Tuesday, November 2nd, 2010, 1:37 pm
Moving From MATLAB to Octave
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feel as though I must apologise for hasty remarks that I made in yesterday’s audiocast when we discussed GNU Octave (so I posted an update). I was basing my assessment on a very old experience and my understanding, as I found it out today, is that more and more MALTAB users consider moving to Octave due to the increasing cost of MATLAB. Another person whose background is in Mathematica taught me some more about the state of Octave. To quote from IRC:
| *Quadrescence (~Quad@unaffiliated/quadrescence) has joined #boycottnovell-social | Nov 01 22:25 | |
| FurnaceBoy | Quadrescence: wb // schestowitz look who’s here | Nov 01 22:26 |
|---|---|---|
| Quadrescence | hi | Nov 01 22:26 |
| schestowitz | Hey | Nov 01 22:28 |
| schestowitz | I was contacted by octave dev | Nov 01 22:28 |
| schestowitz | Did you use it? | Nov 01 22:28 |
| schestowitz | I just need to be able to deal with DICOM in it | Nov 01 22:28 |
| schestowitz | Problem is, octave might not have good 3d visualisation tools | Nov 01 22:28 |
| Quadrescence | I am pretty sure Octave just uses gnuplot | Nov 01 22:29 |
| schestowitz | sjvn: “@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.” | Nov 01 22:29 |
| schestowitz | Quadrescence: yeah | Nov 01 22:29 |
| schestowitz | which is rather primitive compared to binary junk | Nov 01 22:30 |
| schestowitz | So I need to use the junk | Nov 01 22:30 |
| Quadrescence | schestowitz: What do you mean? | Nov 01 22:30 |
| schestowitz | “@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.” | Nov 01 22:30 |
| schestowitz | I think it’s not true. He still boosts Windows (gralla) | Nov 01 22:31 |
| schestowitz | “@schestowitz thanks anyway. I already knew about octave-bioinfo, but it’s functionality is quite limited…” | Nov 01 22:31 |
| schestowitz | Quadrescence: re mathematica | Nov 01 22:31 |
| schestowitz | You though of leaving it? | Nov 01 22:31 |
| schestowitz | maple and matlab are similar | Nov 01 22:31 |
| Quadrescence | schestowitz: Sorry, I don’t know what you mean | Nov 01 22:33 |
| Quadrescence | schestowitz: Are you saying gnuplot is primitive compared to mathematica/maple/matlab? | Nov 01 22:34 |
| schestowitz | for plotting I think it’s lacking in comparison | Nov 01 22:35 |
| schestowitz | The octave guy admitted it | Nov 01 22:35 |
| schestowitz | I work with images a lot | Nov 01 22:35 |
| schestowitz | for just plain stats I could use octave | Nov 01 22:35 |
| Quadrescence | Actually I’d say gnuplot is rather phenomenal. | Nov 01 22:35 |
| FurnaceBoy | pics or gtfo | Nov 01 22:36 |
| Quadrescence | An alternative to gnuplot would be to use Sage: http://i.imgur.com/71Hr3.png | Nov 01 22:36 |
| TechrightsBot-sc | Title: Not a web page! Aborting image/png type .::. Size~: 0 KB | Nov 01 22:36 |
| Quadrescence | P and Q are plots. To plot them together, just do P+Q | Nov 01 22:36 |
| Quadrescence |  |
Nov 01 22:36 |
| schestowitz | Nice | Nov 01 22:36 |
| schestowitz | Maybe it has improved | Nov 01 22:36 |
| Quadrescence | I don’t think that is gnuplot tho | Nov 01 22:36 |
| Quadrescence | In fact, I know it isn’t | Nov 01 22:36 |
| MinceR | gnupowder plot | Nov 01 22:37 |
| schestowitz | gnuspamassassin plot | Nov 01 22:37 |
| Quadrescence | gnuplot is still great: http://gnuplot.sourceforge.net/demo_svg/singulr.html | Nov 01 22:38 |
| TechrightsBot-sc | Title: gnuplot demo script: singulr.dem .::. Size~: 8.92 KB | Nov 01 22:38 |
| Quadrescence | http://gnuplot.sourceforge.net/demo_svg/contours.html | Nov 01 22:39 |
| TechrightsBot-sc | Title: gnuplot demo script: contours.dem .::. Size~: 10.67 KB | Nov 01 22:39 |
| Quadrescence | stuff in general: http://gnuplot.sourceforge.net/demo_svg/ | Nov 01 22:39 |
| TechrightsBot-sc | Title: Demo scripts for SVG terminal in gnuplot version 4.4 .::. Size~: 5.63 KB | Nov 01 22:39 |
| Quadrescence | opacity: http://gnuplot.sourceforge.net/demo/transparent_solids.2.png | Nov 01 22:40 |
| TechrightsBot-sc | Title: Not a web page! Aborting image/png type .::. Size~: 0 KB | Nov 01 22:40 |
| Quadrescence | Anyway, the best thing about gnuplot is that it’s incredibly fast/lightweight. | Nov 01 22:41 |
| Quadrescence | Mathematica has a tendency of blowing 2GB of RAM just to get a decent surface plot | Nov 01 22:41 |
| Quadrescence | MathGL is an incredible open source library for making absolutely spectacular plots: http://mathgl.sourceforge.net/pictures.html | Nov 01 22:42 |
| TechrightsBot-sc | Title: MathGL – pictures .::. Size~: 4.34 KB | Nov 01 22:42 |
| Quadrescence | *and* you can use it with Octave | Nov 01 22:43 |
| FurnaceBoy | Quadrescence: that is impressive (the svg stuff) | Nov 01 22:53 |
| *FurnaceBoy lieks svg | Nov 01 22:53 | |
| schestowitz | abeNd-org: syntax compatible? | Nov 01 22:56 |
| schestowitz | Quadrescence ^^ | Nov 01 22:56 |
| schestowitz | Could I attempt to run old matlab programs with gnuplot and octave? | Nov 01 22:57 |
| schestowitz | FurnaceBoy: <SFT have VML | Nov 01 22:57 |
| schestowitz | SVG scares them cause it ain’t THEIRS. | Nov 01 22:57 |
| schestowitz | *MSFT I meant | Nov 01 22:57 |
| FurnaceBoy | schestowitz: fine , let it scare them | Nov 01 22:58 |
| Quadrescence | schestowitz: it is mostly compatible | Nov 01 22:59 |
| *Ender2070 (~Ender2070@CPE00222d6e3608-CM00222d6e3605.cpe.net.cable.rogers.com) has joined #boycottnovell-social | Nov 01 23:04 | |
| schestowitz | FurnaceBoy: they ‘joined’ this year | Nov 01 23:04 |
| schestowitz | Only to keep pushing VML | Nov 01 23:04 |
| schestowitz | They need to intervene in the competition too | Nov 01 23:04 |
| schestowitz | To bend it | Nov 01 23:05 |
| schestowitz | See MSODF for example | Nov 01 23:05 |
| FurnaceBoy | bend -> break. | Nov 01 23:05 |
| schestowitz | Microsoft fragmented ODF | Nov 01 23:05 |
| FurnaceBoy | hehe | Nov 01 23:05 |
| FurnaceBoy | tried w/ java | Nov 01 23:05 |
| FurnaceBoy | + html | Nov 01 23:05 |
| schestowitz | got sued | Nov 01 23:05 |
| schestowitz | They try again now | Nov 01 23:05 |
| schestowitz | AZune [sic] cloud | Nov 01 23:05 |
| FurnaceBoy | yes, they only have one trick | Nov 01 23:05 |
| schestowitz | Inviting Java dvs | Nov 01 23:05 |
| schestowitz | *devs | Nov 01 23:05 |
It turns out that my employer may also allow me to move from MALTAB to Octave, thus using only Free software in my research. In fact, I’m installing Octave at this very moment.
November 3rd, 2010 at 4:42 am
Oh yes, gnuplot is wonderful free software. I prefer to use it’s generate from file capability and call it from scripts or have scripts craft the files, then call it for each set of data. This is a very powerful way of plotting lots of data quickly. The Los Alamos lab site shows you how to do just about anything you care to do. For analysis, I like png output. eps output does a good job with pdf output from latex.
You should also look into OpenDX for 3D plotting and it’s image format, which I was once told will replace dicom. Here is an interesting starter that links to this practical use page that will jump start scripted use. OpenDX does surface plots and 3D data clouds.
Dicom is a tricky “extensible standard” which vendors violate at will, so you will have problems with it. There is purpose built free software like Aeskulap, which also works with pacs. I’ve also been told that ImageJ can deal with dicom, but I have not tried it. Aeskulap was unable to see the images that come from the scanners I have to work with.
You should also check out Debian Medical, where all sorts of medical software is being packaged for Debian. The people running it are great.
I never got sucked into matlab because it was non free and expensive at the time I found it. The main draw to it is not the language, it’s the community that makes useful examples. There are similar communities around other non free visualization tools, but I think people are better off with the even larger community using free tools. The more you look, the more you find.
November 3rd, 2010 at 2:41 pm
Thanks for all the pointers. I am going to use them and write a lot more on the subject in days to come.