r20579 - /branches/peak_intensities/user_functions/spectrum.py -- August 13, 2013 - 11:58

Author: bugman
Date: Tue Aug 13 11:58:38 2013
New Revision: 20579

URL: http://svn.gna.org/viewcvs/relax?rev=20579&view=rev
Log:
Modification of the spectrum.read_intensities user function front end.

The heteronuc and proton arguments have been eliminated.  Instead the new dim 
argument is used to
associate the data with the spins of any dimension in the peak list.


Modified:
    branches/peak_intensities/user_functions/spectrum.py

Modified: branches/peak_intensities/user_functions/spectrum.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/user_functions/spectrum.py?rev=20579&r1=20578&r2=20579&view=diff
==============================================================================
--- branches/peak_intensities/user_functions/spectrum.py (original)
+++ branches/peak_intensities/user_functions/spectrum.py Tue Aug 13 11:58:38 
2013
@@ -238,18 +238,12 @@
     desc = "The unique spectrum ID string or list of strings to associate 
with the peak intensity values.  If 'auto' is provided for a NMRPipe 
seriesTab formatted file, the IDs are auto generated in form of Z_A{i}."
 )
 uf.add_keyarg(
-    name = "heteronuc",
-    default = "N",
-    py_type = "str",
-    desc_short = "heteronucleus name",
-    desc = "The name of the heteronucleus as specified in the peak intensity 
file."
-)
-uf.add_keyarg(
-    name = "proton",
-    default = "HN",
-    py_type = "str",
-    desc_short = "proton name",
-    desc = "The name of the proton as specified in the peak intensity file."
+    name = "dim",
+    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."
 )
 uf.add_keyarg(
     name = "int_method",
@@ -328,7 +322,7 @@
     name = "spin_id",
     py_type = "str",
     desc_short = "spin ID string",
-    desc = "The spin ID string used by the generic intensity file format to 
restrict the loading of data to certain spin subsets.",
+    desc = "The spin ID string used to restrict the loading of data to 
certain spin subsets.",
     can_be_none = True
 )
 uf.add_keyarg(
@@ -342,7 +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 heteronucleus and proton should be set 
respectively to the name of the heteronucleus and proton in the file.  Only 
those lines which match these labels will be used.")
+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 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.
@@ -364,7 +358,7 @@
 uf.backend = spectrum.read
 uf.menu_text = "&read_intensities"
 uf.gui_icon = "oxygen.actions.document-open"
-uf.wizard_height_desc = 140
+uf.wizard_height_desc = 160
 uf.wizard_size = (1000, 750)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'