Tuesday, March 31, 2020

Using jumphost to scp and ssh without ssh / scp twice

Jumphost comes handy in the cases where A (source) -> C (dest) direct ssh or scp is not possible due to firewall policies. So it is achieved via a Jumphost B, rather than repeating the process twice, A -> B and then B -> C.

scp -o 'ProxyJump me@jumphost.bmi.emory.edu' test.log pkathi2@desthost.bmi.emory.edu:/opt/localdrive

Sunday, March 29, 2020

Pandemic Atlanta Lockdown - Week 2

Some music videos in my projector

We are the new Wuhan

When the outbreak happened in Wuhan, everyone was curious to know how the feeling of getting locked down is. There were some Quora threads from those in Wuhan, documenting their daily life. Now, the USA has become the most affected country and we are all Wuhan. Perhaps Atlanta is still fine. But New York is suffering more. I don't see ambulances roaming around my community so far. I hope it stays that way. But it is uncertain as the pandemic continues to spread rapidly across the western world.

Entering the Week 3

We are entering the 3rd week of WFH. The first 2 weeks were not much of a difference than the regular weeks. I miss going out and meeting friends, colleagues, and overall random humans. I also had to cancel my flight and bookings to Bolivia for the last weekend (+2 additional days) and postponed my Suriname travel plan indefinitely. But other than that, weeks were busy with work. I miss my family and I wish they were here locked down with me. But on the other hand, it seems the USA is going to be the riskiest country during the pandemic. So probably it is good they are not here for now.

Food as usual

I cooked and had my meals as usual. The groceries still had regular vegetables. Ground meat and canned food have mostly run out. But I rarely buy them anyway. Food perspective - nothing changed so far for me. I eat regular Sri Lankan food that I cook for myself. Although I work from home, I did not indulge in snacks. Probably my tea intake may have increased slightly. But that too green tea with honey, but no milk in it. In fact, we went to have hot chocolate or a cup of coffee like twice a week while at work. So probably my sugar intake is only the honey in the tea and the sugar in my mojito last night.

Work goes on remotely

Like the previous week, we continued the daily standup and weekly progress calls for work. We also had the Friday coffee/liquor hour at 5 pm Friday. I made myself Black Russian. Mostly I drink only on Friday nights and Saturday nights. That means I have sufficient drinks for quite a long time. I am thankful that we can work from home and support each other remotely.

Grocery shopping

I ordered some vegetables and meat from Amazon PrimeNow WholeFoods. It was contactless doorstep delivery. The expected delivery time window was 5 - 7 pm. But the order was delivered at 4:41 pm. The delivery person left the products stealthily not even knocking the door. Usually, they knock the door and quickly leave - just to notify that the products are delivered. I think, this is to ensure no contact. That's good. That means less than an hour since I placed the order. Much faster than the regular days. That's quite interesting. Most of the things I ordered were available, except for bananas. I asked for 6 bananas. But at check-out time, the quantity reduced to 1, stating there is not sufficient stock available to deliver more than 1. Not even two bananas in Whole Foods? That's strange. But not unexpected during a pandemic of this scale.

Twitter and updates

These days Twitter has been a communication medium and entertainment channel for most of us. It also has become more negative and people are less patient on Twitter now. I can understand that the pandemic has made everyone more pessimist. I don't blame them.
I kept updating Twitter with my feelings. My feelings are darker now during the pandemic. I want to cut down spreading negativity. Therefore, I decided to reduce updates to Twitter. However, I will keep these weekly blog posts for my future reference and as historical evidence if needed in the future.

I also watch music videos on my projector during the nights after work. It is fun for a change. I must note that my taste in music videos has slightly changed towards lyrics or tunes with overall sadness. Maybe it is normal. Maybe not.

Kiss me baby I'll must be stay here Day by Day...

Where are we now?

There is also a dashboard that shows the current status of the pandemic. I check it frequently. Quite depressing to see it change rapidly to the worse, to be honest. I used to check the updates from GlobalTimes frequently. But now that the pandemic has moved to other countries, those China-based updates are less relevant now.

Everyone, please stay home and take care of yourself and your family if you are lucky enough to be around your family during these days, unlike me. I seriously have no clue how the pandemic will progress and when we will return to normalcy. Let's wait and see. Hope for the best!

Wednesday, March 25, 2020

PNG conversion for jpeg compressed DICOM images

Due to an existing bug in pydicom, the png conversion of (tested with jpeg lossless compression) compressed dcm images were failing.

A few steps to fix the issue (tested on Mac).

2. Close and open your terminal.

3. pip install pydicom image numpy pandas pypng

4. conda install -c conda-forge -y gdcm

5. Now run your python script again and see it works.

Tuesday, March 24, 2020

Pandemic Atlanta Lockdown - Week 1

Lonely railway track near Lindberg station
So we have completed the first week of the pandemic WFH. I planned a few personal policies to follow during the pandemic. Some of them worked, some of them didn't.

1. Work from a specific "office" area at home
This worked. I rearranged my table and I am also using my projector. 

2. Use the office laptop for office work only.
It was quite hard not to use the laptop for some music out of convenience. But I avoided that during the regular work hours.

3. Wake up and work at the same time as usual
I am waking up early as usual, except for a slight delay since I do not have to commute to work. I start working around the same time (7:25 am). But since my collaborators work until late, I cannot stop working at 4:45 pm as I planned (and I am used to, while working from the office). I kind of worked longer than I expected. Blurred work-life boundaries made this worse. But it is not that bad as I had nothing else to do anyway, staying home alone - working, cooking and eating, learning Portuguese, listening to music, and sleeping.

4. No music
Yes, I did not play music during regular work hours.
My home workspace

5. No Twitter
This did not work. Twitter is my news source and also some human interaction especially when we are isolated.

6. Wear proper clothes
Yes, it worked.

7. No alcohol
Worked. We had a coffee/tea/liquor hour last Friday evening at 3 pm to mark the close of the week. It lasted 75 minutes, and I enjoyed the White Russian cocktail I made for myself.

8. Follow the lunch timing

9. No personal calls
Worked. I had some calls. But the regular amounts as if I were working from the office. Lasted only around 5 - 10 minutes maximum a day.

10. Make random meaningless coffee-time video calls to my colleagues
We have weekly update calls 11 - 12 pm on Mondays and daily calls 11 - 11:15 am. Those are not meaningless calls since we discuss the progress. We also had some random calls.

Go for coffee with colleagues
The situation deteriorated fast within a week. With strict social distancing measures in place, this won't happen. During the past week (including the weekend), I only went out once - that is, to buy groceries from Kroger. I may go out once a week or once in 2 weeks during these days for grocery shopping.

12. Track how everything goes
Yes, and I hope to maintain these weekly blog posts. I used to do that when I moved to Portugal in 2012 and continued to do so until 2013 summer vacation (see all posts tagged Lisbon). Those days were the most exciting days. COVID-19 lockdown days are the opposite. Most boring days ever. Yet, I think the blog posts give me some records for the future.

I hope everyone stays safe at home. Hope we all overcome this pandemic soon and move on with our regular happy life.

Saturday, March 14, 2020

Coronavirus pandemic and working from home

The novel coronavirus has turned this year upside down with a pandemic. Starting the coming Monday, we all decided to work from home to minimize human interactions. We are not sure when we will go back to work from the office. I have rarely worked from home except during my MSc/Ph.D. days. So this period brings me back my memories.

Although I have worked from home rarely during the past ~2 years in Atlanta, those were often only a day in a few months. Since this time is going to be a continuous long-term work from home, I decided to set up some own self-policies to ensure I work a sufficient amount of time, while also not overworking. With deadline-induced panic, during my Ph.D. days, I have overworked at times, like 60 hours non-stop with no sleep in between once. But then I also had more flexibility to take days off following such stints. It was well-balanced. But now, we are preparing for an outbreak. I will keep these personal work hours policies updated with amendments if the work-from-home drags on for a long time.

Personal work hour policies during the work-from-home era of the Coronavirus pandemic

I made these policies to emulate my work habits as if I am working from my actual office.

1. Work from a specific "office" area at home
My "home office."
Today I brought back my office laptop home. I have a home laptop with all the stuff I needed to do my office work configured. But, since this is going to be a long time, I will work only on my office laptop during work hours. I have also set up our dining table as my office table. My other laptop table remains in my room with my personal laptop on it.

2. Use the office laptop for office work only.
I will use it for work only, and everything else on my personal laptop. Conversely, I won't use my own laptop to do office work during these days.

3. Wake up and work at the same time as usual
Every day I arrive at work at 7:25 a.m. and leave at 4:45 p.m. I will continue the same work hours during these days. Similarly, during the weekdays, I will continue to wake up at the same time (6 a.m).

4. No music
I like to listen to music. Mainly Romanian, Chinese, and Indian music. But I never listen to music at work (except with an exception during my time in Saudi Arabia where I used music and an earphone to combat the background noise). I like quiet environments to work. My apartment is quiet, especially given that currently, I am home alone. I will maintain it by not introducing any music.

5. No Twitter
Twitter is the only active social media I currently use. I will not use Twitter except during lunchtime while I am working at home. Although I still check Twitter once in a while at work from my office, I will avoid that when I work from home to avoid getting dragged into a long conversation. These days, with the pandemic and panic going on, it is easy to lose track of time on Twitter.

6. Wear proper clothes 
When I am working from home, I will wear regular clothes, instead of working in underwear.

7. No alcohol
I always have some alcohol in my fridge. I am not addicted. I drink when I want to. I am very alcohol-tolerant. But as a practice, I won't drink during my work hours. 

8. Follow the lunch timing
Usually, I cook during the evenings after work for my dinner and lunch the next day. I pack the lunch for the next day in a lunch box so that I can use the microwave to heat it. I will continue this practice, rather than trying to cook during lunch hours.

9. No personal calls
Unless it is a quick one. Typically, I do not make calls from the office since there is no place to make calls from. That means, lack of privacy, and if I did make a call that would disturb others.

10. Make random meaningless coffee-time video calls to my colleagues
This one actually depends on my colleagues. If they do not agree, this won't work. :P I like people - I am an extrovert since 2012. I do not want to be away from humanity for too long. At work, we often make our small fun activities, like making poems and talking nonsense. It is nice to continue the tradition. These calls are not the same as the progress meetings or weekly standups. Those meetings have a purpose.

11. Go for coffee with colleagues
In case of a severe outbreak, this would break the purpose of working from home. But I think at least for now, a coffee walk with my colleagues who live close by is not a big problem (as long as they are up for that). At work, we often go for coffee at least once a week.

12. Track how everything goes
I just want to work as usual. Not to work slower or not to work to death. I still estimate we have 2 more weeks of regular life. But if things get worse by then, we need to be ready for a bumpy ride.

This year so far has been horrible. Previously 2016 and 2007 were the only two years I felt hopeless. This pandemic and some other problems made my 2020 go bad. But today, I met my mentor, and her positive words made me optimistic again. I believe we all will overcome this pandemic together. Whatever that doesn't wipe the humanity off the earth, will make us stronger.

Friday, March 13, 2020

Some beach songs during the pandemic

I am a fan of Romanian music, and I like INNA's music. I decided to share a few of my favorite songs that have a beach video and summer vibes in this post since we are stuck by a horrible never-ending pandemic. :) These songs are primarily from Romanian singers and artists.

1. INNA - Amazing

This song was released during my first summer in Lisboa - mid-June 2013. I still remember going to the Praia dos Matosinhos in Porto, and falling in love with Porto. It was quite sad, going back to Sri Lanka from Portugal for the summer vacation. Interestingly, this song was shot in Praia das Maçãs in Sintra. While we were living in Portugal, somehow we failed to visit this beach. I visited this beach only when I went back to Portugal in 2019 for my Ph.D. defense. It was cloudy, and the beach was smaller than I expected. The video made it look never-ending. But overall, the village, the small train, and the beach environment with a stream were all good.

2. INNA - Shining Star

One of my favorites. I like the lyrics because of the memories I have with this song. The song was released in February 2013 when I was still early in Lisboa. Great memories.

3. ANTONIA - Iubirea Mea

During the summer 2017, we were visiting Timișoara, Romania. It was nice to listen to Romanian music while we were in Romania!

4. Mia Martina - Latin Moon

Relatively an old one. But I like that sunset vibes and Mia Martina's voice.

Finally, I hope the COVID-19 coronavirus pandemic ends soon so that we all can get back to our life soon.