Author: bugman
Date: Fri May 3 20:27:35 2013
New Revision: 19656
URL: http://svn.gna.org/viewcvs/relax?rev=19656&view=rev
Log:
Merged revisions 19650-19655 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19650 | bugman | 2013-05-03 19:36:30 +0200 (Fri, 03 May 2013) | 3 lines
Modified the Value.test_value_copy system test to check the copying of
errors as well.
........
r19651 | bugman | 2013-05-03 19:49:43 +0200 (Fri, 03 May 2013) | 5 lines
Added the error flag argument to all of the specific analysis API
set_param_values() methods.
This will allow parameter errors as well as values to be set.
........
r19652 | bugman | 2013-05-03 19:54:55 +0200 (Fri, 03 May 2013) | 3 lines
The Value.test_value_copy system test now checks all of the values and
errors.
........
r19653 | bugman | 2013-05-03 20:08:55 +0200 (Fri, 03 May 2013) | 5 lines
Added the error flag argument to the value.set user function.
This will allow for parameter errors to be set by the user.
........
r19654 | bugman | 2013-05-03 20:10:28 +0200 (Fri, 03 May 2013) | 5 lines
Bug fix for the value.copy user function.
The user function can now handle parameter errors, and the values are set
in the correct data pipe.
........
r19655 | bugman | 2013-05-03 20:11:07 +0200 (Fri, 03 May 2013) | 3 lines
The specific analysis API _return_value_general() method now returns errors
even when values are missing.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/value.py
branches/relax_disp/specific_analyses/api_base.py
branches/relax_disp/specific_analyses/api_common.py
branches/relax_disp/specific_analyses/model_free/main.py
branches/relax_disp/specific_analyses/n_state_model.py
branches/relax_disp/test_suite/system_tests/value.py
branches/relax_disp/user_functions/value.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri May 3 20:27:35 2013
@@ -1,1 +1,1 @@
-/trunk:1-19648
+/trunk:1-19655
Modified: branches/relax_disp/pipe_control/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/value.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/value.py (original)
+++ branches/relax_disp/pipe_control/value.py Fri May 3 20:27:35 2013
@@ -53,6 +53,7 @@
pipe_from = pipes.cdp_name()
if pipe_to == None:
pipe_to = pipes.cdp_name()
+ pipe_orig = pipes.cdp_name()
# The second pipe does not exist.
pipes.test(pipe_to)
@@ -77,16 +78,25 @@
if value != None or error != None:
raise RelaxValueError(param, pipe_to)
+ # Switch to the data pipe to copy values to.
+ pipes.switch(pipe_to)
+
# Copy the values.
for spin, spin_id in spin_loop(pipe=pipe_from, return_id=True):
# Get the value and error from pipe_from.
value, error = return_value(spin, param)
# Set the values of pipe_to.
- set(spin_id=spin_id, val=value, error=error, param=param)
+ if value != None:
+ set(spin_id=spin_id, val=value, param=param, pipe=pipe_to)
+ if error != None:
+ set(spin_id=spin_id, val=error, param=param, pipe=pipe_to,
error=True)
# Reset all minimisation statistics.
minimise.reset_min_stats(pipe_to)
+
+ # Switch back to the original current data pipe.
+ pipes.switch(pipe_orig)
def display(param=None, scaling=1.0):
@@ -343,19 +353,19 @@
minimise.reset_min_stats()
-def set(val=None, param=None, error=None, pipe=None, spin_id=None,
force=True, reset=True):
+def set(val=None, param=None, pipe=None, spin_id=None, error=False,
force=True, reset=True):
"""Set global or spin specific data values.
@keyword val: The parameter values.
@type val: None or list
@keyword param: The parameter names.
@type param: None, str, or list of str
- @keyword error: The parameter errors.
- @type error: None, number, or list of numbers
@keyword pipe: The data pipe the values should be placed in.
@type pipe: None or str
@keyword spin_id: The spin identification string.
@type spin_id: str
+ @keyword error: A flag which if True will allow the parameter errors
to be set instead of the values.
+ @type error: bool
@keyword force: A flag forcing the overwriting of current values.
@type force: bool
@keyword reset: A flag which if True will cause all minimisation
statistics to be reset.
@@ -414,7 +424,7 @@
raise RelaxParamSetError(param[i])
# Set the parameter values.
- set_param_values(param=param, value=val, spin_id=spin_id, force=force)
+ set_param_values(param=param, value=val, spin_id=spin_id, error=error,
force=force)
# Reset all minimisation statistics.
if reset:
Modified: branches/relax_disp/specific_analyses/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/api_base.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/api_base.py (original)
+++ branches/relax_disp/specific_analyses/api_base.py Fri May 3 20:27:35 2013
@@ -655,7 +655,7 @@
raise RelaxImplementError('set_error')
- def set_param_values(self, param=None, value=None, spin_id=None,
force=True):
+ def set_param_values(self, param=None, value=None, spin_id=None,
error=False, force=True):
"""Set the model parameter values.
@keyword param: The parameter name list.
@@ -664,6 +664,8 @@
@type value: list
@keyword spin_id: The spin identification string, only used for
spin specific parameters.
@type spin_id: None or str
+ @keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
+ @type error: bool
@keyword force: A flag which if True will cause current values
to be overwritten. If False, a RelaxError will raised if the parameter value
is already set.
@type force: bool
"""
Modified: branches/relax_disp/specific_analyses/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/api_common.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/api_common.py (original)
+++ branches/relax_disp/specific_analyses/api_common.py Fri May 3 20:27:35
2013
@@ -364,9 +364,9 @@
if hasattr(spin, object_name):
value = getattr(spin, object_name)
- # The error.
- if hasattr(spin, object_error):
- error = getattr(spin, object_error)
+ # The spin error.
+ if hasattr(spin, object_error):
+ error = getattr(spin, object_error)
# The global value.
elif hasattr(cdp, object_name):
@@ -435,7 +435,7 @@
inc = inc + 1
- def _set_param_values_global(self, param=None, value=None, spin_id=None,
force=True):
+ def _set_param_values_global(self, param=None, value=None, spin_id=None,
error=False, force=True):
"""Set the global parameter values in the top layer of the data pipe.
@keyword param: The parameter name list.
@@ -444,6 +444,8 @@
@type value: list
@keyword spin_id: The spin identification string (unused).
@type spin_id: None
+ @keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
+ @type error: bool
@keyword force: A flag which if True will cause current values
to be overwritten. If False, a RelaxError will raised if the parameter value
is already set.
@type force: bool
"""
@@ -461,6 +463,10 @@
if not obj_name:
raise RelaxError("The parameter '%s' is not valid for this
data pipe type." % param[i])
+ # Error object.
+ if error:
+ obj_name += '_err'
+
# Is the parameter already set.
if not force and hasattr(cdp, obj_name) and getattr(cdp,
obj_name) != None:
raise RelaxError("The parameter '%s' already exists, set the
force flag to True to overwrite." % param[i])
@@ -469,7 +475,7 @@
setattr(cdp, obj_name, value[i])
- def _set_param_values_spin(self, param=None, value=None, spin_id=None,
force=True):
+ def _set_param_values_spin(self, param=None, value=None, spin_id=None,
error=False, force=True):
"""Set the spin specific parameter values.
@keyword param: The parameter name list.
@@ -478,6 +484,8 @@
@type value: list
@keyword spin_id: The spin identification string, only used for
spin specific parameters.
@type spin_id: None or str
+ @keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
+ @type error: bool
@keyword force: A flag which if True will cause current values
to be overwritten. If False, a RelaxError will raised if the parameter value
is already set.
@type force: bool
"""
@@ -498,8 +506,13 @@
if not spin.select:
continue
+ # The object name.
+ obj_name = param[i]
+ if error:
+ obj_name += '_err'
+
# Set the parameter.
- setattr(spin, param[i], value[i])
+ setattr(spin, obj_name, value[i])
def _set_selected_sim_global(self, model_info, select_sim):
Modified: branches/relax_disp/specific_analyses/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/model_free/main.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/model_free/main.py (original)
+++ branches/relax_disp/specific_analyses/model_free/main.py Fri May 3
20:27:35 2013
@@ -2207,7 +2207,7 @@
inc = inc + 1
- def set_param_values(self, param=None, value=None, spin_id=None,
force=True):
+ def set_param_values(self, param=None, value=None, spin_id=None,
error=False, force=True):
"""Set the model-free parameter values.
@keyword param: The parameter name list.
@@ -2216,6 +2216,8 @@
@type value: list
@keyword spin_id: The spin identification string, only used for
spin specific parameters.
@type spin_id: None or str
+ @keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
+ @type error: bool
@keyword force: A flag which if True will cause current values
to be overwritten. If False, a RelaxError will raised if the parameter value
is already set.
@type force: bool
"""
@@ -2232,7 +2234,10 @@
# Diffusion tensor parameter.
diff_obj = diffusion_tensor.return_data_name(param[i])
if diff_obj:
- diff_params.append(param[i])
+ if error:
+ diff_params.append(param[i] + '_err')
+ else:
+ diff_params.append(param[i])
diff_vals.append(value[i])
# Model-free parameter.
@@ -2252,6 +2257,10 @@
# Check if it is a model-free parameter.
if obj_name not in self.data_names(set='params', scope='spin')
and obj_name not in self.data_names(set='generic', scope='spin'):
raise RelaxError("The parameter '%s' is unknown. It should
be one of %s or %s" % (mf_params[i], self.data_names(set='params',
scope='spin'), self.data_names(set='generic', scope='spin')))
+
+ # The error object name.
+ if error:
+ obj_name += '_err'
# Set the parameter.
for spin in spin_loop(spin_id):
Modified: branches/relax_disp/specific_analyses/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/n_state_model.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/n_state_model.py (original)
+++ branches/relax_disp/specific_analyses/n_state_model.py Fri May 3
20:27:35 2013
@@ -2596,7 +2596,7 @@
return getattr(tensor, names[param_index]+'_err')
- def set_param_values(self, param=None, value=None, spin_id=None,
force=True):
+ def set_param_values(self, param=None, value=None, spin_id=None,
error=False, force=True):
"""Set the N-state model parameter values.
@keyword param: The parameter name list.
@@ -2605,6 +2605,8 @@
@type value: list
@keyword spin_id: The spin identification string (unused).
@type spin_id: None
+ @keyword error: A flag which if True will allow the parameter
errors to be set instead of the values.
+ @type error: bool
@keyword force: A flag which if True will cause current values
to be overwritten. If False, a RelaxError will raised if the parameter value
is already set.
@type force: bool
"""
@@ -2621,6 +2623,10 @@
# Is the parameter is valid?
if not obj_name:
raise RelaxError("The parameter '%s' is not valid for this
data pipe type." % param[i])
+
+ # Error object.
+ if error:
+ obj_name += '_err'
# Set the indexed parameter.
if obj_name in ['probs', 'alpha', 'beta', 'gamma']:
Modified: branches/relax_disp/test_suite/system_tests/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/value.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/value.py (original)
+++ branches/relax_disp/test_suite/system_tests/value.py Fri May 3 20:27:35
2013
@@ -45,8 +45,11 @@
self.interpreter.spin.create(mol_name='test mol', res_name='Gly',
res_num=2, spin_name='N')
self.interpreter.spin.create(mol_name='test mol', res_name='Gly',
res_num=3, spin_name='N')
- # Add some values.
+ # Add some values and errors.
self.interpreter.value.set(val=0.8, param='s2', spin_id=':1,2')
+ self.interpreter.value.set(val=0.1, param='s2', spin_id=':1',
error=True)
+ self.interpreter.value.set(val=0.2, param='s2', spin_id=':2',
error=True)
+ self.interpreter.value.set(val=0.3, param='s2', spin_id=':3',
error=True)
# Create a new data pipe.
self.interpreter.pipe.create('new', 'mf')
@@ -54,3 +57,18 @@
# Copy the sequence data and value.
self.interpreter.sequence.copy(pipe_from='orig', pipe_to='new')
self.interpreter.value.copy(pipe_from='orig', pipe_to='new',
param='s2')
+
+ # Loop over both the new and old pipes to check the data.
+ for pipe in ['orig', 'new']:
+ # Printout.
+ print("Checking the values of the '%s' data pipe." % pipe)
+
+ # Check the values.
+ self.assertEqual(ds[pipe].mol[0].res[0].spin[0].s2, 0.8)
+ self.assertEqual(ds[pipe].mol[0].res[1].spin[0].s2, 0.8)
+ self.assert_(not hasattr(ds[pipe].mol[0].res[2].spin[0], 's2'))
+
+ # Check the errors.
+ self.assertEqual(ds[pipe].mol[0].res[0].spin[0].s2_err, 0.1)
+ self.assertEqual(ds[pipe].mol[0].res[1].spin[0].s2_err, 0.2)
+ self.assertEqual(ds[pipe].mol[0].res[2].spin[0].s2_err, 0.3)
Modified: branches/relax_disp/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/value.py?rev=19656&r1=19655&r2=19656&view=diff
==============================================================================
--- branches/relax_disp/user_functions/value.py (original)
+++ branches/relax_disp/user_functions/value.py Fri May 3 20:27:35 2013
@@ -330,6 +330,13 @@
desc_short = "spin ID to restrict value setting to",
desc = "The spin ID string to restrict value setting to.",
can_be_none = True
+)
+uf.add_keyarg(
+ name = "error",
+ default = False,
+ py_type = "bool",
+ desc_short = "error flag",
+ desc = "A flag which if True will cause the error rather than parameter
to be set."
)
# Description.
uf.desc.append(Desc_container())
r19656 - in /branches/relax_disp: ./ pipe_control/ specific_analyses/ specific_analyses/model_free/ test_suite/system_tests/...