Define a function with inline Ruby code in QSoas

QSoas can read and execute Ruby code directly, while reading command files, or even at the command prompt. For that, just write plain Ruby code inside a ruby...ruby end block. Probably the most useful possibility is to define elaborated functions directly from within QSoas, or, preferable, from within a script; this is an alternative to defining a function in a completely separated Ruby-only file using ruby-run. For instance, you can define a function for plain Michaelis-Menten kinetics with a file containing:

ruby
def my_func(x, vm, km)
  return vm/(1 + km/x)
end
ruby end

This defines the function my_func with three parameters, $x$, $v_m$ (vm) and $K_m$(km), with the formula: $\frac{v_m}{1 + K_m/x}$

You can then test that the function has been correctly defined running for instance:

QSoas> eval my_func(1.0,1.0,1.0)
 => 0.5
QSoas> eval my_func(1e4,1.0,1.0)
 => 0.999900009999

This yields the correct answer: the first command evaluates the function with x = 1.0, vm = 1.0 and km = 1.0. For $x = K_m$, the result is $v_m/2$ (here 0.5). For $x \gg K_m$, the result is almost $v_m$. You can use the newly defined my_func in any place you would use any ruby code, such as in the optional argument to generate-buffer, or for arbitrary fits:

QSoas> generate-buffer 0 10 my_func(x,3.0,0.6)
QSoas> fit-arb my_func(x,vm,km)

To redefine my_func, just run the ruby code again with a new definition, such as:

ruby
def my_func(x, vm, km)
  return vm/(1 + km/x**2)
end
ruby end

The previous version is just erased, and all new uses of my_func will refer to your new definition.

See for yourself

The code for this example can be found there. Browse the qsoas-goodies github repository for more goodies !

About QSoas

QSoas is a powerful open source data analysis program that focuses on flexibility and powerful fitting capacities. It is released under the GNU General Public License. It is described in Fourmond, Anal. Chem., 2016, 88 (10), pp 5050–5052. Current version is 2.1. You can download its source code or buy precompiled versions for MacOS and Windows there.

Extract many attachement from many mails in one go using ripmime

I was recently looking for a way to extract many attachments from a series of emails. I first had a look at the AttachmentExtractor thunderbird plugin, but it seems very old and not maintained anymore. So I've come up with another very simple solution that also works with any other mail client.

Just copy all the mails you want to extract attachments from to a single (temporary) mail folder, find out which file holds the mail folder and use ripmime on that file (ripmime is packaged for Debian). For my case, it looked like:

~ ripmime -i .icedove/XXXXXXX.default/Mail/pop.xxxx/tmp -d target-directory

Simple solution, but it saved me quite some time. Hope it helps !

Screen that hurts my eyes, take 2

Six month ago, I wrote a lengthy post about my new computer hurting my eyes. I haven't made any progress with that, but I've accidentally upgraded my work computer from Kernel 4.4 to 4.8 and the nvidia drivers from 340.96-4 to 375.66-2. Well, my work computer now hurts, I've switched back to the previous kernel and drivers, I hope it'll be back to normal.

Any ideas of something specific that changed, either between 4.4 and 4.8 (kernel startup code, default framebuffer modes, etc ?), or between the 340.96 and the 375.66 drivers ? In any case, I'll try that specific combination of kernels/drivers home to see if I can get it to a useable state.

Update, July 23rd

I reverted to the earlier drivers/kernel, to no avail. But it seems in fact the problem with my work computer is linked to an allergy of some kind, since antihistamine drugs have an effect (there are construction works in my lab, perhaps they are the cause ?). No idea still for my home computer, for which the problem is definitely not solved.

Run QSoas complely non-interactively

QSoas can run scripts, and, since version 2.0, it can be run completely without user interaction from the command-line (though an interface may be briefly displayed). This possibility relies on the following command-line options:

• --run, which runs the command given on the command-line;
• --exit-after-running, which closes automatically QSoas after all the commands specified by --run were run;
• --stdout (since version 2.1), which redirects QSoas's terminal directly to the shell output.

If you create a script.cmds file containing the following commands:

generate-buffer -10 10 sin(x)
save sin.dat

and run the following command from your favorite command-line interpreter:

~ QSoas --stdout --run '@ script.cmds' --exit-after-running

This will create a sin.dat file containing a sinusoid. However, if you run it twice, a Overwrite file 'sin.dat' ? dialog box will pop up. You can prevent that by adding the /overwrite=true option to save. As a general rule, you should avoid all commands that may ask questions in the scripts; a /overwrite=true option is also available for save-buffers for instance.

I use this possibility massively because I don't like to store processed files, I prefer to store the original data files and run a script to generate the processed data when I want to plot or to further process them. It can also be used to generate fitted data from saved parameters files. I use this to run automatic tests on Linux, Windows and Mac for every single build, in order to quickly spot platform-specific regressions.

To help you make use of this possibility, here is a shell function (Linux/Mac users only, add to your $HOME/.bashrc file or equivalent, and restart a terminal) to run directly on QSoas command files:

qs-run () {
        QSoas --stdout --run "@ $1" --exit-after-running
}

To run the script.cmds script above, just run

~ qs-run script.cmds

About QSoas

QSoas is a powerful open source data analysis program that focuses on flexibility and powerful fitting capacities. It is described in Fourmond, Anal. Chem., 2016, 88 (10), pp 5050–5052. Current version is 2.1

make-theme-image: a script to make yourself an idea of a icon theme

I created some time ago a utils repository on github to publish miscellaneous scripts, but it's only recently that I have started to really populate it. One of my recent work is make-theme-image script, that downloads an icon them package, grabs relevant, user-specifiable, icons, and arrange them in a neat montage. The images displayed are the results of running

~ make-theme-image gnome-icon-theme moblin-icon-theme

This is quite useful to get a good idea of the icons available in a package. You can select the icons you want to display using the -w option. The following command should provide you with a decent overview of the icon themes present in Debian:

apt search -- -icon-theme | grep / | cut -d/ -f1 | xargs make-theme-image

I hope you find it useful ! In any case, it's on github, so feel free to patch and share.

Variations around ls -lrt

I have been using almost compulsively ls -lrt for a long time now. As per the ls man page, this command lists the files of the current directory, with the latest files at the end, so that they are the ones that show up just above your next command-line. This is very convenient to work with, hmmm, not-so-well-organized directories, because it just shows what you're working on, and you can safely ignore the rest. Typical example is a big Downloads directory, for instance, but I use it everywhere. I quickly used alias lrt="ls -lrt" to make it easier, but... I though I might have as well a reliable way to directly use what I saw. So I came up with the following shell function (zsh, but probably works with most Bourne-like shells):

lrt() {
    ls -lrt "$@"
    lrt="$(ls -rt "$@" | tail -n1)"
}

This small function runs ls -lrt as usual, but also sets the $lrt shell variable to the latest file, so you can use it in your next commands ! Especially useful for complex file names. Demonstration:

22:05 vincent@ashitaka ~/Downloads lrt
[...]
-rw-r--r-- 1 vincent vincent   1490027 Apr  2 15:44 k.zip
-rw-r--r-- 1 vincent vincent    668566 Apr  3 22:05 1-s2.0-S0013468617305947-main.pdf
22:06 vincent@ashitaka ~/Downloads cp -v $lrt ~/nice-paper.pdf
'1-s2.0-S0013468617305947-main.pdf' -> '/home/vincent/nice-paper.pdf'

This saves typing the name of the 1-s2.0-S0013468617305947-main.pdf: in this case, automatic completion doesn't help much, since many files in my Downloads directory start with the same orefix... I hope this helps !

Extended dataset generation possibilities of QSoas

While the main focus of QSoas is the processing of experimental data, it also features commands to generate (calculate) datasets. The command generate-buffer creates a dataset of equally spaced points (you can change their number using the option /samples) between to limiting values, as below:

QSoas> generate-buffer -2 2

By default, the $y$ values are taken equal to $x$. However, generate-buffer also takes an optional formula to directly set the $y$ values:

QSoas> generate-buffer -10 10 sin(x)

From version 2.0, it is possible to generate several datasets in a row using the /number option, and to color them using the /style option (but only since version 2.1). Each dataset is generated according to the formula, and number is a special number that starts at 0 and increases by 1 for each dataset. Here's what I used to generate the picture on the right:

QSoas> generate-buffer -2 2 sin(PI*x)**(number+1) /number=30 /style=red-to-blue

About QSoas

QSoas is an open source data analysis program that focuses on flexibility and powerful fitting capacities. It is described in Fourmond, Anal. Chem., 2016, 88 (10), pp 5050–5052.

Version 2.1 of QSoas is out

I have just released QSoas version 2.1. It brings in a new solve command to solve arbitrary non-linear equations of one unknown. I took advantage of this command in the figure to solve the equation $\exp(x\,y)-x = 0$ for $y$. It also provides a new way to reparametrize fits using the reparametrize-fit command, a new series of fits to model the behaviour of an adsorbed 1- or 2-electrons catalyst on an electrode (these fits are discussed in great details in our recent review (DOI: 10.1016/j.coelec.2016.11.002), improvements in various commands, the possibility to now compile using Ruby 2.3 and the most recent version of the GSL library, and sketches for an emacs major mode, which you can activate (for QSoas script files, ending in .cmds) using the following snippet in $HOME/.emacs:

(autoload 'qsoas-mode "$HOME/Prog/QSoas/misc/qsoas-mode.el" nil t)
(add-to-list 'auto-mode-alist '("\\.cmds$" . qsoas-mode))

Of course, you'll have to adapt the path $HOME/Prog/QSoas/misc/qsoas-mode.el to the actual location of qsoas-mode.el.

As before, you can download the source code from our website, and purchase the pre-built binaries following the links from that page too. Enjoy !

RFH: screen that hurts my eyes

Short summary:

My eyes hurt when I use my home desktop computer - but only with this computer. This has been very long and frustrating for me, so if you think you can help, read the whole story just below, or skip to what I've tried and what I suspect might be the problem, and post comments below, or send me a mail (my adress should be quite obvious in this page).

Whole story:

Two years ago, I bought myself a new fancy motherboard (a Asus B85M-G C2) with a new fancy Intel-based processor with built-in graphics (an Intel Core i7-4770) and memory to go with it. I installed it in the place of my old AMD-based motherboard, keeping everything else (my hoard of hard drives and such) excepted the graphics card, which was not needed anymore. I immediately noticed my eyes were aching when using the computer. I was quite surprised since I had been using the screen very heavily for almost 10 years before that, without any problems. I attributed that to Intel Graphics, so I tried putting back the old graphics card, but it did not help. The situation was very frustrating, since working on the computer for an hour or so was making my eyes hurt for several days. This problem was specific to this computer, I could keep on using my computer at work and my laptop without problems.

I could use the computer using SSH from my laptop, so I could profit from the faster processor, but, hey, that wasn't how it was meant to happen. I bought another screen, also tried with one from the work, without any change. I tried using two screens at the same time (this is what I have at work), also without success, so I just kept not using the computer directly. I moved recently to a new place and tried to get that working back again, but didn't get any luck. Frustrated, I got another desktop computer and another screen, and I still have the same problem ! I also tried remounting the old motherboard with the AMD processor and the old graphics card, but that didn't bring any improvement. I just don't get it. This situation is rather frustrating for me, and it's been holding me back in my software projects for two years now (which partly explains my lack of involvement in Debian over the past few years). This post is here in the hope someone will have a idea, but also for me to keep track of what I've done and what I should.

What is puzzling me is that the computer I had before was perfectly fine, and that I have a very very similar setup at work (also with a NVIDIA graphics card) that doesn't hurt my eyes at all.

What I've tried:

Here is what I tried, you need to keep in mind that when a trial fails, my eyes keep on hurting for several days, and might trigger false positives.

• putting back the old (NVIDIA) graphics card, buying a new one (NVIDIA as well);
• putting back the old motherboard (but with a new OS, but maybe my eyes were too sore for a clean test);
• using another screen (a new one from the same brand, Samsung), a Dell and a HP from my work, and a brand new Phillips;
• using two screens at the same time;
• using a completely different (new, based on Xeon processors and a NVIDIA graphics card) computer (with new mouse, keyboard, hard drives and so on);
• changing house, including changing the lighting conditions, the desk, the internet provider (no, I didn't do that just because of my computer problems !);
• changing the way I drive the screens between VGA, DVI and HDMI;
• copying the system I have in my workplace to the new computer and booting from that system (after a few adaptations, though).

As you can guess, none of those brought any improvement.

Wild hypotheses:

• Is that a software thing ? Is there something wrong for me in the versions of Debian dating from August 2014 and after ?
• Is that a BIOS problem with recent computers ?
• Is that linked to some waves (bluetooth shoudln't be on, but maybe I didn't check well enough ?)
• Is that linked to EFI (but I also have the problems when I use legacy BIOS for booting)
• Something weird in my home ?
• Anything else ?

Any help will be greatly appreciated, but please don't advise going to see a doctor, I don't see how this could be a medical condition specific to my home desktop computer, unless this is a very specific psychosomatic problem.