Author: bugman
Date: Thu Aug 21 11:23:28 2014
New Revision: 25159
URL: http://svn.gna.org/viewcvs/relax?rev=25159&view=rev
Log:
Merged revisions 25152-25158 via svnmerge from
svn+ssh://[email protected]/svn/relax/trunk
........
r25152 | bugman | 2014-08-21 10:37:38 +0200 (Thu, 21 Aug 2014) | 3 lines
Created the MODEL_LIST_FIT_R1 variable to keep track of dispersion models
with R1 fitting support.
........
r25153 | bugman | 2014-08-21 10:40:26 +0200 (Thu, 21 Aug 2014) | 6 lines
The is_r1_optimised() function now checks MODEL_LIST_FIT_R1.
If the model is not in MODEL_LIST_FIT_R1, i.e. R1 optimisation is not
supported, then the function
will return False.
........
r25154 | bugman | 2014-08-21 10:42:58 +0200 (Thu, 21 Aug 2014) | 5 lines
Bug fix for the updating of the Model_class.params list with 'r1'.
The is_r1_optimised() function needs to be called!
........
r25155 | bugman | 2014-08-21 10:59:02 +0200 (Thu, 21 Aug 2014) | 3 lines
Removed some unused imports to allow the test_variables unit tests to pass.
........
r25156 | bugman | 2014-08-21 11:05:12 +0200 (Thu, 21 Aug 2014) | 5 lines
Removed all of the MODEL_*_FIT_R1 from the remaining unit tests.
These are for the tests of the specific_analyses.relax_disp.model module.
........
r25157 | bugman | 2014-08-21 11:08:52 +0200 (Thu, 21 Aug 2014) | 5 lines
Fix for the test_nesting_param_5 unit test.
The 'r1' parameter is now dynamic and hence will not be present in the
initial list.
........
r25158 | bugman | 2014-08-21 11:21:12 +0200 (Thu, 21 Aug 2014) | 5 lines
One final fix for the Model_class.params list with 'r1'.
The is_r1_optimised() function is now called with the model name argument, as
required.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Aug 21 11:23:28 2014
@@ -1 +1 @@
-/trunk:1-25150
+/trunk:1-25158
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/data.py?rev=25159&r1=25158&r2=25159&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/relax_disp/data.py Thu Aug
21 11:23:28 2014
@@ -79,7 +79,7 @@
from pipe_control import value
import specific_analyses
from specific_analyses.relax_disp.checks import check_exp_type,
check_interpolate_offset_cpmg_model, check_missing_r1, check_mixed_curve_types
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_DESC_CPMG_DQ,
EXP_TYPE_DESC_CPMG_MQ, EXP_TYPE_DESC_CPMG_PROTON_MQ,
EXP_TYPE_DESC_CPMG_PROTON_SQ, EXP_TYPE_DESC_CPMG_SQ, EXP_TYPE_DESC_CPMG_ZQ,
EXP_TYPE_DESC_R1RHO, EXP_TYPE_LIST, EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO,
EXP_TYPE_R1RHO, MODEL_B14, MODEL_B14_FULL, MODEL_DPL94, MODEL_LIST_MMQ,
MODEL_LIST_NUMERIC_CPMG, MODEL_LIST_R1RHO_FULL, MODEL_LIST_R1RHO_ON_RES,
MODEL_LIST_R1RHO_OFF_RES, MODEL_MP05, MODEL_NS_R1RHO_2SITE, MODEL_PARAMS,
MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, PARAMS_R20
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_DESC_CPMG_DQ,
EXP_TYPE_DESC_CPMG_MQ, EXP_TYPE_DESC_CPMG_PROTON_MQ,
EXP_TYPE_DESC_CPMG_PROTON_SQ, EXP_TYPE_DESC_CPMG_SQ, EXP_TYPE_DESC_CPMG_ZQ,
EXP_TYPE_DESC_R1RHO, EXP_TYPE_LIST, EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO,
EXP_TYPE_R1RHO, MODEL_B14, MODEL_B14_FULL, MODEL_DPL94, MODEL_LIST_FIT_R1,
MODEL_LIST_MMQ, MODEL_LIST_NUMERIC_CPMG, MODEL_LIST_R1RHO_FULL,
MODEL_LIST_R1RHO_ON_RES, MODEL_LIST_R1RHO_OFF_RES, MODEL_MP05,
MODEL_NS_R1RHO_2SITE, MODEL_PARAMS, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02,
PARAMS_R20
from stat import S_IRWXU, S_IRGRP, S_IROTH
from os import chmod, sep
@@ -1026,6 +1026,10 @@
@return: True if the R1 values should be optimised, False if loaded
values should be used instead.
@rtype: bool
"""
+
+ # Return False for all models which do not support R1 optimisation.
+ if model not in MODEL_LIST_FIT_R1:
+ return False
# Firstly use the R1 fit flag as an override.
if hasattr(cdp, 'r1_fit'):
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/model.py?rev=25159&r1=25158&r2=25159&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/relax_disp/model.py Thu Aug
21 11:23:28 2014
@@ -58,7 +58,7 @@
# model parameters.
self.params = MODEL_PARAMS[self.model]
- if is_r1_optimised and 'r1' not in self.params:
+ if is_r1_optimised(model=model) and 'r1' not in self.params:
self.params.insert(0, 'r1')
# model number of parameters.
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py?rev=25159&r1=25158&r2=25159&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
Thu Aug 21 11:23:28 2014
@@ -407,6 +407,9 @@
MODEL_LIST_DW_MIX_QUADRUPLE = [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]
"""Models using parameters with mixed dw, and has four variables. For example
with both dw_AB, dw_BC, dwH_AB and dwH_BC."""
+
+# The models which currently support R1 fitting via target function switching.
+MODEL_LIST_FIT_R1 = [MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03,
MODEL_MP05, MODEL_NS_R1RHO_2SITE]
# The defined models, which is used for nesting.
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py?rev=25159&r1=25158&r2=25159&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
(original)
+++
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
Thu Aug 21 11:23:28 2014
@@ -21,8 +21,8 @@
# relax module imports.
from specific_analyses.relax_disp.model import nesting_model, nesting_param,
sort_models
-from specific_analyses.relax_disp.variables import MODEL_B14, MODEL_B14_FULL,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94_FIT_R1, MODEL_IT99, MODEL_MMQ_CR72,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_MP05_FIT_R1, MODEL_NOREX,
MODEL_NOREX_R1RHO_FIT_R1, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_2SITE_FIT_R1,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF,
MODEL_TAP03_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TSMFK01
-from specific_analyses.relax_disp.variables import MODEL_PARAMS_B14_FULL,
MODEL_PARAMS_CR72, MODEL_PARAMS_CR72_FULL, MODEL_PARAMS_LM63,
MODEL_PARAMS_LM63_3SITE, MODEL_PARAMS_MMQ_CR72, MODEL_PARAMS_MP05_FIT_R1,
MODEL_PARAMS_NS_MMQ_2SITE, MODEL_PARAMS_NS_MMQ_3SITE,
MODEL_PARAMS_NS_MMQ_3SITE_LINEAR, MODEL_PARAMS_NS_R1RHO_2SITE,
MODEL_PARAMS_NS_R1RHO_3SITE, MODEL_PARAMS_NS_R1RHO_3SITE_LINEAR,
MODEL_PARAMS_TAP03_FIT_R1
+from specific_analyses.relax_disp.variables import MODEL_B14, MODEL_B14_FULL,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_MMQ_CR72,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_MP05, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import MODEL_PARAMS_B14_FULL,
MODEL_PARAMS_CR72, MODEL_PARAMS_CR72_FULL, MODEL_PARAMS_LM63,
MODEL_PARAMS_LM63_3SITE, MODEL_PARAMS_MMQ_CR72, MODEL_PARAMS_MP05,
MODEL_PARAMS_NS_MMQ_2SITE, MODEL_PARAMS_NS_MMQ_3SITE,
MODEL_PARAMS_NS_MMQ_3SITE_LINEAR, MODEL_PARAMS_NS_R1RHO_2SITE,
MODEL_PARAMS_NS_R1RHO_3SITE, MODEL_PARAMS_NS_R1RHO_3SITE_LINEAR,
MODEL_PARAMS_TAP03
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -337,13 +337,13 @@
def test_nesting_model_r1rho_1(self):
"""Unit test of function nesting_model, which determine which model to
nest from, testing for R1rho experiments."""
- ## Test MODEL_MP05_FIT_R1 model request, when models are all R1rho
models with fitted R1.
- # Define all the models tested in the analysis.
- self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1,
MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_MP05_FIT_R1,
MODEL_NS_R1RHO_2SITE_FIT_R1]
-
- # Define which current model is selected
- model = MODEL_MP05_FIT_R1
- model_nest = MODEL_TAP03_FIT_R1
+ ## Test MODEL_MP05 model request, when models are all R1rho models
with fitted R1.
+ # Define all the models tested in the analysis.
+ self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94,
MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
+
+ # Define which current model is selected
+ model = MODEL_MP05
+ model_nest = MODEL_TAP03
print("self.models is:", self_models)
print("Current model to analyse is:", model)
@@ -356,12 +356,12 @@
def test_nesting_model_r1rho_2(self):
"""Unit test of function nesting_model, which determine which model to
nest from, testing for R1rho experiments."""
- ## Test MODEL_TP02_FIT_R1 model request, when models are all R1rho
models with fitted R1, and MODEL_NS_R1RHO_2SITE_FIT_R1 was fitted first.
- # Define all the models tested in the analysis.
- self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1, MODEL_R2EFF,
MODEL_NOREX_R1RHO_FIT_R1, MODEL_NS_R1RHO_2SITE_FIT_R1, MODEL_TP02_FIT_R1]
-
- # Define which current model is selected
- model = MODEL_TP02_FIT_R1
+ ## Test MODEL_TP02 model request, when models are all R1rho models
with fitted R1, and MODEL_NS_R1RHO_2SITE was fitted first.
+ # Define all the models tested in the analysis.
+ self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_R2EFF,
MODEL_NOREX_R1RHO, MODEL_NS_R1RHO_2SITE, MODEL_TP02]
+
+ # Define which current model is selected
+ model = MODEL_TP02
model_nest = None
print("self.models is:", self_models)
@@ -375,12 +375,12 @@
def test_nesting_model_r1rho_3(self):
"""Unit test of function nesting_model, which determine which model to
nest from, testing for R1rho experiments."""
- ## Test MODEL_DPL94_FIT_R1 model request, when models are all R1rho
models with fitted R1, and MODEL_NS_R1RHO_2SITE_FIT_R1 was fitted first.
- # Define all the models tested in the analysis.
- self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1,
MODEL_NS_R1RHO_2SITE_FIT_R1, MODEL_DPL94_FIT_R1]
-
- # Define which current model is selected
- model = MODEL_DPL94_FIT_R1
+ ## Test MODEL_DPL94 model request, when models are all R1rho models
with fitted R1, and MODEL_NS_R1RHO_2SITE was fitted first.
+ # Define all the models tested in the analysis.
+ self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_NS_R1RHO_2SITE,
MODEL_DPL94]
+
+ # Define which current model is selected
+ model = MODEL_DPL94
model_nest = None
print("self.models is:", self_models)
@@ -394,12 +394,12 @@
def test_nesting_model_r1rho_4(self):
"""Unit test of function nesting_model, which determine which model to
nest from, testing for R1rho experiments."""
- ## Test MODEL_TP02_FIT_R1 model request, when model are all R1rho
models with fitted R1, and MODEL_DPL94_FIT_R1 was fitted first.
- # Define all the models tested in the analysis.
- self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1,
MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1]
-
- # Define which current model is selected
- model = MODEL_TP02_FIT_R1
+ ## Test MODEL_TP02 model request, when model are all R1rho models with
fitted R1, and MODEL_DPL94 was fitted first.
+ # Define all the models tested in the analysis.
+ self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02]
+
+ # Define which current model is selected
+ model = MODEL_TP02
model_nest = None
print("self.models is:", self_models)
@@ -509,20 +509,19 @@
"""Unit test of function nesting_param, which determine how model
parameters are converted for nesting."""
# Define parameters
- model_params = MODEL_PARAMS_TAP03_FIT_R1
- nested_model_params = MODEL_PARAMS_MP05_FIT_R1
-
- # Get the dictionary of parameter conversion.
- par_dic = nesting_param(model_params=model_params,
nested_model_params=nested_model_params)
-
- # Test the number of elements in the dictionary.
- self.assertEqual(len(par_dic), len(model_params))
-
- print("model parameters", model_params)
- print("nested_model_params", nested_model_params)
-
- # Test content of dictionary.
- self.assertEqual(par_dic['r1'], 'r1')
+ model_params = MODEL_PARAMS_TAP03
+ nested_model_params = MODEL_PARAMS_MP05
+
+ # Get the dictionary of parameter conversion.
+ par_dic = nesting_param(model_params=model_params,
nested_model_params=nested_model_params)
+
+ # Test the number of elements in the dictionary.
+ self.assertEqual(len(par_dic), len(model_params))
+
+ print("model parameters", model_params)
+ print("nested_model_params", nested_model_params)
+
+ # Test content of dictionary.
self.assertEqual(par_dic['r2'], 'r2')
self.assertEqual(par_dic['pA'], 'pA')
self.assertEqual(par_dic['dw'], 'dw')
@@ -670,8 +669,8 @@
## Test sort of models, when models are all R1rho models with fitted
R1.
# Define all the models tested in the analysis.
- self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1,
MODEL_DPL94_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_MP05_FIT_R1,
MODEL_NS_R1RHO_2SITE_FIT_R1]
- expected_result = [MODEL_R2EFF, MODEL_NOREX_R1RHO_FIT_R1,
MODEL_MP05_FIT_R1, MODEL_TAP03_FIT_R1, MODEL_TP02_FIT_R1, MODEL_DPL94_FIT_R1,
MODEL_NS_R1RHO_2SITE_FIT_R1]
+ self_models = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94,
MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
+ expected_result = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_MP05,
MODEL_TAP03, MODEL_TP02, MODEL_DPL94, MODEL_NS_R1RHO_2SITE]
# Test the return.
self.assertEqual(sort_models(models=self_models), expected_result)
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py?rev=25159&r1=25158&r2=25159&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
(original)
+++
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
Thu Aug 21 11:23:28 2014
@@ -20,7 +20,7 @@
###############################################################################
# relax module imports.
-from specific_analyses.relax_disp.variables import MODEL_B14, MODEL_B14_FULL,
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94_FIT_R1, MODEL_IT99, MODEL_MMQ_CR72,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_MP05_FIT_R1, MODEL_NOREX,
MODEL_NOREX_R1RHO_FIT_R1, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_2SITE_FIT_R1,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF,
MODEL_TAP03_FIT_R1, MODEL_TP02_FIT_R1, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_MMQ_CR72,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_3SITE
from specific_analyses.relax_disp.variables import MODEL_EXP_TYPE, MODEL_EQ,
MODEL_PARAMS, MODEL_SITES, MODEL_YEAR
from test_suite.unit_tests.base_classes import UnitTestCase
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