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
