On Clouds, Poems, Python and more...

Google Reader is dead!

2013-06-30T09:39:00.000-07:00

Google has finally pulled the plug on the Reader. It is time to move on another feed reader. In the meantime, here is the last screenshot from the Trends page:

More than 45k read items since October 2008. Looking forward 450k more to read :)

Thanks to Mihai Parparita's Python scripts I archived all there is to archive from the Reader.

Happy news reading!!!

Issues with GDL Python module

2012-11-07T13:01:00.000-08:00

1-) Importing GDL segfaults in IPython

$ ii # this is alias for ipython --pylab

Python 2.7, IPython 0.14.dev

I1 import GDL

I2 Segmentation fault (core dumped)

however, works fine in Python shell

>>> import GDL

>>> GDL.findgen(5)

>>> GDL.function('findgen',5)

array([ 0., 1., 2., 3., 4.], dtype=float32)

possibly readline module issue? Interestingly, works fine in Spyder's IPython console.

2-) Source compiled (with --enable-python_module option) GDL Python module fails to work

>>> import GDL

Traceback (most recent call last):

File "", line 1, in

ImportError: ./GDL.so: invalid ELF header

possibly, due to wrong lib arch use, during compilation?

3-) GDL's dindgen yields wrong result while accessed through its Python module

>>> GDL.function('dindgen',10)

array([ 0.00000000e+000, 1.00000000e+000, 2.00000000e+000,

3.00000000e+000, 4.00000000e+000, 0.00000000e+000,

5.92878775e-323, 3.30571061e-313, 6.94380683e-310,

4.03179200e-313])

Posted this issue on dindgen with GDL python module

Calling IDL, GDL, and FL from Python

2012-11-07T12:57:00.001-08:00

Thanks to Anthony Smith's pIDLy module, accessing IDL, and its clones GDL and FL from within Python becomes really easy.

Launch an IPython session, then typing these example lines to see pidly in action:

I1 import pidly

I2 idl = pidly.IDL()

I3 fl = pidly.IDL('fl', idl_prompt='FL> ')

I4 gdl = pidly.IDL('gdl', idl_prompt='GDL> ')

I5 idl.findgen(10)

O5 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I6 fl.findgen(10)

O6 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I7 gdl.findgen(10)

O7 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I8 np.arange(10, dtype='float32')

O8 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

Testing these with:

I2 pidly.__version__

O2 '0.2.4+'

I3 np.__version__

O3 '1.8.0.dev-82c0bb8'

$ idl

$ gdl # the version that ships with Fedora 16

GDL - GNU Data Language, Version 0.9.2

$ fl # latest development snapshot (10/Oct/2012)

Example access to an IDL procedure:

I5 idl.pro('cgplot', np.sin(np.linspace(0, 6*np.pi, 1000)))

I6 idl.pro('iplot', np.sin(np.linspace(0, 6*np.pi, 1000)))

For more information, just read the quick usage guide on pidly's web-site, or clone the source from https://github.com/anthonyjsmith/pIDLy

Worldcloud for ccnworks

2012-11-07T09:57:00.002-08:00

Here is a worldcloud created for my code repository on:

http://code.google.com/p/ccnworks/

First get the commit message history into a text file (the last commit is r287):

svn log >> test.txt

Then with a bit of VIM trick and manual step, remove unwanted lines:

sort u

Select of all the text, and import into

http://www.wordle.net/create

Tadaaa, here comes the result :)

Indeed, we are data scientists here in atmospheric science!

Alternative wordcloud implementation comes from Andreas Mueller. I saw his A Wordcloud in Python titled posting via Planet SciPy. In order to run his wordcloud.py I needed to change unsigned int[:,:] integral_image -> unsigned long[:,:] integral_image in query_integral_image.pyx to get past 'ValueError: Buffer dtype mismatch, expected 'unsigned int' but got 'unsigned long''.

Then feeding the same log data I get the following image, which is nicer looking than the wordle's image :)

Python videos

2012-02-11T15:13:00.000-08:00

# from AMS

Reading, writing and visualizing GRIB and netCDF data with Python (invited) (91st American Meteorological Society Annual Meeting)

Porting radar simulation software to Python: a case study in the benefits of Python (91st American Meteorological Society Annual Meeting)

WxMAP2—a python-based system for model diagnosis and weather forecast tool development (91st American Meteorological Society Annual Meeting)

Using CDAT for model development and analysis of large data sets (invited) (91st American Meteorological Society Annual Meeting)

Community Tools for the Analysis and Visualization of Geoscientific Data (invited) (91st American Meteorological Society Annual Meeting)

DV3D: 3D Climate data visualization using python and VTK (91st American Meteorological Society Annual Meeting)

HootPy: A Console-Based Processing and Visualization Package for Meteorological Models and Observations (91st American Meteorological Society Annual Meeting)

Python Adoption at the Naval Research Laboratory (91st American Meteorological Society Annual Meeting)

# PyCon10 Videos

Introduction to Python Profiling

PyCon 2010:Python's Dusty Corners (#182)
PyCon 2010:Keynote: Relentlessly Pursuing Opportunities With Python, or why the AIs will Spare Us Al
PyCon 2010:The Mighty Dictionary (#55)
PyCon 2010:Keynote: State of CPython
PyCon 2010:Deconstruction of an Object (#62)
The Ring of Python (#189)
Debating 'til Dawn: Topics to keep you up all night (#183)

# PyCon2009 videos

Eggs and Buildout Deployment in Python (Part 001)
Eggs and Buildout Deployment in Python (Part 002)
Eggs and Buildout Deployment in Python (Part 003)

Introduction to Python Profiling
Leveraging ReStructuredText in your Projects
The State of the Python Community: Leading the Python tribe
Keynote: Guido van Rossum
How Python is Developed

An Introduction to Object-Oriented Programming (Part 001)
An Introduction to Object-Oriented Programming (Part 002)
An Introduction to Object-Oriented Programming (Part 003)

Python 401: Some Advanced Topics (Part 001)
Python 401: Some Advanced Topics (Part 002)
Python 401: Some Advanced Topics (Part 003)

Python 101 (Part 001)
Python 101 (Part 002)

Python 102 (Part 001)
Python 102 (Part 002)
Python 102 (Part 003)

# various

sagedays29: Fernando Perez -- Scientific Computing Using Python

SciPy 2010 - Travis Oliphant - Moving Forward from the Last Decade of SciPy

SciPy 2010 - David Beazley - Python Concurrency
Getting Started with Numpy Arrays in Python

PyAtl November 2009: "Python Data Structures" by Brandon Rhodes

Google's Python Class

Python for Scientific and High Performance Computing (1 of 4)

What is Python? by Wesley Chun

Advanced Python or Understanding Python

The Importance of Programming Literacy (PyCon 2007)

Google I/O 2008 - Painless Python Part 1 of 2
Google I/O 2008 - Painless Python Part 2 of 2

Sage: Unifying Mathematical Software, video part 1, video part 2

A Demonstration of the 'IPython' Interactive Shell

Various open-source videos

2012-02-11T15:06:00.000-08:00

What's under the hat? A sneak peek at Fedora 13 by Jesse Keating
Git er done with GIT by Jesse Keating

Keynote: MeeGo: A Free & Standard Linux OS for the Mobile Industry

Google I/O 2009 - The Myth of the Genius Programmer
Google I/O 2009 - Do You Believe in the Users?
Google I/O 2008 - Project Hosting on Google Code
Google I/O 2008 - Open Source Projects and Poisonous People
Google I/O 2008 - Open Source is Magic
What's In It for Me? Benefits from Open Sourcing Code
Learning from StackOverflow.com

Paul Graham - Great Hackers (2004)
Paul Graham - Open Source Software Development (2005)

# resources

http://docs.sfepy.org/euroscipy-tutorials/tutorials/index.html
Euroscipy 2010 tutorials
RCE 48: NumPy
The Pragmatic Bookshelf | List of Tips
Code Like a Pythonista: Idiomatic Python
NumPy MedKit by Stéfan van der Walt (.tar.gz)
PEP 3099 -- Things that will Not Change in Python 3000
Building Skills in Python

NumPy 1.5 Beginner's Guide review

2011-12-26T09:44:00.000-08:00

This new NumPy book provides an easy start to NumPy for those who want to churn numbers in Python programming language, whether you don't have much programming background or you are switching from your favorite language. The author of the book uses quite a friendly tone throughout the book. Most of the important aspects of NumPy is well covered with well explained examples. The examples provided are step by step explained, starting from the basic array/matrix creation to more complex tasks like signal analysis and linear algebra related calculations.

To get best out of this book, it is recommended that you would try out the examples and challenge yourself with the exercises given in have a go sections of the book. If you are feeling lazy for some reason, you can get the source code from the book's page. I finished perusing the book in about a week (having a few years of NumPy experience has definitely role in this). For me reading and understanding through stock market related examples were a bit boring, but if you are in to financial business you might enjoy putting NumPy in your toolstack with the help of this book. Notably, besides the basic NumPy beginners chapters, the book extends into basic Matplotlib and SciPy lands. A lot of examples use Matplotlib to create plots and better illustrate the operations at hand (e.g. curve fitting, statistical distributions) It is a bit surprising to see MaskedArray module didn't get any mention in the book. However, with the basics you gained, it should be fairly easy to start experimenting with masked array functions of NumPy.

Overall, if you are looking for a book to get started in NumPy in about 200 pages, you might give this one a chance. It is available in both print and electronic formats. Further on, you can try their advanced matplotlib and and Sage books, if you are willing to enhance your scientific Python skills.

Final Note: I received a review copy from the publisher. Thanks to Packt publishing for their contributions to open-source literature and providing me a free copy of the book.

Virgin Adaları'ndan dönüş

2011-07-28T22:49:00.000-07:00

Buradan oraya gidiş oradan buraya gelişten daha kolaydı nedense. Yükseklik farkından olsa gerek herhalde. Taa 2000 üstü metrelerden deniz seviyesine varmak nispeten daha kolayca oldu. O kadar bisikletimi götürmeyi istesem de adaya, bu isteğimi bir türlü gerçekleştiremedim. Halbuki onca zamandır da bisikletin içinde geldiği kutusunu saklamaktayım, olurda bir gün bir adaya giderim, olurda bisikletimi götürmek isterim diye. Ne adada bisiklete binebildim, ne de adanın çevresini koşarak ya da kanoyla kürek çekerek dolaşma hayalim gerçek oldu. Artık bu hayaller başka bir zamana kaldı. Karayipler’de 7000’i aşkın irili ufaklı ada varmış. Bir gün yine denk gelir adalar etrafında bulutları çalışmak isteyen ve bulutlardaki yağış oluşumunu anlayama çalışan birileri.

Bu aşağıdaki ilginç şekilli ada (her ne kadar konunun genelinden biraz uzak olsa da) KK adlı okur ve arkadaşa gidiyor. Gerçi her ne kadar adanın tapusu bende olmasa da, kendisinin adanın yer bilgisini bulması karşılığında bir sonraki sefere görüşmemizde bir şişe “Cruzan rum” garantilediğini bilmesini isterim. KK, ister desen tanıma kullanabilir, isterse resme ait bilgilerinden uçağın o anki yerini tespit etmeye çalışabilir, ya da olmadı eşe dosta sorabilir, tercih tamamen kendisinin.

Bugün ayın 28’i olmuş. 17 gün ne çabukta gelip geçmiş. Arda kalan günlerde gezip görüleni ve çalışılıp işleneni kısaca özetlemek için bir güzel sözsüz şarkıyla eşlik edilmiş bir resim şovu hazırladım. Şarkı yaklaşık 4 dakika 28 saniye sürüyor. Saniyeler güne tuttu, hadi öyleyse izlenen resim sayısı da adada geçen gün sayısı ile şarkının dakikasından türeyip 17x4 = 68 olsun. Tıklayıp keyifli seyirler dilerim (bu kapanışta çok fazla AA ile seyahat etmekten bir etkilenme olsa gerek :)

Virgin Adaları Günlüğü: -3. Gün

2011-07-25T07:43:00.001-07:00

Bugün adaya gelişimin 2. haftası. Bunca zaman geçmesine rağmen ilk kez C-130'de uçuş fırsatını yakaladım. Çoktan beri aksatılmış günlüğün bu bölümünü yazarken 10. görevin eve dönüşüne yaklaşık 1.5 saat var. İçerisi bolca gürültülü, kulaklık takmaksızın, kulakları tıkamaksızın yolculuk etmek pek mümkün değil. Gerçi bu uçağın amacı yolculuk etmekten ziyade, bulutların içine uçup onların özelliklerini ölçmek. BUZ-T isminden de anlaşılacağı üzere asıl gaye bulutlardaki buzu ölçmek (gerek miktar, gerek şekil, gerekse de yapısal olarak) ve buzun yağış oluşumundaki işlevini daha detaylıca anlamaya çalışmak.

Uçak bulutları ziyaret ederken ayrıcalıklı ön koltuklarda oturmadıkça, dışarıyı görmek pek mümkün değil. Bugünde ileriye bakan kamera arızalı olduğu için ekranlara kamera resimleri yansımadı --uçağın altına bakan kameradan gelenler hariç. Ziyareti söz konusu olan bulutlar epeyce gelişmiş olduklarından içerlerine doğru dikey hava hareketi epey güçleniyor. Bu sebeple emniyet (bu kelime önemli) kemerlerini açıp dolaşmak pek akıl karı bir iş değil. Bana göre “Havaların Kralı” ile bulutları ziyaret daha eğlenceliydi çünkü içerdeki herkes dışarıdaki durumu rahatça görebiliyordu, ama bu uçakta bulutları anlamamıza yardımcı olan çok daha fazla sayıda araç gereç mevcut. Mesela bu ucuşta kaydedilen veri sayısı yaklaşık olarak 500 ve 6 saatten uzun süren yolculuğun ardından her saniyede bir kez örneklenmiş verilerden oluşan dosyanın boyutu yaklaşık 130MB civarında.

Sağ yanımda iki tane büyük hava tüpü, önümde bulut çekirdeği sayma ve ölçme cihazı, sol yanımda önündeki cihazlarla ve bilgisayarla meşgul biri, dişlerimin arasında az önce yediğim elmadan sadece geriye kalan sapı, başımda içinden bulut alakalı konuşmalar geçen kocaman bir kulaklık ve, ve aklımda bir türlü çıkmak bilmeyen bir güzel S, daha hala 1 saatlik yol var geri dönüşümüze...

Virgin Adaları Günlüğü - 2. Gün

2011-07-13T20:51:00.000-07:00

Dün pek bir değişik etkinliği olmayan bir gündü. Gözlükler yine buğulandı, garip kuşlar yine ötüp durdu, deniz sakinliğini korudu, bilgisayar başında yapılan çalışmalar devam etti, 5. araştırma ucuşun ardından 36 kişi bir odada bir araya gelip uçuş değerlendirmesinde bulundu ama gece yağmur yoktu. Günün önemli olaylarından biri uçuşlara katılabilmem için gerekli kısa güvenlik eğitimini tamamlamış olmamdı. Öğlen bunu yazarken gürültüsü bol, içinde ve dışında bir dünya ölçüm araç ve gereci olduğundan bahsettiğim uçağın içindeyiz. Bugün uçuş yok ama içerde olağan koşuşturmacalar sürmekte, bulutlarında istemesiyle bir-iki güne uçuşa gidiş yakındır.

Virgin Islands Diary - Day 1

2011-07-12T06:51:00.000-07:00

Today I have once again realized that, I can't think the same way in Turkish as I do in English and vice versa. Yesterday night, and this morning I tried to translate my first diary posting to English, but to no avail. Neither I was able to list the words as nicely I did in Turkish nor my sleepy eyes were able to fight more. So I have decided to alternate these island blogs in between languages. Writing Turkish for even days and English for odd days unlike I originally planned to write dual language for all days. Unlike me, Erden Eruç can handle dual language blogging (as well as circumnavigating the earth) very well with using the beautiful intricacies of both languages. Three years of staying in an English speaking country apparently is not enough for me, still lots of grammar mistakes, still asking toothbrush instead of toothpaste and filling in arrival dates instead of departure dates in forms. Of course, fatigue from long travel and not getting proper sleep, high humidity and trying to focus on writing and improving an important research related text and the rash of trying to response for those who wonders about me using this turtle speed internet connection. Tell me please, where is my grammar fairy?

Day 1 goes fast indeed. Waking up 7:30 and trying to cope with the high humidity and heat aren't as easy as it looks. Think of it like living in your bathroom while your hot shower is on. Luckily these rooms have air conditioning to make life easier. It feels like changing climates from going inside and out and outside in. I don’t remember glasses getting fogged in summer, like you step inside a warmer place from a colder place. It was a busy day today. Finally we have created an almost page long draft that describes our efforts about numerical cloud parcel model experiments that will go in a report. It took many hours indeed to finalize those few paragraphs. Each sentence triggered a new question and each question lead to a new thought provoking discussion. In our case, even jokes turned into deep intellectual conversations and sometimes deep intellectual conversations into jokes. Anyone out can tell me what "exact non-equilibrium thermodynamics" really means? :) or how Thales' deductive reasoning could play role in explaining your thought process while delving deep into the explanation of internal cloud model interactions? Probably floating on the ocean while sipping a cold drink might cause similar triggers in one's mind. Still yet to try if this claim is true or not. Students of science occupation tend to verify things, don't they?

Even though I wasn’t able to fly today, I had chance to connect to the C-130 data system to see the measurements in real-time. This is great since without being in the aircraft you can observe how things are looking out there, except experiencing some cloud bumpiness and sharp research maneuvers. Today they performed the 4th research flight. The previous 3 research flights have already been processed and shared. Meaning I have more data to study and understand. I like variety yes, and I have atmospheric dataset collections from many different locations of the earth. When I want to go the South Pacific or Arabia or even to the central US (actually, I just go there instead of all these buzz :D), I just browse into my folders and have a fresh look at what those probes tell me, what the radar reveal, and how their imagers capture clouds like. More research is on the way, so better tigthen my mind.

Those flurries have visited us again at around the same time like they did last night. Free nightly washing service. No wonder this tropical island is so green :)

Virgin Adaları Günlüğü - 0. Gün

2011-07-11T06:04:00.000-07:00

Bir kez daha SciPy konferansına gitmek isterken, yolum başka bir yöne düşüyor. Gerçi bu kez gidilen yer okyanus aşırı değil, aksine okyanus içinde bir yerde: Virgin adalarında. Bir dünya dolusu atmosferik ölçüm cihazı bulunan bir uçakla buzun yağış oluşumundaki etkisini araştırmak daha cazip geldi sanırım bu sefer :) Hem C-130 ile ilk defa uçacak olmak hem de birkaç zamandır okuduğum makalelerin yazarları ile tanışacak olmak bu işi gerçekten çok heyecan verici kılıyor.

Adaya ulaşması epey zaman aldı. İki uçak ve bir otobüste geçen, beklemelerle birlikte 15-16 saat süren bir yolculuk oldu. Sonrasında uykulu gözlerle gecenin köründe yazılan bu yazı ve yazılması gereken bir paragrafı bitirmenin telaşı. Keşke sadece bitmeyenler bunlar olsa: geride SciPy11 zamanında tamamlamayı planladığım basit bir bulut modeli, yolculuk sırasında bitiririm dediğim “Termodinamik Yasalarına Çok Kısa Bir Giriş” isimli sesli kitap (bilin bakalım 0. gün ismi nereden çıktı), ve diferensiyal denklemlerin hızlı bir tekrarını yapmamı sağlayan görüntülü ders notlarının son birkaç bölümü hala beni beklemekte.

Öyle ya da böyle bugünden itibaren ikinci saha araştırmama merhaba diyorum. Daha önce Arabistan’da bulutlara uçmuştuk, simdi sıra Karayipler’de gezinen bulutlarda. Kendime ve takım arkadaşlarıma ölçüme müsait, bol bulutlu, tropik fırtınasız günler diliyorum. Beni bekleyen ya da bir sebepten beni bekleyemeyen herkese de çok selam şimdiden. Gecenin bu geç saatinde, dışarısı 25 °C’ye yakın sıcak iken, birden başlayan sağanak yağmur buradaki zamanın çok hareketli geçeceğini haber ediyor sanki. Biz burada BUZ-T dolayısıyla meşgulken sizlere de buzu eksik olmayan günler diliyorum :)

Records number of citations

2011-05-19T00:09:00.000-07:00

It has been a little more than a year since I mentioned about "Record number of equations" in a book about cloud microphysics. This time, the record holder is in a different category, that is the number of references used in a journal article. In her 2003 review article*, Prof. Finlayson-Pitts references a total of 367 articles.

If you are not much in the chemical aspects of the sea salt aerosol but want to learn more about the physical and measurement sides of the subject then you can consult to your one-of-the-high-citing books (over 1800 references) from Lewis and Schwarts (2005)**.

With number of my local article collection reaching over 400 and citation listings reaching up to upper 2 and sometimes 3 digits in most of them, scientific literacy has a great place in the life of a PhD student in atmospheric sciences.

References:
*Finlayson-Pitts, B. J., 2003: The tropospheric chemistry of sea salt: A molecular-level view of the chemistry of NaCl and NaBr. Chem. Rev., 103, 4801-4822.

**Lewis, E. R., and S. E. Schwartz, 2005: Sea Salt Aerosol Production: Mechanisms, Methods, Measurements, and Models. American Geophysical Union, Washington, DC.

Precipitation Diagram

2011-05-16T22:31:00.000-07:00

from: http://weatherfaqs.org.uk/node/160

Aerosol effects figure in IPCC Climate Change 2007 report

2011-05-13T11:20:00.000-07:00

Figure 2.10. Schematic diagram showing the various radiative mechanisms associated with cloud effects that have been identified as significant in relation to aerosols (modified from Haywood and Boucher, 2000). The small black dots represent aerosol particles; the larger open circles cloud droplets. Straight lines represent the incident and reflected solar radiation, and wavy lines represent terrestrial radiation. The filled white circles indicate cloud droplet number concentration (CDNC). The unperturbed cloud contains larger cloud drops as only natural aerosols are available as cloud condensation nuclei, while the perturbed cloud contains a greater number of smaller cloud drops as both natural and anthropogenic aerosols are available as cloud condensation nuclei (CCN). The vertical grey dashes represent rainfall, and LWC refers to the liquid water content.

IPCC: Climate Change 2007: The Physical Science Basis, in: Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, edited by: Solomon, S., Qin, D., Manning, M., Chen, Z., Marquis, M., Averyt, K. B., Tignor, M., and Miller, H. L., Cambridge University Press, Cambridge, UK and New York, NY, USA, 2007.

Seminar on clouds

2010-10-29T15:33:00.000-07:00

Yesterday, I gave a seminar talk to our department faculty and students, titled as "An Aerosol - Cloud Condensation Nuclei and Cloud Droplet Concentration Closure Study" that is summarizing a majority of my thesis related work on aerosol and cloud micro-physical research, starting and finishing with the presentation slides shown above and at the very end of this post.

One of the most exciting parts of the talk was after I finished demonstrating my research results and showed a few of the technicalities of the research. First of all, thanks go to Dr. Jefferson R. Snider for providing his IDL-based parcel model code and being patient with me while I was re-writing the model in Python. Both versions of the code could be accessed through ccnworks by browsing the source tab, and looking under the thesis folder or alternatively, directly contacting to Dr. Snider to get the latest updated version of the model.

When I was working on the model conversion, at one point I had stuck getting similar outputs from the two languages using the same initial conditions, and with the almost identically progressing code. (Some might object on the definitions of two conditions' being "the same" and "almost identical" in the land of high-precision floating point arithmetic.) Continuing in my numerical instability problem, I had created a simple animation to better demonstrate the issue I was experiencing. As some eyes might easily catch, the droplets in parcel model reaching to so bigger sizes comparing to the results produced by IDL, solely based on condensational growth theory. It took a while to find and correct the variable that was updating its original reference while it was supposed to be operating on a copy of the content instead. This issue and a few other discrepancies were fixed in around May 2010. As a personal important todo note at this point is to restructure the parcel model code so that it behaves as an external library, thus making all the important thermodynamical and cloud micro-physics related functions greatly re-usable. This is when I figure passing dictionaries (or changing the structure of the code) to outer scope of the original file that they are declared in.

The final technicality demonstration comes from the work of Dobashi et. al., (2008) (Their "Feedback Control of Cumuliform Cloud Formation based on Computational Fluid Dynamics" titled work.) Those are by far the most realistic cloud appearances I have ever seen in a physical cloud formation processes applied simulation study. Although cloud modellers are usually interested in studying temporal and spatial statistical properties of clouds rather than synthesizing their realistic shapes and appearances, such a similar work would have a great educational use in visualising and thus better demonstrating the physical processes governing the cloud formation and further precipitation development. I can say that the authors should have prototyped their simulations using a C-like language in order to make low level access to CPU/GPU because of the high computation demands, but there are fast computation techniques available in Python that would make this undertaking possible to be realized be it simulating a research flight or playing in between sequences of a simulation to probe important properties of the formation.

For the curious, I share high-quality PDF version of the slides. Note that I had to take out a couple pages from this original presentation in order to fit 45 minutes allocated presentation time, and it was unfortunate that one of the expected audience was not in the classroom to see a few indistinguishably minute research unrelated points. All analyses and plots in my slides are performed/created using Python and its scientific tool-stack with some additional annotation help from OpenOffice on the slides using DejaVu-Sans font; for the first time with full consistency. There is one exception to the pure Python code, that is when the Python based model calculations taking up five to ten times more than the original IDL-based code, and that is where exactly Cython magic were sought and applied to boost million-times executed functions. Here, I greet the community once more, for making the scientific computation freely, publicly, and easily available to everyone without putting any restrictions in both code and verbal discussions level as how this core work should really be in its very essence within the science endeavor.

I also salute Matthew Turk and his work for that fantastic presentation style even though I couldn't copy his great architectural design throughout my slides. Yet not him, I have other masters around me for letting me embrace Tufte's sayings :)

My work on clouds is on-going and leading me to a PhD level research after successful completion of my Masters thesis within the next month. Feel free to say hi or ask more clouds if you share any research similarities.

Now, it is time for some abstraction: Youth Uprising - Rarefaction

Please keep up imagination and creativity flames are burning all along...

Vim magic2 - search and replace in visual selection

2010-10-19T09:13:00.000-07:00

Since I thought making generic analysis and plotting routines would have been harder for 8-9 different source airborne data, I am showing some pure uniqueness and laziness of variable name selections on the given screenshot. Like in many cases VIM is here to my rescue :) First we switch to line selection mode by Shift-V combination and highlight the area of interest and then hitting ":" and continuing typing by s/06/08/g in the command insertion area. The magic is done --all the "06" instances are replaced by "08"s readying the code for our April08 case.

Vim magic: Synchronized scrolling

2010-10-14T11:00:00.000-07:00

As shown in this screen capture, I have two minor modifications to my original closure-fitting code. The original code runs using the lab PCASP size ranges and excluding the first PCASP channels data, "zair-fit" version uses the field calibrated PCASP size bins, and still excluding the first two channels. The final file "zair-fit2" runs the code with the size bins and including the pseudo-problematic first two channel PCASP concentration data.

VIM provides me a very practical way to synchronized scrolling of all open windows so that I can easily compare the results from those well-formatted table structure outputs. Solution is simple: execute the following line in each window as shown in this blog entry.

:set scrollbind

Damlalar her yerde

2010-09-01T17:30:00.000-07:00

Evet, hepsini içmek serbest hatta kendi sıvınızda dahil. Olur ya kurak bir yerde mahsur kalarsınız diye Les Stroud’un Kalahari çölündeki bölümünü izleyebilirsiniz ya da burda kalıp okumaya devam ederek kendinize banyo yaparken soracak yeni sorular edinebilirsiniz.

Duş almaktan söz ediyoruz ya, ilk soru şöyle belirdi: sıcak bir duşta, pek bir havalandırması olmayan bir odanın içinde, yukarıya lamba tarafına doğru bakınca havada asılı danseden bir sürü parçacık göze çarpıyor. Gerçektende havada asılı duran parçacıklar, üfleyince bile uçuşuveriyorlar. Soruyorum, bu parçacıklar ne ölçüde aktifleşmiş? İçerideki ortam hangi oranda neme doymuştur? Sonraki soru bir şekilde banyo duvarına ya da perdesine sıçramış parçacıkların büyümesini, süzülüşünü ve diğerlerine karışıp akıp kaybolmasını izlerken aklıma geliyor. Çok sayıda küçük damlacık ve az sayıda büyük parçacık. Gamma ve Marshall-Pallmer dağılımları ne kadar doğru tanımlamakta bu parçacık dizilimini? (Diğer dağılımlara Kolmogorov–Smirnov testi yapmak isteyen?) Son sorularsa en ilginci. Bu kez damlacıkların üstümden sıçramasını izlerken düşünüyorum ve seyre dalıyorum. Çarpan yüzeyden seken damlacıklar (bu durumda benim omzum) ne şekilde parçalanıyor ve nasıl bir yörünge takip ediyor, ne zaman sonra çiseleyerek yere doğru düşüyor ve ne kadarı buharlaşıverip ya da yan duvarda kümeleşen parçacıklara yapışıp etkisiz hale geliyor?

Ya bu kapta yoğunlaşan parçacıklara ne demeli? Nedir gerçekte onları bu şekilde dengede tutan? Nasıl bir etkileşimle öyle değişik şekiller alabilmekteler ve ne kadar büyümeleri gerekir tutundukları zeminden aşağıya kaymaya başlayıncaya kadar.

Bazıları Percy W. Bridgman’ın “Eğer ölçemiyorsak büyük ihtimalle ne demek istediğimizi bilmiyoruz” sözünü fazlasıyla dikkate alaraktan ya da Meinrat O. Andreae’nin bir konuşmasında alıntıladığı gibi “Gözlemleyerek öğrenmeyecek şey yoktur” sözünün büyüsüne fazlasıyla kendilerini kaptırdıklarından, yukarıdaki soruların bazılarının yanıtlarına ulaşmışlar gibi. Tabii bu bazıları dediklerim akışkanlar mekaniği ve yağış fiziği konularında ileri seviyede bilgisi olup dahası bu minik dünyalardaki hareketlilikleri çok yüksek hızlarda izleyebilecek araç-gerece sahip kişilerdir.

Böyle bir uğraşın sonucunda ortaya çıkanlar ise sadece bir su damlacığını analiz ederek yağmur damlalarının genel dağılımı hakkında bir görüye ulaşılabileceğini gösteriyor. (“Bilinen bir konu üstüne çalışarak, yeni bir olguyu keşfetme.” Bu alıntının nereden geldiğini çözemediyseniz sizi James Burke’nin “Evrenin değistiği gün” belgeselinin ilk bölümüne alalım.) Devam edersek, düşen yağmur parçacıklarının parçalanmaya başlamadan önce teorik olarak ulaşabilecekleri çapın en fazla 6-7 mm dolayında olabileceği (bazı istisnaları ile birlikte). En ilginci ise, her ne kadar Galileo zamanından beri bilinen ve yağış ile ilgili kaynaklarda damlaların belli bir hızın üstüne gidemeyeceği bilgisinin (en azından benim böyle bilişim) yerel olarak doğruluğunu yitirişi. Parçalanış esnasında anne damladan kopan parçacıkların tekrar dengeye ulaşıncaya kadar limit hızdan aşırı hızlarda hareket ediyor oluşu. Detaylarını merak edenler şu makaleyle devam edebilirler, ya da şu bağlantıdan görüntülenmiş bir parçacığın dansını seyredebilirler.

Buradan karşısı daha mavi

2010-06-29T02:20:00.000-07:00

Yok yok, buranın karşısı değil. Bu taraf geçen haftanın macerası idi. Dağın maceracısı çokmuş: kimi normal yoldan çıkıp, bisikletle patikalardan inermiş, kimileri de dağdan aşağıya atıyor kendini paraşüte güvenip :)

Evet işte o tepelerin ardı deniz. Şehir bir dağ ile bir tepe arasında alabildiğine uzanmış. Ne güzel bir gün öncesinden karşı taraf kendini açıkça gösteriyordu, fakat oradan dağa bakınca pek açık bir görüntü almak mümkün olmadı. Kirlilikten mi desem, buluttan mı yoksa bulut olamamış parçacıklardan mı desem dağ kendini göstermedi ertesi günü. Yandan uzanan el bana gidilecek tarafları gösteriyor: Gündoğdu, oradan aşağı Kurşunlu, sonra yan yan Mudanya.

(Son cümle tamamlanamadan bir bölünme oldu, annem tarafından ekmek ve yufka almaya gitmem gerekçesiyle, yazı bekler patatesler kızarıyor neticesinde :) Ben yolda, acaba diyorum şimdi Texas'daki SciPy10 eğlencesinde olmak nasıl olurdu diye söyleniyorum kendi kendime, ya da Oregon'daki Bulut Fiziği konferansında geziniyor olup, poster sunmak, makalelerde ve kitaplarda adlarını gördüğümüz kişilerle karşılaşıp iki laf yapmak hiç fena olmazdı.)

Karşısı yalnızca daha mavi değil, ayrıca daha da yeşil. Yol boyu isteyene zeytinlik, sahibine incirlik, yoldan geçenine çamlıklar dizili. Kimi dut vardı, kimi erik, şeftali, armut yemek isteyenine. Ara ara çeşmelerde vardı yol boyunda, ama su içmek isteyeni dağa çıkmalı...

Bu resmi yukarıdakinin önüne koyunca körfeze baktığımız anlaşılıyordur sanırım. Aslında tepeden denize inince kanoya tekneye binip karşı tarafa kürek çekmek vardı. Belki ileride; tepeler yeşilini, deniz de mavisini korumaya devam ederse...

Her inişin bir çıkışı varmış. Gerçi bisikletler güzel güzel poz verse de, elde taşındılar epeyce. Özellikle bu çıkış dağa çıkışın çok benzeri, yalnız bir farkla; burası 5-10 dakikada tükenip yine aşağıya akıyor, fakat dağ yolunda buna benzer en az 100 tanesi aşılmayı bekleyen.

Bu sefer N900'ün şarjı tam doluydu yola çıkmadan. Bizim gezi yaklaşık 10 saat sürsede hem resimler hem de yol koordinatları bu kez bir aksiliğe uğramadılar. Bu yukarıdaki Runsaturday sitesinden; GPS olunca gezi daha başka bir hal oluyor. Gerçi yol boyu halinden memnun olmayanlar olsa da, bol iniş-çıkışlı ve bol manzaralı, yine son dönüş kısmı geceye kalan eğlenceli bir bisiklet turu oldu.

A is for Acceleration

2010-06-25T04:51:00.000-07:00

I was reading the comments for Best Way To Publish an "Indie" Research Paper? entry on Slashdot. Then I have jumped to The Journal of Irreproducible Results. Somehow I have ended up meeting the Annals of Improbable Research magazine. Among the titles I semi-randomly clicked on their March-April 2007 Theoretical Figures issue. "Stress Analysis of Gawn" has kept me busy for a little while (keeping my comments private, no worries) Here comes a part of the poem in the same issue. See the free PDF if you are curious to read the rest...

You’d think there were enough. You’d think
There were no need for tricks.
The letters of our alphabet
Seem plenty— twenty-six.

The choices should be obvious
When making letters stand
For quantities of physics. Well,
Things weren’t quite that well-planned.

The quantities are many,
And the letters not enough.
Some choices feel intuitive,
But some feel off-the-cuff.

Yes, some are fairly obvious,
But others feel make-do.
In case you have forgotten, kids,
Let’s do a quick review.

A is for acceleration.
B, magnetic feld.
C is for the speed of light
That prism tests revealed.

On my way to the summit

2010-06-21T04:24:00.000-07:00

This is the story of my unsuccessful attempt to reach to the peak of Uludağ on Saturday, June 19. I had to give up my ascent about 200 m below the summit. I had to give up because I ran out battery on my N900 where I was logging my coordinates, communicating with my family down in the city of Bursa, and capturing all those beautiful moments that I came across along the way. To my luck, the battery died just at the point where I photographed the little summit without being saved to the device memory. Coincidentally, this was the point where I stopped climbing any further.

I was readying myself to greet Erden Eruç from the top for his amazing solo journey. Along with him, I was going to send some special messages to a few people in my life, and to a few that I have met in the last couple of years in my life. Unfortunately I couldn't touch the sky from the summit; I couldn't keep the sun up for two more hours nor managed to last my batteries to document all my progress. However I managed to got back home safely; without being eaten by wolves or birds while biking in the dark from the mountain top to the almost downtown area. I returned with beautiful stories and beautiful pictures. Sometimes reaching the destination isn't all about, but it is the journey what matters most (What!, you haven't read the Alchemist yet?).

Here on, the real story begins. We started ascending (me and my bike in the same cabin) in a famous aerial tramway. I spent about 8$ for one-way two stage trip for both myself and the bike. It takes about 15-20 minutes without to reach up to Sarıalan and as seen in the above picture the trip is highly scenic but a scary one especially if you feel fear from looking down high heights.

This is the Sarıalan plateau, and also showing where I was heading to. Although the mini-buses on the front was waiting for passengers to go to the hotels region, I have passed my chance for the next time to experience the scenery as closely as possible and to mimic Erden's style a bit. The sub-motivation of this trip was to see if the white looking parts on the slope of the summit was really snow packs or some sort of rocks.

Wasn't I right? It is all green in between lovely bird songs. This was one my most beautiful biking path I have ever taken. Although after less than a kilometer pedaling the slope of the road got steeper, I reached to a point that I was after in about 3 km more biking.

Finally, my bike is at the crossroad. It is actually my cousin's bike. I stressed the bike probably more than what its manufacturer had done on it. Through wet or dry, bumpy or straight, rocky or sandy roads, day or night and blazingly fast or turtle slow, in climbing or descending it never broke down, and never had me to touch on it once. Thank you Bisan, you really know how to make a durable mountain bike at very affordable prices.

Water water everywhere, and all drops for drinking. This was another pure joy moment. I should have stopped my climb after washing my head under this fridge cold spring. I know of myself being content with small things most of the time. Apparently, this was not of those moments. I ended up continuing upwards and instead the bike carrying me I had to carry it on the very harsh roads. On the way up there was many small creaks flowing downwards conveniently freeing me from carrying water. I gave about 4-5 water breaks. Could those be any signs of melting rocks? :) Although the nature was very generous to water me any time I needed, there wasn't much to eat around the grass and on trees.

Here comes the challenges. I felt like playing the latest Prince of Persia game when I came by these missing bridges. The trail was getting rougher; partially eroded by the flowing water mostly, and covered by rocks at its particular places. The first pass was the easier one, since the columns were as if specially designed for bikers in mind. When I came to the next one, I paused for a moment and Damian Walter's clip started playing in my head, immediately. I saved this part for him; one wrong move could have stranded me there. I took the easier path and walked around the bridge by spending 2 extra minutes, refreshing myself once again from that fresh snow water.

This photo was my final summit capture. It was taken about half an hour before I reach my bridge challenges. At point A, I left my bike behind departing from the trail a bit uphill. It took me about another half an hour to get to the point B. If "C" had located on one down the right, I would have continued and touched there in a good one hour in spite of lack of all the supplies. I saw two hikers and a car parked on one hill along the way. Definitely, I would camp somewhere on the hills if I had enough equipments and companied by a good friend.

   And a bonus sunset. I was lucky enough to see double suns appearing in the sky. I should improve my ability to interpret universe's language. (Haven't I mentioned somewhere above about the Alchemist?) When the nature has sent me omens like above I should have been wiser and not to turn my back at them. Clearly, one of the suns (illusion or not) was setting and telling me it's time to go back home.
   After about three hours ascent, in almost an hour I managed to return to the hotels region safely. Only at one point, I was stopped by a watchdog and had to veer off to bushes. I was not sure whether the dog was leashed or not. He barked a few times and stepped a few feet towards me, while I was backing up at the same time. Later on, I stopped for a short snack break.
   It was after 45 minutes fast descent, when I called my dad to pick me up by the İnkaya sycamore about 10 minutes biking distance before I could reach to the downtown. (You still don't know the story of the Alchemist starts by a sycamore? :) Through the dark, water splash, wind whispering, dog barking, car lighting, and half moon lit ways my 25-30 km descent was completed within 45 minutes, slowing down at a few points but without ever once stopping. It could be argued if it was smart to take this adventure alone at night, but one thing is for sure; there is a lot to learn facing the darkness. In case someone still wonders, this bike proved me once again that a bike's most essential feature is its tires turning unceasingly when one most needs them to be.
   Final words are taken from a verse attributed to Imam al-Shafi which I heard in the The Man Who Walked Across the World titled documentary made for the Islamic seyyah Ibn Battuta:

Travel! Set out for pastures new

Life tastes richer when you have road-worn feet.

No water that stagnates is fit to drink,

For only that which flows is truly sweet.

Celebrating the first year of IPython logging

2010-04-16T19:58:00.000-07:00

It was last year today when I first started logging my IPython sessions explicitly using Pierre Raybaut's idea. All you need to do is just to make the changes/additions described in this piece of documentation (Logging to a file) on its soon-to-be-change LP repository. (Applies to IPython 0.10 and below)

You get a time-stamped log file (in your ~/ipython/ or wherever your IPython home directory is set at) created per day that looks like below:

#!/usr/bin/env python
# 2009-04-16.py
# IPython automatic logging file
# 13:15
# =================================
d = loadtxt(file, skiprows=30)
plot([d[i][8:] for i in range(12)])
# =================================
# 14:08
# =================================
boxplot(d[:][8:])

As of writing this entry I count almost 300 separate logs and combining them into one file using this little script yields about 37.5 k-lines (including lots of multiple entries, time-stamps, empty comments, many copy-paste codes that I haven't actually typed in)

Besides having this combined file as a rough measure for myself there is another good use for it as triggered with this question: How to exit IPython properly? IPython internal history file forgets what was in the session if you accidentally or intentionally kill your IPython session without issuing an Exit at the exit :) That new combined history file comes to our help.

First we will append all the time-stamp logs into one file (rename it to "history" so that IPython can load it at the start-up) Then from iplib.py comment the readline.set_history_length(1000) line to prevent 1000 lines limit in your history file. Now I can access all my previous coding history from within IPython again no matter how I end my sessions. (Providing that I will stitch my logs periodically)

Lazy coding at its best!

It would be great if IPython could handle history lines more smartly to read multiple lines back properly. Who knows maybe an IPython super user has a solution for that laziness as well.

By the way anyone knows how to remove duplicate lines from a file without actually sorting it?

GVIM+IPython with Conque plug-in

2010-04-05T15:22:00.000-07:00

Here is an alternative way to bridge (G)VIM and IPython applications. GVIM is my editor-of-choice and IPython is a great interactive Python interpreter. If you are a user of these two environments, this simple integration technique could greatly boost your programming / prototyping speeds.

First go to conque (Thanks to Nico Raffo for the plug-in and helping me to include IPython functionality in it) page and install the plug-in following the simple installation instructions. (In my Fedora 12 system, I pulled the latest tar.gz package from the download list section and extracted it under ~/.vim folder.) Next grab the latest conque_term_pylab.vim file from the same section and place under ~/.vim/plugin directory.

When you open a simple Python script you can easily launch an "IPython -pylab" instance by hitting F6 and execute the whole script content by F8, use F9 to send a visual selection. The IPython inside the buffer acts as a part of GVIM, so you can easily switch between buffers and copy/move text from/to buffers. You can modify the IPython switch, default window position, mapped keys editing conque_term_pylab.vim

The screenshot below shows the bridge in action:

Hint: Add the following line into your vimrc file to get equally spaced buffer windows independent of the main GVIM window size.

autocmd VimResized * wincmd =

Currently only %run magic of IPython is implemented. Here are some of the ideas that could be added to improve this IPython + VIM integration:

Add %whos key-mapping
Launch IPython -pylab on start-up automatically if a Python script is opened.
If "run" command is sent before an IPy launched instantiate one automatically.
Make sure only one instance of IPython is running!
GUI integration, create GVIM menus, reading %whos values back into a separate window and changing values.

These last points could be well achieved by working on PIDA project. It is very possible to have an VIM + IPython powered IDE that is especially suited towards scientific use.

Scenes from under a microscope window

2010-04-03T08:50:00.000-07:00

This photo is showing about 40 μm dry soda lime glass microspheres. They are perfectly spherical indeed. We use these particles to calibrate optical particle detectors e.g. Forward Scattering Spectrometer Probe (FSSP) The picture with less beads shows even tinier particles -- I will say sizes down to 5-10 μm from the same bottle. However these are the smallest sizes it gets from the microscope we used. It is not possible to detect by eye the sphericity of microspheres from the 2.1 μm bottle.

The microscope we used is a Nikon SMZ-U (Zoom 1:10) Unfortunately, our efforts were not successful in trying to show the more sphericity of Ammonium Sulfate {(NH₄)₂SO₄} particles than Salt (NaCl) crystals. We definitely need a powerful electron microscope to confirm this riddle. See the rest of the images at my Particles titled Picasa album.

PS: In one of the pictures the hands belong to Julia Beard. Without those hands it would take me a day to finish this work. Thanks Julia for your patience and tolerating my never-ending requests.

PPS: This posting has really nothing to do with Dream Theater's Scenes from a Memory album :)