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
