Warning !

Soas is no longer maintained. You are strongly encouraged to switch to its successor, QSoas

Step by step tutorial: analysis of a non catalytic CV

This section shows a typical/minimal analysis of a non-catalytic voltammogram, with links to the later sections in the manual for more details.

We analyze the file 3.OCW. Let's first move to the directory containing the file.

/home/lc/ 137 > cd dummy/
/home/lc/dummy/ 138 >

List the files to check you're in the right directory.

/home/lc/dummy/ 138 > ls
3.OCW

Start soas:

/home/lc/dummy/ 139 > soas -ffGPES

A black graphic windows appears and your terminal goes:

SOAS (version x.x.x -- Revision: xx). Sorry for the name, that's Kerensa's idea.
For Help, type h or see file: http://bip.cnrs-mrs.fr/bip06/
INFO : reading command line options...
INFO : editor set to pico.
INFO : file format set to GPES.
Working directory is /home/lc. Type G to change it.

 Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B),
 peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).
Soas>

You get a small menu with the short list of the most useful commands. You first want to load a file; type l. [load command] The data files should then be listed.

Soas> l
Cannot access *.[dD][aA][tT]: No such file or directory
3.OCW
Data filename ([return to abort]) :

Note that the default choice is written between square braquets. When SOAS asks something and offers alternative choices (e.g. 'Do you wish to quit ([y]/n) ?'), the default choice is written between square brackets and can be selected just by hitting the return key.

Type the name of the file you want to load `3.OCW' (case sensitive):

Data filename ([return to abort]) : 3.OCW

and return, you get back the menu,

Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

and the voltammogram is plotted on the graphic window.



The name of the buffer (data set) is written (in yellow) in the graphic window.

Let's say you want to analyze the oxidative part of the scan, you have to `cut' the data first, type c and return, you get:

Soas> c   
use left/right buttons or b/e for limits
use mid button or q to Quit deleting outer range
type u qUit deleting inner range

and the current is now plotted against `time' in the graphic window. The vertical white lines mark the limits of the part of the data you want to keep. Change them using the mouse: click with the left button at X=50, and with the right button at X=600. You need to keep a significant part of the data where the faradaic current is zero, (so don't cut too close to the peak). [cut command]



Type q or use the middle button of the mouse to quit. The new data set is now plotted, and you get back the menu.



Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

Let's remove the noise using a Fourier filter. Type f

Soas> f
use left/right buttons or d/i to decrease/increase filter size,
use 1/2 to decrease/increase quickly filter size,
use r to turn off/on the display of the raw data,
use p to toggle the display of the power spectrum,
...  then left button to select frequency (low-pass),
...  or b to bandpass,
use c to switch between Gaussian and heavyside cutoff filters,
mid button or q to quit.

The upper window shows the raw data in yellow, and the smoothed data overlaid in blue. The difference (residuals) are plotted in the lower box. [filter commands]



To change the size of the filter, the easiest way is to display the power spectrum (PS) of the data = magnitude of the signal as a function of frequency. Type p, the lower box changes. The PS of the raw data now is plotted in yellow, that of the smoothed data overlaid in blue.



Smoothing means cutting off the high frequencies (i.e. the noise). You want to keep only the left part of the PS (the low, relevant frequencies).

Click at X = 2 10**(-2) on the lower box. This increases the filter size to 50 (in units of `time interval between points' i.e. inverse of frequency). This new value is written on top of the main box.

Type p again to get back the residuals in the lower box: you want to make sure that the residuals are evenly distributed around Y=0, i.e. that you're not over-filtering.

Type q to quit. You get the smoothed data full screen, and the small menu in the text window.



Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

You now want to compute a non-catalytic baseline. Type b.

Soas> b
s,x,o to switch between Smooth/eXact/Off_data
left   button or a to Add a marker
right  button or r to Remove the nearest marker
middle button or q to Quit and subtract baseline
m to get More commands.

and you get the cursor in the main window. Click (left button) several times to set at least three markers on the data. They should be on either side of the peak, where you think there is no faradaic current (i.e. not too close from the peak). [baseline command]

Once more than three markers are set, the interpolated base line is plotted in blue, and the lower box shows the baseline subtracted data.



Add (left button) / remove (right button) markers until you're happy with the baseline. Then quit (type q) to get the baseline subtracted data full screen.



INFO : area is now     0.4256E-09

Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

You might want to save the baseline subtracted data . Type s [save command]

Soas> s
Cannot access *.[dD][aA][tT]: No such file or directory
Filename ([3.DAT],q to abort) :

Type the name: e.g.

Filename ([3.DAT],q to abort) : 3.oxscan.dat
INFO : data saved in 3.oxscan.dat

Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

Now let's find the position of the (single) peak. Type 1:

Soas> 1
position   0.8679E-01 current   0.4076E-08 width   0.1036     area   0.4677E-09
INFO : saved in out.dat

Load (l) Save (s) Cut (c) Filter (f) Base line non-cat/cat data (b/B), 
peak search (1) Undo (u) Redo (r) Help (h) Quit (q), More commands (m).

Soas>

The peak is marked with white lines (position and width). [1-peak search command]



The file `out.dat' is created, it contains more information than that written on the screen: position, height, width, left-width, right-width, area, left-area, right-area, filename.

Now you want to repeat everything with the reductive part of the scan. Type u (undo) 4 times, until you get back the raw voltammogram, or load it again typing l and giving its name.

Use c to cut the reductive part of the scan, f to remove the noise, b to remove the baseline, s to save the baseline subtracted data, 1 to measure the position of the peak and append out.dat, load a new file...

...

This is the minimum you'll need. Go through the help file to see which are the different commands you might like to use. Waste a bit of time trying everything, and get back to me in case of trouble.

Warning !

Soas is no longer maintained. You are strongly encouraged to switch to its successor, QSoas
Christophe Leger 2009-02-24