Hi Edward. It's fine for me!
I think it is the very best, to have these values collected in one-table. Also for documentation! These are values is what would go looking for, if I am the smallest interested in what is happening. Also the linear constraints should be there. And maybe also the scaling... Best Troels 2014-05-28 16:36 GMT+02:00 Edward d'Auvergne <[email protected]>: > That could be a default, using grid_lower and grid_upper for the > mapping. But an override of map_lower and map_upper would be very > useful, even in the dispersion analysis. This would be required for > the kex parameter, as grid_lower is set to 1.0, whereas map_lower > should be 0.0. The tex parameter as well. > > Regards, > > Edward > > > On 28 May 2014 16:29, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Edward. >> >> I don't know much about the Model free. >> >> But I guess these values could be added to: >> specific_values/XXX/parameter_object.py >> >> But as a start, the map values could be the grid values? >> >> Best >> Troels >> >> >> 2014-05-28 16:19 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> Hi, >>> >>> What did you think about the map bounds in the parameter_object >>> specific analysis API? In addition to the grid_lower and grid_upper >>> arguments, also have map_lower and map_upper arguments? If you look >>> at specific_analyses/model_free/api.py and >>> specific_analyses/model_free/optimisation.py, you will see that these >>> are all set to different values for the model-free analysis. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 28 May 2014 15:59, Edward d'Auvergne <[email protected]> wrote: >>>> Hi, >>>> >>>> Exactly, but it would need to be in a branch (to keep the trunk >>>> stable) and then done for all analyses (to keep the API clean). I.e. >>>> the same steps as I mentioned before >>>> (http://thread.gmane.org/gmane.science.nmr.relax.devel/5987). You've >>>> already done half of the work with the changes at >>>> http://article.gmane.org/gmane.science.nmr.relax.devel/5986. But it >>>> must really be done for all analyses. The parameter_object is a major >>>> part of the specific analysis API. Most of the work is in the base >>>> parameter_object anyway, rather than in the specific analyses which >>>> just require hardcoded values shifted from >>>> specific_analyses/*/optimisation.py into >>>> specific_analyses/*/parameter_object.py which is simply 39 pairs of >>>> numbers: >>>> >>>> $ grep lower.append specific_analyses/*/* | wc -l >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 28 May 2014 15:47, Troels Emtekær Linnet <[email protected]> wrote: >>>>> Hm. >>>>> >>>>> That is too much work. >>>>> >>>>> Can I write the default values into the >>>>> specific_analysis/relax_disp/parameter_object.py. >>>>> >>>>> So I can simply call: >>>>> >>>>> from specific_analyses.relax_disp.parameter_object import >>>>> Relax_disp_params >>>>> PARAMS = Relax_disp_params() >>>>> PARAMS.default_value('pA') >>>>> PARAMS.grid_upper('pA') >>>>> >>>>> Then I wont touch the API. >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> 2014-05-28 15:30 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>>>> Hi, >>>>>> >>>>>> If you have the time and would like to implement this, such a change >>>>>> must be done for the entire specific API. It cannot be just for the >>>>>> relaxation dispersion analysis. The API change must be complete - >>>>>> otherwise the changes will not be accepted as that will result in huge >>>>>> amounts of maintenance work for me in the future, much more than the >>>>>> effort of making the API consistent for all analyses. Though if you >>>>>> set up one analysis type, the rest should be easy (half don't perform >>>>>> minimisation, so the grid limits are not defined). The best way to >>>>>> implement this would be: >>>>>> >>>>>> - Create a new svn branch from the trunk for the developments. >>>>>> - Add the self._grid_lower and self._grid_upper objects and >>>>>> corresponding arguments to specific_analyses.parameter_objects. >>>>>> - Go into specific_analyses, and run 'grep lower.append */*' to see >>>>>> all the places this needs changing. >>>>>> - Shift all of these hard coded values into the specific >>>>>> parameter_object modules. >>>>>> - Import the parameter_object singleton into the modules requiring the >>>>>> default bounds. >>>>>> - Replace all the hard coded values with the >>>>>> parameter_object.grid_lower() and parameter_object.grid_upper() >>>>>> function calls. Note the places where the limits are dynamically >>>>>> changed - these must remain. >>>>>> - Make sure the test suite passes. >>>>>> - Ask for the branch to be merged back. >>>>>> >>>>>> The API function grid_lower() should not be added, as these methods >>>>>> are really designed for use outside of the specific API. If you wish >>>>>> to do this, feel free. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 28 May 2014 15:00, Troels Emtekær Linnet <[email protected]> >>>>>> wrote: >>>>>>> Hi Ed. >>>>>>> >>>>>>> I would like to collect the grid seach lower and upper bounds into the >>>>>>> table of >>>>>>> specific_analysis/relax_disp/parameter_object.py >>>>>>> >>>>>>> This is to make one place, where such details are collected. >>>>>>> >>>>>>> And the lower and upper bounds can be extracted for unit tests, and >>>>>>> for example dx.map more easily. >>>>>>> >>>>>>> I have worked it out for lower bounds of pA, and tested it. >>>>>>> >>>>>>> --- a/specific_analyses/api_base.py >>>>>>> +++ b/specific_analyses/api_base.py >>>>>>> @@ -314,6 +314,22 @@ class API_base(object): >>>>>>> raise RelaxImplementError('grid_search') >>>>>>> >>>>>>> >>>>>>> + def grid_lower(self, param): >>>>>>> + """Return the default lower bounds of paramater for the grid >>>>>>> search. >>>>>>> + >>>>>>> + This basic method will first search for a global parameter >>>>>>> and, if not found, then a spin parameter. >>>>>>> + >>>>>>> + >>>>>>> + @param param: The specific analysis parameter. >>>>>>> + @type param: str >>>>>>> + @return: The default value. >>>>>>> + @rtype: float >>>>>>> + """ >>>>>>> + >>>>>>> + # Return the value. >>>>>>> + return self._PARAMS.grid_lower(param) >>>>>>> + >>>>>>> + >>>>>>> def has_errors(self): >>>>>>> """Test if errors exist for the current data pipe. >>>>>>> >>>>>>> diff --git a/specific_analyses/parameter_object.py >>>>>>> b/specific_analyses/parameter_object.py >>>>>>> index b626a83..8e7abab 100644 >>>>>>> --- a/specific_analyses/parameter_object.py >>>>>>> +++ b/specific_analyses/parameter_object.py >>>>>>> @@ -54,6 +54,7 @@ class Param_list(object): >>>>>>> self._scope = {} >>>>>>> self._string = {} >>>>>>> self._defaults = {} >>>>>>> + self._grid_lowers = {} >>>>>>> self._units = {} >>>>>>> self._desc = {} >>>>>>> self._py_types = {} >>>>>>> @@ -92,7 +93,7 @@ class Param_list(object): >>>>>>> return cls._instance >>>>>>> >>>>>>> >>>>>>> - def _add(self, name, scope=None, string=None, default=None, >>>>>>> units=None, desc=None, py_type=None, set='all', conv_factor=None, >>>>>>> grace_string=None, err=False, sim=False): >>>>>>> + def _add(self, name, scope=None, string=None, default=None, >>>>>>> grid_lower=None, units=None, desc=None, py_type=None, set='all', >>>>>>> conv_factor=None, grace_string=None, err=False, sim=False): >>>>>>> """Add a parameter to the list. >>>>>>> >>>>>>> @param name: The name of the parameter. This will >>>>>>> be used as the variable name. >>>>>>> @@ -103,6 +104,8 @@ class Param_list(object): >>>>>>> @type string: None or str >>>>>>> @keyword default: The default value of the parameter. >>>>>>> @type default: anything >>>>>>> + @keyword grid_lower: The default lower bounds of the grid >>>>>>> search. >>>>>>> + @type grid_lower: float >>>>>>> @keyword units: A string representing the parameters >>>>>>> units. >>>>>>> @type units: None or str >>>>>>> @keyword desc: The text description of the parameter. >>>>>>> @@ -134,6 +137,7 @@ class Param_list(object): >>>>>>> self._names.append(name) >>>>>>> self._scope[name] = scope >>>>>>> self._defaults[name] = default >>>>>>> + self._grid_lowers[name] = grid_lower >>>>>>> self._units[name] = units >>>>>>> self._desc[name] = desc >>>>>>> self._py_types[name] = py_type >>>>>>> @@ -540,6 +544,22 @@ class Param_list(object): >>>>>>> return self._grace_string[name] >>>>>>> >>>>>>> >>>>>>> + def grid_lower(self, name): >>>>>>> + """Return the default lower bounds of paramater for the grid >>>>>>> search. >>>>>>> + >>>>>>> + @param name: The name of the parameter. >>>>>>> + @type name: str >>>>>>> + @return: The default value. >>>>>>> + @rtype: None or str >>>>>>> + """ >>>>>>> + >>>>>>> + # Parameter check. >>>>>>> + self.check_param(name) >>>>>>> + >>>>>>> + # Return the default value. >>>>>>> + return self._grid_lowers[name] >>>>>>> + >>>>>>> + >>>>>>> def is_spin_param(self, name): >>>>>>> """Determine whether the given parameter is spin specific. >>>>>>> >>>>>>> diff --git a/specific_analyses/relax_disp/optimisation.py >>>>>>> b/specific_analyses/relax_disp/optimisation.py >>>>>>> index a92922e..82bd364 100644 >>>>>>> --- a/specific_analyses/relax_disp/optimisation.py >>>>>>> +++ b/specific_analyses/relax_disp/optimisation.py >>>>>>> @@ -38,6 +38,7 @@ from lib.errors import RelaxError >>>>>>> from lib.text.sectioning import subsection >>>>>>> from multi import Memo, Result_command, Slave_command >>>>>>> from pipe_control.mol_res_spin import spin_loop >>>>>>> +from specific_analyses.api import return_api >>>>>>> from specific_analyses.relax_disp.checks import check_disp_points, >>>>>>> check_exp_type, check_exp_type_fixed_time >>>>>>> from specific_analyses.relax_disp.data import average_intensity, >>>>>>> count_spins, find_intensity_keys, has_exponential_exp_type, >>>>>>> has_proton_mmq_cpmg, loop_exp, loop_exp_frq_offset_point, >>>>>>> loop_exp_frq_offset_point_time, loop_frq, loop_offset, loop_time, >>>>>>> pack_back_calc_r2eff, return_cpmg_frqs, return_offset_data, >>>>>>> return_param_key_from_data, return_r1_data, return_r2eff_arrays, >>>>>>> return_spin_lock_nu1 >>>>>>> from specific_analyses.relax_disp.parameters import >>>>>>> assemble_param_vector, assemble_scaling_matrix, >>>>>>> disassemble_param_vector, linear_constraints, loop_parameters, >>>>>>> param_conversion, param_num >>>>>>> @@ -296,6 +297,9 @@ def grid_search_setup(spins=None, spin_ids=None, >>>>>>> param_vector=None, lower=None, >>>>>>> elif isinstance(inc, int): >>>>>>> inc = [inc]*n >>>>>>> >>>>>>> + # The specific analysis API object. >>>>>>> + api = return_api() >>>>>>> + >>>>>>> # Set up the default bounds. >>>>>>> if not lower: >>>>>>> # Init. >>>>>>> @@ -357,7 +361,9 @@ def grid_search_setup(spins=None, spin_ids=None, >>>>>>> param_vector=None, lower=None, >>>>>>> if spins[si].model == MODEL_M61B: >>>>>>> lower.append(0.85) >>>>>>> else: >>>>>>> - lower.append(0.5) >>>>>>> + #lower.append(0.5) >>>>>>> + lower.append(api.grid_lower('pA')) >>>>>>> + #lower.append(api.default_value('pA')) >>>>>>> upper.append(1.0) >>>>>>> >>>>>>> # The population of state B (for 3-site exchange). >>>>>>> diff --git a/specific_analyses/relax_disp/parameter_object.py >>>>>>> b/specific_analyses/relax_disp/parameter_object.py >>>>>>> index 936d2b1..21dfe99 100644 >>>>>>> --- a/specific_analyses/relax_disp/parameter_object.py >>>>>>> +++ b/specific_analyses/relax_disp/parameter_object.py >>>>>>> @@ -61,7 +61,7 @@ class Relax_disp_params(Param_list): >>>>>>> self._add('r2', scope='spin', default=10.0, desc='The >>>>>>> transversal relaxation rate', set='params', py_type=dict, >>>>>>> grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) >>>>>>> self._add('r2a', scope='spin', default=10.0, desc='The >>>>>>> transversal relaxation rate for state A in the absence of exchange', >>>>>>> set='params', py_type=dict, grace_string='\\qR\\s2,A\\N\\Q >>>>>>> (rad.s\\S-1\\N)', err=True, sim=True) >>>>>>> self._add('r2b', scope='spin', default=10.0, desc='The >>>>>>> transversal relaxation rate for state B in the absence of exchange', >>>>>>> set='params', py_type=dict, grace_string='\\qR\\s2,B\\N\\Q >>>>>>> (rad.s\\S-1\\N)', err=True, sim=True) >>>>>>> - self._add('pA', scope='spin', default=0.90, desc='The >>>>>>> population for state A', set='params', py_type=float, >>>>>>> grace_string='\\qp\\sA\\N\\Q', err=True, sim=True) >>>>>>> + self._add('pA', scope='spin', default=0.90, grid_lower=0.6, >>>>>>> desc='The population for state A', set='params', py_type=float, >>>>>>> grace_string='\\qp\\sA\\N\\Q', err=True, sim=True) >>>>>>> self._add('pB', scope='spin', default=0.5, desc='The >>>>>>> population for state B', set='params', py_type=float, >>>>>>> grace_string='\\qp\\sB\\N\\Q', err=True, sim=True) >>>>>>> self._add('pC', scope='spin', default=0.5, desc='The >>>>>>> population for state C', set='params', py_type=float, >>>>>>> grace_string='\\qp\\sC\\N\\Q', err=True, sim=True) >>>>>>> self._add('phi_ex', scope='spin', default=5.0, desc='The >>>>>>> phi_ex = pA.pB.dw**2 value (ppm^2)', set='params', py_type=float, >>>>>>> grace_string='\\xF\\B\\sex\\N = \\q >>>>>>> p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True, >>>>>>> sim=True) >>>>>>> >>>>>>> Best >>>>>>> Troels >>>>>>> >>>>>>> _______________________________________________ >>>>>>> relax (http://www.nmr-relax.com) >>>>>>> >>>>>>> This is the relax-devel mailing list >>>>>>> [email protected] >>>>>>> >>>>>>> To unsubscribe from this list, get a password >>>>>>> reminder, or change your subscription options, >>>>>>> visit the list information page at >>>>>>> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
