Author: bugman
Date: Mon Jul 2 12:21:06 2012
New Revision: 17118
URL: http://svn.gna.org/viewcvs/relax?rev=17118&view=rev
Log:
Merged revisions 17114-17116 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17114 | bugman | 2012-07-02 11:14:28 +0200 (Mon, 02 Jul 2012) | 5 lines
Created a system test to replicate Romel Bobby's bug #19887.
This is the bug report at https://gna.org/bugs/?19887.
........
r17115 | bugman | 2012-07-02 12:03:02 +0200 (Mon, 02 Jul 2012) | 11 lines
Partial fix for bug #19887 (https://gna.org/bugs/?19887).
The problem is that the number of peak height values was not the same for
all spins!
The error message was being caused by the math_fns.relax_fit C object
'setup' function being feed in
incorrect values, causing relax to fail directly after the setup() call in
specific_fns.relax_fit.minimise(). The number of points was being taken
from cdp.relax_times, but
in the Relax_fit.test_bug_19887_curvefit_fail system test, one of the 3
spins has 4 points rather
than 5. Now the correct number is sent into setup().
........
r17116 | bugman | 2012-07-02 12:17:23 +0200 (Mon, 02 Jul 2012) | 6 lines
A final fix for bug #19887 (https://gna.org/bugs/?19887).
Now a RelaxError is raised if the number of peak intensities is not the
same for all spins. This
occurs in the relaxation curve-fitting overfit_deselect() method.
........
Added:
branches/interatomic/test_suite/shared_data/peak_lists/bug_19887/
- copied from r17116, trunk/test_suite/shared_data/peak_lists/bug_19887/
branches/interatomic/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
- copied unchanged from r17116,
trunk/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
Modified:
branches/interatomic/ (props changed)
branches/interatomic/specific_fns/relax_fit.py
branches/interatomic/test_suite/system_tests/relax_fit.py
Propchange: branches/interatomic/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Jul 2 12:21:06 2012
@@ -1,1 +1,1 @@
-/trunk:1-17044
+/trunk:1-17117
Modified: branches/interatomic/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/relax_fit.py?rev=17118&r1=17117&r2=17118&view=diff
==============================================================================
--- branches/interatomic/specific_fns/relax_fit.py (original)
+++ branches/interatomic/specific_fns/relax_fit.py Mon Jul 2 12:21:06 2012
@@ -707,7 +707,7 @@
# The relaxation times.
times.append(cdp.relax_times[key])
- setup(num_params=len(spin.params),
num_times=len(cdp.relax_times), values=values, sd=errors, relax_times=times,
scaling_matrix=scaling_matrix.tolist())
+ setup(num_params=len(spin.params), num_times=len(values),
values=values, sd=errors, relax_times=times,
scaling_matrix=scaling_matrix.tolist())
# Setup the minimisation algorithm when constraints are present.
@@ -824,11 +824,17 @@
if not hasattr(spin, 'intensities'):
warn(RelaxDeselectWarning(spin_id, 'missing intensity data'))
spin.select = False
+ continue
# Require 3 or more data points.
elif len(spin.intensities) < 3:
warn(RelaxDeselectWarning(spin_id, 'insufficient data, 3 or
more data points are required'))
spin.select = False
+ continue
+
+ # Check that the number of relaxation times is complete.
+ if len(spin.intensities) != len(cdp.relax_times):
+ raise RelaxError("The %s peak intensity points of the spin
'%s' does not match the expected number of %s (the IDs %s do not match %s)."
% (len(spin.intensities), spin_id, len(cdp.relax_times),
spin.intensities.keys(), cdp.spectrum_ids))
def return_data(self, spin):
Modified: branches/interatomic/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/relax_fit.py?rev=17118&r1=17117&r2=17118&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/relax_fit.py (original)
+++ branches/interatomic/test_suite/system_tests/relax_fit.py Mon Jul 2
12:21:06 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2011 Edward d'Auvergne
#
+# Copyright (C) 2006-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -31,6 +31,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.mol_res_spin import spin_index_loop, spin_loop
from generic_fns import pipes
+from relax_errors import RelaxError
from status import Status; status = Status()
@@ -140,6 +141,18 @@
self.assertNotEqual(float(lines[index+1][2]), 0.0)
+ def test_bug_19887_curvefit_fail(self):
+ """Test for the failure of relaxation curve-fitting, replicating bug
#19887."""
+
+ # Execute the script.
+ try:
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'curve_fitting'+sep+'bug_19887_curvefit_fail.py')
+
+ # A RelaxError is expected (but assertRaises() does not work with
the script_exec method).
+ except RelaxError:
+ pass
+
+
def test_curve_fitting_height(self):
"""Test the relaxation curve fitting C modules."""
r17118 - in /branches/interatomic: ./ specific_fns/ test_suite/shared_data/peak_lists/bug_19887/ test_suite/system_tests/ te...