taskGNU Health - Tasks: task #15167, Orthanc DICOM module


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task #15167: Orthanc DICOM module

Submitter:  Chris Zimmerman <teffalump>
Submitted:  Thu 31 Jan 2019 09:35:16 PM UTC
Should Start On:  Thu 31 Jan 2019 12:00:00 AM UTC Should be Finished on:  Wed 01 May 2019 12:00:00 AM UTC
Category:  Functionality Priority:  5 - Normal
Status:  Done Privacy:  Public
Assigned to:  teffalump Percent Complete:  100%
Open/Closed:  Closed Release:  3.5.0
Module:  health_orthanc Component:  None

Jump to the original submission

Fri 19 Apr 2019 11:02:43 PM UTC, comment #11: 

I updated the imaging documentation to a minimum level. Automatic linking to specific test is difficult and not necessary given studies can be manually linked to the imaging results. The clinical workflow can include this step when generating the studies, etc.

Possible future considerations:

- Remote reports
- Better viewer integration

But currently complete.

Chris Zimmerman <teffalump>
Group Member
Sun 31 Mar 2019 01:34:07 AM UTC, comment #10: 


Added a link between orthanc studies and imaging test results. Instead of adding images to the ir.attachment model, can just point to relevant orthanc study on the form view.

TODO: Feasible, or not, to make automatic linking to specific test request.

Chris Zimmerman <teffalump>
Group Member
Sun 31 Mar 2019 12:06:06 AM UTC, comment #9: 

Integrating the structured report/final read syncing is a possible future goal but not realistic at the moment. There are standards for storing these reports in DICOM but less confident that they are consistently used.

My next goal is to be able to point to the Orthanc studies as part of the health_imaging test result. Also, I want to expand the report section of the imaging result.

Chris Zimmerman <teffalump>
Group Member
Sun 24 Feb 2019 06:00:35 AM UTC, comment #8: 



- Add direct url links to server, patient, and study
- Remove provider read permission to server model


- Retrieve interpretation/final report

I need to do more testing on the attachments endpoint to see if I can quickly determine the report information. Testing needs to be done, but this seems a minimally functional module now.

Chris Zimmerman <teffalump>
Group Member
Sun 24 Feb 2019 04:34:38 AM UTC, comment #7: 


Added documentation for orthanc integration. Also, did not see Imaging section, so created it. I'll add documentation for the basic, local workflow soon.

Chris Zimmerman <teffalump>
Group Member
Thu 21 Feb 2019 03:12:09 AM UTC, comment #6: 



- Update existing patients (and automatically connect with patients if IDs match)
- Other fixes and small changes

I've also written documentation (with appropriate screenshots) that I will add to the Wiki.

I can code a direct link to the study/patient for the DICOMweb plugin. Although, a separate DICOM viewer would be better, so this may be unnecessary. Another idea is to retrieve the final read/report attached to the study and save the interpretation locally. A separate setup.py file still on TODO.

Chris Zimmerman <teffalump>
Group Member
Sun 10 Feb 2019 05:17:50 AM UTC, comment #5: 



- Add validated boolean for successfully validated server details
- When changing domain, username, or password triggers validation check
- Ignore non-validated servers when syncing
- Wizard to add new servers (with validation and full sync)


- Documentation
- Setup.py file
- Sync updates on existing patients and studies
- Provide link to remote server for DICOM viewer/webDICOM

Chris Zimmerman <teffalump>
Group Member
Sun 03 Feb 2019 08:12:33 AM UTC, comment #4: 


These commits:
 - added requirements.txt file (for 2 required libraries)
 - return local language duration in words
 - full_sync for initial sync (gets all patients and studies at once) instead of querying changes database
 - refactor functions so will be able to update current patients and studies in future commit
  - various other small changes (library calls, logging, etc)

Chris Zimmerman <teffalump>
Group Member
Fri 01 Feb 2019 08:46:49 PM UTC, comment #3: 


Moved the data to separate data directory.

On the TODO list:

- Documentation (I will hopefully start soon)
- Provide direct link to the remote server (ie, click --> open up in browser to webDICOM instance)
    - Also, we could recommend some FOSS DICOM viewers to install, etc - thoughts?
- Better authentication handling and workflow
- Sync updates on existing patients and changes from the remote server (not just new patients and studies)
- And further ideas?

Chris Zimmerman <teffalump>
Group Member
Fri 01 Feb 2019 11:22:13 AM UTC, comment #2: 

Excellent, Chris !

Definitely the missing part to make the link between GNU Health and Orthanc !

Let's put the xml data files under the "health_orthanc/data" dir to be consistent with the other packages.

Can't wait to play with it :)


Luis Falcon <meanmicio>
Group administrator
Fri 01 Feb 2019 03:32:48 AM UTC, comment #1: 


Sync patients and studies from remote Orthanc servers via REST API

- trytond-cron job to poll changes endpoint(s) for new studies and patients
- Automatically connects local patients to remote patients with same PUID
- Patient and study view
- Config view to manage servers and credentials with manual sync button
- Other basics: access rights, icon, etc

Chris Zimmerman <teffalump>
Group Member
Thu 31 Jan 2019 09:35:16 PM UTC, original submission:  

A module to support remote Orthanc DICOM servers through Orthanc's REST API. Possibly more intimate integration in the future.

Chris Zimmerman <teffalump>
Group Member


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    Follow 12 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2019-04-19 teffalump StatusIn Progress Done
        Percent Complete90% 100%
        Open/ClosedOpen Closed
    2019-03-31 teffalump StatusDone In Progress
    2019-03-31 teffalump Should be Finished on2019-03-31 2019-05-01
        StatusIn Progress Done
        Percent Complete80% 90%
    2019-02-21 teffalump Percent Complete70% 80%
    2019-02-10 teffalump Percent Complete30% 70%
    2019-02-01 meanmicio Release3.4.0 3.5.0
    2019-02-01 teffalump Percent Complete0% 30%
        ReleaseNone 3.4.0

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