Author: bugman
Date: Wed Jul 19 07:06:51 2006
New Revision: 2510
URL: http://svn.gna.org/viewcvs/relax?rev=2510&view=rev
Log:
Added a test (AIC model selection between diffusion tensors) to the relax
test-suite.
This test triggers the problem reported by Chris MacRaild at
https://mail.gna.org/public/relax-devel/2006-04/msg00020.html. The test has
been added to aid in
the removal of bug #5746 located at
https://gna.org/bugs/?func=detailitem&item_id=5746.
Added:
1.2/test_suite/model_selection.py
Modified:
1.2/test_suite/test_suite.py
Added: 1.2/test_suite/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/model_selection.py?rev=2510&view=auto
==============================================================================
--- 1.2/test_suite/model_selection.py (added)
+++ 1.2/test_suite/model_selection.py Wed Jul 19 07:06:51 2006
@@ -1,0 +1,86 @@
+###############################################################################
+#
#
+# Copyright (C) 2006 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+import sys
+
+
+class Modsel:
+ def __init__(self, relax, test_name):
+ """Class for testing model selection."""
+
+ self.relax = relax
+
+ # Diffusion tensor selection.
+ if test_name == 'diff tensor':
+ # The name of the test.
+ self.name = "AIC model selection between two diffusion tensors"
+
+ # The test.
+ self.test = self.diff
+
+
+ def diff(self, run):
+ """The test of selecting between diffusion tensors using AIC."""
+
+ # Create the three runs.
+ self.relax.generic.runs.create('sphere', 'mf')
+ self.relax.generic.runs.create('spheroid', 'mf')
+ self.relax.generic.runs.create('aic', 'mf')
+
+ # Path of the files.
+ path = sys.path[-1] +
'/test_suite/data/model_free/S2_0.970_te_2048_Rex_0.149'
+
+ # Read the sequence.
+ self.relax.interpreter._Sequence.read('sphere', file='r1.600.out',
dir=path)
+ self.relax.interpreter._Sequence.read('spheroid', file='r1.600.out',
dir=path)
+
+ # Select the model.
+ self.relax.interpreter._Model_free.select_model('sphere', model='m4')
+ self.relax.interpreter._Model_free.select_model('spheroid',
model='m4')
+
+ # Read the relaxation data.
+ self.relax.interpreter._Relax_data.read('sphere', 'R1', '600', 600.0
* 1e6, 'r1.600.out', dir=path)
+ self.relax.interpreter._Relax_data.read('sphere', 'R2', '600', 600.0
* 1e6, 'r2.600.out', dir=path)
+ self.relax.interpreter._Relax_data.read('sphere', 'NOE', '600',
600.0 * 1e6, 'noe.600.out', dir=path)
+ self.relax.interpreter._Relax_data.read('sphere', 'R1', '500', 500.0
* 1e6, 'r1.500.out', dir=path)
+ self.relax.interpreter._Relax_data.read('sphere', 'R2', '500', 500.0
* 1e6, 'r2.500.out', dir=path)
+ self.relax.interpreter._Relax_data.read('sphere', 'NOE', '500',
500.0 * 1e6, 'noe.500.out', dir=path)
+ self.relax.interpreter._Relax_data.copy('sphere', 'spheroid')
+
+ # Set the diffusion tensors.
+ self.relax.interpreter._Diffusion_tensor.init('sphere', 1e-9,
fixed=0)
+ self.relax.interpreter._Diffusion_tensor.init('spheroid', (1e-9, 0,
0, 0), fixed=0)
+
+ # Set some global stats.
+ self.relax.data.chi2['sphere'] = 200
+ self.relax.data.chi2['spheroid'] = 0
+
+ # Model selection.
+ self.relax.interpreter._Modsel.model_selection(method='AIC',
modsel_run='aic')
+
+ # Test if the spheroid has been selected.
+ if not self.relax.data.diff.has_key('aic') or not
self.relax.data.diff['aic'].type == 'spheroid':
+ print "\nThe spheroid diffusion tensor has not been selected."
+ return
+
+ # Success.
+ return 1
Modified: 1.2/test_suite/test_suite.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/test_suite.py?rev=2510&r1=2509&r2=2510&view=diff
==============================================================================
--- 1.2/test_suite/test_suite.py (original)
+++ 1.2/test_suite/test_suite.py Wed Jul 19 07:06:51 2006
@@ -30,6 +30,7 @@
from generic import Generic
from jw_mapping import Jw
from model_free import Mf
+from model_selection import Modsel
from relax_fit import Relax_fit
from run_create import Run_create
from sequence import Sequence
@@ -165,6 +166,22 @@
self.exec_tests(self.jw_test_array)
+ # Model selection tests.
+ ########################
+
+ # Heading.
+ self.heading("The model selection tests")
+
+ # Initialise the array containing each test element.
+ self.modsel_test_array = []
+
+ # The tests.
+ self.modsel_test_array.append(Modsel(self.relax, 'diff tensor'))
+
+ # Execute the tests.
+ self.exec_tests(self.modsel_test_array)
+
+
# Generic tests.
################
@@ -322,6 +339,17 @@
self.summary_line(test)
+ # Model selection tests.
+ ########################
+
+ # Heading.
+ sys.stdout.write("\nThe model selection tests:\n")
+
+ # Loop over the tests.
+ for test in self.modsel_test_array:
+ self.summary_line(test)
+
+
# Generic tests.
################
r2510 - in /1.2/test_suite: model_selection.py test_suite.py