Author: bugman
Date: Fri Apr 11 10:35:18 2014
New Revision: 22712
URL: http://svn.gna.org/viewcvs/relax?rev=22712&view=rev
Log:
Eliminated the return_data_name() concept from the specific analysis API.
The parameter names can now only have one value, i.e. 's2' is different from
'S2'. In addition, a
number of related functions have been deleted form the pipe_control.minimise
module as these are now
handled by the parameter list object. The deleted functions are
return_conversion_factor() and
return_value().
Modified:
trunk/pipe_control/minimise.py
trunk/pipe_control/opendx.py
trunk/pipe_control/plotting.py
trunk/pipe_control/value.py
trunk/specific_analyses/api_base.py
trunk/specific_analyses/api_common.py
trunk/specific_analyses/model_free/api.py
trunk/specific_analyses/n_state_model/api.py
Modified: trunk/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/minimise.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/pipe_control/minimise.py (original)
+++ trunk/pipe_control/minimise.py Fri Apr 11 10:35:18 2014
@@ -319,18 +319,6 @@
spin.warning = None
-def return_conversion_factor(stat_type):
- """Dummy function for returning 1.0.
-
- @param stat_type: The name of the statistic. This is unused!
- @type stat_type: str
- @return: A conversion factor of 1.0.
- @rtype: float
- """
-
- return 1.0
-
-
return_data_name_doc = Desc_container("Minimisation statistic data type
string matching patterns")
table = uf_tables.add_table(label="table: min data type patterns",
caption="Minimisation statistic data type string matching patterns.")
table.add_headings(["Data type", "Object name", "Patterns"])
@@ -341,93 +329,6 @@
table.add_row(["Hessian call count", "'h_count'", "'^[Hh].*[ -_][Cc]ount'"])
return_data_name_doc.add_table(table.label)
-def return_data_name(name):
- """Return a unique identifying string for the minimisation parameter.
-
- @param name: The minimisation parameter.
- @type name: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Chi-squared.
- if search('^[Cc]hi2$', name) or search('^[Cc]hi[-_ ][Ss]quare', name):
- return 'chi2'
-
- # Iteration count.
- if search('^[Ii]ter', name):
- return 'iter'
-
- # Function call count.
- if search('^[Ff].*[ -_][Cc]ount', name):
- return 'f_count'
-
- # Gradient call count.
- if search('^[Gg].*[ -_][Cc]ount', name):
- return 'g_count'
-
- # Hessian call count.
- if search('^[Hh].*[ -_][Cc]ount', name):
- return 'h_count'
-
-
-def return_value(spin=None, stat_type=None, sim=None):
- """Function for returning the minimisation statistic corresponding to
'stat_type'.
-
- @param spin: The spin data container if spin specific data is to
be reset.
- @type spin: SpinContainer
- @param stat_type: The name of the statistic to return the value for.
- @type stat_type: str
- @param sim: The index of the simulation to return the value for.
If None, then the
- normal value is returned.
- @type sim: None or int
- """
-
- # Get the object name.
- object_name = return_data_name(stat_type)
-
- # The statistic type does not exist.
- if not object_name:
- raise RelaxError("The statistic type " + repr(stat_type) + " does
not exist.")
-
- # The simulation object name.
- object_sim = object_name + '_sim'
-
- # Get the global statistic.
- if spin == None:
- # Get the statistic.
- if sim == None:
- if hasattr(cdp, object_name):
- stat = getattr(cdp, object_name)
- else:
- stat = None
-
- # Get the simulation statistic.
- else:
- if hasattr(cdp, object_sim):
- stat = getattr(cdp, object_sim)[sim]
- else:
- stat = None
-
- # Residue specific statistic.
- else:
- # Get the statistic.
- if sim == None:
- if hasattr(spin, object_name):
- stat = getattr(spin, object_name)
- else:
- stat = None
-
- # Get the simulation statistic.
- else:
- if hasattr(spin, object_sim):
- stat = getattr(spin, object_sim)[sim]
- else:
- stat = None
-
- # Return the statistic (together with None to indicate that there are no
errors associated with the statistic).
- return stat, None
-
set_doc = """
Minimisation statistic set details
@@ -449,29 +350,26 @@
@type spin_id: str
"""
- # Get the parameter name.
- param_name = return_data_name(param)
-
# Global minimisation stats.
if spin_id == None:
# Chi-squared.
- if param_name == 'chi2':
+ if param == 'chi2':
cdp.chi2 = val
# Iteration count.
- elif param_name == 'iter':
+ elif param == 'iter':
cdp.iter = val
# Function call count.
- elif param_name == 'f_count':
+ elif param == 'f_count':
cdp.f_count = val
# Gradient call count.
- elif param_name == 'g_count':
+ elif param == 'g_count':
cdp.g_count = val
# Hessian call count.
- elif param_name == 'h_count':
+ elif param == 'h_count':
cdp.h_count = val
# Residue specific minimisation.
@@ -480,21 +378,21 @@
spin = return_spin(spin_id)
# Chi-squared.
- if param_name == 'chi2':
+ if param == 'chi2':
spin.chi2 = val
# Iteration count.
- elif param_name == 'iter':
+ elif param == 'iter':
spin.iter = val
# Function call count.
- elif param_name == 'f_count':
+ elif param == 'f_count':
spin.f_count = val
# Gradient call count.
- elif param_name == 'g_count':
+ elif param == 'g_count':
spin.g_count = val
# Hessian call count.
- elif param_name == 'h_count':
+ elif param == 'h_count':
spin.h_count = val
Modified: trunk/pipe_control/opendx.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/opendx.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/pipe_control/opendx.py (original)
+++ trunk/pipe_control/opendx.py Fri Apr 11 10:35:18 2014
@@ -119,7 +119,6 @@
# Alias the specific functions.
self.calculate = api.calculate
self.model_statistics = api.model_statistics
- self.return_data_name = api.return_data_name
self.map_bounds = []
self.return_conversion_factor = []
self.return_units = []
@@ -230,8 +229,8 @@
# Loop over the parameters.
for i in range(self.n):
- # Get the parameter name.
- name = self.return_data_name(self.params[i])
+ # Alias the parameter name.
+ name = self.params[i]
# Diffusion tensor parameter.
if pipes.get_type() == 'mf':
Modified: trunk/pipe_control/plotting.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/plotting.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/pipe_control/plotting.py (original)
+++ trunk/pipe_control/plotting.py Fri Apr 11 10:35:18 2014
@@ -28,7 +28,6 @@
# relax module imports.
from lib.errors import RelaxError
-from pipe_control import minimise
from pipe_control.mol_res_spin import spin_loop
from specific_analyses.api import return_api
@@ -610,10 +609,6 @@
if data_name in ['res_num', 'spin_num']:
return None, None
- # A minimisation statistic.
- if minimise.return_data_name(data_name):
- return minimise.return_value, minimise.return_conversion_factor
-
# Analysis specific value returning functions.
else:
api = return_api()
@@ -633,11 +628,6 @@
if data_name in ['res_num', 'spin_num']:
return int
- # A minimisation statistic.
- if minimise.return_data_name(data_name):
- return int
-
# Analysis specific value returning functions.
- else:
- api = return_api()
- return api.data_type(data_name)
+ api = return_api()
+ return api.data_type(data_name)
Modified: trunk/pipe_control/value.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/value.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/pipe_control/value.py (original)
+++ trunk/pipe_control/value.py Fri Apr 11 10:35:18 2014
@@ -282,19 +282,6 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Minimisation parameter.
- if minimise.return_data_name(param):
- # Minimisation statistic flag.
- min_stat = True
-
- # Specific value and error returning function.
- return_value = minimise.return_value
-
- # Specific set function.
- set_fn = minimise.set
-
- # Normal parameter.
- else:
# Minimisation statistic flag.
min_stat = False
@@ -354,7 +341,7 @@
write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums,
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values,
data_name=param, error=errors, error_name='%s_error'%param)
# Reset the minimisation statistics.
- if not min_stat:
+ if api.set(param) == 'min':
minimise.reset_min_stats()
@@ -421,7 +408,7 @@
# Loop over the parameters, getting the default values.
val = []
for i in range(len(param)):
- val.append(api.default_value(api.return_data_name(param[i])))
+ val.append(api.default_value(param[i]))
# Check that there is a default.
if val[-1] == None:
Modified: trunk/specific_analyses/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/api_base.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/specific_analyses/api_base.py (original)
+++ trunk/specific_analyses/api_base.py Fri Apr 11 10:35:18 2014
@@ -552,23 +552,6 @@
return self._PARAMS.description(name)
- def return_data_name(self, param):
- """Return a unique identifying string for the given parameter.
-
- @param param: The parameter name.
- @type param: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # No parameter.
- if not self._PARAMS.contains(param):
- return None
-
- # Return the name.
- return param
-
-
def return_error(self, data_id=None):
"""Return the error points corresponding to the data points used in
optimisation.
Modified: trunk/specific_analyses/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/api_common.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/specific_analyses/api_common.py (original)
+++ trunk/specific_analyses/api_common.py Fri Apr 11 10:35:18 2014
@@ -383,21 +383,18 @@
# Initialise.
index = None
- # Get the object name.
- object_name = self.return_data_name(param)
-
# The error, simulation and back calculated names.
- if object_name:
- object_error = object_name + '_err'
- object_sim = object_name + '_sim'
- object_bc = object_name + '_bc'
+ if param:
+ object_error = param + '_err'
+ object_sim = param + '_sim'
+ object_bc = param + '_bc'
key = None
# The data type does not exist.
else:
# Is it a spectrum id?
if hasattr(cdp, 'spectrum_ids') and param in cdp.spectrum_ids:
- object_name = 'intensity'
+ param = 'intensity'
object_error = 'intensity_err'
object_sim = 'intensity_sim'
object_bc = 'intensity_bc'
@@ -413,23 +410,23 @@
# Switch to back calculated data.
if bc:
- object_name = object_bc
+ param = object_bc
# Value or sim value?
if sim != None:
- object_name = object_sim
+ param = object_sim
# The spin value.
- if hasattr(spin, object_name):
- value = getattr(spin, object_name)
+ if hasattr(spin, param):
+ value = getattr(spin, param)
# The spin error.
if hasattr(spin, object_error):
error = getattr(spin, object_error)
# The global value.
- elif hasattr(cdp, object_name):
- value = getattr(cdp, object_name)
+ elif hasattr(cdp, param):
+ value = getattr(cdp, param)
# The error.
if hasattr(cdp, object_error):
@@ -517,23 +514,20 @@
# Loop over the parameters.
for i in range(len(param)):
- # Get the object's name.
- obj_name = self.return_data_name(param[i])
-
# Is the parameter is valid?
- if not obj_name:
+ if not param[i]:
raise RelaxError("The parameter '%s' is not valid for this
data pipe type." % param[i])
# Error object.
if error:
- obj_name += '_err'
+ param[i] += '_err'
# Is the parameter already set.
- if not force and hasattr(cdp, obj_name) and getattr(cdp,
obj_name) != None:
+ if not force and hasattr(cdp, param[i]) and getattr(cdp,
param[i]) != None:
raise RelaxError("The parameter '%s' already exists, set the
force flag to True to overwrite." % param[i])
# Set the parameter.
- setattr(cdp, obj_name, value[i])
+ setattr(cdp, param[i], value[i])
def _set_param_values_spin(self, param=None, value=None, index=None,
spin_id=None, error=False, force=True):
Modified: trunk/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/api.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/api.py (original)
+++ trunk/specific_analyses/model_free/api.py Fri Apr 11 10:35:18 2014
@@ -1921,20 +1921,17 @@
# Set the model-free parameters.
for i in range(len(mf_params)):
- # The object name.
- obj_name = self.return_data_name(mf_params[i])
-
# 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'):
+ if mf_params[i] not in self.data_names(set='params',
scope='spin') and mf_params[i] 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'
+ mf_params[i] += '_err'
# Set the parameter.
for spin in spin_loop(spin_id):
- setattr(spin, obj_name, mf_vals[i])
+ setattr(spin, mf_params[i], mf_vals[i])
def set_selected_sim(self, model_info, select_sim):
Modified: trunk/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/api.py?rev=22712&r1=22711&r2=22712&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/api.py (original)
+++ trunk/specific_analyses/n_state_model/api.py Fri Apr 11 10:35:18
2014
@@ -758,28 +758,23 @@
# Loop over the parameters.
for i in range(len(param)):
- # Get the object's name.
- obj_name = self.return_data_name(param[i])
- print param
- print obj_name
-
# Is the parameter is valid?
- if not obj_name:
+ if not param[i]:
raise RelaxError("The parameter '%s' is not valid for this
data pipe type." % param[i])
# Error object.
if error:
- obj_name += '_err'
+ param[i] += '_err'
# Set the indexed parameter.
- if obj_name in ['probs', 'alpha', 'beta', 'gamma']:
- obj = getattr(cdp, obj_name)
+ if param[i] in ['probs', 'alpha', 'beta', 'gamma']:
+ obj = getattr(cdp, param[i])
obj[index] = value[i]
# Set the spin parameters.
else:
for spin in spin_loop(spin_id):
- setattr(spin, obj_name, value[i])
+ setattr(spin, param[i], value[i])
def sim_init_values(self):
r22712 - in /trunk: pipe_control/ specific_analyses/ specific_analyses/model_free/ specific_analyses/n_state_model/