPInstanceUID: 1.3.12.2.1107.5.2.32.35380.2011090515332091307765751
  Data Set: Not Present
  Status Detail:

# Dicom-Data-Set
# Used TransferSyntax: LittleEndianImplicit
(0000,0902) LO [org.nrg.xnat.helpers.prearchive.SessionException: A record with] #  64, 1 ErrorComment
Releasing Association

Any clues?

Thanks,

-Gabriele

[Archie, Kevin]

Gabriele,

I'm flummoxed by every part of this. I'll continue digging into the DicomBrowser side; could another XNAT dev (Deech?) please take a look at the XNAT side?

Also: this is on CentOS? What version, and what JVM version?

Thanks,

  Kevin

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[deech]

Hi Gabriele,
If you look on the prearchive page in XNAT (I assume you're running version 1.5.x), do you see the session 11.09.05-15:26:56-DST-1.3.12.2.1107.5.2.32.35380?

If you do see it, is there a corresponding timestamp directory '20110905_181016' in your prearchive path?

If that directory exists then there maybe a problem with the prearchive table on the Postgres end. Can you send me an output of the prearchive table in Postgres? It's called "prearchive" and located in "xdat_search" schema.

Thanks ...
-deech

[Gabriele]

Nothing showing up in the prearchive page. Where is the prearchive cache stored in the db?

Of note: there may have been some filesystem issues with this session (permissions issue during the migration), which resulted in the database being in an inconsistent state after a user renamed the already archive session - the db thought the files were in one place, but they had not been moved due to permissions issues. We deleted this session, fixed the back-end permissions, and are trying to resend it, however, it kind of looks like XNAT thinks it should merge the incoming files with a session it thinks still exists in the PreArchive and/or Archive, but which does not because it was deleted.

Thanks,

-Gabriele

[deech]

Hi Gabriele,
The prearchive table is located in the "xdat_search" schema in the "prearchive" table. Could send me the output of:
SELECT * from xdat_search.prearchive

The "url" column shows the relative path to the folder on the filesystem. It would be helpful if you could verify that the folder does in fact exist at the path referred to by the "url" column.

Thanks ...
-deech

[Gabriele]

% select * from xdat_search.prearchive where url like '%20110905_181016%';

 project |    timestamp    |       lastmod       |      uploaded       |      scan_date      | scan_time |         subject          |      foldername       |                       name                       |                           tag                            | status |                             url                              | autoarchive 

---------+-----------------+---------------------+---------------------+---------------------+-----------+--------------------------+-----------------------+--------------------------------------------------+----------------------------------------------------------+--------+--------------------------------------------------------------+-------------

 Limbo   | 20110905_181016 | 2011-09-08 16:27:49 | 2011-09-05 18:10:16 | 2011-09-05 00:00:00 | 15:27:27  | INVALID: 110905_HTT01310 | Investigators_Buckner | 11.09.05-15:26:56-DST-1.3.12.2.1107.5.2.32.35380 | 1.3.12.2.1107.5.2.32.35380.30000011090220502135700000016 | READY  | /XNAT/PreArchive/Limbo/20110905_181016/Investigators_Buckner | 

Though I see nothing in the prearchive view. May I just delete this?

Thanks,

-Gabriele

[deech]

Hi Gabriele,
That's odd that you don't see this in the prearchive view. Before you delete it just a couple more things. First we need to check that this row shows up correctly over the REST API, so please query the following URL:
<xnat-server>/REST/prearchive?format=csv
and make sure that a row corresponding to row in prearchive table the appears in the output.

If it does appear in the output the prearchive page is behaving badly. Is that the only thing in your prearchive? Are other sessions showing up correctly?

Thanks ...
-deech

[Gabriele]

Hi Deech,

Thank for the responses. The user in question has "done a lot of stuff" since my last post without providing much detail, and the database no longer shows the entry I posted. I have yet to try and resend the session, but will update with any new information if there are any issues this time around.

Thanks,

-Gabriele