Author: bugman
Date: Thu Jan 19 10:53:32 2012
New Revision: 15187
URL: http://svn.gna.org/viewcvs/relax?rev=15187&view=rev
Log:
The relaxation curve-fitting specific analysis now uses the new SPIN_PARAMS
list API object.
Modified:
branches/spec_api/auto_analyses/relax_fit.py
branches/spec_api/sample_scripts/relax_fit.py
branches/spec_api/specific_fns/relax_fit.py
branches/spec_api/test_suite/system_tests/scripts/1UBQ_relax_fit.py
branches/spec_api/test_suite/system_tests/scripts/bug_17276_peak_lists.py
branches/spec_api/test_suite/system_tests/scripts/relax_fit.py
Modified: branches/spec_api/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/auto_analyses/relax_fit.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/auto_analyses/relax_fit.py (original)
+++ branches/spec_api/auto_analyses/relax_fit.py Thu Jan 19 10:53:32 2012
@@ -131,8 +131,8 @@
self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr',
dir=self.grace_dir, force=True) # Minimised chi-squared value.
self.interpreter.grace.write(y_data_type='i0', file='i0.agr',
dir=self.grace_dir, force=True) # Initial peak intensity.
self.interpreter.grace.write(y_data_type='rx',
file=self.file_root+'.agr', dir=self.grace_dir, force=True) # Relaxation
rate.
- self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', file='intensities.agr', dir=self.grace_dir, force=True)
# Average peak intensities.
- self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', norm=True, file='intensities_norm.agr',
dir=self.grace_dir, force=True) # Average peak intensities (normalised).
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='intensities', file='intensities.agr', dir=self.grace_dir,
force=True) # Average peak intensities.
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='intensities', norm=True, file='intensities_norm.agr',
dir=self.grace_dir, force=True) # Average peak intensities (normalised).
# Display the Grace plots if selected.
if self.view_plots:
Modified: branches/spec_api/sample_scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/relax_fit.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/sample_scripts/relax_fit.py (original)
+++ branches/spec_api/sample_scripts/relax_fit.py Thu Jan 19 10:53:32 2012
@@ -104,8 +104,8 @@
grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
-grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.agr', force=True) # Average peak intensities.
-grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.agr', force=True) # Average peak intensities
(normalised).
+grace.write(x_data_type='relax_times', y_data_type='intensities',
file='intensities.agr', force=True) # Average peak intensities.
+grace.write(x_data_type='relax_times', y_data_type='intensities', norm=True,
file='intensities_norm.agr', force=True) # Average peak intensities
(normalised).
# Display the Grace plots.
grace.view(file='chi2.agr')
Modified: branches/spec_api/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/relax_fit.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/specific_fns/relax_fit.py (original)
+++ branches/spec_api/specific_fns/relax_fit.py Thu Jan 19 10:53:32 2012
@@ -55,6 +55,8 @@
self.base_data_loop = self._base_data_loop_spin
self.model_loop = self._model_loop_spin
self.return_conversion_factor = self._return_no_conversion_factor
+ self.return_data_name = self._return_data_name_spin
+ self.return_grace_string = self._return_grace_string_spin
self.return_value = self._return_value_general
self.set_error = self._set_error_spin
self.set_param_values = self._set_param_values_spin
@@ -62,6 +64,13 @@
self.sim_init_values = self._sim_init_values_spin
self.sim_return_param = self._sim_return_param_spin
self.sim_return_selected = self._sim_return_selected_spin
+
+ # Set up the spin parameters.
+ self.SPIN_PARAMS.add('rx', default=8.0, grace_string='\\qR\\sx\\Q')
+ self.SPIN_PARAMS.add('intensities', grace_string='\\qPeak
intensities\\Q')
+ self.SPIN_PARAMS.add('i0', default=10000.0,
grace_string='\\qI\\s0\\Q')
+ self.SPIN_PARAMS.add('iinf', default=0.0,
grace_string='\\qI\\sinf\\Q')
+ self.SPIN_PARAMS.add('relax_times', grace_string='\\qRelaxation time
period (s)\\Q')
def _assemble_param_vector(self, spin=None, sim_index=None):
@@ -647,27 +656,6 @@
"""]
- def default_value(self, param):
- """Return the default relaxation curve-fitting parameter values.
-
- @param param: The relaxation curve-fitting parameter.
- @type param: str
- @return: The default value.
- @rtype: float
- """
-
- # Relaxation rate.
- if param == 'rx':
- return 8.0
-
- # Initial intensity.
- if param == 'i0':
- return 10000.0
-
- # Intensity at infinity.
- if param == 'iinf':
- return 0.0
-
def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
"""The exponential curve fitting grid search method.
@@ -925,52 +913,23 @@
return_data_name_doc = ["Relaxation curve fitting data type string
matching patterns", """
-
__________________________________________________________________________________________
- | | |
|
- | Data type | Object name |
Patterns |
-
|___________________________________|______________________|_____________________________|
- | | |
|
- | Relaxation rate | 'rx' |
'^[Rr]x$' |
- | | |
|
- | Peak intensities (series) | 'intensities' |
'^[Ii]nt$' |
- | | |
|
- | Initial intensity | 'i0' |
'^[Ii]0$' |
- | | |
|
- | Intensity at infinity | 'iinf' |
'^[Ii]inf$' |
- | | |
|
- | Relaxation period times (series) | 'relax_times' |
'^[Rr]elax[ -_][Tt]imes$' |
-
|___________________________________|______________________|_____________________________|
+ ____________________________________________________________
+ | | |
+ | Data type | Object name |
+ |___________________________________|______________________|
+ | | |
+ | Relaxation rate | 'rx' |
+ | | |
+ | Peak intensities (series) | 'intensities' |
+ | | |
+ | Initial intensity | 'i0' |
+ | | |
+ | Intensity at infinity | 'iinf' |
+ | | |
+ | Relaxation period times (series) | 'relax_times' |
+ |___________________________________|______________________|
"""]
-
- def return_data_name(self, param):
- """Return a unique identifying string for the relaxation
curve-fitting parameter.
-
- @param param: The relaxation curve-fitting parameter.
- @type param: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Relaxation rate.
- if match('^[Rr]x$', param):
- return 'rx'
-
- # Peak intensities (series)
- if match('^[Ii]nt$', param):
- return 'intensities'
-
- # Initial intensity.
- if match('^[Ii]0$', param):
- return 'i0'
-
- # Intensity at infinity.
- if match('^[Ii]inf$', param):
- return 'iinf'
-
- # Relaxation period times (series).
- if match('^[Rr]elax[ -_][Tt]imes$', param):
- return 'relax_times'
def return_error(self, data_id):
@@ -990,44 +949,6 @@
return spin.intensity_err
- def return_grace_string(self, param):
- """Return the Grace string representation of the parameter.
-
- This is used for axis labelling.
-
- @param param: The relaxation curve-fitting parameter.
- @type param: str
- @return: The Grace string representation of the parameter.
- @rtype: str
- """
-
- # Get the object name.
- object_name = self.return_data_name(param)
-
- # Relaxation rate.
- if object_name == 'rx':
- grace_string = '\\qR\\sx\\Q'
-
- # Peak intensities.
- elif object_name == 'intensities':
- grace_string = '\\qPeak intensities\\Q'
-
- # Initial intensity.
- elif object_name == 'i0':
- grace_string = '\\qI\\s0\\Q'
-
- # Intensity at infinity.
- elif object_name == 'iinf':
- grace_string = '\\qI\\sinf\\Q'
-
- # Relaxation period times (series).
- elif object_name == 'relax_times':
- grace_string = '\\qRelaxation time period (s)\\Q'
-
- # Return the Grace string.
- return grace_string
-
-
def return_units(self, param):
"""Dummy method which returns None as the stats have no units.
Modified: branches/spec_api/test_suite/system_tests/scripts/1UBQ_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/1UBQ_relax_fit.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/scripts/1UBQ_relax_fit.py
(original)
+++ branches/spec_api/test_suite/system_tests/scripts/1UBQ_relax_fit.py Thu
Jan 19 10:53:32 2012
@@ -101,8 +101,8 @@
grace.write(y_data_type='chi2', file='chi2.agr', dir=ds.tmpdir, force=True)
# Minimised chi-squared value.
grace.write(y_data_type='i0', file='i0.agr', dir=ds.tmpdir, force=True) #
Initial peak intensity.
grace.write(y_data_type='rx', file='rx.agr', dir=ds.tmpdir, force=True) #
Relaxation rate.
-grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.agr', dir=ds.tmpdir, force=True) # Average peak
intensities.
-grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.agr', dir=ds.tmpdir, force=True) # Average peak
intensities (normalised).
+grace.write(x_data_type='relax_times', y_data_type='intensities',
file='intensities.agr', dir=ds.tmpdir, force=True) # Average peak
intensities.
+grace.write(x_data_type='relax_times', y_data_type='intensities', norm=True,
file='intensities_norm.agr', dir=ds.tmpdir, force=True) # Average peak
intensities (normalised).
# Save the program state.
state.save('rx.save', dir=ds.tmpdir, force=True)
Modified:
branches/spec_api/test_suite/system_tests/scripts/bug_17276_peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/bug_17276_peak_lists.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/scripts/bug_17276_peak_lists.py
(original)
+++ branches/spec_api/test_suite/system_tests/scripts/bug_17276_peak_lists.py
Thu Jan 19 10:53:32 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -106,8 +106,8 @@
#grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
#grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
#grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
-#grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.agr', force=True) # Average peak intensities.
-#grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.agr', force=True) # Average peak intensities
(normalised).
+#grace.write(x_data_type='relax_times', y_data_type='intensities',
file='intensities.agr', force=True) # Average peak intensities.
+#grace.write(x_data_type='relax_times', y_data_type='intensities',
norm=True, file='intensities_norm.agr', force=True) # Average peak
intensities (normalised).
#
## Display the Grace plots.
#grace.view(file='chi2.agr')
Modified: branches/spec_api/test_suite/system_tests/scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/relax_fit.py?rev=15187&r1=15186&r2=15187&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/scripts/relax_fit.py (original)
+++ branches/spec_api/test_suite/system_tests/scripts/relax_fit.py Thu Jan 19
10:53:32 2012
@@ -107,8 +107,8 @@
grace.write(y_data_type='chi2', file='devnull', force=True) # Minimised
chi-squared value.
grace.write(y_data_type='i0', file='devnull', force=True) # Initial peak
intensity.
grace.write(y_data_type='rx', file='devnull', force=True) # Relaxation
rate.
-grace.write(x_data_type='relax_times', y_data_type='int', file='devnull',
force=True) # Average peak intensities.
-grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='devnull', force=True) # Average peak intensities (normalised).
+grace.write(x_data_type='relax_times', y_data_type='intensities',
file='devnull', force=True) # Average peak intensities.
+grace.write(x_data_type='relax_times', y_data_type='intensities', norm=True,
file='devnull', force=True) # Average peak intensities (normalised).
# Save the program state.
state.save('devnull', force=True)
r15187 - in /branches/spec_api: auto_analyses/ sample_scripts/ specific_fns/ test_suite/system_tests/scripts/