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7 July 2021

Vincent Fourmond: Upcoming features of QSoas and github repository

For the past years, most of the development has happened behind the scene in a private repository, and the code has appeared in the public repository only a couple of months before the release, in the release branch. I have now decided to publish the current code of QSoas in the github repository (in the public branch). This way, you can follow and use all the good things that were developed since the last release, and also verify whether any bug you have is still present in the currently developed version !

Upcoming features
This is the occasion to write a bit about the some of the features that have been added since the publication of the 3.0 release. Not all of them are polished nor documented yet, but here are a few teasers. The current version in github has: Check out the github repository if you want to know more about the new features !

As of now, no official date is planned for the 3.1 release, but this could happen during fall.

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 3.0. You can download its source code there (or clone from the GitHub repository) and compile it yourself, or buy precompiled versions for MacOS and Windows there.

11 March 2021

Vincent Fourmond: All tips and tricks about QSoas

I've decided to post regular summaries of all the articles written here about QSoas; this is the first post of this kind. All the articles related to QSoas can be found here also. The articles written here can be separated into several categories. Tutorials to analyze real data These are posts about how to reproduce the data analysis of published articles, including links to the original data so you can fully reproduce our results. These posts all have the label tutorial. All about fits QSoas has a particularly powerful interface for non-linear least square minimisations (fits): Meta-data Meta data describe the conditions in which experiments were performed. Quiz and their solutions Quiz are small problems that take some skill to solve; they can teach you a lot about how to work with QSoas. Other tips and tricks Release annoucements These have generally lot of general information about the possibilities in QSoas:
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 3.0. You can download its source code there (or clone from the GitHub repository) and compile it yourself, or buy precompiled versions for MacOS and Windows there.

16 February 2021

Vincent Fourmond: QSoas tips and tricks: permanently storing meta-data

It is one thing to acquire and process data, but the data themselves are most often useless without the context, the conditions in which the experiments were made. These additional informations can be called meta-data. In a previous post, we have already described how one can set meta-data to data that are already loaded, and how one can make use of them. QSoas is already able to figure out some meta-data in the case of electrochemical data, most notably in the case of files acquired by GPES, ECLab or CHI potentiostats. However, only a small number of constructors are supported as of now[1], and there are a number of experimental details that the software is never going to be able to figure out for you, such as the pH, the sample, what you were doing... The new version of QSoas provides a means to permanently store meta-data for experimental data files:
QSoas> record-meta pH 7 file.dat
This command uses record-meta to permanently store the information pH = 7 for the file file.dat. Any time QSoas loads the file again, either today or in one year, the meta-data will contain the value 7 for the field pH. Behind the scenes, QSoas creates a single small file, file.dat.qsm, in which the meta-data are stored (in the form of a JSON dictionnary). You can set the same meta-data to many files in one go, using wildcards (see load for more information). For instance, to set the pH=7 meta-data to all the .dat files in the current directory, you can use:
QSoas> record-meta pH 7 *.dat
You can only set one meta-data for each call to record-meta, but you can use it as many times as you like. Finally, you can use the /for-which option to load or browse to select only the files which have the meta you need:
QSoas> browse /for-which=$meta.pH<=7
This command browses the files in the current directory, showing only the ones that have a pH meta-data which is 7 or below.

[1] I'm always ready to implement the parsing of other file formats that could be useful for you. If you need parsing of special files, please contact me, sending the given files and the meta-data you'd expect to find in those. 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 3.0. You can download its source code there (or clone from the GitHub repository) and compile it yourself, or buy precompiled versions for MacOS and Windows there.

14 December 2020

Vincent Fourmond: Version 3.0 of QSoas is out

After almost two years of development, version 3.0 of QSoas is finally out ! It brings in a number of new features. An expert mode for fitting Undoubtedly the most important feature in the new version is a complete upgrade of the fit system, which now features an expert mode, turned on by using the /expert=true option with the fit commands. The expert mode features a command prompt that looks like the normal command prompt, in which it is possible: The latter feature is very important when running fits with many parameters. In that case, there are a number of local minima, and it is necessary to try a number of different starting parameters to really find the best parameters. The new parameter space exploration feature makes it much easier than before, with an interface that allows easily finding the best parameters tried so far and reuse them.
A new documentation system Another very important update is the inclusion of a new, offline, documentation system. The documentation features browsing via table of contents, a command index and text search. It also features the possibility to copy commands from the help to the command prompt, or even run them directly. To top it all, it comes with a series of startup tips that might teach you a thing or two about QSoas (try hitting Show random to learn new tricks !).
Many other features For the full list of changes, please see the changelog. Apart from the changes described above, these are my favorites:
To get the new version, you can just download the source code from the downloads page, where you can also purchase precompiled versions for Windows and MacOS. You can also clone the source from the GitHub repository. About QSoasQSoas 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 3.0. You can download its source code there (or clone from the GitHub repository) and compile it yourself, or buy precompiled versions for MacOS and Windows there.

17 August 2015

Iustin Pop: Nikkor 300mm f/4E tests and happy dogs!

I recently got a new lens, which I'm still trying to learn how to properly use . The new lens is the Nikon 300m f/4E PF ED VR (wow, that's a mouthful of acronyms ) and it's as good as I expected, except that it seems that it's too good for the person using it (me). Physically, the lens is indeed very light and very easy to hand-hold; it's barely heavier and longer than the 70-300mm f/4-5.6 zoom, although a bit more bulky. I was fearing something "bigger" and heavier for a fixed-aperture lens, even after hearing all the good reports about it, but it was better than I expected. I was also slightly concerned, this being a prime lens, about finding the subject fast, especially if smaller or far away. It turned out that if the lens is focused at somewhat the right distance (not at the opposite end), it is not a real problem. So, as the first test/learning exercise, I did a couple of hour long walks outdoor, photographing random subjects. First day I used the lens by itself, on the second day I added the Nikon TC-14E(III) tele-converter, for a 420mm focal length. All pictures below except the Huskies are non-cropped, just down-sampled (they have the original field of view); the Husky pictures were cropped. In all cases, camera was set to semi-manual mode, mostly at 1/1000s or 1/2000s, various apertures between f/4 and f/8; this means wide open or stopped down one (when with the tele-converter) or two stops. Semi-manual as auto-ISO was on. Lens focus limiter on, VR either active or sport (to help with the viewfinder image mostly, at this speed), camera set to AF-C and group mode most of the time. Also, all pictures were shot hand-held, with bad technique - until somebody stopped me, turns out he was a photographer, and showed me how to properly hold a telephoto lens; thanks, whoever you were! The "random subjects" parts worked only somewhat, as (at first) the subjects were not too interesting; air-plane flying high above - check, fast focus (although it is easy to focus on a plane in clear sky), or close, static subjects: Airplane in the sky Test of close focusing Birds flying around - almost check, fast focus (both with just the lens and with the TC), although I learned that shooting flying birds while panning needs 1/2000s - my initial attempt at 1/1000s was not enough to eliminate either panning blur or wing-tip blur (both depend on the speed of the respective action); in any case, initial focus acquisition is speedy enough for me. A couple of examples (first without, second with the TC; in the second one, I was unprepared when the I saw the bird from the corner of my eye, and managed to bring up the camera and take exactly one photo before the bird was gone): Not enough speed Too much blur Another attempt was to focus on dogs jumping in the water. Here the problem was different: focusing on the correct object! The splashing around meant that there were lots of water droplets both in front and behind the dog, the dog being partially obscured by them. I don't know what AF settings would have helped here (maybe 3D tracking pre-focused on the black dog)? I had a low success rate on the first attempt, so I'll have to try again. The lens did correctly track the wrong thing, though . Examples: Almost focused Wrong focus Once the dog caught its target, the lens focused well enough, of course, but not perfect; it might need some AF fine-tuning or photographer upgrade : Not quite perfect focus At one point, I was lucky to have a dog running towards me; focus tracking on a subject approaching the camera is a good test for the lens (and camera) auto-focus performance. I was pleasantly surprised, given my failure to track left-to-right flying birds (which should be easier!): Run! Not yet tired! In any case, I was walking and thinking on how to improve on my technique, when I saw in the distance a pair of dogs (Husky's, I believe) which were very active. This case was relatively easy for the camera and lens, since they were moving only left-to-right, instead of forward-backward, so the focus distance was mostly constant, and I just had to pan. Full gallery here, two examples: Jump! Play over, going home These two dogs had an education value beyond the "how is the lens performing"; they were so fast, active (they kept going at it non-stop for a good number of minutes) and playful that they made my day brighter . So, that concludes my first test of this lens and the 1.4 tele-converter. Conclusion: equipment good, need to upgrade the photographer!