Tuesday, October 23, 2018

Installing Standalone Viewer of OHIF


You can install an OHIF Simple Viewer by following the below steps:

1) Install Meteor
$ curl https://install.meteor.com/ | sh


2) Clone the Viewers repository
$ git clone https://github.com/OHIF/Viewers.git

 
3) Go to the SimpleViewer directory
$ cd Viewers/StandaloneViewer/StandaloneViewer/


4) Run the Standalone viewer
$ METEOR_PACKAGE_DIRS="../../Packages" meteor --settings ../../config/dcm4cheeDIMSE.json

Make sure that your JSON file consisting of the URLs of DICOM images (i.e., series instances) is placed inside the directory Viewers/StandaloneViewer/StandaloneViewer/public
as in
Viewers/StandaloneViewer/StandaloneViewer/public/big.json
 
5) Access the viewer from the browser.
You may access it from localhost:3000 followed by the url of a JSON file consisting of Dicom images.
http://localhost:3000/?url=https://raw.githubusercontent.com/OHIF/Viewers/master/StandaloneViewer/StandaloneViewer/private/testData/PTCTStudy.json
or access your local json files consisting of the DICOM instances, as in,
http://localhost:3000/?url=big.json

Wednesday, September 26, 2018

Restaurant Scams in Atlanta

This weekend we had dinner at an Indian restaurant. My bill came as 37$ for the food we consumed for 29$ (11+ 15 + 3). The additional 8$ includes the sales tax and 20% service charge. (We were a group - but asked for individual bills). Since there was already a 20% service charge, I put 0$ on the tip. I clearly also indicated 37$ as the total in the bill (37 + 0.00 = 37).


Initially, my bank showed 37$ as pending. Now it shows 43$ as the completed amount. Mistakenly, or intentionally, the restaurant charged 6$ as the tip. I have a hard time to believe this is an honest mistake, since I also wrote down the total amount as 37$, after putting 0$ under the tip.


Also, a 20% service charge for a lousy service was not something I was planning to do. The food was below average too - and overpriced. Of course, from the menu, it looked 29$ for two, and with sales tax and 20% mandatory service charge, it came to 37$. Add the 20% service charge, why would I pay another 6$ to make a 40% tip in total for this below-average experience? Seriously?!


I have disputed this additional 6$ charge with my bank. The bank said, generally, they charge for the disputes, though they can make it free for me this time since this is my first dispute. However, they recommended to contact the restaurant and resolve this dispute with them.


So I called them. Judging from the voice, the first guy to answer the call was the waiter who served us (the second one). I explained to him my situation. He insisted I visit the restaurant with the bill to get a refund. He pretended that he could not find their copy of the receipt, while I was waiting for him searching through the records. He also verified what I had, where we sat down, and how much each cost, etc. Like security questions. :P I told him "I am busy to come to the restaurant to get the refund." when he repeated as if that is the only way. He said, "come on, you have time to call for 6$, and you tell me you are busy?" sarcastically. His intention was to shame me and make me give up. Now I realized he was the one who intentionally made the 0 to 6$ to get the 6$ for himself. I told him that I have already disputed this with the bank. Then he said, "Ok, give me your name and phone number. We will call you back if we find out what you say is correct". Then he also asked me to spell my name! Come on. :D He was also very unapologetic.


Within a few minutes, they called back. This time it must be a senior or a manager. He was polite and apologetic, and he accepted that it was their mistake. He said, "Your zero gave the one who entered to put a 6" (not sure what he meant. Did he mean the employee was a fraud or was it an honest mistake? It was unclear). He said they would send me a cheque for the 6$.

Update: I received a cheque from the restaurent on the 28th/Friday, 3 days from the 25th/Tuesday since I complained. This issue is resolved!


Anyway, lesson learned. Next time, I would not put 0.00 $ and write the same amount down, if I choose not to tip. I always tip. But not when a 20% service charge is already added to my bill. I would make sure just to cut the section standing for "tip" if I were to give no tip!

Luckily I paid attention. I am not sure how many customers lost their money to this scam.


Summary
1. Keep your receipts safe, especially when the waiter takes your card away from your view, and especially when there is a potential for them to seek a tip from your card.

2. Check your bank accounts online every day, and keep track of the balance, to make sure there are no weird transactions.

3. Report to the bank instantly if you find something weird.

4. Be extra vigilant if you are a tourist. You cannot spend time and money making international calls, and your bank may have limited control over a foreign transaction. Also, if your transaction is in a different currency, it will make the things even more complicated. If I were not living in Atlanta, even if they send me a cheque, I won't be able to receive it anyway - giving me no choice other than to give up.

Monday, September 17, 2018

Configuring Orthanc with Postgres backend with a network data directory

So we hve configured Orthanc with a Postgres backend. To support a large-scale data store, we mapped a network directory as the data directory of Postgres. Then we configured Orthanc to have Postgres as its backend data store, instead of its default SQLite backend, using the Postgres plugin. There is also an option for a MySQL/MariaDB backend, which we found not stable with MySQL in a network directory.

However, since we have the configured Postgres in a network directory, we have to make sure everything is running fine. Unfortunately, when we reboot, often the network directory does not mount on its own. Therefore, despite our configuration to start Postgres and Orthanc at the boot time, they both fail.

Data directory unaccessible → Postgres fails to start. Postgres failed to start → Orthanc fails to start.

We have to configure the below services in Centos, following the same order.

1) Postgresql
$ sudo systemctl start postgresql

$ sudo systemctl enable postgresql

$ sudo systemctl status postgresql

● postgresql.service - PostgreSQL database server
   Loaded: loaded (/usr/lib/systemd/system/postgresql.service; enabled; vendor preset: disabled)
   Active: active (running) since Mon 2018-09-17 14:46:41 EDT; 11min ago
 Main PID: 2655 (postgres)
   CGroup: /system.slice/postgresql.service
           ├─2655 /usr/bin/postgres -D /opt/pacs/postgres -p 5432
           ├─2657 postgres: logger process
           ├─2701 postgres: checkpointer process
           ├─2702 postgres: writer process
           ├─2703 postgres: wal writer process
           ├─2704 postgres: autovacuum launcher process
           ├─2705 postgres: stats collector process
           ├─2754 postgres: postgres orthanc ::1(48534) idle
           └─2755 postgres: postgres orthanc ::1(48536) idle

Sep 17 14:45:59 HOST.NAME systemd[1]: Starting PostgreSQL database server...
Sep 17 14:45:59 HOST.NAME pg_ctl[2652]: pg_ctl: another server might be running; trying to start server anyway
Sep 17 14:46:41 HOST.NAME systemd[1]: Started PostgreSQL database server.


2) Orthanc
$ sudo systemctl start orthanc

$ sudo systemctl enable orthanc

$ sudo systemctl status orthanc

● orthanc.service - Orthanc DICOM server
   Loaded: loaded (/usr/lib/systemd/system/orthanc.service; enabled; vendor preset: disabled)
   Active: active (running) since Mon 2018-09-17 14:47:14 EDT; 8min ago
     Docs: man:Orthanc(1)
           http://www.orthanc-server.com/
 Main PID: 2753 (Orthanc)
   CGroup: /system.slice/orthanc.service
           └─2753 /usr/sbin/Orthanc /etc/orthanc/orthanc.json

Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.399045 ServerContext.cpp:167] Reloading the jobs from the last execution of Orthanc
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.399776 JobsEngine.cpp:281] The jobs engine has started with 2 threads
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.400023 ServerContext.cpp:293] Disk compression is disabled
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.400050 ServerIndex.cpp:1437] No limit on the number of stored patients
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.400490 ServerIndex.cpp:1454] No limit on the size of the storage area
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.400995 LuaContext.cpp:103] Lua says: Lua toolbox installed
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.403966 main.cpp:848] DICOM server listening with AET BMIPACS on port: 4242
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.404382 MongooseServer.cpp:1087] HTTP compression is enabled
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.405872 MongooseServer.cpp:1001] HTTP server listening on port: 8042 (HTTPS encryption is disabled, remote access is allowed)
Sep 17 14:47:15 HOST.NAME Orthanc[2753]: W0917 14:47:15.405915 main.cpp:667] Orthanc has started






To clean the data from Orthanc entirely

 

The easy way is to drop the Orthanc database.

First connect to the postgres client:
$ psql -U postgres
Password for user postgres:
psql (9.2.24)
Type "help" for help.


postgres-# \l
                                 List of databases
   Name    |  Owner   | Encoding |  Collate   |   Ctype    |   Access privileges
-----------+----------+----------+------------+------------+-----------------------
 dcm4chee  | dcm4chee | UTF8     | en_US.utf8 | en_US.utf8 |
 mytest    | postgres | UTF8     | en_US.utf8 | en_US.utf8 |
 orthanc   | postgres | UTF8     | en_US.utf8 | en_US.utf8 |
 postgres  | postgres | UTF8     | en_US.utf8 | en_US.utf8 |
 template0 | postgres | UTF8     | en_US.utf8 | en_US.utf8 | =c/postgres          +
           |          |          |            |            | postgres=CTc/postgres
 template1 | postgres | UTF8     | en_US.utf8 | en_US.utf8 | =c/postgres          +
           |          |          |            |            | postgres=CTc/postgres
 testtest  | postgres | UTF8     | en_US.utf8 | en_US.utf8 |
(7 rows)

Then go to another database to be able to drop the Orthanc database
orthanc=# \c mytest
You are now connected to database "mytest" as user "postgres".

mytest=# drop database orthanc;
ERROR:  database "orthanc" is being accessed by other users
DETAIL:  There are 2 other sessions using the database.

Yes, first we need to stop Orthanc!

[root@researchpacs postgres]# systemctl stop orthanc

Now drop the database. 
mytest=# drop database orthanc;
DROP DATABASE
mytest=#

Create the database again.

mytest=# create database orthanc;
CREATE DATABASE

Now you may start Orthanc again!

[root@researchpacs postgres]# systemctl start orthanc



You can also access your data via a browser, using the HTTP Port:

http://HOST.NAME:8042/app/explorer.html

Tuesday, September 11, 2018

Configuring Kong API Gateway for your Service Endpoints

Kong provides a complete documentation on its installation and a quick-start guide to start using it, such as configuring a service in Kong

In this post we will briefly look into configuring Kong using its Docker container as an API gateway for your backend services. This document uses Kong version 0.14.0-alpine, which is the current latest version of Kong. Kong can be configured with Postgres or Cassandra backend for its persistent storage. Here we will configure Kong with Postgres.

Install and Start Kong with Postgres

You have 2 options. If you want to get it done quick, I recommend choosing the option #2 - installing via Docker containers.

1. Download Kong's native installation for your operating system

Download and install Kong for your respective operating system 

Configure with Postgres:
$ psql -U postgres
postgres=# CREATE USER kong; CREATE DATABASE kong OWNER kong;


Run the Kong migrations:
$ kong migrations up

Start Kong
$ kong start

You may choose to start with verbose logs:
$ kong start -vv

You may need to create a kong configuration file to load Kong with custom configurations:
$ sudo mkdir /etc/kong

$ sudo touch /etc/kong/kong.conf

Now your Kong is running. Confirm that by,

 

2.  Install Kong via Docker containers.

We have our own "kong-ldap" repository with scripts that will install and configure Kong with Postgres in a container. 

$ cd kong-ldap

$ sh buildRun.sh

Optionally, you may also use these scripts to configure OpenDJ LDAP directory as a Docker container a well, connected to Docker. However, the commands are commented out - therefore you will need to uncomment the relevant commands in the script buildRun script to get it working.

Kong has two interfaces. One is the user-facing interface and the other one is the admin interface. The admin interface by default listens to the port 8001 and should not be exposed to the public. The admin interface is used by the administrators to create and configure the routes to the services in the Kong API gateway. The user-facing interface by default listens to the port 8000. It is exposed to the public, and the users can consume the services defined by the admin previously using the user-facing interface. The user-facing interface is completely separated by Kong from the admin interface.

Configure Kong for your Services

Configuring Kong as an API gateway for your services is a 2-step procedure, starting from Kong 0.14. Previous versions of Kong provided a unified approach through its "api" objects, which is current depreciated and replaced by two entities known as "services" and "routes".

Make sure that you have Kong up and running. Then,  execute the below two commands from the server that hosts Kong.

First, you need to define a "service" in Kong to each of your service/API groups (i.e., your backend applications or web services).


1) Create a Kong Service using the Kong Admin API

$ curl -i -X POST --url http://localhost:8001/services/ --data 'name=radiology' --data 'url=http://172.20.11.223:9099/services/v4/TCIA/query/'

Above, we assume your web application is hosted in http://172.20.11.223:9099/  and it has a set of services under the base path /services/v4/TCIA/query/. We pass the complete url of the backend of the original service deployments through the "url" flag, as shown above. We create a service named "radiology" in Kong for these services, using the Kong admin interface for the creation of services. Here, we assume Kong is hosted in localhost, with its admin interface using the default port option of 8001. /services/ let you create/modify the service definitions in Kong.


Second, you should add a "route" to the "radiology" service that you created.

2) Add a Route to the Kong Service

$ curl -i -X POST --url http://localhost:8001/services/radiology/routes --data 'paths=/radiology'

 As shown above, we use the KONG-ADMIN-INTERFACE/services/SERVICE-NAME/routes to configure the routes to the service that we defined above. Here the SERVICE-NAME is "radiology" as we defined above in the previous step. The "paths" flag indicate the paths that Kong should match to the service that we defined in the previous step.


Accessing your services via Kong

Now, you may access your services via Kong
http://172.20.11.222:8000/radiology/getImage
the same way you access it directly
http://172.20.11.223:9099/services/v4/TCIA/query/getImage

Here, we assume that you have deployed Kong in a server with a public address http://172.20.11.222 and your services are in http://172.20.11.223.

You may of course do additional tasks such as rate limiting, request/response transformations, logging, and analytics with the Kong API Gateway. You may refer to the Kong documentation on pointers to achieving this.

Friday, August 24, 2018

Export Confluence HTML to Github Wiki

Confluence allows its HTML pages to be exported in a single zip. There is a Confluence-to-Github-Markdown tool that allows automatic export of these HTML files to markdown .md files with a single command from the core directory:
$ confluence-to-github-markdown

Now you can create separate pages in the GitHub wiki with these md files. However, there are a certain limitations that need to be manually handled to complete the process.

1. Image. GitHub wiki does not support uploading images. Images are posted via URLs in the wiki. Therefore, currently we need to upload the images to a public location and access the URL from there.

2. Metadata. The tool also converts metadata (which is actually good I think) to md. We need to manually remove them wherever unnecessary instead of showing them as plain text in the GitHub wiki.

3. The converter tool creates the name of the md file from the html title. If you have ' or any special characters in the title of your html, it will fail to convert and throw js errors. To fix, change the title header from something such as "Rakshak’s RESTful API" to "Rakshak RESTful API" before executing the converter tool.

4. Internal links (links to named anchors in the markdown) are not handled by the converter.  The anchors must be manually added.

5. Links to other pages in the confluence wiki are preserved as it is, rather than having them as a relative link. Therefore they need to be replaced by the respective new link in the markdown wiki.

6. Video embedding is not supported in Markdown. Therefore, the converter tool simply ignores any video files embedded in the HTML. To fix this, in the final wiki pages, manually add the videos as a simple HTML links as in, [screencast](https://www.youtube.com/embed/S8juo0Dx68I).