30 June 2012

Re-reading (and re-reading again) the wavelet transform

So, a quick update: the lombcoeff function, which implements the Lomb unnormalized transform at one frequency, has been written and has a doc string; there was actually no problem with my code, I needed to reboot Octave; I may try compiling all of the Fortran libraries for x64 (or check if they already are, since I installed a 64-bit only system on the computer in question) and build Octave with 64-bit support; finally, I'll be writing a batch of tests this weekend based around a sum of a few sine curves, just to show how the function works (and I'll apply them across the whole suite, too. Once I've got sample data, it's pretty quick to extend.) The next step there is to write a test script using the Vostok data, and then I need to write a documentation file clearing up the source of that data (collected and documented by JR Petit et al, published in Nature, and available in tab-separated values from the NOAA's paleoclimatology site.) Currently in the /data folder is a CSV export of the .rda archives from the Mathias paper, but I think I may re-export them with a text file explaining each column, since the R export included various nonsense values around the data.

As for the nurealwavelet and fastnurealwavelet commands, I will need to study the code and the paper a few more times (I think I've read it at least five times so far) because neither section actually makes any sense to me. There is no nurealwavelet.R file, so nurealwavelet() in fastnu.c is not actually accessible from R, while the fast- version seems to have other problems. I get the feeling that I'm better off writing using only the paper as a guide when it comes to this transform, and I may not implement the fast- variation, since thus far the "fast" implementations have been orders of magnitude slower than their supposedly slower brethren (although I have a few ideas about accelerating them, mostly by changing how some math is handled and changing to switches from my current control structure. The second is easier to implement, and I will add that change before the more intricate changes I'm planning.)

In short, I'm back to work as usual, except for scratching my head over the wavelet transform. (I'll take some time now to read the paper Mathias cited, An introduction to wavelets, as it is available online and will most likely make my life easier.)

25 June 2012

Examining current results

Well, the methods all run. That's a nice thing. The not-so-nice thing is that their results are not exactly in line with what the R code suggests they should be. Specifically, in the case of lscomplex, all of the R results are compressed into the first 400 values, taking omegamax = 1, 20 octaves and 100 coefficients per octave, while the next 1600 values are all infinitesimally small frequencies which are in essence garbage values ... oh, and my code generates values 283.42 times larger than the R results. (Other oddities are cropping up in the fast methods as well, but I'd rather break it down in the ordinary methods first.)

In short, I'm slightly confused and need to work out what exactly is going wrong here. I have a feeling this will involve the rest of the day.

Just a few thoughts this morning

So, I ran mkoctfile on the fast transforms this morning; fastlscomplex works fine and cleanly (and fast, on this processor!) Unfortunately, I've left some error in fastlsreal still, and it segfaults with a SIGSEGV 11 — Address Boundary Error; I'll figure that out this morning, and I'll check the output of fastlscomplex against the reference R implementation.

UPDATE: Found the problem, fixed it. There was an accidental call to a zero address (whoops.)

UPDATE 2: There's now the excellent question of what to do about the fact that the results produced vary in some areas, occasionally by spectacular amounts. I'm going to do some analysis on the results today, including generating the cosine functions indicated and comparing them to the data.

21 June 2012

Progress? Absolutely.

Well, I'm about to commit some code that compiles without a hitch for fastlsreal, definitely a plus. Once I set up a clean environment to build the necessary R code, I'll generate the results to compare against my .oct files (as I've gotten behind on that front.) Finally, I'll write the documentation for the functions from the past two weeks, and that'll be it!

17 June 2012

Sorry about the radio silence

So, on Wednesday I had a bunch of stuff stolen out of my locker at the gym, including my laptop and various other important things. This halted my work for a little while as I reassembled my life, but I have a computer again and am currently running ./configure to build Octave; I should be completely set up to get to work again later today.

In code-related news, everything I've written up to this point (except for edits to the lombnormcoeff.m file) was stored in the octave-forge svn, so nothing was lost (other than time, money, a sense of privacy, and my general peace of mind) when the thief got at my stuff. That's the upside of offsite storage! To my mentors, I'll be back at work tomorrow, and once I get everything really rebuilt I'll have more code to submit (I'll test fastlscomplex tomorrow and then write fastlsreal as it's just a few additional steps on top of fastlscomplex.)

08 June 2012


I just uploaded fastlscomplex.cc in its current version, and it works. It generates what looked to me to be correct results, I'll do a few spot-tests later. So far, it doesn't implement any sanity checks, so if run with bad input, it will segfault right now; again, I'll add sanity checks this afternoon. (The other thing is, it's much slower than lscomplex, most likely because I didn't hard-code many optimisations yet. Some functions could be accelerated by changing the number of operations used, for instance. I'll look into reducing the complexity of some sections during the buffer time before OctConf, while I'm also cleaning up documentation.

In the meantime, I'm just happy to have a working function!

07 June 2012

Rewritten code and irregular segfaults

So, I decided on Monday that the best option was to completely rewrite fastlscomplex from scratch; the code took a day to write, and on Wednesday morning, it compiled just fine. One minor problem is that it causes segfaults. (Okay, more than just minor. But it runs, sometimes.) I've figured out where the segfault is, after abusing std::cout as a way to check that it's running. The segfault-causing error is somewhere in the merging code, so I'm going to remove the output I added to check on what output was generated so far, and focus my attention on the merging code so that I can determine why it's failing.

The other problem with this code currently is that it doesn't actually output results. When it does run, it generates a long vector of the correct size, all of whose elements are zero. That's ... not exactly the result I was expecting, so while I know the actual answer-generating code is not killing the process, there's obviously a problem in it somewhere. That's what I'll be focusing on this afternoon, after I find a way to keep the code from randomly going ballistic on me.

02 June 2012

Sometimes macros are more of a pain than you expect.

Right now, I have most of the fastlscomplex method structured the way I want it to be upon completion, however it still requires some tweaking to manage the shift from C to C++ — after a few applications of replace-string, most of the mkoctfile errors vanished (apparently it didn't like a macro that was used in the original code). In short, the code I'm working with still doesn't compile, but it's very close at this point, and I should have a fully operational fastlscomplex by early next week. (Even with this slowdown, I'm still almost a week ahead!)

Once I've gotten fastlscomplex running, I'll spend a little time cleaning up other functions, adding tests and other error-response components, so that I've got a lesser load later on to finish that.