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
