specific_fns.api

35 """A special object for handling global and spin parameters.""" 36

37 - def __init__(self, spin_data=True):

38 """Set up the class. 39 40 @keyword spin_data: A flag which if True indicates that the specific analysis operates with spins. 41 @type spin_data: bool 42 """ 43 44 # Store the flags. 45 self.spin_data = spin_data 46 47 # Initialise the lists and dictionaries for the parameter info. 48 self._names = [] 49 self._scope = {} 50 self._string = {} 51 self._defaults = {} 52 self._units = {} 53 self._desc = {} 54 self._py_types = {} 55 self._conv_factor = {} 56 self._grace_string = {} 57 self._set = {} 58 self._err = {} 59 self._sim = {} 60 61 # Add some spin specific objects. 62 if self.spin_data: 63 self.add('select', scope='spin', desc='The spin selection flag', py_type=bool, sim=True) 64 self.add('fixed', scope='spin', desc='The fixed flag', py_type=bool)

65 66

67 - def add(self, name, scope=None, string=None, default=None, units=None, desc=None, py_type=None, set='generic', conv_factor=None, grace_string=None, err=False, sim=False):

68 """Add a parameter to the list. 69 70 @param name: The name of the parameter. This will be used as the variable name. 71 @type name: str 72 @keyword scope: The parameter scope. This can be set to 'global' for parameters located within the global scope of the current data pipe. Or set to 'spin' for spin specific parameters. Alternatively the value 'both' indicates that there are both global and specific versions of this parameter. 73 @type scope: str 74 @keyword string: The string representation of the parameter. 75 @type string: None or str 76 @keyword default: The default value of the parameter. 77 @type default: anything 78 @keyword units: A string representing the parameters units. 79 @type units: None or str 80 @keyword desc: The text description of the parameter. 81 @type desc: None or str 82 @keyword py_type: The Python type that this parameter should be. 83 @type py_type: Python type object 84 @keyword set: The set of object names. This can be set to 'all' for all names, to 'generic' for generic object names, 'params' for analysis specific parameter names, or to 'min' for minimisation specific object names. 85 @type set: str 86 @keyword conv_factor: The factor of conversion between different parameter units. 87 @type conv_factor: None, float or func 88 @keyword grace_string: The string used for the axes in Grace plots of the data. 89 @type grace_string: None or str 90 @keyword err: A flag which if True indicates that the parameter name + '_err' error data structure can exist. 91 @type err: bool 92 @keyword sim: A flag which if True indicates that the parameter name + '_sim' Monte Carlo simulation data structure can exist. 93 @type sim: bool 94 """ 95 96 # Checks. 97 if scope == None: 98 raise RelaxError("The parameter scope must be set.") 99 if py_type == None: 100 raise RelaxError("The parameter type must be set.") 101 allowed_sets = ['all', 'generic', 'params', 'min'] 102 if set not in allowed_sets: 103 raise RelaxError("The parameter set '%s' must be one of %s." % (set, allowed_sets)) 104 105 # Add the values. 106 self._names.append(name) 107 self._scope[name] = scope 108 self._defaults[name] = default 109 self._units[name] = units 110 self._desc[name] = desc 111 self._py_types[name] = py_type 112 self._set[name] = set 113 self._conv_factor[name] = conv_factor 114 self._err[name] = err 115 self._sim[name] = sim 116 117 # The parameter string. 118 if string: 119 self._string[name] = string 120 else: 121 self._string[name] = name 122 123 # The Grace string. 124 if grace_string: 125 self._grace_string[name] = grace_string 126 else: 127 self._grace_string[name] = name

128 129

130 - def add_min_data(self, min_stats_global=False, min_stats_spin=False):

131 """Add minimisation specific objects. 132 133 @keyword min_stats_global: A flag which if True will include the parameters 'chi2', 'iter', 'f_count', 'g_count', 'h_count', 'warning' in the list of global parameters. 134 @type min_stats_global: bool 135 @keyword min_stats_spin: A flag which if True will include the parameters 'chi2', 'iter', 'f_count', 'g_count', 'h_count', 'warning' in the list of spin parameters. 136 @type min_stats_spin: bool 137 """ 138 139 # Store the flags. 140 self.min_stats_global = min_stats_global 141 self.min_stats_spin = min_stats_spin 142 143 # Global minimisation data. 144 if self.min_stats_global or self.min_stats_spin: 145 # The scope. 146 if self.min_stats_global and self.min_stats_spin: 147 scope = 'both' 148 elif self.min_stats_global: 149 scope = 'global' 150 else: 151 scope = 'spin' 152 153 # The minimisation parameters. 154 self.add('chi2', scope=scope, desc='Chi-squared value', py_type=float, set='min', err=False, sim=True) 155 self.add('iter', scope=scope, desc='Optimisation iterations', py_type=int, set='min', err=False, sim=True) 156 self.add('f_count', scope=scope, desc='Number of function calls', py_type=int, set='min', err=False, sim=True) 157 self.add('g_count', scope=scope, desc='Number of gradient calls', py_type=int, set='min', err=False, sim=True) 158 self.add('h_count', scope=scope, desc='Number of Hessian calls', py_type=int, set='min', err=False, sim=True) 159 self.add('warning', scope=scope, desc='Optimisation warning', py_type=str, set='min', err=False, sim=True)

160 161

162 - def base_loop(self, set=None, scope=None):

163 """An iterator method for looping over all the base parameters. 164 165 @keyword set: The set of object names to return. This can be set to 'all' for all names, to 'generic' for generic object names, 'params' for analysis specific parameter names, or to 'min' for minimisation specific object names. 166 @type set: str 167 @keyword scope: The scope of the parameter to return. If not set, then all will be returned. If set to 'global' or 'spin', then only the parameters within that scope will be returned. 168 @type scope: str or None 169 @returns: The parameter names. 170 @rtype: str 171 """ 172 173 # Loop over the parameters. 174 for name in self._names: 175 # Skip the parameter if the set does not match. 176 if set == 'generic' and self._set[name] != 'generic': 177 continue 178 if set == 'params' and self._set[name] != 'params': 179 continue 180 if set == 'min' and self._set[name] != 'min': 181 continue 182 183 # Skip the parameter is outside of the scope. 184 if scope == 'global' and self._scope[name] == 'spin': 185 continue 186 if scope == 'spin' and self._scope[name] == 'global': 187 continue 188 189 # Yield the parameter name. 190 yield name

191 192

193 - def check_param(self, name):

194 """Check if the parameter exists. 195 196 @param name: The name of the parameter to search for. 197 @type name: str 198 @raises RelaxError: If the parameter does not exist. 199 """ 200 201 # Check. 202 if name not in self._names: 203 raise RelaxError("The parameter '%s' does not exist." % name)

204 205

206 - def contains(self, name):

207 """Determine if the given name is within the parameter list. 208 209 @param name: The name of the parameter to search for. 210 @type name: str 211 @return: True if the parameter is within the list, False otherwise. 212 @rtype: bool 213 """ 214 215 # Check. 216 if name in self._names: 217 return True 218 219 # No match. 220 return False

221 222

223 - def get_conv_factor(self, name):

224 """Return the conversion factor. 225 226 @param name: The name of the parameter. 227 @type name: str 228 @return: The conversion factor. 229 @rtype: float 230 """ 231 232 # Parameter check. 233 self.check_param(name) 234 235 # No factor. 236 if self._conv_factor[name] == None: 237 return 1.0 238 239 # Function. 240 if isinstance(self._conv_factor[name], FunctionType) or isinstance(self._conv_factor[name], MethodType): 241 return self._conv_factor[name]() 242 243 # Value. 244 return self._conv_factor[name]

245 246

247 - def get_default(self, name):

248 """Return the default value of the parameter. 249 250 @param name: The name of the parameter. 251 @type name: str 252 @return: The default value. 253 @rtype: None or str 254 """ 255 256 # Parameter check. 257 self.check_param(name) 258 259 # Return the default value. 260 return self._defaults[name]

261 262

263 - def get_desc(self, name):

264 """Return the description of the parameter. 265 266 @param name: The name of the parameter. 267 @type name: str 268 @return: The description. 269 @rtype: None or str 270 """ 271 272 # Skip error and simulation structures. 273 if name not in ['ri_data_err'] and (search('_err$', name) or search('_sim$', name)): 274 return None 275 276 # Parameter check. 277 self.check_param(name) 278 279 # Return the description. 280 return self._desc[name]

281 282

283 - def get_err(self, name):

284 """Return the error flag for the parameter. 285 286 @param name: The name of the parameter. 287 @type name: str 288 @return: The error flag for the parameter. 289 @rtype: bool 290 """ 291 292 # Parameter check. 293 self.check_param(name) 294 295 # Return the type. 296 return self._err[name]

297 298

299 - def get_grace_string(self, name):

300 """Return the Grace string for the parameter. 301 302 @param name: The name of the parameter. 303 @type name: str 304 @return: The Grace string. 305 @rtype: str 306 """ 307 308 # Parameter check. 309 self.check_param(name) 310 311 # Return the value. 312 return self._grace_string[name]

313 314

315 - def get_set(self, name):

316 """Return the parameter set that the parameter belongs to. 317 318 @param name: The name of the parameter. 319 @type name: str 320 @return: The parameter set. 321 @rtype: str 322 """ 323 324 # Parameter check. 325 self.check_param(name) 326 327 # Return the type. 328 return self._set[name]

329 330

331 - def get_sim(self, name):

332 """Return the Monte Carlo simulation flag for the parameter. 333 334 @param name: The name of the parameter. 335 @type name: str 336 @return: The Monte Carlo simulation flag for the parameter. 337 @rtype: bool 338 """ 339 340 # Parameter check. 341 self.check_param(name) 342 343 # Return the type. 344 return self._sim[name]

345 346

347 - def get_type(self, name):

348 """Return the Python type for the parameter. 349 350 @param name: The name of the parameter. 351 @type name: str 352 @return: The Python type. 353 @rtype: Python type object 354 """ 355 356 # Parameter check. 357 self.check_param(name) 358 359 # Return the Python type. 360 return self._py_types[name]

361 362

363 - def get_units(self, name):

364 """Return the units string for the parameter. 365 366 @param name: The name of the parameter. 367 @type name: str 368 @return: The units string. 369 @rtype: str 370 """ 371 372 # Parameter check. 373 self.check_param(name) 374 375 # Function. 376 if isinstance(self._conv_factor[name], FunctionType) or isinstance(self._conv_factor[name], MethodType): 377 return self._units[name]() 378 379 # Return the value. 380 return self._units[name]

381 382

383 - def loop(self, set=None, scope=None, error_names=False, sim_names=False):

384 """An iterator method for looping over all the parameters. 385 386 @keyword set: The set of object names to return. This can be set to 'all' for all names, to 'generic' for generic object names, 'params' for analysis specific parameter names, or to 'min' for minimisation specific object names. 387 @type set: str 388 @keyword scope: The scope of the parameter to return. If not set, then all will be returned. If set to 'global' or 'spin', then only the parameters within that scope will be returned. 389 @type scope: str or None 390 @keyword error_names: A flag which if True will add the error object names as well. 391 @type error_names: bool 392 @keyword sim_names: A flag which if True will add the Monte Carlo simulation object names as well. 393 @type sim_names: bool 394 @returns: The parameter names. 395 @rtype: str 396 """ 397 398 # Loop over and yield the parameters. 399 for name in self.base_loop(set=set, scope=scope): 400 yield name 401 402 # Error names. 403 if error_names: 404 for name in self.base_loop(set=set): 405 if self.get_err(name): 406 yield name + '_err' 407 408 # Sim names. 409 if sim_names: 410 for name in self.base_loop(set=set): 411 if self.get_sim(name): 412 yield name + '_sim'

Source Code for Module specific_fns.api_objects