Friday, January 24, 2020

Quickly view your DICOM files locally

Install Kheops and OHIF Viewer with Docker
$ docker run -p 3000:80 ohif/viewer:latest
  
Now, OHIF Viewer can be accessed from http://localhost:3000 and Kheops from http://localhost:8042/

Load any Dicom files to your Kheops and click the "Open OHIF"

It will take you to a long URL of the hosted OHIF Viewer online. Most likely this won't work.

https://ohif.kheops.online/viewer/?url=http%3A%2F%2Flocalhost%3A8042%2Fapi%2Flink. ....

In the above URL, replace https://ohif.kheops.online/ with http://localhost:3000 as in

http://localhost:3000/viewer/?url=http%3A%2F%2Flocalhost%3A8042%2Fapi%2Flink. ....

Now you see the DICOM images in your own OHIF Viewer deployment.

Thursday, January 23, 2020

Configuring Keycloak for Kheops

Install Keycloak with Docker, together with a user account

docker run -e KEYCLOAK_USER= -e KEYCLOAK_PASSWORD= jboss/keycloak

sudo docker run -p 8081:8080 -e KEYCLOAK_USER=pradeeban -e KEYCLOAK_PASSWORD=password jboss/keycloak

Now go to https://localhost:8081

Log in with the user name and password you specified before.


Now to configure a log in connect for Kheops

1. Keycloak KHEOPS Login Client

Click the "Clients" tab, and choose the "Create" option.

Client ID = loginConnect

Click "Save", which will then open more configurations for the "LoginConnect" that you just created.

Turn on the option "Implicit Flow Enabled"

Turn off the "Direct Access Grants Enabled"

Valid Redirect URIs: https://localhost:8081/*

Web origin: https://localhost:8081

Click "Save" again.


2. Client Scope (kheops)

Click the "Client Scopes" tab, and choose the "Create" option.

Name: kheops

Turn off the "Display On Consent Screen"

Click "Save"


Click "Clients" again and go to "LoginConnect"

Go to the "Client Scopes" tab.

Choose "kheops" from the Available Client Scopes and choose the "Add selected" option.



3. Service Account

Create another client "kheopsAuthorization".

Save, and then disable "Standard Flow Enabled" and "Direct Access Grants Enabled".

Under the "Client Scopes" choose "Kheops", and click the "Scope" mapping.

Choose "kheopsAuthorization" for "Client Roles".

4. Logging Impersonations

Under the "LoginConnect" client's Mappers tab, click "Add Bulletin", and add the Impersonator User ID."

Change the "Token Claim Name" to "act.sub". Then disable "Add to ID token" option.

Finally, click "Save". This is supposed to conclude the configurations unless I missed something.

Tuesday, January 21, 2020

Setting up Kheops - the docker projects

Kheops deployment consists of several Docker projects. This post lists them, adopted from the CI docker-compose.

UI 
1) kheops-ui:
    image: osirixfoundation/kheops-ui:${KHEOPS_UI_IMAGE_TAG}
    https://github.com/OsiriX-Foundation/KheopsUI

Reverse Proxy
2) kheops-reverse-proxy:
    image: osirixfoundation/kheops-reverse-proxy:${KHEOPS_REVERSE_PROXY_IMAGE_TAG}

Authorization
3) kheops-database (postgresql):
    image: osirixfoundation/kheops-database:${KHEOPS_DATABASE_IMAGE_TAG}
    https://github.com/OsiriX-Foundation/KheopsDatabase

4) kheops-authorization:
    image: osirixfoundation/kheops-authorization:${KHEOPS_AUTHORIZATION_IMAGE_TAG}

5) kheops-dicomweb-proxy:
    image: osirixfoundation/kheops-dicomweb-proxy:${KHEOPS_DICOMWEB_PROXY_IMAGE_TAG}

Zipper
6) kheops-zipper:
    image: osirixfoundation/kheops-zipper:${KHEOPS_ZIPPER_IMAGE_TAG}

Authorization Proxy
7) pacs-authorization-proxy:
    image: osirixfoundation/pacs-authorization-proxy:${PACS_AUTHORIZATION_PROXY_IMAGE_TAG}


DCM4CHEE PACS
8) ldap: LDAP Server initalized for the DICOM Archive
    image: dcm4che/slapd-dcm4chee:${PACS_LDAP_IMAGE_TAG}

DCM4CHEE LDAP also internally uses its own Postgresql database.

9) archive:
    image: osirixfoundation/kheops-dcm4chee-arc-psql:${KHEOPS_ARC_IMAGE_TAG}

In addition to these 9 docker containers, Keycloak runs in another VM and communicate with these containers.

We need to fit the dockers in an appropriate number of VMs.

A conservative approach would be, 2 VMs.
1 with Keycloak and everything else with the Docker containers on the 2nd.

I think the Kheops proposed approach would be 7 VMs.
1. Keycloak
2. Kheops UI
3. Kheops Authorization
4. Reverse Proxy
5. Zipper
6. Authorization Proxy
7. DCM4Chee PACS

But maybe, Kheops UI and Kheops Authorization can be merged into a single Kheops VM. In that case, we can also move zipper into that Kheops VM. Probably Authorization Proxy should just live with dcm4chee PACS.

Then we have 4 VMs:
1. Keycloak
2. Kheops containers (kheops-ui, kheops-database, kheops-authorization, kheops-dicomweb-proxy, and kheops-zipper)
3. Reverse Proxy container (kheops-reverse-proxy)
4. DCM4Chee containers (slapd-dcm4chee, kheops-dcm4chee-arc-psql, and pacs-authorization-proxy)

I think the 4 VM route is decent.

Monday, January 20, 2020

The Birkman Method

We recently had a Birkman session at the university. This is the summary map I got. So I am usually an extrovert - which I think is correct.

Image
 The detailed components go like this.
Image

Then my interests are as below.

Image
 Finally, my top career areas to explore:

Image

That's it folks. Birkman uncle told me I should manage a Sri Lanka restaurant. lol. Restaurante Sri Lanka em Parque das Nações (Ano 2048) 😇

Friday, January 10, 2020

Stop the small talk if you need information

I hate small talk online and offline - especially when it doesn't go anywhere and performs zero information exchange despite consuming considerable time. This post talks about why I hate small talk online.

They: Hi
Me: Hi
They: How r u?
Me: Good, thanks, and you?
They: Good too. 

So what's next? Do I need to continue this chat? Note how I was the one who typed more characters above despite them starting the convo. Come to the point directly! I am not here to lead and drive the communication that you started (unless we are close and we know each other very well). If you are chatting online with me through LinkedIn, very likely there is a reason. You don't message someone without a purpose, especially a stranger -- that too using professional network platforms such as LinkedIn.

These days, if the message comes from an unknown youth, I cut them short to help both of us. 

They: Hi 
Me: Hi 
They: How r u? 
Me: Anything I can help with? 
They: I want to apply to GSoC. How to proceed? 

See, I have prevented that unnecessary bluff and waste of network bandwidth.

My suggestion to the youngsters, don't ask to ask. Just ask. If someone has responded to your chat/message, you have already achieved their attention. Most people have a little attention span. Don't lose that to small talk. Instead, come to the point instantly. Although chats are synchronous technically, they work more asynchronously in practice. I am not glued to my computer to slowly receive each piece of message and reply. But if you message the important/core communication at once in brief, it can get you the answer faster.

Often the below communication works better. Shorter and more to the point, but more complete than the previous 2.

They: Hi Pradeeban, I want to apply to GSoC with Emory BMI. How to proceed?
Me: Hi, Thanks for your interest. Please check https://github.com/sharmalab/Emory-BMI-GSoC

All it needed was just one single message exchange. Not three or more as in the second and first cases.