Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    PGF vs PNG vs JPEG 2000 for long-term photo storage/archive

    26th May 2015

    I am using an excellent photo-management suite digiKam, which offers 3 lossless compressed formats for photos versioning and storage: PNG, JPEG 2000, and PGF. I wanted to know which one should I use, which urged me to perform this comparison.

    This post is not intended to be an in-depth comparison, but should be sufficient to choose one of the three file formats for your purposes. For more format details and history simply follow the links provided. File formats are reviewed roughly in “historical” order.

    PNG (Portable Network Graphics) was designed as GIF replacement.

    • It is lossless.
    • It is suitable for photos.
    • PNG is more space-efficient in the case of images with many pixels of the same color, such as diagrams/plots (as compared to PGF and JPEG2000). However, PNG photos are almost always larger than lossless PGF/JPEG2000 photos (real photo example: 9.9 MB in PNG, 7.0 MB in JPEG 2000).
    • PNG is fairly fast at (en|de)coding.
    • PNG is widely supported by web-browsers, image editors, and other software.
    • PNG uses CRCs internally for each data block, so if damage occurs only the damaged block(s) should be lost – theoretically. However, in practice, according to the Just One Bit paper (local copy), PNG is actually much less damage-resilient than JPEG 2000.

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    Posted in Comparison, Links, Misc, Software | No Comments »

    Casio G-Shock: amazing survivalist watches

    14th May 2015

    Casio G-Shock

    Casio G-Shock

    In May 2010 I’ve paid US $118 for Casio G-Shock GW-810D (Atomic/Waveceptor Tough Solar) wrist watch with stainless steel band.
    5 years later, at the end of April 2015, I lost it :( .

    Looking for a replacement, I found that:

    • Casio seems to no longer make affordable models with the same functionality and a metal band – only polymer;
    • a similar used model from Casio (MTG-something) costs upwards of 70 EUR.

    I was quite sad about that. Any survivalist-minded person can easily see why:
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    Posted in Hardware, Misc | No Comments »

    Tools to manage Debian services and start-up scripts

    8th April 2015

    • sysv-rc-conf: text-UI, allows editing multiple runlevels, but seems to be failing recently
    • rcconf: another good-looking text-UI alternative; can only modify current runlevel
    • bum: GUI tool (BootUp Manager)

    More details about these tools and runlevels (in German).

    Posted in *nix, Notepad | No Comments »

    Ender’s Game (the movie)

    29th March 2015

    Just finished watching Ender’s Game. As of this writing, it has IMDB rating 6.7, and I think it is slightly under-rated.

    Ender's Game (2013) on IMDb

    If you love Sci-Fi movies, this one is a definite “should watch”. I’m not sure if it has much “watching again later” value, but for one evening it is very good.
    The story holds well together, has a good (though noticeably compressed) pace, and proceeds in a fairly expected way. Overall, I liked how this movie was made. The music also blended in organically.

    Some share of the reviewers claim that watching this movie does not spoil reading the book after the movie. Some even go as far as to claim that this entire 2-hour movie can be deemed a “trailer” to the book. I had also seen disgruntled reviews of people comparing the movie to the book and complaining about the changes in the movie, and timeline compression. Well, compression was noticeable, but without it the movie would probably be boring. Also, not having read the book, I believe that the changes were necessary to make this movie hold together better. Honest film adaptations of the books are not necessarily good – these are different media, after all. Moreover, if a movie incites interest to read the book (and Ender’s game did!) – this is only for the better. Especially if a movie is like a trailer to the book :)

    Posted in Movies | No Comments »

    Compressors galore: pbzip2, lbzip2, plzip, xz, and lrzip tested on a FASTQ file

    28th March 2015

    About 2 years ago I had already reviewed some parallel (and not) compressing utilities, settling at that time on pbzip2 – it scales quasi-linearly with the number of CPUs/cores, stores compressed data in relatively small 900k blocks, is fast, and has good compression ratio. pbzip2 was (and still is) a very good choice.

    Yesterday I got somewhat distracted, and thus found lbzip2 -

    an independent, multi-threaded implementation of bzip2. It is commonly the fastest SMP (and uniprocessor) bzip2 compressor and decompressor

    - as it says in the Debian package description. Is it really “commonly the fastest” one? How does it compare to pbzip2? Should I use lbzip2 instead of pbzip2?

    This minor distraction had grown into a full-scale web-search and comparison, adding to the mix plzip (a parallel version of lzip), xz, and lrzip. After reading thousands of characters, all of these were put to a simple test: compressing an about 2 gigabyte FASTQ file with default options.

    All the external links and benchmarks, as well as my own mini-benchmark results, are provided below.

    The conclusion is that out of all the tested compressors lbzip2 is indeed the best one (for my practical use). It is only slightly better than the trusty pbzip2, which takes the second place. All the other compressors performed so poorly, that they do not get any place in my practical rating…

    So, let us first ask internet wisdom/foolishness, if lbzip2 or pbzip2 is faster/better?
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    Posted in *nix, Comparison, Links, Misc, Software | 2 Comments »

    Looking for a perfect Android app for TSW/GTD use

    13th March 2015

    I have recently realized that my planning habits are quite similar to what The Secret Weapon promotes. However, my planning is not as elaborate and detailed/structured as TSW, and I am using several tools:

    • Google Keep, an awesome note-taking and to-do lists application with a really good web-interface, and free;
    • Trello, convenient lists/projects/tasks management platform (especially for group work), and free;
    • Google Calendar, the de facto calendar standard for Android phones, and free;
    • my A5 format weekly paper planner, and… the only not free component.

    It is easy to see that I am using too many tools.

    In an effort to use less tools, and also to try some of the features of TSW, I’ve performed a brief search for GTD/TSW-compatible Android apps.

    TSW website is built around the Evernote app. However, I am not sure if this would be a good solution for me, as I have been already using Evernote since several years for longer-term note-keeping, and thus already have a bunch of notepads, notes, and tags there. Moreover, Evernote’s website mentions something about “offline notes” in the Premium (non-free) tier for mobile apps; this hints at the requirement to have internet connectivity to be able to work with TSW+Evernote efficiently through the day.

    Oh, before I forget: all the 4 tools that I am using have their purpose, with overlap between Keep and Trello.
    My A5 format paper planner (weekview compact 2015) is not a simple weekly planner; it has a structure that stimulates goal-oriented planning.
    More specifically, it provides means to plan:
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    Posted in Comparison, Links, Misc, Notepad, Software | No Comments »

    Ukraine: from the Past to the Future (presentation)

    1st March 2015

    Presentation about Ukraine

    • Goal: general introduction of Ukraine.
    • Target audience: German and international students, including PhD students.
    • Duration: approximately 25-30 minutes.
    • Presented: January, 16, 2015, in Canossa, Universität des Saarlandes, Campus, 66123 Saarbrücken, Deutschland, during the Ukrainian Evening (Landerabend Ukraine).
    • Presentation planning group: Dima Panfilenko (Landerabend organizer), Bogdan Tokovenko, Varvara Obolonchykova, Zarema Ibragimova, Ivan Pryvalov.
    • Slides: Dima Panfilenko (initial version of tourism slides and text), Bogdan Tokovenko (all the other slides/text and final tourism slides/text).
    • Useful feedback and criticism: Varvara Obolonchykova.

    Презентація про Україну

    1st slide
    Ukraine: from the Past to the Future (v5 slides, PDF)
    1st slide with notes
    Ukraine: from the Past to the Future (v5 slides with notes and extra information, PDF)

    You can also download slide notes as a text file.
    Original PowerPoint presentation file is available on request.
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    Posted in Kyiv, Life, Society, Ukraine | No Comments »