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Testing Emacs Weblogger Mode
I installed WebloggerMode into Emacs 23.1 and am testing it out. Yes,
right here, live! Typing text into Emacs, even some simple
HTML is much faster and more fun than typing into the
Wordpress text editor. I’ve got all my memorized shortcuts in Emacs to
create my text. Supposedly I can post and publish my entry straight
into my blog site with a few simple keystrokes. I don’t know. I haven’t
tried it yet, but if you are reading this presumably it worked. So this
is just a short testing post; hopefully more will follow from Emacs.
Well, here I am back in the WordPress editor box. My Weblogger post posted fine, only problem was it got assigned to the uncategorized category. Haven’t figured out how to set categories in Weblogger — yet. Otherwise, pretty cool Emacs mode.
Posted in Computers & Software
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What’s Happened To The Bookstores?
If you are a bookstore aficionado you can’t have avoided noticing how they have deteriorated over the last ten years. Fewer books, less variety, more open spaces and chairs, fewer people, most of whom are there to drink coffee and work on their laptops using free Wifi connections — it’s hard to pin it down exactly, but the bookstores today are just not as good as they used to be. Are they going the way of video stores (e.g. Blockbuster which is dying) or CD stores (e.g. Tower Records, already deceased)? I can make a quick judgment of the quality of a bookstore by two tests: how many different Thomas Hardy books they stock and how large their computer book section is. At the Borders near Park Meadows Mall outside of Denver back in the 1990′s every Thomas Hardy book, even the obscure ones, from Desperate Remedies to The Hand of Ethelbertha, was there, alongside the more common Tess of the D’Urbervilles and The Return of the Native, in multiple editions (Penguin, Oxford, others). Nowadays, you’ll find a handful of the latter famous books, in some generic Barnes and Noble edition (Hardy wrote several versions of his books — the Penguin editions contain his first version and the Oxford edition his last, so the edition is important) and none of the more obscure novels. I don’t think there is anything unique about Thomas Hardy books, the same thing is true if you look at Charlotte Bronte (where is a copy of The Professor?), or Thackerary (you might find Vanity Fair, but good luck finding Pendennis), and so forth. The thinning out of the Thomas Hardy selection over time is just a symptom of the general malaise that is afflicting bookstores, gradually sapping them of their strength. The other barometer is the size of the computer book section. Back in the 90′s the computer book section at the above mentioned Borders took up a whole corner of the building. There was shelf after shelf of computer books, whole walls just devoted to C++ books alone. Nowadays at the downtown Borders in Louisville, KY there is one side of one shelf with computer books. That’s it. As for the huge Borders near Park Meadows Mall outside of Denver — it’s closed. Out of Business. Very sad.
Of course it’s all due to economics, to electronic book readers, to the iPad, to the Internet, to Amazon.com, and so forth. And it’s good for the trees. True enough. But I fear the downfall of the traditional bookstore is also due to fewer people reading books, to a general lack of interest in books and reading — in short to illiteracy. I could have written a post “What’s Happened To The Libraries?” to make the same point. Libraries have become a place for free Internet access, much like Starbucks without the coffee. The books are still there, but are ignored. Oh I know there are still plenty of book lovers out there. But we are a dying breed. I remember with great joy going to the Universal Books Store on 5th Street in Philadelphia as a teen and seeing the newly minted glossy covers of the Ace and Ballentine editions of Edgar Rice Burroughs books, or even more special, going downtown to Leary’s Bookstore, where I purchased the Ace book edition of The Fellowship of the Ring when it first came out in the 1960′s. Sure, now I can get any book I want on Amazon — in some ways it is better for a book lover nowadays then back when I was growing up. But I miss the browsing experience, the thrill of discovery, the impulse purchase that opens up a new author and new literary world at a bookstore, and am saddened to see this change.
Posted in Books, Computers & Software, Language
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Singleton Madness
I’ve been spending the last few weeks trying to exorcise a pesky singleton class from EP Simulator. This is the Options class, which contains all the program options that are saved from session to session. There is only one set of Options, so I had naively made the class a singleton. Singletons being what they are, the class soon started infiltrating many other classes, sitting there as a hidden dependency, rendering classes untestable, and generally causing trouble. Having read such posts as Singleton Considered Stupid I realized the error of my ways and I have been diligently trying to exterminate the nasty thing. It’s not easy! The concept behind a singleton seems worthwhile: you only want one instance of the object. So what do you do instead of making a singleton? Just create one instance of the object! Make sure you just are using the same instance throughout your program and it can be an ordinary class, which you can then subclass to create mock classes for unit testing, and which you just pass around as needed to your objects, making the dependency explicit. Don’t hide dependencies in singletons! My advice: if you have singletons mixed into your code, the sooner you remove them, the better. Right now I am tearing the code apart to eliminate the nasty singleton, breaking code right and left, but I know the results will be worth it, eventually.
Posted in Computers & Software, Electrophysiology
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Emacs Tip of the Month
Want real shell mode in Emacs? Using M-x shell only gives terminal emulation, which sometimes doesn’t display things correctly and which, since it supports all Emacs key bindings, makes you do things like use M-p instead of C-p to bring up previous commands in the command buffer ring. Most of the time Shell mode is fine and actually preferable, but if you need a true terminal/shell mode, use M-x term. In this mode it at first appears none of the usual Emacs key-bindings work — How do you change windows?? The secret is to use C-c instead of C-x as your command prefix, e.g. use C-c o instead of C-x o to change windows. To use the M-x commands or any other command, just precede the command with C-c. Thus use C-c M-x compile instead of just M-x compile. Try it. You’ll like it. (Hey I know this is too simple for Emacs gurus with megabyte long .emacs configuration files, but not all of us know these tricks, not even some long time users).
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EP Studios Projects Update
Here’s a rundown of current activity at the EP Studios mothership:
EP Office
EP Office is the flagship project of EP Studios. Version 1.7 is out and basically is the culmination of the original software, which started out as a Microsoft Access version 2 database way back in 1995. It is proprietary software, but very cheap as such things go (less than $100 for the multi-user version). It is basically a Microsoft Office add-on, and as such is tied inextricably to Microsoft Windows. Version 2 of EP Office is a complete rewrite from the ground up, utilizing all the lessons learned from the original program, as well as new perspectives gleaned from my moving from academics to private practice. Version 2 is hosted an a Ruby on Rails platform, is open-source software, and completely web/browser based. Right now the database schema is being designed. As we go along we will upload the program as a demo to the Heroku website.
EP Simulator
EP Simulator despite several years of off and on again work remains in a very alpha-like stage of development. Basically we are trying to work on the Navigator functions first, which have to do with file organization. We are in the process of rewriting the data processing to use a database backbone such as SQLite and MySql. The hard part of EP Simulator, i.e. the actual simulation of arrhythmias, is still somewhat far in the future…
Clickit
We are working on a gui frontend to configure Clickit scripts using Tkinter and Python. This should allow easy customization of number of clicks, time between clicks, etc.
MorbidMeter
MorbidMeter also deserves a gui frontend. We would also like to port it to Android, although that will mean rewriting the program in Java. It’s a small and simple program however and this shouldn’t be too hard.
We have some other projects in mind. Stay tuned.
Posted in Computers & Software, Electrophysiology
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Stupid Bug
Having just spent the last several hours chasing down a weird bug, there is a sense of anticlimax having finally figured it out. I have to say the debugger was less than useless in this matter: various functions mysteriously were not working, although identical code seemed to work elsewhere, variables were listed as “not in scope” when they clearly had to be … it was just weird! Since Qt C++ is not really C++, that is, the language is extended, mostly by using evil MACROS, I was half-convinced there was some bug in the Qt meta-compiler that I would never in a million years solve. Then I was thinking I should be using a mutable iterator instead of a plain one, then I was sure that something was wrong with my copy constructors, then that some global scope library variable was hiding my variable or vice versa, around and around it went. I actually found a few other bugs in trying to fix this, but the ultimate problem eluded me for hours. Until…
There it was, staring me in the face all along:
while (iter.hasNext());
names << iter.next().name();
Unbelievably, a misplaced semicolon at the end of the while() line was causing all the trouble. Sometimes (maybe more than sometimes) C++ can drive you crazy, as much as I love it. It certainly is making me appreciate "cleaner" higher level languages like Python and Ruby.
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Amarok Startup Crash — Solved!
Every since I upgraded to OpenSuse 11.2, a source of frustration was that Amarok was broken, and I couldn’t fix it. Every time I tried to start it, I would immediately get a crash report from KDE. I could solve the problem by downgrading libxine to the version that came with OpenSuse, but that meant no mp3 support (OpenSuse can’t include proprietary codecs). Kaffeine worked fine with mp3 support, but it still bugged me that I couldn’t get Amarok to run. I even downloaded the latest version source code and compiled it but, no dice!
So, just tonight, I fixed it. I tried a lot of useless fixes from the Google, but this site had the answer. It’s simple. I uninstalled phonon-backend-xine and it works now. Go figure.
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When Science Is Proprietary
After working with open source and/or free software (I’ll let the purists argue the difference there), it is jarring to look up scientific papers in the real world for my real job (electrophysiologist). It costs money to read these papers! The results of scientific research, intended to better the world and spread knowledge, costs money to read! Of course, you say, it costs money to do the science, so why not? Because the money you are paying to read an article online or in a journal does not go to the researchers who did the study! They are funded by the government or grants from various institutions or drug companies to do the research. When they submit an article to a journal, they don’t get paid. They sign over the copyright to the journal, which then charges for a subscription or for access to the article. The reviewers who review the article for acceptance into the journal also don’t get paid. They do their job for free, with the hope that doing a lot of reviews will improve their status and get them on some journal’s editorial board, where, again, they will not be paid for their services. So from the scientist’s point of view, besides perhaps an idealist view to improve the world by furthering scientific research, the benefit from doing studies is status based, much like in the open source software community. Yes there are financial rewards for improvement in status, such as getting invited to give paid talks, or getting employed by some biomedical research firm, but the same is true in the open source world. The villains are the publishers. Certainly there was more justification for paying for journals when the only medium for publication was dead trees. Now everything is available online (how about getting rid of the dead tree version?), and publication costs are minimal. Yet if you truly wanted access to all major publications, just in EP alone, you would be subscribing to at least 10 journals, each costing several hundred dollars a year. This is ridiculous — a hurtle for almost every one who needs this information. Even those doctors who subscribe to most of the major journals will find they need to look up some article in some more obscure journal. When it pops up online with a price tag, isn’t it tempting to just peruse the abstract and accept the possibly flawed conclusions, than take out your credit card and examine the actual methods and results?
This is the 21st century. Ignorance appears to run rampant over much of the world, including if not especially the United States. The present peer-reviewed process for publication of scientific studies is a good one. But let’s get rid of middle-man publisher in the age of the Internet. Knowledge should be free.
Posted in Electrophysiology
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Plugging Away At EP Simulator
Just to show that I have been working on this project, here’s another screenshot which I posted at SourceForge.
Source code is hosted at GitHub. I expect to upload Windows and Linux binaries soon for download for those of you who aren’t into compiling source code.
Posted in Computers & Software, Electrophysiology
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