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    Matvey Ezhov
    @ematvey
    Interpolation with keyframes sounds reasonable for the first try.
    I've thought for a long time about the UX for 3D annotation. But it's so hard for humans to think and annotate in volumes. 3D brush is fun to use but not very efficient.
    btw I've tried to deploy locally, but vinlab-api is restarting.
    (base) ➜  docker git:(master) docker-compose ps
          Name                    Command                 State                           Ports
    -----------------------------------------------------------------------------------------------------------------
    vinlab-api         ./bin                            Restarting
    vinlab-dashboard   docker-entrypoint.sh ./run.sh    Up           0.0.0.0:57679->80/tcp
    vinlab-es          /tini -- /usr/local/bin/do ...   Up           0.0.0.0:57698->9200/tcp, 9300/tcp
    vinlab-idgen       ./bin                            Up           0.0.0.0:57677->8080/tcp
    vinlab-keycloak    /opt/jboss/tools/docker-en ...   Up           8080/tcp, 8443/tcp, 0.0.0.0:57676->9090/tcp
    vinlab-minio       /usr/bin/docker-entrypoint ...   Up           0.0.0.0:57671->9000/tcp
    vinlab-nginx       /docker-entrypoint.sh ngin ...   Up           80/tcp, 0.0.0.0:8080->8080/tcp
    vinlab-orthanc     /docker-entrypoint.sh /tmp ...   Up           0.0.0.0:57668->4242/tcp, 0.0.0.0:57669->8042/tcp
    vinlab-redis       docker-entrypoint.sh redis ...   Up           0.0.0.0:57670->6379/tcp
    vinlab-rqlite      docker-entrypoint.sh rqlit ...   Up           0.0.0.0:57673->4001/tcp, 0.0.0.0:57674->4002/tcp
    vinlab-uploader    ./run.sh                         Up           0.0.0.0:57682->8080/tcp
    vinlab-viewer      docker-entrypoint.sh ./run.sh    Up           443/tcp, 0.0.0.0:57681->80/tcp
    Matvey Ezhov
    @ematvey
    Seems to be related to mounting docker/permissions.csv
    Nghia
    @Lego1st
    You try Docker option, right ?
    Matvey Ezhov
    @ematvey
    yep
    Nghia
    @Lego1st
    Oh, please try Kubernetes option instead. It seems that there is an issue that made Docker optiontemporarily not available now. We are working on this issue. @iamatsundere Do you have any idea ?
    Matvey Ezhov
    @ematvey
    this one
    2021/04/06 16:05:57 [INFO] [main.go:75] API is running in [production] mode
    2021/04/06 16:05:57 [INFO] [main.go:96] [http://vinlab-es:9200]
    panic: Cannot connect to ES
    goroutine 1 [running]:
    main.main()
    /opt/app/main.go:103 +0x20a5
    simisimi
    @iamatsundere
    The API need a little bit of time to start, because of waiting for ES. But we recommend you to use Kubernetes instead while we fixing the issue of Docker deployment.
    Matvey Ezhov
    @ematvey
    I'll try that thanks
    simisimi
    @iamatsundere
    @ematvey yeah, ping us if it works (or you need any support) :))
    Matvey Ezhov
    @ematvey
    Great, thanks!
    Can you share your estimates for when 3D annotation will be released?
    I get that it'll be done when it's done) but what do you think? We only need 3D annotation...
    Matvey Ezhov
    @ematvey
    Seems to be a typo in k8s doc: vinbigdata-medical/vindr-lab#1
    Matvey Ezhov
    @ematvey
    Nope, something's not right with the namespaces still.
    Events:
      Type     Reason       Age                  From               Message
      ----     ------       ----                 ----               -------
      Normal   Scheduled    19m                  default-scheduler  Successfully assigned default/apigateway-deployment-d6dcc5d8f-kngb6 to minikube
      Warning  FailedMount  8m43s (x2 over 13m)  kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[default-token-vq7vz apigateway-configmap]: timed out waiting for the condition
      Warning  FailedMount  118s (x6 over 17m)   kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[apigateway-configmap default-token-vq7vz]: timed out waiting for the condition
      Warning  FailedMount  86s (x17 over 19m)   kubelet            MountVolume.SetUp failed for volume "apigateway-configmap" : configmap "apigateway-configmap" not found
    Events:
      Type     Reason       Age                  From               Message
      ----     ------       ----                 ----               -------
      Normal   Scheduled    20m                  default-scheduler  Successfully assigned default/vinlab-api-deployment-d4fbc5c5f-w72xk to minikube
      Warning  FailedMount  4m54s (x2 over 16m)  kubelet            Unable to attach or mount volumes: unmounted volumes=[backend-configmap], unattached volumes=[default-token-vq7vz backend-configmap]: timed out waiting for the condition
      Warning  FailedMount  25s (x7 over 18m)    kubelet            Unable to attach or mount volumes: unmounted volumes=[backend-configmap], unattached volumes=[backend-configmap default-token-vq7vz]: timed out waiting for the condition
      Warning  FailedMount  8s (x18 over 20m)    kubelet            MountVolume.SetUp failed for volume "backend-configmap" : configmap "backend-configmap" not found
    simisimi
    @iamatsundere
    Have you run kubectl apply -f . -n vinlab ? Because I think you run with the default namespace in somewhere
    Matvey Ezhov
    @ematvey
    Nope, I ran kubectl apply -f . following the instructions
    simisimi
    @iamatsundere
    Oh, please follow the instruction from README.md file in vindr-lab-deployment repo. It is the latest version.
    simisimi
    @iamatsundere
    hey @ematvey, how is your deployment, does it work?
    Jan Witowski
    @jwitos
    Hi, just wanted to add a note of interest for 3D annotation tools. Contrary to @ematvey I love 3D Slicer but for personal annotation, not "MLops" / engaging new people to do segmentation. I think simple tools like a brush is sufficient for many use cases. Even something as simple as https://www.medseg.ai/ would work. Thanks for contributing, I've also worked for some time on a similar project when I was at Harvard for a few months (markit.mgh.harvard.edu) so I understand how difficult this can be.
    Jakob Thrane
    @jakthra
    Hello! having some issues uploading DICOM files. I've added an issue to the uploader API endpoint (error not handled). However, if trying to upload a DICOM with the DICM tag, I get hit by the following error
    2021-04-20 07:31:36.613 | ERROR    | middleware.authenticate:get_authentication:60 - error when get info
    2021-04-20 07:31:36.847 | ERROR    | middleware.authenticate:get_authentication:56 - Token is missing the "aud" claim
    simisimi
    @iamatsundere
    @jakthra do you use Docker or Kubernetes?
    Jakob Thrane
    @jakthra
    @iamatsundere Kubernetes
    simisimi
    @iamatsundere
    ok, please login to the Keycloak admin console, go to Clients/vinlab-frontend
    image.png
    and tell me do you see any thing like these
    Jakob Thrane
    @jakthra
    image.png
    Did I miss something in the setup guide?
    simisimi
    @iamatsundere
    No, I think it's my bad, I will update it in the Keycloak document
    But I will support you to get it done now
    pleas click the Add Builtin button
    Jakob Thrane
    @jakthra
    Thanks a lot :)
    simisimi
    @iamatsundere
    and looking for something like audience resolve
    Jakob Thrane
    @jakthra
    I have nothing under "Builtin" with that name. I do however have it under "Create"
    simisimi
    @iamatsundere
    ok, so please click the Create button then setup like this
    image.png
    if you completed it, you should re-login
    Jakob Thrane
    @jakthra
    Ok, thanks, will try :-D
    simisimi
    @iamatsundere
    Ok, notice me if you have any issues or just finish this :)
    21 replies
    guigautier
    @guigautier
    Hi, I m trying to run the application with kubernetes, I met the same problem (vinbigdata-medical/vindr-lab-deployment#5), when I try to create a new project. I think, I miss something during the keycloak installation, but I don’t know what. Any ideas ? Thank tou
    1 reply
    guigautier
    @guigautier
    Everything works fine. Keycloak configuration files are working well. Thanks a lot
    1 reply
    guigautier
    @guigautier
    Hi, I tested your system, the workflow process and the UI are really nice. However I did not succeed to see my labeling annotations after completed it in task mode. (saved labeling annotation are not visible) Maybe I ommitted to do something. I have also a question, how can I retrieve the stored data and associated annotations from the json file ? Thanks
    5 replies
    guigautier
    @guigautier
    Hi, I retested on an other computer with the same configuration, and I got the same issue. I can’t review done annotation.
    Otherwise the app is really nice. Missing some tools for 3D annotations. I saw it’s Work in progress. I will be interested to help you to define the 3D brush tools.
    3 replies
    Rasmus Bonnevie
    @Bonnevie
    Hi, this seems related to the issue mentioned by guigautier. I am using the Kubernetes deployment on Ubuntu 20.04 with the keycloak files you've supplied, and I can access the UI just fine. When annotating, though, (in the medical-view subdomain) it happens that when I press "Save", all my annotations immediately disappear. Is this a lacking permission of some kind?
    6 replies
    Nghia
    @Lego1st
    Hi everyone, after weeks of being busy. We have fixed the saving issues on Github. Please check it out and let me know if everything is ok. :-D
    markcorsi
    @markcorsi
    Hi All - I finished the setup instructions at: https://github.com/vinbigdata-medical/vindr-lab-deployment/blob/master/KEYCLOAK.md At the end of the document says: "And here we go!....." And then nothing. I am sorry. But where do I go? I can login to the account user info, but how do I actually start the software and upload my first study?
    markcorsi
    @markcorsi
    By the way, I noticed one issue with my install that I don't see covered in the documentation. I am trying to install this on a real webserver (e.g. running it from a fqdn not localhost). Is this my problem?
    markcorsi
    @markcorsi
    Hi again! That was exactly the issue. I installed everything on a local vagrant box running ubuntu and everything worked perfectly for 'localhost'. However, I cannot seem to find where I change localhost to a FQDN inside the settings for deploying on the internet. I found four places in the clients 'vinlab-frontend' and 'vinlab-backend' where localhost is part of the URL configurations but changing those to my fqdn still doesn't stop the redirect to localhost when I try to log into the system. Any help will be greatly appreciated! (Oh, and thanks for writing this application! It looks great!!)