r20634 - /trunk/user_functions/spectrum.py -- August 20, 2013 - 16:41

Author: bugman
Date: Tue Aug 20 16:41:30 2013
New Revision: 20634

URL: http://svn.gna.org/viewcvs/relax?rev=20634&view=rev
Log:
Changes for the spectrum.read_intensities user function dim argument.

The default is now w1, the indirect dimension in a 2D experiment.  The 
description has also been
fixed.


Modified:
    trunk/user_functions/spectrum.py

Modified: trunk/user_functions/spectrum.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/spectrum.py?rev=20634&r1=20633&r2=20634&view=diff
==============================================================================
--- trunk/user_functions/spectrum.py (original)
+++ trunk/user_functions/spectrum.py Tue Aug 20 16:41:30 2013
@@ -239,11 +239,11 @@
 )
 uf.add_keyarg(
     name = "dim",
-    default = 2,
+    default = 1,
     py_type = "int",
     min = 1,
     desc_short = "spectral dimension to read",
-    desc = "Associate the data with the spins of any dimension in the peak 
list.  This defaults to w2, the heteronucleus in HSQC type experiments."
+    desc = "Associate the data with the spins of any dimension in the peak 
list.  This defaults to w1, the heteronucleus in HSQC type experiments."
 )
 uf.add_keyarg(
     name = "int_method",
@@ -336,7 +336,7 @@
 uf.desc.append(Desc_container())
 uf.desc[-1].add_paragraph("The peak intensity can either be from peak 
heights or peak volumes.")
 uf.desc[-1].add_paragraph("The spectrum ID is a label which is subsequently 
utilised by other user functions.  If this identifier matches that of a 
previously loaded set of intensities, then this indicates a replicated 
spectrum.")
-uf.desc[-1].add_paragraph("The spectral dimension is used to specify if the 
intensity data should be loaded into the spins identified by the first 
dimension, second dimension, etc.")
+uf.desc[-1].add_paragraph("The spectral dimension is used to specify if the 
intensity data should be loaded into the spins identified by the first 
dimension w1, second dimension w2, etc.")
 uf.desc[-1].add_paragraph("The integration method is required for the 
subsequent error analysis.  When peak heights are measured, this should be 
set to 'height'.  Volume integration methods are a bit varied and hence two 
values are accepted.  If the volume integration involves pure point 
summation, with no deconvolution algorithms or other methods affecting peak 
heights, then the value should be set to 'point sum'.  All other volume 
integration methods, e.g. line shape fitting, the value should be set to 
'other'.")
 uf.desc[-1].add_paragraph("If a series of intensities extracted from Bruker 
FID files processed in Topspin or XWinNMR are to be compared, the ncproc 
parameter may need to be supplied.  This is because this FID is stored using 
integer representation and is scaled using ncproc to avoid numerical 
truncation artifacts.  If two spectra have significantly different maximal 
intensities, then ncproc will be different for both.  The intensity scaling 
is binary, i.e. 2**ncproc. Therefore if spectrum A has an ncproc of 6 and and 
spectrum B a value of 7, then a reference intensity in B will be double that 
of A.  Internally, relax stores the intensities scaled by 2**ncproc.")
 # File formats.