Re: r8138 - /1.3/generic_fns/spectrum.py -- December 05, 2008

Hi Ed,

What about making the code recognize automatically which columns are what ?

We could, for example, have the code determine the number of fields and
then search the header for strings as 'res_num' or 'res_name', etc, and
when all searched fields recognized, assume that the remaining fields
are intensities to extract... The absent fields could be given a default
value such as 'None'. For this, we would need to have the header sent to
the intensity_generic() function (from the autodetect_format() function).

I think this would be great because it could allow users not to input
column numbers and have their files automatically parsed, in whatever
fields the data is...

What do you think of this approach ? Do you see any problem with it ?

Let me know what you think.

Regards,


Séb  :)



Edward d'Auvergne wrote:

Sorry, this task of the generic formatted file is far more complicated
than I thought.  It's structure should be modelled after the
generic_fns.value.read() function, as this takes a similarly formatted
file.  Flexibility here is key - any int arguments for the
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col
should be acceptable.  I.e. you can put this information at the end of
the file if you are crazy enough.  But most of the code in
generic_fns.value.read() can be used.  It just needs to be shifted
into functions of generic_fns.spectrum such as
number_of_header_lines() and intensity_generic().

In the future I might write some functions in generic_fns.mol_res_spin
to parse any spin specific but generically formatted file.  But for
now, the generic_fns.value.read() function needs to be mimicked.  This
is an insanely complex task, considering the additional flexibility I
talked about in
https://mail.gna.org/public/relax-devel/2008-12/msg00016.html
especially the automatic reading with the spin specific columns being
allowed to be anywhere.  So if you think this is too much, I can take
over at any point.

Regards,

Edward



On Thu, Dec 4, 2008 at 7:30 PM,  <sebastien.morin.1@xxxxxxxxx> wrote:

Author: semor
Date: Thu Dec  4 19:30:11 2008
New Revision: 8138

URL: http://svn.gna.org/viewcvs/relax?rev=8138&view=rev
Log:
Modified the autodetection code for the generic format.

This now recognizes the most generic format as in
'test_suite/shared_data/peak_lists/generic_intensity2.txt'.


Modified:
   1.3/generic_fns/spectrum.py

Modified: 1.3/generic_fns/spectrum.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=8138&r1=8137&r2=8138&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Thu Dec  4 19:30:11 2008
@@ -254,7 +254,7 @@
            break

    # Generic format.
-    if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', 
'spin_name']:
+    if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', 
'spin_name'] or line[0] in ['Num', 'Name']:
        return 'generic'

    # Sparky format.


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Re: r8138 - /1.3/generic_fns/spectrum.py

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