Author: bugman
Date: Tue Apr 16 10:56:57 2013
New Revision: 19484
URL: http://svn.gna.org/viewcvs/relax?rev=19484&view=rev
Log:
Merged revisions 19474,19483 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19474 | bugman | 2013-04-13 18:25:14 +0200 (Sat, 13 Apr 2013) | 5 lines
Added a warning for the spectrum.read user function if a peak intensity of
zero is encountered.
This value can cause singular matrix failures in certain optimisation.
........
r19483 | bugman | 2013-04-16 10:51:48 +0200 (Tue, 16 Apr 2013) | 6 lines
The spectrum.error_analysis user function can now be performed on a subset
of all spectra.
The subset argument has been added to allow the error analysis to be
restricted to a subset of all
loaded spectral data.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/spectrum.py
branches/relax_disp/user_functions/spectrum.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Apr 16 10:56:57 2013
@@ -1,1 +1,1 @@
-/trunk:1-19463
+/trunk:1-19483
Modified: branches/relax_disp/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/spectrum.py?rev=19484&r1=19483&r2=19484&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/spectrum.py (original)
+++ branches/relax_disp/pipe_control/spectrum.py Tue Apr 16 10:56:57 2013
@@ -60,9 +60,11 @@
spin.intensity_err = spin.baseplane_rmsd
-def __errors_repl(verbosity=0):
+def __errors_repl(subset=None, verbosity=0):
"""Calculate the errors for peak intensities from replicated spectra.
+ @keyword subset: The list of spectrum ID strings to restrict the
analysis to.
+ @type subset: list of str
@keyword verbosity: The amount of information to print. The higher the
value, the greater the verbosity.
@type verbosity: int
"""
@@ -82,8 +84,14 @@
cdp.sigma_I = {}
cdp.var_I = {}
+ # The subset.
+ subset_flag = False
+ if not subset:
+ subset_flag = True
+ subset = cdp.spectrum_ids
+
# Loop over the spectra.
- for id in cdp.spectrum_ids:
+ for id in subset:
# Skip non-replicated spectra.
if not repl[id]:
continue
@@ -172,7 +180,10 @@
# Average across all spectra if there are time points with a single
spectrum.
if not all_repl:
# Print out.
- print("\nVariance averaging over all spectra.")
+ if subset_flag:
+ print("\nVariance averaging over the spectra subset.")
+ else:
+ print("\nVariance averaging over all spectra.")
# Initialise.
var_I = 0.0
@@ -192,7 +203,7 @@
var_I = var_I / float(num_dups)
# Assign the average value to all time points.
- for id in cdp.spectrum_ids:
+ for id in subset:
cdp.var_I[id] = var_I
# Print out.
@@ -213,7 +224,7 @@
spin.intensity_err = cdp.sigma_I
-def __errors_volume_no_repl():
+def __errors_volume_no_repl(subset=None):
"""Calculate the errors for peak volumes when no spectra are
replicated."""
# Loop over the spins and set the error to the RMSD of the base plane
noise.
@@ -365,8 +376,12 @@
del spin.intensities[spectrum_id]
-def error_analysis():
- """Determine the peak intensity standard deviation."""
+def error_analysis(subset=None):
+ """Determine the peak intensity standard deviation.
+
+ @keyword subset: The list of spectrum ID strings to restrict the
analysis to.
+ @type subset: list of str
+ """
# Test if the current pipe exists
pipes.test()
@@ -378,6 +393,12 @@
# Test if spectra have been loaded.
if not hasattr(cdp, 'spectrum_ids'):
raise RelaxError("Error analysis is not possible, no spectra have
been loaded.")
+
+ # Check the IDs.
+ if subset:
+ for id in subset:
+ if id not in cdp.spectrum_ids:
+ raise RelaxError("The spectrum ID '%s' has not been loaded
into relax." % id)
# Peak height category.
if cdp.int_method == 'height':
@@ -390,12 +411,14 @@
print("Replicated spectra: Yes.")
# Set the errors.
- __errors_repl()
+ __errors_repl(subset=subset)
# No replicated spectra.
else:
# Print out.
print("Replicated spectra: No.")
+ if subset:
+ print("Spectra ID subset ignored.")
# Set the errors.
__errors_height_no_repl()
@@ -411,7 +434,7 @@
print("Replicated spectra: Yes.")
# Set the errors.
- __errors_repl()
+ __errors_repl(subset=subset)
# No replicated spectra.
else:
@@ -648,6 +671,10 @@
# Extract the data.
H_name, X_name, spin_id, intensity, line = intensity_data[i]
+ # Sanity check.
+ if intensity == 0.0:
+ warn(RelaxWarning("A peak intensity of zero has been encountered
for the spin '%s' - this could be fatal later on." % spin_id))
+
# Skip data.
if (X_name and X_name != heteronuc) or (H_name and H_name != proton):
warn(RelaxWarning("Proton and heteronucleus names do not match,
skipping the data %s." % line))
Modified: branches/relax_disp/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/spectrum.py?rev=19484&r1=19483&r2=19484&view=diff
==============================================================================
--- branches/relax_disp/user_functions/spectrum.py (original)
+++ branches/relax_disp/user_functions/spectrum.py Tue Apr 16 10:56:57 2013
@@ -113,9 +113,19 @@
uf = uf_info.add_uf('spectrum.error_analysis')
uf.title = "Perform an error analysis for peak intensities."
uf.title_short = "Peak intensity error analysis."
+uf.add_keyarg(
+ name = "subset",
+ py_type = "str_list",
+ desc_short = "subset spectrum IDs",
+ desc = "The list of spectrum ID strings to restrict the error analysis
to.",
+ wiz_combo_iter = spectrum.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
+)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This user function must only be called after all
peak intensities have been loaded and all other necessary spectral
information set. This includes the baseplane RMSD and the number of points
used in volume integration, both of which are only used if spectra have not
been replicated.")
+uf.desc[-1].add_paragraph("The error analysis can be restricted to a subset
of the loaded spectral data. This is useful, for example, if half the
spectra have been collected on one spectrometer and the other half on a
different spectrometer.")
uf.desc[-1].add_paragraph("Six different types of error analysis are
supported depending on whether peak heights or volumes are supplied, whether
noise is determined from replicated spectra or the RMSD of the baseplane
noise, and whether all spectra or only a subset have been duplicated. These
are:")
table = uf_tables.add_table(label="table: peak intensity error analysis",
caption="The six peak intensity error analysis types.")
table.add_headings(["Int type", "Noise source", "Error scope"])
@@ -156,7 +166,7 @@
uf.backend = spectrum.error_analysis
uf.menu_text = "&error_analysis"
uf.gui_icon = "oxygen.categories.applications-education"
-uf.wizard_height_desc = 550
+uf.wizard_height_desc = 530
uf.wizard_size = (1000, 700)
uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
uf.wizard_apply_button = False
r19484 - in /branches/relax_disp: ./ pipe_control/spectrum.py user_functions/spectrum.py