Author: bugman
Date: Mon May 7 23:20:00 2012
New Revision: 16081
URL: http://svn.gna.org/viewcvs/relax?rev=16081&view=rev
Log:
Converted the model_selection user function to the auto-generation design.
Added:
branches/uf_redesign/user_functions/model_selection.py
- copied, changed from r16068,
branches/uf_redesign/prompt/model_selection.py
Removed:
branches/uf_redesign/prompt/model_selection.py
Modified:
branches/uf_redesign/prompt/__init__.py
branches/uf_redesign/prompt/interpreter.py
branches/uf_redesign/user_functions/__init__.py
Modified: branches/uf_redesign/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/prompt/__init__.py?rev=16081&r1=16080&r2=16081&view=diff
==============================================================================
--- branches/uf_redesign/prompt/__init__.py (original)
+++ branches/uf_redesign/prompt/__init__.py Mon May 7 23:20:00 2012
@@ -36,7 +36,6 @@
'interpreter',
'jw_mapping',
'model_free',
- 'model_selection',
'molecule',
'molmol',
'monte_carlo',
Modified: branches/uf_redesign/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/prompt/interpreter.py?rev=16081&r1=16080&r2=16081&view=diff
==============================================================================
--- branches/uf_redesign/prompt/interpreter.py (original)
+++ branches/uf_redesign/prompt/interpreter.py Mon May 7 23:20:00 2012
@@ -60,7 +60,6 @@
from fix import Fix
from gpl import GPL
from reset import Reset
-from model_selection import Modsel
from sys_info import Sys_info
from temperature import Temp
@@ -200,7 +199,6 @@
eliminate = Eliminate()
fix = Fix()
reset = Reset()
- modsel = Modsel()
opendx = OpenDX()
sys_info = Sys_info()
temp = Temp()
@@ -209,7 +207,6 @@
objects['eliminate'] = eliminate.eliminate
objects['fix'] = fix.fix
objects['reset'] = reset.reset
- objects['model_selection'] = modsel.model_selection
objects['sys_info'] = sys_info.sys_info
objects['temperature'] = temp.set
Removed: branches/uf_redesign/prompt/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/prompt/model_selection.py?rev=16080&view=auto
==============================================================================
--- branches/uf_redesign/prompt/model_selection.py (original)
+++ branches/uf_redesign/prompt/model_selection.py (removed)
@@ -1,109 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2012 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
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module containing the 'model_selection' user function class."""
-__docformat__ = 'plaintext'
-
-# relax module imports.
-import arg_check
-from generic_fns import model_selection
-from status import Status; status = Status()
-
-
-class Modsel:
- """Class containing the function for selecting which model selection
method should be used."""
-
- def model_selection(self, method=None, modsel_pipe=None, pipes=None):
- """Function for model selection.
-
- Keyword arguments
- ~~~~~~~~~~~~~~~~~
-
- method: The model selection technique (see below).
-
- modsel_pipe: The name of the new data pipe which will be created by
this user function by
- the copying of the selected data pipe.
-
- pipes: An array containing the names of all data pipes to include
in model selection.
-
-
- Description
- ~~~~~~~~~~~
-
- The following model selection methods are supported:
-
- AIC: Akaike's Information Criteria.
-
- AICc: Small sample size corrected AIC.
-
- BIC: Bayesian or Schwarz Information Criteria.
-
- Bootstrap: Bootstrap model selection.
-
- CV: Single-item-out cross-validation.
-
- Expect: The expected overall discrepancy (the true values of
the parameters are
- required).
-
- Farrow: Old model-free method by Farrow et al., 1994.
-
- Palmer: Old model-free method by Mandel et al., 1995.
-
- Overall: The realised overall discrepancy (the true values of
the parameters are
- required).
-
- For the methods 'Bootstrap', 'Expect', and 'Overall', the function
'monte_carlo' should have
- previously been executed with the type argument set to the
appropriate value to modify its
- behaviour.
-
- If the pipes argument is not supplied then all data pipes will be
used for model selection.
-
-
- Example
- ~~~~~~~
-
- For model-free analysis, if the preset models 1 to 5 are minimised
and loaded into the
- program, the following commands will carry out AIC model selection
and to place the selected
- results into the 'mixed' data pipe, type one of:
-
- relax> model_selection('AIC', 'mixed')
- relax> model_selection(method='AIC', modsel_pipe='mixed')
- relax> model_selection('AIC', 'mixed', ['m1', 'm2', 'm3', 'm4',
'm5'])
- relax> model_selection(method='AIC', modsel_pipe='mixed',
pipes=['m1', 'm2', 'm3', 'm4', 'm5'])
- """
-
- # Function intro text.
- if status.prompt_intro:
- text = status.ps3 + "model_selection("
- text = text + "method=" + repr(method)
- text = text + ", modsel_pipe=" + repr(modsel_pipe)
- text = text + ", pipes=" + repr(pipes) + ")"
- print(text)
-
- # The argument checks.
- arg_check.is_str(method, 'model selection method')
- arg_check.is_str(modsel_pipe, 'model selection data pipe name')
- arg_check.is_str_list(pipes, 'data pipes', can_be_none=True,
list_of_lists=True)
-
- # Execute the functional code.
- model_selection.select(method=method, modsel_pipe=modsel_pipe,
pipes=pipes)
Modified: branches/uf_redesign/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/__init__.py?rev=16081&r1=16080&r2=16081&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/__init__.py (original)
+++ branches/uf_redesign/user_functions/__init__.py Mon May 7 23:20:00 2012
@@ -42,6 +42,7 @@
'dasha',
'diffusion_tensor',
'minimisation',
+ 'model_selection',
'palmer',
'pipe',
'relax_data',
@@ -57,6 +58,7 @@
import user_functions.dasha
import user_functions.diffusion_tensor
import user_functions.minimisation
+import user_functions.model_selection
import user_functions.palmer
import user_functions.pipe
import user_functions.relax_data
Copied: branches/uf_redesign/user_functions/model_selection.py (from r16068,
branches/uf_redesign/prompt/model_selection.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/model_selection.py?p2=branches/uf_redesign/user_functions/model_selection.py&p1=branches/uf_redesign/prompt/model_selection.py&r1=16068&r2=16081&rev=16081&view=diff
==============================================================================
--- branches/uf_redesign/prompt/model_selection.py (original)
+++ branches/uf_redesign/user_functions/model_selection.py Mon May 7
23:20:00 2012
@@ -21,89 +21,94 @@
###############################################################################
# Module docstring.
-"""Module containing the 'model_selection' user function class."""
-__docformat__ = 'plaintext'
+"""Module containing the 'model_selection' user function data."""
# relax module imports.
-import arg_check
-from generic_fns import model_selection
-from status import Status; status = Status()
+from generic_fns import model_selection, pipes
+from graphics import WIZARD_IMAGE_PATH
+from user_functions.data import Uf_info; uf_info = Uf_info()
-class Modsel:
- """Class containing the function for selecting which model selection
method should be used."""
+# The model_selection user function.
+uf = uf_info.add_uf('model_selection')
+uf.title = "Select the best model from a set of optimised models."
+uf.title_short = "Model selection."
+uf.display = True
+uf.add_keyarg(
+ name = "method",
+ py_type = "str",
+ desc_short = "model selection method",
+ desc = "The model selection technique (see below).",
+ wiz_element_type = 'combo',
+ wiz_combo_choices = [
+ "Akaike's Information Criteria",
+ "Small sample size corrected AIC",
+ "Bayesian or Schwarz Information Criteria",
+ "Bootstrap model selection",
+ "Single-item-out cross-validation",
+ "Expected overall discrepancy",
+ "Farrow et al., 1994",
+ "Mandel et al., 1995",
+ "Realised overall discrepancy"
+ ],
+ wiz_combo_data = [
+ "AIC",
+ "AICc",
+ "BIC",
+ "Bootstrap",
+ "CV",
+ "Expect",
+ "Farrow",
+ "Palmer",
+ "Overall"
+ ],
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "modsel_pipe",
+ py_type = "str",
+ desc_short = "model selection data pipe name",
+ desc = "The name of the new data pipe which will be created by this user
function by the copying of the selected data pipe."
+)
+uf.add_keyarg(
+ name = "pipes",
+ py_type = "str_list_of_lists",
+ desc_short = "data pipes",
+ desc = "An array containing the names of all data pipes to include in
model selection.",
+ wiz_element_type = 'combo_list',
+ wiz_combo_iter = pipes.pipe_names,
+ wiz_read_only = True,
+ can_be_none = True
+)
+uf.desc = """
+The following model selection methods are supported:
- def model_selection(self, method=None, modsel_pipe=None, pipes=None):
- """Function for model selection.
+ AIC: Akaike's Information Criteria.
+ AICc: Small sample size corrected AIC.
+ BIC: Bayesian or Schwarz Information Criteria.
+ Bootstrap: Bootstrap model selection.
+ CV: Single-item-out cross-validation.
+ Expect: The expected overall discrepancy (the true values of the
parameters are required).
+ Farrow: Old model-free method by Farrow et al., 1994.
+ Palmer: Old model-free method by Mandel et al., 1995.
+ Overall: The realised overall discrepancy (the true values of the
parameters are required).
- Keyword arguments
- ~~~~~~~~~~~~~~~~~
+For the methods 'Bootstrap', 'Expect', and 'Overall', the function
'monte_carlo' should have previously been executed with the type argument set
to the appropriate value to modify its behaviour.
- method: The model selection technique (see below).
+If the pipes argument is not supplied then all data pipes will be used for
model selection.
+"""
+uf.prompt_examples = """
+For model-free analysis, if the preset models 1 to 5 are minimised and
loaded into the
+program, the following commands will carry out AIC model selection and to
place the selected
+results into the 'mixed' data pipe, type one of:
- modsel_pipe: The name of the new data pipe which will be created by
this user function by
- the copying of the selected data pipe.
-
- pipes: An array containing the names of all data pipes to include
in model selection.
-
-
- Description
- ~~~~~~~~~~~
-
- The following model selection methods are supported:
-
- AIC: Akaike's Information Criteria.
-
- AICc: Small sample size corrected AIC.
-
- BIC: Bayesian or Schwarz Information Criteria.
-
- Bootstrap: Bootstrap model selection.
-
- CV: Single-item-out cross-validation.
-
- Expect: The expected overall discrepancy (the true values of
the parameters are
- required).
-
- Farrow: Old model-free method by Farrow et al., 1994.
-
- Palmer: Old model-free method by Mandel et al., 1995.
-
- Overall: The realised overall discrepancy (the true values of
the parameters are
- required).
-
- For the methods 'Bootstrap', 'Expect', and 'Overall', the function
'monte_carlo' should have
- previously been executed with the type argument set to the
appropriate value to modify its
- behaviour.
-
- If the pipes argument is not supplied then all data pipes will be
used for model selection.
-
-
- Example
- ~~~~~~~
-
- For model-free analysis, if the preset models 1 to 5 are minimised
and loaded into the
- program, the following commands will carry out AIC model selection
and to place the selected
- results into the 'mixed' data pipe, type one of:
-
- relax> model_selection('AIC', 'mixed')
- relax> model_selection(method='AIC', modsel_pipe='mixed')
- relax> model_selection('AIC', 'mixed', ['m1', 'm2', 'm3', 'm4',
'm5'])
- relax> model_selection(method='AIC', modsel_pipe='mixed',
pipes=['m1', 'm2', 'm3', 'm4', 'm5'])
- """
-
- # Function intro text.
- if status.prompt_intro:
- text = status.ps3 + "model_selection("
- text = text + "method=" + repr(method)
- text = text + ", modsel_pipe=" + repr(modsel_pipe)
- text = text + ", pipes=" + repr(pipes) + ")"
- print(text)
-
- # The argument checks.
- arg_check.is_str(method, 'model selection method')
- arg_check.is_str(modsel_pipe, 'model selection data pipe name')
- arg_check.is_str_list(pipes, 'data pipes', can_be_none=True,
list_of_lists=True)
-
- # Execute the functional code.
- model_selection.select(method=method, modsel_pipe=modsel_pipe,
pipes=pipes)
+relax> model_selection('AIC', 'mixed')
+relax> model_selection(method='AIC', modsel_pipe='mixed')
+relax> model_selection('AIC', 'mixed', ['m1', 'm2', 'm3', 'm4', 'm5'])
+relax> model_selection(method='AIC', modsel_pipe='mixed', pipes=['m1', 'm2',
'm3', 'm4', 'm5'])
+"""
+uf.backend = model_selection.select
+uf.menu_text = "m&odel_selection"
+uf.gui_icon = "relax.discrepancy_curve"
+uf.wizard_size = (800, 600)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'discrepancy_curve.png'
r16081 - in /branches/uf_redesign: prompt/ user_functions/