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

 
 

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task #15167: Orthanc DICOM module

Submitted by:  Chris Zimmerman <teffalump>
Submitted on:  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
Percent Complete:  100% Assigned to:  Chris Zimmerman <teffalump>
Open/Closed:  Closed Release:  3.5.0
Module:  health_orthanc

( 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>
Project MemberIn charge of this item.
Sun 31 Mar 2019 01:34:07 AM UTC, comment #10: 

https://hg.savannah.gnu.org/hgweb/health/rev/1deffd26078b

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>
Project MemberIn charge of this item.
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>
Project MemberIn charge of this item.
Sun 24 Feb 2019 06:00:35 AM UTC, comment #8: 

https://hg.savannah.gnu.org/hgweb/health/rev/7e2c77dac653
https://hg.savannah.gnu.org/hgweb/health/rev/797737d12d6c

Changes:

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

TODO:

- 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>
Project MemberIn charge of this item.
Sun 24 Feb 2019 04:34:38 AM UTC, comment #7: 

https://en.wikibooks.org/wiki/GNU_Health/Imaging

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>
Project MemberIn charge of this item.
Thu 21 Feb 2019 03:12:09 AM UTC, comment #6: 

https://hg.savannah.gnu.org/hgweb/health/rev/48c32daa1a49
https://hg.savannah.gnu.org/hgweb/health/rev/f600a8a3db44
https://hg.savannah.gnu.org/hgweb/health/rev/eb0ea4b8b795
https://hg.savannah.gnu.org/hgweb/health/rev/3c8aa357f08d
https://hg.savannah.gnu.org/hgweb/health/rev/22b36ac203b5
https://hg.savannah.gnu.org/hgweb/health/rev/ed41e03a7cba

Changes:

- 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>
Project MemberIn charge of this item.
Sun 10 Feb 2019 05:17:50 AM UTC, comment #5: 

https://hg.savannah.gnu.org/hgweb/health/rev/5a25b62eeebb
https://hg.savannah.gnu.org/hgweb/health/rev/f6f8e54213cd
https://hg.savannah.gnu.org/hgweb/health/rev/40b3470c3b75

Changes:

- 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)

TODO:

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

Chris Zimmerman <teffalump>
Project MemberIn charge of this item.
Sun 03 Feb 2019 08:12:33 AM UTC, comment #4: 

https://hg.savannah.gnu.org/hgweb/health/rev/5099415c8a08
https://hg.savannah.gnu.org/hgweb/health/rev/d3d1c96d090f
https://hg.savannah.gnu.org/hgweb/health/rev/d96481be0c5a

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>
Project MemberIn charge of this item.
Fri 01 Feb 2019 08:46:49 PM UTC, comment #3: 

https://hg.savannah.gnu.org/hgweb/health/rev/8feb85dc762c

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>
Project MemberIn charge of this item.
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 :)

Best
Luis

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

https://hg.savannah.gnu.org/hgweb/health/rev/7293408b973a

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>
Project MemberIn charge of this item.
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>
Project MemberIn charge of this item.

 

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Items that depend on this one: None found

 

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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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