Tutorial- lesson 10 - Script file

Not a lot of user practice Visual Spec in console mode. This console allows you to enter command lines. It is now possible to link them into a text file and run this as a script to automatize some processings. Automatization of spectral processing shall be done with care. Make sure your results are consistent and less accurate than the manual, traditional, longer process

List of console command dir List the file in the current working directory cd nomrepertoire Change directory load nomfichier Load the file, do not put the directory, it is the current working directory by default save nomfichier Save the file with the nomfichier name in the current working directory affserie nomserie Select and display the serie with the name seriename formatx l1 l2 Force all the profile opened to be displayed between l1 and l2, l1 and l2 are on the x axis allformatx Force all series and all profiles opened to be displayed between l1 and l2 decoupe l1 l2 Crop the profile between the l1 and l2 values, x axis norma l1 l2 Normalize the current active serie by taking the average continuum between l1 and l2 comp 'operation' l1 l2 Compute the following operation between the values l1 and l2, x axis a:surface b:barycentre c:centre e:standard deviation f:fwmh i:intensity l:equivalent width m:average s:signal-to-noise ratio gaussfit l1 l2 Fit a gaussian to the profile section comprise between l1 and l2 serie_sel s1 Select the serie by its number s1 Serie number s1 are coded as followed: - Intensity: 3 - Ref1:4 - Ref2:5 - Normalise:6 - added temporary series, incremented as they are added, first add start at 8 div s1 Divide the current active serie by the serie of number s1 file_sel nomfenetre Make the profile in the window name nomfenetre the active profile document div_sel nomfenetre Divide the current serie of the current profile by the serie active of the profile in the window name nomfenetre cont_l Compute the continuum from point list stored previously in the Liste.txt file cont_z Compute the continuum by eliminating zone from the list stored previously in the Listezone.txt file smooth p1 Smooth by spline function the current active serie, the smooth coefficient is p1 replace s1 Replace the serie of serienumber s1 by the current active serie run nomprog.pgm p1 p2 p3 Run the script nomprog.pgm, can support 3 parameters

How to build / run a script -Test your command sequence first in the single command mode in the console -Open a text file, edit the command list, one command by line, up to 3 parameters $1, $2, $3 can be used -Save the text file with a .pgm extension - the file shall be stored in the vspec.exe directory -Run the script from the console by typing run nompgm (without .pgm) and the parameters if you have included them

A simple example In this example, the script will load the $1 file, perform a zone continuum correction followed by a spline smooth with $3 smooth coefficient, select the intensity serie and divided it by the serie "8" which is the added serie "continuum.fit". It then normalize the profile, move the current serie in the intensity serie, save the file under the $2 name and reload it to display the result load $1 conti_z smooth $3 serie_sel 3 div 8 norma 6590 6640 replace 3 save $2 load $2 The most important to know here is have previously stored the list of profile zone to eliminated before the continuum fit on a previous profile, this having being done the traditional way. The same way, the smooth coef $3 wold have been determined from another similar object processed manually. It may not be absolutly the same from one profile to another one... that's the limitation of automatisation. Here are the files to process by the script I picked the profile which exhibits the highest number of lines, to make sure all the zones where lines can be present are captured and eliminated. I choose the profile of alp cam. This profile is then processed "manually" - first, extract the continuum Then, eliminate the zone where there are lines When done, just run the continuum extraction, and get the smooth box displayed - pick and note the smooth coefficient you can stop here, or go up to the end, just to check that your process will be ok Display the console Enter the command to run the script with the name of the file to process as parameter 1, the name of file under you want to save the result as the second parameter and the smooth coefficient, which is 5 (the highest it is the smoother it will be). Run... and observe the sequence, at the end, the file with the resulting processed spectrum is saved and displayed. The list of commands executed are printed in green in the console. You can repeat the script entering new object names - you can just edit the names on the same line, then select only few characters of the line and hit enter - the command will be run again. You can also cut and paste to repeat the same script in a long text file with the different names of the object you want to process. And run just once... In all case, this is the reult of the automatisation of the continuum correction. Not too bad... Now, it is just "Imagination at Work (c)"