[f32d144] | 1 | """ |
---|
| 2 | Class that holds a fit page state |
---|
| 3 | """ |
---|
[a95ae9a] | 4 | # TODO: Refactor code so we don't need to use getattr/setattr |
---|
[5062bbf] | 5 | ################################################################################ |
---|
[a95ae9a] | 6 | # This software was developed by the University of Tennessee as part of the |
---|
| 7 | # Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
---|
| 8 | # project funded by the US National Science Foundation. |
---|
[5062bbf] | 9 | # |
---|
[a95ae9a] | 10 | # See the license text in license.txt |
---|
[5062bbf] | 11 | # |
---|
[a95ae9a] | 12 | # copyright 2009, University of Tennessee |
---|
[5062bbf] | 13 | ################################################################################ |
---|
[11a7e11] | 14 | import time |
---|
| 15 | import os |
---|
| 16 | import sys |
---|
[abcbe09] | 17 | import wx |
---|
[6f023e8] | 18 | import copy |
---|
[11a7e11] | 19 | import logging |
---|
[9a5097c] | 20 | import numpy as np |
---|
[7673ecd] | 21 | import traceback |
---|
[c77d859] | 22 | |
---|
[35b556d] | 23 | import xml.dom.minidom |
---|
[ac5b69d] | 24 | from xml.dom.minidom import parseString |
---|
[11a7e11] | 25 | from lxml import etree |
---|
| 26 | |
---|
[8898558b] | 27 | from sasmodels import convert |
---|
[6c382da] | 28 | import sasmodels.weights |
---|
| 29 | |
---|
[b699768] | 30 | import sas.sascalc.dataloader |
---|
| 31 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader |
---|
| 32 | from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node |
---|
[a95ae9a] | 33 | from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector |
---|
| 34 | from sas.sascalc.dataloader.data_info import Process, Aperture |
---|
[4387385] | 35 | |
---|
[463e7ffc] | 36 | logger = logging.getLogger(__name__) |
---|
[c155a16] | 37 | |
---|
[a95ae9a] | 38 | # Information to read/write state as xml |
---|
[61cada5] | 39 | FITTING_NODE_NAME = 'fitting_plug_in' |
---|
| 40 | CANSAS_NS = "cansas1d/1.0" |
---|
| 41 | |
---|
[4387385] | 42 | CUSTOM_MODEL = 'Plugin Models' |
---|
| 43 | CUSTOM_MODEL_OLD = 'Customized Models' |
---|
| 44 | |
---|
[b1e609c] | 45 | LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"], |
---|
| 46 | ["group_id", "data_group_id", "string"], |
---|
| 47 | ["data_name", "data_name", "string"], |
---|
| 48 | ["data_id", "data_id", "string"], |
---|
| 49 | ["name", "name", "string"], |
---|
| 50 | ["data_name", "data_name", "string"]] |
---|
[acf8e4a5] | 51 | LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"], |
---|
[b1e609c] | 52 | ["qmax", "qmax", "float"], |
---|
| 53 | ["npts", "npts", "float"], |
---|
| 54 | ["categorycombobox", "categorycombobox", "string"], |
---|
[c8e1996] | 55 | ["formfactorcombobox", "formfactorcombobox", |
---|
| 56 | "string"], |
---|
| 57 | ["structurecombobox", "structurecombobox", |
---|
| 58 | "string"], |
---|
[b1e609c] | 59 | ["multi_factor", "multi_factor", "float"], |
---|
| 60 | ["magnetic_on", "magnetic_on", "bool"], |
---|
| 61 | ["enable_smearer", "enable_smearer", "bool"], |
---|
| 62 | ["disable_smearer", "disable_smearer", "bool"], |
---|
| 63 | ["pinhole_smearer", "pinhole_smearer", "bool"], |
---|
| 64 | ["slit_smearer", "slit_smearer", "bool"], |
---|
| 65 | ["enable_disp", "enable_disp", "bool"], |
---|
| 66 | ["disable_disp", "disable_disp", "bool"], |
---|
| 67 | ["dI_noweight", "dI_noweight", "bool"], |
---|
| 68 | ["dI_didata", "dI_didata", "bool"], |
---|
| 69 | ["dI_sqrdata", "dI_sqrdata", "bool"], |
---|
| 70 | ["dI_idata", "dI_idata", "bool"], |
---|
| 71 | ["enable2D", "enable2D", "bool"], |
---|
| 72 | ["cb1", "cb1", "bool"], |
---|
| 73 | ["tcChi", "tcChi", "float"], |
---|
| 74 | ["smearer", "smearer", "float"], |
---|
| 75 | ["smear_type", "smear_type", "string"], |
---|
[c8e1996] | 76 | ["dq_l", "dq_l", "float"], |
---|
| 77 | ["dq_r", "dq_r", "float"], |
---|
[d85f1d8a] | 78 | ["dx_percent", "dx_percent", "float"], |
---|
[b1e609c] | 79 | ["dxl", "dxl", "float"], |
---|
| 80 | ["dxw", "dxw", "float"]] |
---|
| 81 | |
---|
| 82 | LIST_OF_MODEL_ATTRIBUTES = [["values", "values"], |
---|
[11a7e11] | 83 | ["weights", "weights"]] |
---|
| 84 | |
---|
[b1e609c] | 85 | DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]] |
---|
[2296316] | 86 | |
---|
[b1e609c] | 87 | LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"], |
---|
[f32d144] | 88 | ["str_parameters", "str_parameters"], |
---|
[61cada5] | 89 | ["orientation_parameters", "orientation_params"], |
---|
[c8e1996] | 90 | ["dispersity_parameters", |
---|
| 91 | "orientation_params_disp"], |
---|
[f32d144] | 92 | ["fixed_param", "fixed_param"], |
---|
| 93 | ["fittable_param", "fittable_param"]] |
---|
[b1e609c] | 94 | LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"], |
---|
[f32d144] | 95 | ["xmax", "xmax", "float"], |
---|
| 96 | ["ymin", "ymin", "float"], |
---|
| 97 | ["ymax", "ymax", "float"], |
---|
| 98 | ["_xaxis", "_xaxis", "string"], |
---|
[df7ed14] | 99 | ["_xunit", "_xunit", "string"], |
---|
[f32d144] | 100 | ["_yaxis", "_yaxis", "string"], |
---|
| 101 | ["_yunit", "_yunit", "string"], |
---|
| 102 | ["_zaxis", "_zaxis", "string"], |
---|
| 103 | ["_zunit", "_zunit", "string"]] |
---|
[b1e609c] | 104 | LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"], |
---|
| 105 | ["qy_data", "qy_data", "float"], |
---|
| 106 | ["dqx_data", "dqx_data", "float"], |
---|
| 107 | ["dqy_data", "dqy_data", "float"], |
---|
| 108 | ["data", "data", "float"], |
---|
| 109 | ["q_data", "q_data", "float"], |
---|
| 110 | ["err_data", "err_data", "float"], |
---|
| 111 | ["mask", "mask", "bool"]] |
---|
[61cada5] | 112 | |
---|
[f32d144] | 113 | |
---|
| 114 | def parse_entry_helper(node, item): |
---|
[0b12abb5] | 115 | """ |
---|
| 116 | Create a numpy list from value extrated from the node |
---|
[2f4b430] | 117 | |
---|
[0b12abb5] | 118 | :param node: node from each the value is stored |
---|
| 119 | :param item: list name of three strings.the two first are name of data |
---|
[f32d144] | 120 | attribute and the third one is the type of the value of that |
---|
[0b12abb5] | 121 | attribute. type can be string, float, bool, etc. |
---|
[2f4b430] | 122 | |
---|
[0b12abb5] | 123 | : return: numpy array |
---|
| 124 | """ |
---|
| 125 | if node is not None: |
---|
| 126 | if item[2] == "string": |
---|
| 127 | return str(node.get(item[0]).strip()) |
---|
| 128 | elif item[2] == "bool": |
---|
| 129 | try: |
---|
[e3d1423] | 130 | return node.get(item[0]).strip() == "True" |
---|
[c8e1996] | 131 | except Exception: |
---|
[0b12abb5] | 132 | return None |
---|
| 133 | else: |
---|
| 134 | try: |
---|
| 135 | return float(node.get(item[0])) |
---|
[c8e1996] | 136 | except Exception: |
---|
[0b12abb5] | 137 | return None |
---|
[2f4b430] | 138 | |
---|
| 139 | |
---|
[cfc0913] | 140 | class PageState(object): |
---|
[c77d859] | 141 | """ |
---|
[5062bbf] | 142 | Contains information to reconstruct a page of the fitpanel. |
---|
[c77d859] | 143 | """ |
---|
[61cada5] | 144 | def __init__(self, parent=None, model=None, data=None): |
---|
[f32d144] | 145 | """ |
---|
[5062bbf] | 146 | Initialize the current state |
---|
[2f4b430] | 147 | |
---|
[5062bbf] | 148 | :param model: a selected model within a page |
---|
[f32d144] | 149 | :param data: |
---|
[2f4b430] | 150 | |
---|
[c77d859] | 151 | """ |
---|
[61cada5] | 152 | self.file = None |
---|
[a95ae9a] | 153 | # Time of state creation |
---|
[11a7e11] | 154 | self.timestamp = time.time() |
---|
[a95ae9a] | 155 | # Data member to store the dispersion object created |
---|
[c77d859] | 156 | self._disp_obj_dict = {} |
---|
[a95ae9a] | 157 | # ------------------------ |
---|
| 158 | # Data used for fitting |
---|
[c77d859] | 159 | self.data = data |
---|
[2296316] | 160 | # model data |
---|
| 161 | self.theory_data = None |
---|
[a95ae9a] | 162 | # Is 2D |
---|
[2296316] | 163 | self.is_2D = False |
---|
| 164 | self.images = None |
---|
[2f4b430] | 165 | |
---|
[a95ae9a] | 166 | # save additional information on data that dataloader.reader |
---|
| 167 | # does not read |
---|
[61cada5] | 168 | self.is_data = None |
---|
| 169 | self.data_name = "" |
---|
[c0ff8cc] | 170 | |
---|
[61cada5] | 171 | if self.data is not None: |
---|
| 172 | self.data_name = self.data.name |
---|
| 173 | self.data_id = None |
---|
| 174 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 175 | self.data_id = self.data.id |
---|
| 176 | self.data_group_id = None |
---|
| 177 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 178 | self.data_group_id = self.data.group_id |
---|
[2f4b430] | 179 | |
---|
[a95ae9a] | 180 | # reset True change the state of existing button |
---|
[61cada5] | 181 | self.reset = False |
---|
[2f4b430] | 182 | |
---|
[c77d859] | 183 | # flag to allow data2D plot |
---|
[cfc0913] | 184 | self.enable2D = False |
---|
[c77d859] | 185 | # model on which the fit would be performed |
---|
| 186 | self.model = model |
---|
[93f0a862] | 187 | self.m_name = None |
---|
[a95ae9a] | 188 | # list of process done to model |
---|
[dce84c0] | 189 | self.process = [] |
---|
[a95ae9a] | 190 | # fit page manager |
---|
[c77d859] | 191 | self.manager = None |
---|
[a95ae9a] | 192 | # Store the parent of this panel parent |
---|
[c77d859] | 193 | # For this application fitpanel is the parent |
---|
[f32d144] | 194 | self.parent = parent |
---|
[c77d859] | 195 | # Event_owner is the owner of model event |
---|
| 196 | self.event_owner = None |
---|
[a95ae9a] | 197 | # page name |
---|
[cfc0913] | 198 | self.page_name = "" |
---|
[c8e1996] | 199 | # Contains link between model, its parameters, and panel organization |
---|
[61cada5] | 200 | self.parameters = [] |
---|
[fb59ed9] | 201 | # String parameter list that can not be fitted |
---|
| 202 | self.str_parameters = [] |
---|
[f32d144] | 203 | # Contains list of parameters that cannot be fitted and reference to |
---|
[a95ae9a] | 204 | # panel objects |
---|
[61cada5] | 205 | self.fixed_param = [] |
---|
[f32d144] | 206 | # Contains list of parameters with dispersity and reference to |
---|
[a95ae9a] | 207 | # panel objects |
---|
[61cada5] | 208 | self.fittable_param = [] |
---|
[a95ae9a] | 209 | # orientation parameters |
---|
[61cada5] | 210 | self.orientation_params = [] |
---|
[a95ae9a] | 211 | # orientation parameters for gaussian dispersity |
---|
[61cada5] | 212 | self.orientation_params_disp = [] |
---|
[a95ae9a] | 213 | # smearer info |
---|
[61cada5] | 214 | self.smearer = None |
---|
[7609f1a] | 215 | self.smear_type = None |
---|
| 216 | self.dq_l = None |
---|
| 217 | self.dq_r = None |
---|
[d85f1d8a] | 218 | self.dx_percent = None |
---|
[096181d] | 219 | self.dx_old = False |
---|
[db8fd5b] | 220 | self.dxl = None |
---|
| 221 | self.dxw = None |
---|
[a95ae9a] | 222 | # list of dispersion parameters |
---|
[f32d144] | 223 | self.disp_list = [] |
---|
[61cada5] | 224 | if self.model is not None: |
---|
[71f0373] | 225 | self.disp_list = self.model.getDispParamList() |
---|
[2296316] | 226 | |
---|
[61cada5] | 227 | self.disp_cb_dict = {} |
---|
[2296316] | 228 | self.values = {} |
---|
| 229 | self.weights = {} |
---|
[2f4b430] | 230 | |
---|
[a95ae9a] | 231 | # contains link between a model and selected parameters to fit |
---|
[61cada5] | 232 | self.param_toFit = [] |
---|
[a95ae9a] | 233 | # dictionary of model type and model class |
---|
[cfc0913] | 234 | self.model_list_box = None |
---|
[a95ae9a] | 235 | # save the state of the context menu |
---|
[61cada5] | 236 | self.saved_states = {} |
---|
[a95ae9a] | 237 | # save selection of combobox |
---|
[3b9e023] | 238 | self.formfactorcombobox = None |
---|
[ea5fa58] | 239 | self.categorycombobox = None |
---|
[f32d144] | 240 | self.structurecombobox = None |
---|
[c0ff8cc] | 241 | |
---|
[a95ae9a] | 242 | # radio box to select type of model |
---|
| 243 | # self.shape_rbutton = False |
---|
| 244 | # self.shape_indep_rbutton = False |
---|
| 245 | # self.struct_rbutton = False |
---|
| 246 | # self.plugin_rbutton = False |
---|
| 247 | # the indice of the current selection |
---|
[b787e68c] | 248 | self.disp_box = 0 |
---|
[a95ae9a] | 249 | # Qrange |
---|
| 250 | # Q range |
---|
[61cada5] | 251 | self.qmin = 0.001 |
---|
| 252 | self.qmax = 0.1 |
---|
[a95ae9a] | 253 | # reset data range |
---|
[0b12abb5] | 254 | self.qmax_x = None |
---|
| 255 | self.qmin_x = None |
---|
[2f4b430] | 256 | |
---|
[cfc0913] | 257 | self.npts = None |
---|
[61cada5] | 258 | self.name = "" |
---|
[4523b68] | 259 | self.multi_factor = None |
---|
[318b5bbb] | 260 | self.magnetic_on = False |
---|
[a95ae9a] | 261 | # enable smearering state |
---|
[cfc0913] | 262 | self.enable_smearer = False |
---|
[fc6ea43] | 263 | self.disable_smearer = True |
---|
[7609f1a] | 264 | self.pinhole_smearer = False |
---|
[f32d144] | 265 | self.slit_smearer = False |
---|
[55bb249c] | 266 | # weighting options |
---|
| 267 | self.dI_noweight = False |
---|
| 268 | self.dI_didata = True |
---|
| 269 | self.dI_sqrdata = False |
---|
[f32d144] | 270 | self.dI_idata = False |
---|
[a95ae9a] | 271 | # disperity selection |
---|
[61cada5] | 272 | self.enable_disp = False |
---|
| 273 | self.disable_disp = True |
---|
[2f4b430] | 274 | |
---|
[a95ae9a] | 275 | # state of selected all check button |
---|
[cfc0913] | 276 | self.cb1 = False |
---|
[a95ae9a] | 277 | # store value of chisqr |
---|
[61cada5] | 278 | self.tcChi = None |
---|
[9e0aa69a] | 279 | self.version = (1,0,0) |
---|
[2f4b430] | 280 | |
---|
[6f023e8] | 281 | def clone(self): |
---|
[61cada5] | 282 | """ |
---|
[5062bbf] | 283 | Create a new copy of the current object |
---|
[61cada5] | 284 | """ |
---|
| 285 | model = None |
---|
| 286 | if self.model is not None: |
---|
[6f023e8] | 287 | model = self.model.clone() |
---|
[bb70474] | 288 | model.name = self.model.name |
---|
[61cada5] | 289 | obj = PageState(self.parent, model=model) |
---|
| 290 | obj.file = copy.deepcopy(self.file) |
---|
[6f023e8] | 291 | obj.data = copy.deepcopy(self.data) |
---|
[61cada5] | 292 | if self.data is not None: |
---|
| 293 | self.data_name = self.data.name |
---|
| 294 | obj.data_name = self.data_name |
---|
| 295 | obj.is_data = self.is_data |
---|
[dcf29d7] | 296 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
---|
[2f4b430] | 297 | |
---|
[ea5fa58] | 298 | obj.categorycombobox = self.categorycombobox |
---|
[61cada5] | 299 | obj.formfactorcombobox = self.formfactorcombobox |
---|
[f32d144] | 300 | obj.structurecombobox = self.structurecombobox |
---|
[2f4b430] | 301 | |
---|
[a95ae9a] | 302 | # obj.shape_rbutton = self.shape_rbutton |
---|
| 303 | # obj.shape_indep_rbutton = self.shape_indep_rbutton |
---|
| 304 | # obj.struct_rbutton = self.struct_rbutton |
---|
| 305 | # obj.plugin_rbutton = self.plugin_rbutton |
---|
[2f4b430] | 306 | |
---|
[dcf29d7] | 307 | obj.manager = self.manager |
---|
| 308 | obj.event_owner = self.event_owner |
---|
[71f0373] | 309 | obj.disp_list = copy.deepcopy(self.disp_list) |
---|
[2f4b430] | 310 | |
---|
[c477b31] | 311 | obj.enable2D = copy.deepcopy(self.enable2D) |
---|
[cfc0913] | 312 | obj.parameters = copy.deepcopy(self.parameters) |
---|
[fb59ed9] | 313 | obj.str_parameters = copy.deepcopy(self.str_parameters) |
---|
[cfc0913] | 314 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
---|
| 315 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
---|
[f32d144] | 316 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
---|
[c8e1996] | 317 | obj.orientation_params_disp = \ |
---|
| 318 | copy.deepcopy(self.orientation_params_disp) |
---|
[b787e68c] | 319 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
---|
[fc6ea43] | 320 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
---|
[0aeabc6] | 321 | obj.tcChi = self.tcChi |
---|
[2f4b430] | 322 | |
---|
[f32d144] | 323 | if len(self._disp_obj_dict) > 0: |
---|
| 324 | for k, v in self._disp_obj_dict.iteritems(): |
---|
| 325 | obj._disp_obj_dict[k] = v |
---|
| 326 | if len(self.disp_cb_dict) > 0: |
---|
| 327 | for k, v in self.disp_cb_dict.iteritems(): |
---|
| 328 | obj.disp_cb_dict[k] = v |
---|
| 329 | if len(self.values) > 0: |
---|
| 330 | for k, v in self.values.iteritems(): |
---|
[2296316] | 331 | obj.values[k] = v |
---|
[f32d144] | 332 | if len(self.weights) > 0: |
---|
| 333 | for k, v in self.weights.iteritems(): |
---|
[2296316] | 334 | obj.weights[k] = v |
---|
[b787e68c] | 335 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
---|
[fc6ea43] | 336 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
---|
[7609f1a] | 337 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
---|
| 338 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
---|
| 339 | obj.smear_type = copy.deepcopy(self.smear_type) |
---|
[55bb249c] | 340 | obj.dI_noweight = copy.deepcopy(self.dI_noweight) |
---|
| 341 | obj.dI_didata = copy.deepcopy(self.dI_didata) |
---|
| 342 | obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata) |
---|
| 343 | obj.dI_idata = copy.deepcopy(self.dI_idata) |
---|
[7609f1a] | 344 | obj.dq_l = copy.deepcopy(self.dq_l) |
---|
| 345 | obj.dq_r = copy.deepcopy(self.dq_r) |
---|
[d85f1d8a] | 346 | obj.dx_percent = copy.deepcopy(self.dx_percent) |
---|
[096181d] | 347 | obj.dx_old = copy.deepcopy(self.dx_old) |
---|
[db8fd5b] | 348 | obj.dxl = copy.deepcopy(self.dxl) |
---|
[2f4b430] | 349 | obj.dxw = copy.deepcopy(self.dxw) |
---|
[b787e68c] | 350 | obj.disp_box = copy.deepcopy(self.disp_box) |
---|
| 351 | obj.qmin = copy.deepcopy(self.qmin) |
---|
| 352 | obj.qmax = copy.deepcopy(self.qmax) |
---|
[c0ff8cc] | 353 | obj.multi_factor = self.multi_factor |
---|
[318b5bbb] | 354 | obj.magnetic_on = self.magnetic_on |
---|
[f32d144] | 355 | obj.npts = copy.deepcopy(self.npts) |
---|
[b787e68c] | 356 | obj.cb1 = copy.deepcopy(self.cb1) |
---|
[3370922] | 357 | obj.smearer = copy.deepcopy(self.smearer) |
---|
[fa487d93] | 358 | obj.version = copy.deepcopy(self.version) |
---|
[2f4b430] | 359 | |
---|
[a074145] | 360 | for name, state in self.saved_states.iteritems(): |
---|
| 361 | copy_name = copy.deepcopy(name) |
---|
| 362 | copy_state = state.clone() |
---|
[f32d144] | 363 | obj.saved_states[copy_name] = copy_state |
---|
[6f023e8] | 364 | return obj |
---|
[2f4b430] | 365 | |
---|
[a321c52] | 366 | def _old_first_model(self): |
---|
[8898558b] | 367 | """ |
---|
[0de74af] | 368 | Handle save states from 4.0.1 and before where the first item in the |
---|
| 369 | selection boxes of category, formfactor and structurefactor were not |
---|
| 370 | saved. |
---|
[8898558b] | 371 | :return: None |
---|
| 372 | """ |
---|
[71601312] | 373 | if self.categorycombobox == CUSTOM_MODEL_OLD: |
---|
| 374 | self.categorycombobox = CUSTOM_MODEL |
---|
[1c6bad0] | 375 | if self.formfactorcombobox == '': |
---|
[6d2b50b] | 376 | FIRST_FORM = { |
---|
| 377 | 'Shapes' : 'BCCrystalModel', |
---|
| 378 | 'Uncategorized' : 'LineModel', |
---|
| 379 | 'StructureFactor' : 'HardsphereStructure', |
---|
| 380 | 'Ellipsoid' : 'core_shell_ellipsoid', |
---|
| 381 | 'Lamellae' : 'lamellar', |
---|
| 382 | 'Paracrystal' : 'bcc_paracrystal', |
---|
| 383 | 'Parallelepiped' : 'core_shell_parallelepiped', |
---|
| 384 | 'Shape Independent' : 'be_polyelectrolyte', |
---|
| 385 | 'Sphere' : 'adsorbed_layer', |
---|
| 386 | 'Structure Factor' : 'hardsphere', |
---|
[4387385] | 387 | CUSTOM_MODEL : '' |
---|
[6d2b50b] | 388 | } |
---|
| 389 | if self.categorycombobox == '': |
---|
| 390 | if len(self.parameters) == 3: |
---|
| 391 | self.categorycombobox = "Shape-Independent" |
---|
| 392 | self.formfactorcombobox = 'PowerLawAbsModel' |
---|
| 393 | elif len(self.parameters) == 9: |
---|
| 394 | self.categorycombobox = 'Cylinder' |
---|
| 395 | self.formfactorcombobox = 'barbell' |
---|
| 396 | else: |
---|
| 397 | msg = "Save state does not have enough information to load" |
---|
| 398 | msg += " the all of the data." |
---|
[c155a16] | 399 | logger.warning(msg=msg) |
---|
[6d2b50b] | 400 | else: |
---|
| 401 | self.formfactorcombobox = FIRST_FORM[self.categorycombobox] |
---|
[8898558b] | 402 | |
---|
[12361fd] | 403 | @staticmethod |
---|
[ca224b1] | 404 | def param_remap_to_sasmodels_convert(params, is_string=False): |
---|
[3d8c49a] | 405 | """ |
---|
[1c6bad0] | 406 | Remaps the parameters for sasmodels conversion |
---|
[3d8c49a] | 407 | |
---|
[1c6bad0] | 408 | :param params: list of parameters (likely self.parameters) |
---|
| 409 | :return: remapped dictionary of parameters |
---|
[3d8c49a] | 410 | """ |
---|
| 411 | p = dict() |
---|
[1c6bad0] | 412 | for fittable, name, value, _, uncert, lower, upper, units in params: |
---|
[3d8c49a] | 413 | if not value: |
---|
[9a5097c] | 414 | value = np.nan |
---|
[9eb8fae] | 415 | if not uncert or uncert[1] == '' or uncert[1] == 'None': |
---|
[3d8c49a] | 416 | uncert[0] = False |
---|
[9a5097c] | 417 | uncert[1] = np.nan |
---|
[9eb8fae] | 418 | if not upper or upper[1] == '' or upper[1] == 'None': |
---|
[3d8c49a] | 419 | upper[0] = False |
---|
[9a5097c] | 420 | upper[1] = np.nan |
---|
[9eb8fae] | 421 | if not lower or lower[1] == '' or lower[1] == 'None': |
---|
[3d8c49a] | 422 | lower[0] = False |
---|
[9a5097c] | 423 | lower[1] = np.nan |
---|
[0633048] | 424 | if is_string: |
---|
| 425 | p[name] = str(value) |
---|
| 426 | else: |
---|
| 427 | p[name] = float(value) |
---|
[64c7f39] | 428 | p[name + ".fittable"] = bool(fittable) |
---|
| 429 | p[name + ".std"] = float(uncert[1]) |
---|
| 430 | p[name + ".upper"] = float(upper[1]) |
---|
| 431 | p[name + ".lower"] = float(lower[1]) |
---|
| 432 | p[name + ".units"] = units |
---|
[1c6bad0] | 433 | return p |
---|
| 434 | |
---|
[12361fd] | 435 | @staticmethod |
---|
[ca224b1] | 436 | def param_remap_from_sasmodels_convert(params): |
---|
[1c6bad0] | 437 | """ |
---|
| 438 | Converts {name : value} map back to [] param list |
---|
| 439 | :param params: parameter map returned from sasmodels |
---|
| 440 | :return: None |
---|
| 441 | """ |
---|
| 442 | p_map = [] |
---|
| 443 | for name, info in params.iteritems(): |
---|
| 444 | if ".fittable" in name or ".std" in name or ".upper" in name or \ |
---|
| 445 | ".lower" in name or ".units" in name: |
---|
| 446 | pass |
---|
| 447 | else: |
---|
| 448 | fittable = params.get(name + ".fittable", True) |
---|
| 449 | std = params.get(name + ".std", '0.0') |
---|
| 450 | upper = params.get(name + ".upper", 'inf') |
---|
| 451 | lower = params.get(name + ".lower", '-inf') |
---|
| 452 | units = params.get(name + ".units") |
---|
[9a5097c] | 453 | if std is not None and std is not np.nan: |
---|
[1c6bad0] | 454 | std = [True, str(std)] |
---|
| 455 | else: |
---|
| 456 | std = [False, ''] |
---|
[9a5097c] | 457 | if lower is not None and lower is not np.nan: |
---|
[1c6bad0] | 458 | lower = [True, str(lower)] |
---|
| 459 | else: |
---|
| 460 | lower = [True, '-inf'] |
---|
[9a5097c] | 461 | if upper is not None and upper is not np.nan: |
---|
[1c6bad0] | 462 | upper = [True, str(upper)] |
---|
| 463 | else: |
---|
| 464 | upper = [True, 'inf'] |
---|
| 465 | param_list = [bool(fittable), str(name), str(info), |
---|
| 466 | "+/-", std, lower, upper, str(units)] |
---|
| 467 | p_map.append(param_list) |
---|
| 468 | return p_map |
---|
[377c19a2] | 469 | |
---|
[1c6bad0] | 470 | def _convert_to_sasmodels(self): |
---|
| 471 | """ |
---|
| 472 | Convert parameters to a form usable by sasmodels converter |
---|
| 473 | |
---|
| 474 | :return: None |
---|
| 475 | """ |
---|
| 476 | # Create conversion dictionary to send to sasmodels |
---|
[a321c52] | 477 | self._old_first_model() |
---|
[1c6bad0] | 478 | p = self.param_remap_to_sasmodels_convert(self.parameters) |
---|
[9e0aa69a] | 479 | structurefactor, params = convert.convert_model(self.structurecombobox, |
---|
| 480 | p, False, self.version) |
---|
| 481 | formfactor, params = convert.convert_model(self.formfactorcombobox, |
---|
| 482 | params, False, self.version) |
---|
[1c6bad0] | 483 | if len(self.str_parameters) > 0: |
---|
[0633048] | 484 | str_pars = self.param_remap_to_sasmodels_convert( |
---|
| 485 | self.str_parameters, True) |
---|
| 486 | formfactor, str_params = convert.convert_model( |
---|
[fa487d93] | 487 | self.formfactorcombobox, str_pars, False, self.version) |
---|
[0633048] | 488 | for key, value in str_params.iteritems(): |
---|
| 489 | params[key] = value |
---|
[3d8c49a] | 490 | |
---|
[fa487d93] | 491 | if self.formfactorcombobox == 'SphericalSLDModel': |
---|
| 492 | self.multi_factor += 1 |
---|
| 493 | self.formfactorcombobox = formfactor |
---|
| 494 | self.structurecombobox = structurefactor |
---|
| 495 | self.parameters = [] |
---|
| 496 | self.parameters = self.param_remap_from_sasmodels_convert(params) |
---|
[3d8c49a] | 497 | |
---|
[61cada5] | 498 | def _repr_helper(self, list, rep): |
---|
| 499 | """ |
---|
[5062bbf] | 500 | Helper method to print a state |
---|
[61cada5] | 501 | """ |
---|
| 502 | for item in list: |
---|
[f32d144] | 503 | rep += "parameter name: %s \n" % str(item[1]) |
---|
| 504 | rep += "value: %s\n" % str(item[2]) |
---|
| 505 | rep += "selected: %s\n" % str(item[0]) |
---|
| 506 | rep += "error displayed : %s \n" % str(item[4][0]) |
---|
| 507 | rep += "error value:%s \n" % str(item[4][1]) |
---|
| 508 | rep += "minimum displayed : %s \n" % str(item[5][0]) |
---|
| 509 | rep += "minimum value : %s \n" % str(item[5][1]) |
---|
| 510 | rep += "maximum displayed : %s \n" % str(item[6][0]) |
---|
| 511 | rep += "maximum value : %s \n" % str(item[6][1]) |
---|
| 512 | rep += "parameter unit: %s\n\n" % str(item[7]) |
---|
[240b9966] | 513 | return rep |
---|
[2f4b430] | 514 | |
---|
[61cada5] | 515 | def __repr__(self): |
---|
[f32d144] | 516 | """ |
---|
[5062bbf] | 517 | output string for printing |
---|
[11a7e11] | 518 | """ |
---|
[f32d144] | 519 | rep = "\nState name: %s\n" % self.file |
---|
[11a7e11] | 520 | t = time.localtime(self.timestamp) |
---|
[deff488] | 521 | time_str = time.strftime("%b %d %Y %H;%M;%S ", t) |
---|
[c0ff8cc] | 522 | |
---|
[f32d144] | 523 | rep += "State created: %s\n" % time_str |
---|
[998ca90] | 524 | rep += "State form factor combobox selection: %s\n" % \ |
---|
| 525 | self.formfactorcombobox |
---|
| 526 | rep += "State structure factor combobox selection: %s\n" % \ |
---|
| 527 | self.structurecombobox |
---|
[f32d144] | 528 | rep += "is data : %s\n" % self.is_data |
---|
| 529 | rep += "data's name : %s\n" % self.data_name |
---|
| 530 | rep += "data's id : %s\n" % self.data_id |
---|
[a95ae9a] | 531 | if self.model is not None: |
---|
[93f0a862] | 532 | m_name = self.model.__class__.__name__ |
---|
| 533 | if m_name == 'Model': |
---|
| 534 | m_name = self.m_name |
---|
[f32d144] | 535 | rep += "model name : %s\n" % m_name |
---|
[74dc0a4] | 536 | else: |
---|
| 537 | rep += "model name : None\n" |
---|
[f32d144] | 538 | rep += "multi_factor : %s\n" % str(self.multi_factor) |
---|
[2f4b430] | 539 | rep += "magnetic_on : %s\n" % str(self.magnetic_on) |
---|
[ea5fa58] | 540 | rep += "model type (Category) selected: %s\n" % self.categorycombobox |
---|
[f32d144] | 541 | rep += "data : %s\n" % str(self.data) |
---|
[a95ae9a] | 542 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % \ |
---|
[c8e1996] | 543 | (str(self.qmin), str(self.qmax), str(self.npts)) |
---|
[f32d144] | 544 | rep += "Dispersion selection : %s\n" % str(self.disp_box) |
---|
| 545 | rep += "Smearing enable : %s\n" % str(self.enable_smearer) |
---|
| 546 | rep += "Smearing disable : %s\n" % str(self.disable_smearer) |
---|
| 547 | rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer) |
---|
| 548 | rep += "Slit smearer enable : %s\n" % str(self.slit_smearer) |
---|
| 549 | rep += "Dispersity enable : %s\n" % str(self.enable_disp) |
---|
| 550 | rep += "Dispersity disable : %s\n" % str(self.disable_disp) |
---|
| 551 | rep += "Slit smearer enable: %s\n" % str(self.slit_smearer) |
---|
[2f4b430] | 552 | |
---|
[f32d144] | 553 | rep += "dI_noweight : %s\n" % str(self.dI_noweight) |
---|
| 554 | rep += "dI_didata : %s\n" % str(self.dI_didata) |
---|
| 555 | rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata) |
---|
| 556 | rep += "dI_idata : %s\n" % str(self.dI_idata) |
---|
[2f4b430] | 557 | |
---|
[f32d144] | 558 | rep += "2D enable : %s\n" % str(self.enable2D) |
---|
[c8e1996] | 559 | rep += "All parameters checkbox selected: %s\n" % self.cb1 |
---|
[f32d144] | 560 | rep += "Value of Chisqr : %s\n" % str(self.tcChi) |
---|
[c8e1996] | 561 | rep += "Smear object : %s\n" % self.smearer |
---|
| 562 | rep += "Smear type : %s\n" % self.smear_type |
---|
[f32d144] | 563 | rep += "dq_l : %s\n" % self.dq_l |
---|
| 564 | rep += "dq_r : %s\n" % self.dq_r |
---|
[d85f1d8a] | 565 | rep += "dx_percent : %s\n" % str(self.dx_percent) |
---|
[db8fd5b] | 566 | rep += "dxl : %s\n" % str(self.dxl) |
---|
[2f4b430] | 567 | rep += "dxw : %s\n" % str(self.dxw) |
---|
[f32d144] | 568 | rep += "model : %s\n\n" % str(self.model) |
---|
[2296316] | 569 | temp_parameters = [] |
---|
| 570 | temp_fittable_param = [] |
---|
| 571 | if self.data.__class__.__name__ == "Data2D": |
---|
| 572 | self.is_2D = True |
---|
| 573 | else: |
---|
| 574 | self.is_2D = False |
---|
| 575 | if self.data is not None: |
---|
| 576 | if not self.is_2D: |
---|
| 577 | for item in self.parameters: |
---|
[a95ae9a] | 578 | if item not in self.orientation_params: |
---|
[2296316] | 579 | temp_parameters.append(item) |
---|
| 580 | for item in self.fittable_param: |
---|
[a95ae9a] | 581 | if item not in self.orientation_params_disp: |
---|
[2296316] | 582 | temp_fittable_param.append(item) |
---|
| 583 | else: |
---|
| 584 | temp_parameters = self.parameters |
---|
| 585 | temp_fittable_param = self.fittable_param |
---|
[2f4b430] | 586 | |
---|
[a95ae9a] | 587 | rep += "number parameters(self.parameters): %s\n" % \ |
---|
| 588 | len(temp_parameters) |
---|
[f32d144] | 589 | rep = self._repr_helper(list=temp_parameters, rep=rep) |
---|
[a95ae9a] | 590 | rep += "number str_parameters(self.str_parameters): %s\n" % \ |
---|
| 591 | len(self.str_parameters) |
---|
[f32d144] | 592 | rep = self._repr_helper(list=self.str_parameters, rep=rep) |
---|
[a95ae9a] | 593 | rep += "number fittable_param(self.fittable_param): %s\n" % \ |
---|
| 594 | len(temp_fittable_param) |
---|
[f32d144] | 595 | rep = self._repr_helper(list=temp_fittable_param, rep=rep) |
---|
[61cada5] | 596 | return rep |
---|
[2296316] | 597 | |
---|
| 598 | def set_report_string(self): |
---|
| 599 | """ |
---|
[f32d144] | 600 | Get the values (strings) from __str__ for report |
---|
[2296316] | 601 | """ |
---|
[d06ae30] | 602 | # Dictionary of the report strings |
---|
[2296316] | 603 | repo_time = "" |
---|
| 604 | model_name = "" |
---|
| 605 | title = "" |
---|
| 606 | title_name = "" |
---|
| 607 | file_name = "" |
---|
| 608 | param_string = "" |
---|
| 609 | paramval_string = "" |
---|
| 610 | chi2_string = "" |
---|
| 611 | q_range = "" |
---|
| 612 | strings = self.__repr__() |
---|
| 613 | lines = strings.split('\n') |
---|
| 614 | |
---|
| 615 | # get all string values from __str__() |
---|
| 616 | for line in lines: |
---|
| 617 | value = "" |
---|
| 618 | content = line.split(":") |
---|
| 619 | name = content[0] |
---|
| 620 | try: |
---|
| 621 | value = content[1] |
---|
[7673ecd] | 622 | except Exception: |
---|
[c8e1996] | 623 | msg = "Report string expected 'name: value' but got %r" % line |
---|
[c155a16] | 624 | logger.error(msg) |
---|
[b7c6a4a] | 625 | if name.count("State created"): |
---|
| 626 | repo_time = "" + value |
---|
[2296316] | 627 | if name.count("parameter name"): |
---|
| 628 | val_name = value.split(".") |
---|
| 629 | if len(val_name) > 1: |
---|
| 630 | if val_name[1].count("width"): |
---|
| 631 | param_string += value + ',' |
---|
| 632 | else: |
---|
| 633 | continue |
---|
| 634 | else: |
---|
| 635 | param_string += value + ',' |
---|
| 636 | if name == "value": |
---|
| 637 | param_string += value + ',' |
---|
[c8e1996] | 638 | fixed_parameter = False |
---|
[b1e609c] | 639 | if name == "selected": |
---|
| 640 | if value == u' False': |
---|
| 641 | fixed_parameter = True |
---|
[2296316] | 642 | if name == "error value": |
---|
[b1e609c] | 643 | if fixed_parameter: |
---|
| 644 | param_string += '(fixed),' |
---|
| 645 | else: |
---|
[d06ae30] | 646 | param_string += value + ',' |
---|
[2296316] | 647 | if name == "parameter unit": |
---|
[f32d144] | 648 | param_string += value + ':' |
---|
[2296316] | 649 | if name == "Value of Chisqr ": |
---|
| 650 | chi2 = ("Chi2/Npts = " + value) |
---|
| 651 | chi2_string = CENTRE % chi2 |
---|
| 652 | if name == "Title": |
---|
| 653 | if len(value.strip()) == 0: |
---|
| 654 | continue |
---|
| 655 | title = value + " [" + repo_time + "]" |
---|
| 656 | title_name = HEADER % title |
---|
| 657 | if name == "data ": |
---|
| 658 | try: |
---|
[b1e609c] | 659 | file_value = ("File name:" + content[2]) |
---|
| 660 | file_name = CENTRE % file_value |
---|
[2296316] | 661 | if len(title) == 0: |
---|
| 662 | title = content[2] + " [" + repo_time + "]" |
---|
| 663 | title_name = HEADER % title |
---|
[7673ecd] | 664 | except Exception: |
---|
[6c382da] | 665 | msg = "While parsing 'data: ...'\n" |
---|
[c155a16] | 666 | logger.error(msg + traceback.format_exc()) |
---|
[74dc0a4] | 667 | if name == "model name ": |
---|
| 668 | try: |
---|
| 669 | modelname = "Model name:" + content[1] |
---|
| 670 | except: |
---|
| 671 | modelname = "Model name:" + " NAN" |
---|
[f32d144] | 672 | model_name = CENTRE % modelname |
---|
[2f4b430] | 673 | |
---|
[2296316] | 674 | if name == "Plotting Range": |
---|
| 675 | try: |
---|
| 676 | q_range = content[1] + " = " + content[2] \ |
---|
| 677 | + " = " + content[3].split(",")[0] |
---|
| 678 | q_name = ("Q Range: " + q_range) |
---|
| 679 | q_range = CENTRE % q_name |
---|
[7673ecd] | 680 | except Exception: |
---|
[6c382da] | 681 | msg = "While parsing 'Plotting Range: ...'\n" |
---|
[c155a16] | 682 | logger.error(msg + traceback.format_exc()) |
---|
[2296316] | 683 | paramval = "" |
---|
[f32d144] | 684 | for lines in param_string.split(":"): |
---|
[2296316] | 685 | line = lines.split(",") |
---|
[f32d144] | 686 | if len(lines) > 0: |
---|
| 687 | param = line[0] |
---|
[2296316] | 688 | param += " = " + line[1] |
---|
| 689 | if len(line[2].split()) > 0 and not line[2].count("None"): |
---|
| 690 | param += " +- " + line[2] |
---|
| 691 | if len(line[3].split()) > 0 and not line[3].count("None"): |
---|
| 692 | param += " " + line[3] |
---|
| 693 | if not paramval.count(param): |
---|
[f32d144] | 694 | paramval += param + "\n" |
---|
[2296316] | 695 | paramval_string += CENTRE % param + "\n" |
---|
[2f4b430] | 696 | |
---|
[a95ae9a] | 697 | text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \ |
---|
| 698 | (title, file, q_name, chi2, paramval) |
---|
[2f4b430] | 699 | |
---|
[f5bdb4a] | 700 | title_name = self._check_html_format(title_name) |
---|
| 701 | file_name = self._check_html_format(file_name) |
---|
| 702 | title = self._check_html_format(title) |
---|
[2f4b430] | 703 | |
---|
[2296316] | 704 | html_string = title_name + "\n" + file_name + \ |
---|
[f32d144] | 705 | "\n" + model_name + \ |
---|
[2296316] | 706 | "\n" + q_range + \ |
---|
| 707 | "\n" + chi2_string + \ |
---|
| 708 | "\n" + ELINE + \ |
---|
| 709 | "\n" + paramval_string + \ |
---|
| 710 | "\n" + ELINE + \ |
---|
| 711 | "\n" + FEET_1 % title + \ |
---|
[f32d144] | 712 | "\n" + FEET_2 |
---|
[2f4b430] | 713 | |
---|
[2296316] | 714 | return html_string, text_string, title |
---|
[2f4b430] | 715 | |
---|
[f5bdb4a] | 716 | def _check_html_format(self, name): |
---|
| 717 | """ |
---|
| 718 | Check string '%' for html format |
---|
| 719 | """ |
---|
| 720 | if name.count('%'): |
---|
| 721 | name = name.replace('%', '%') |
---|
[2f4b430] | 722 | |
---|
[f5bdb4a] | 723 | return name |
---|
[2f4b430] | 724 | |
---|
[2296316] | 725 | def report(self, figs=None, canvases=None): |
---|
| 726 | """ |
---|
| 727 | Invoke report dialog panel |
---|
[2f4b430] | 728 | |
---|
[2296316] | 729 | : param figs: list of pylab figures [list] |
---|
| 730 | """ |
---|
[d85c194] | 731 | from sas.sasgui.perspectives.fitting.report_dialog import ReportDialog |
---|
[2296316] | 732 | # get the strings for report |
---|
| 733 | html_str, text_str, title = self.set_report_string() |
---|
| 734 | # Allow 2 figures to append |
---|
| 735 | if len(figs) == 1: |
---|
[f32d144] | 736 | add_str = FEET_3 |
---|
[2296316] | 737 | elif len(figs) == 2: |
---|
[f32d144] | 738 | add_str = ELINE |
---|
| 739 | add_str += FEET_2 % ("%s") |
---|
| 740 | add_str += ELINE |
---|
| 741 | add_str += FEET_3 |
---|
[2296316] | 742 | elif len(figs) > 2: |
---|
[f32d144] | 743 | add_str = ELINE |
---|
| 744 | add_str += FEET_2 % ("%s") |
---|
| 745 | add_str += ELINE |
---|
| 746 | add_str += FEET_2 % ("%s") |
---|
| 747 | add_str += ELINE |
---|
| 748 | add_str += FEET_3 |
---|
[2296316] | 749 | else: |
---|
| 750 | add_str = "" |
---|
[c0ff8cc] | 751 | |
---|
[2296316] | 752 | # final report html strings |
---|
| 753 | report_str = html_str % ("%s") + add_str |
---|
| 754 | |
---|
| 755 | # make plot image |
---|
| 756 | images = self.set_plot_state(figs, canvases) |
---|
[f32d144] | 757 | report_list = [report_str, text_str, images] |
---|
[6f16e25] | 758 | dialog = ReportDialog(report_list, None, wx.ID_ANY, "") |
---|
[d838715] | 759 | dialog.Show() |
---|
[2f4b430] | 760 | |
---|
[c8e1996] | 761 | def _to_xml_helper(self, thelist, element, newdoc): |
---|
[61cada5] | 762 | """ |
---|
[5062bbf] | 763 | Helper method to create xml file for saving state |
---|
[61cada5] | 764 | """ |
---|
[eddb6ec] | 765 | for item in thelist: |
---|
[61cada5] | 766 | sub_element = newdoc.createElement('parameter') |
---|
| 767 | sub_element.setAttribute('name', str(item[1])) |
---|
| 768 | sub_element.setAttribute('value', str(item[2])) |
---|
| 769 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
---|
| 770 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
---|
| 771 | sub_element.setAttribute('error_value', str(item[4][1])) |
---|
| 772 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
---|
| 773 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
---|
| 774 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
---|
| 775 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
---|
| 776 | sub_element.setAttribute('unit', str(item[7])) |
---|
| 777 | element.appendChild(sub_element) |
---|
[2f4b430] | 778 | |
---|
[c8e1996] | 779 | def to_xml(self, file="fitting_state.fitv", doc=None, |
---|
| 780 | entry_node=None, batch_fit_state=None): |
---|
[61cada5] | 781 | """ |
---|
[a95ae9a] | 782 | Writes the state of the fit panel to file, as XML. |
---|
[2f4b430] | 783 | |
---|
[5062bbf] | 784 | Compatible with standalone writing, or appending to an |
---|
[998ca90] | 785 | already existing XML document. In that case, the XML document is |
---|
| 786 | required. An optional entry node in the XML document may also be given. |
---|
[2f4b430] | 787 | |
---|
[5062bbf] | 788 | :param file: file to write to |
---|
| 789 | :param doc: XML document object [optional] |
---|
[998ca90] | 790 | :param entry_node: XML node within the XML document at which we |
---|
| 791 | will append the data [optional] |
---|
[c8e1996] | 792 | :param batch_fit_state: simultaneous fit state |
---|
[61cada5] | 793 | """ |
---|
| 794 | from xml.dom.minidom import getDOMImplementation |
---|
[71f0373] | 795 | |
---|
[61cada5] | 796 | # Check whether we have to write a standalone XML file |
---|
| 797 | if doc is None: |
---|
| 798 | impl = getDOMImplementation() |
---|
[f32d144] | 799 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
---|
[61cada5] | 800 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
---|
| 801 | top_element = newdoc.documentElement |
---|
| 802 | else: |
---|
| 803 | # We are appending to an existing document |
---|
| 804 | newdoc = doc |
---|
[ac5b69d] | 805 | try: |
---|
| 806 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
| 807 | except: |
---|
| 808 | string = etree.tostring(doc, pretty_print=True) |
---|
| 809 | newdoc = parseString(string) |
---|
| 810 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
[61cada5] | 811 | if entry_node is None: |
---|
| 812 | newdoc.documentElement.appendChild(top_element) |
---|
| 813 | else: |
---|
[ac5b69d] | 814 | try: |
---|
| 815 | entry_node.appendChild(top_element) |
---|
| 816 | except: |
---|
| 817 | node_name = entry_node.tag |
---|
| 818 | node_list = newdoc.getElementsByTagName(node_name) |
---|
| 819 | entry_node = node_list.item(0) |
---|
| 820 | entry_node.appendChild(top_element) |
---|
[2f4b430] | 821 | |
---|
[61cada5] | 822 | attr = newdoc.createAttribute("version") |
---|
[27109e5] | 823 | from sas import sasview |
---|
[9e0aa69a] | 824 | attr.nodeValue = sasview.__version__ |
---|
| 825 | # attr.nodeValue = '1.0' |
---|
[61cada5] | 826 | top_element.setAttributeNode(attr) |
---|
[2f4b430] | 827 | |
---|
[61cada5] | 828 | # File name |
---|
| 829 | element = newdoc.createElement("filename") |
---|
| 830 | if self.file is not None: |
---|
| 831 | element.appendChild(newdoc.createTextNode(str(self.file))) |
---|
| 832 | else: |
---|
| 833 | element.appendChild(newdoc.createTextNode(str(file))) |
---|
| 834 | top_element.appendChild(element) |
---|
[2f4b430] | 835 | |
---|
[11a7e11] | 836 | element = newdoc.createElement("timestamp") |
---|
| 837 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
---|
| 838 | attr = newdoc.createAttribute("epoch") |
---|
| 839 | attr.nodeValue = str(self.timestamp) |
---|
| 840 | element.setAttributeNode(attr) |
---|
| 841 | top_element.appendChild(element) |
---|
[a95ae9a] | 842 | |
---|
[61cada5] | 843 | # Inputs |
---|
| 844 | inputs = newdoc.createElement("Attributes") |
---|
| 845 | top_element.appendChild(inputs) |
---|
[2f4b430] | 846 | |
---|
[61cada5] | 847 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 848 | self.data_group_id = self.data.group_id |
---|
| 849 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
| 850 | self.is_data = self.data.is_data |
---|
| 851 | if self.data is not None: |
---|
| 852 | self.data_name = self.data.name |
---|
| 853 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 854 | self.data_id = self.data.id |
---|
[2f4b430] | 855 | |
---|
[b1e609c] | 856 | for item in LIST_OF_DATA_ATTRIBUTES: |
---|
[0b12abb5] | 857 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 858 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
---|
[f32d144] | 859 | inputs.appendChild(element) |
---|
[2f4b430] | 860 | |
---|
[b1e609c] | 861 | for item in LIST_OF_STATE_ATTRIBUTES: |
---|
[26f3dd5] | 862 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 863 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
---|
[26f3dd5] | 864 | inputs.appendChild(element) |
---|
[2f4b430] | 865 | |
---|
[f32d144] | 866 | # For self.values ={ disp_param_name: [vals,...],...} |
---|
| 867 | # and for self.weights ={ disp_param_name: [weights,...],...} |
---|
[b1e609c] | 868 | for item in LIST_OF_MODEL_ATTRIBUTES: |
---|
[11a7e11] | 869 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 870 | value_list = getattr(self, item[1]) |
---|
| 871 | for key, value in value_list.iteritems(): |
---|
[2296316] | 872 | sub_element = newdoc.createElement(key) |
---|
| 873 | sub_element.setAttribute('name', str(key)) |
---|
| 874 | for val in value: |
---|
[b1e609c] | 875 | sub_element.appendChild(newdoc.createTextNode(str(val))) |
---|
[2f4b430] | 876 | |
---|
[f32d144] | 877 | element.appendChild(sub_element) |
---|
[11a7e11] | 878 | inputs.appendChild(element) |
---|
[2f4b430] | 879 | |
---|
[2296316] | 880 | # Create doc for the dictionary of self._disp_obj_dic |
---|
[6c382da] | 881 | for tagname, varname, tagtype in DISPERSION_LIST: |
---|
| 882 | element = newdoc.createElement(tagname) |
---|
| 883 | value_list = getattr(self, varname) |
---|
| 884 | for key, value in value_list.iteritems(): |
---|
[f32d144] | 885 | sub_element = newdoc.createElement(key) |
---|
| 886 | sub_element.setAttribute('name', str(key)) |
---|
| 887 | sub_element.setAttribute('value', str(value)) |
---|
| 888 | element.appendChild(sub_element) |
---|
| 889 | inputs.appendChild(element) |
---|
[2f4b430] | 890 | |
---|
[b1e609c] | 891 | for item in LIST_OF_STATE_PARAMETERS: |
---|
[61cada5] | 892 | element = newdoc.createElement(item[0]) |
---|
[c8e1996] | 893 | self._to_xml_helper(thelist=getattr(self, item[1]), |
---|
| 894 | element=element, newdoc=newdoc) |
---|
[61cada5] | 895 | inputs.appendChild(element) |
---|
[2f4b430] | 896 | |
---|
[a95ae9a] | 897 | # Combined and Simultaneous Fit Parameters |
---|
| 898 | if batch_fit_state is not None: |
---|
| 899 | batch_combo = newdoc.createElement('simultaneous_fit') |
---|
| 900 | top_element.appendChild(batch_combo) |
---|
| 901 | |
---|
| 902 | # Simultaneous Fit Number For Linking Later |
---|
| 903 | element = newdoc.createElement('sim_fit_number') |
---|
| 904 | element.setAttribute('fit_number', str(batch_fit_state.fit_page_no)) |
---|
| 905 | batch_combo.appendChild(element) |
---|
| 906 | |
---|
| 907 | # Save constraints |
---|
| 908 | constraints = newdoc.createElement('constraints') |
---|
| 909 | batch_combo.appendChild(constraints) |
---|
| 910 | for constraint in batch_fit_state.constraints_list: |
---|
[998ca90] | 911 | if constraint.model_cbox.GetValue() != "": |
---|
[c8e1996] | 912 | # model_cbox, param_cbox, egal_txt, constraint, |
---|
| 913 | # btRemove, sizer |
---|
[998ca90] | 914 | doc_cons = newdoc.createElement('constraint') |
---|
| 915 | doc_cons.setAttribute('model_cbox', |
---|
| 916 | str(constraint.model_cbox.GetValue())) |
---|
| 917 | doc_cons.setAttribute('param_cbox', |
---|
| 918 | str(constraint.param_cbox.GetValue())) |
---|
| 919 | doc_cons.setAttribute('egal_txt', |
---|
| 920 | str(constraint.egal_txt.GetLabel())) |
---|
| 921 | doc_cons.setAttribute('constraint', |
---|
| 922 | str(constraint.constraint.GetValue())) |
---|
| 923 | constraints.appendChild(doc_cons) |
---|
[a95ae9a] | 924 | |
---|
| 925 | # Save all models |
---|
| 926 | models = newdoc.createElement('model_list') |
---|
| 927 | batch_combo.appendChild(models) |
---|
| 928 | for model in batch_fit_state.model_list: |
---|
| 929 | doc_model = newdoc.createElement('model_list_item') |
---|
| 930 | doc_model.setAttribute('checked', str(model[0].GetValue())) |
---|
| 931 | keys = model[1].keys() |
---|
| 932 | doc_model.setAttribute('name', str(keys[0])) |
---|
| 933 | values = model[1].get(keys[0]) |
---|
| 934 | doc_model.setAttribute('fit_number', str(model[2])) |
---|
| 935 | doc_model.setAttribute('fit_page_source', str(model[3])) |
---|
| 936 | doc_model.setAttribute('model_name', str(values.model.id)) |
---|
| 937 | models.appendChild(doc_model) |
---|
| 938 | |
---|
| 939 | # Select All Checkbox |
---|
| 940 | element = newdoc.createElement('select_all') |
---|
| 941 | if batch_fit_state.select_all: |
---|
| 942 | element.setAttribute('checked', 'True') |
---|
| 943 | else: |
---|
| 944 | element.setAttribute('checked', 'False') |
---|
| 945 | batch_combo.appendChild(element) |
---|
| 946 | |
---|
[61cada5] | 947 | # Save the file |
---|
| 948 | if doc is None: |
---|
| 949 | fd = open(file, 'w') |
---|
| 950 | fd.write(newdoc.toprettyxml()) |
---|
| 951 | fd.close() |
---|
| 952 | return None |
---|
| 953 | else: |
---|
[ac5b69d] | 954 | return newdoc |
---|
[2f4b430] | 955 | |
---|
[c8e1996] | 956 | def _from_xml_helper(self, node, list): |
---|
[61cada5] | 957 | """ |
---|
[5062bbf] | 958 | Helper function to write state to xml |
---|
[61cada5] | 959 | """ |
---|
| 960 | for item in node: |
---|
[0b12abb5] | 961 | try: |
---|
| 962 | name = item.get('name') |
---|
| 963 | except: |
---|
| 964 | name = None |
---|
| 965 | try: |
---|
| 966 | value = item.get('value') |
---|
| 967 | except: |
---|
| 968 | value = None |
---|
| 969 | try: |
---|
[3ad91de] | 970 | selected_to_fit = (item.get('selected_to_fit') == "True") |
---|
[0b12abb5] | 971 | except: |
---|
| 972 | selected_to_fit = None |
---|
| 973 | try: |
---|
[3ad91de] | 974 | error_displayed = (item.get('error_displayed') == "True") |
---|
[0b12abb5] | 975 | except: |
---|
| 976 | error_displayed = None |
---|
[f32d144] | 977 | try: |
---|
[0b12abb5] | 978 | error_value = item.get('error_value') |
---|
| 979 | except: |
---|
| 980 | error_value = None |
---|
| 981 | try: |
---|
[f32d144] | 982 | minimum_displayed = (item.get('minimum_displayed') == "True") |
---|
[0b12abb5] | 983 | except: |
---|
| 984 | minimum_displayed = None |
---|
| 985 | try: |
---|
| 986 | minimum_value = item.get('minimum_value') |
---|
| 987 | except: |
---|
| 988 | minimum_value = None |
---|
| 989 | try: |
---|
[3ad91de] | 990 | maximum_displayed = (item.get('maximum_displayed') == "True") |
---|
[0b12abb5] | 991 | except: |
---|
| 992 | maximum_displayed = None |
---|
| 993 | try: |
---|
| 994 | maximum_value = item.get('maximum_value') |
---|
| 995 | except: |
---|
| 996 | maximum_value = None |
---|
| 997 | try: |
---|
| 998 | unit = item.get('unit') |
---|
| 999 | except: |
---|
| 1000 | unit = None |
---|
[2296316] | 1001 | list.append([selected_to_fit, name, value, "+/-", |
---|
| 1002 | [error_displayed, error_value], |
---|
[f32d144] | 1003 | [minimum_displayed, minimum_value], |
---|
| 1004 | [maximum_displayed, maximum_value], unit]) |
---|
[2f4b430] | 1005 | |
---|
[c8e1996] | 1006 | def from_xml(self, file=None, node=None): |
---|
[61cada5] | 1007 | """ |
---|
[5062bbf] | 1008 | Load fitting state from a file |
---|
[2f4b430] | 1009 | |
---|
[5062bbf] | 1010 | :param file: .fitv file |
---|
| 1011 | :param node: node of a XML document to read from |
---|
[61cada5] | 1012 | """ |
---|
| 1013 | if file is not None: |
---|
[11a7e11] | 1014 | msg = "PageState no longer supports non-CanSAS" |
---|
| 1015 | msg += " format for fitting files" |
---|
| 1016 | raise RuntimeError, msg |
---|
[2f4b430] | 1017 | |
---|
[9e0aa69a] | 1018 | if node.get('version'): |
---|
[fa487d93] | 1019 | # Get the version for model conversion purposes |
---|
[9e0aa69a] | 1020 | self.version = tuple(int(e) for e in |
---|
| 1021 | str.split(node.get('version'), ".")) |
---|
[fa487d93] | 1022 | # The tuple must be at least 3 items long |
---|
| 1023 | while len(self.version) < 3: |
---|
| 1024 | ver_list = list(self.version) |
---|
| 1025 | ver_list.append(0) |
---|
| 1026 | self.version = tuple(ver_list) |
---|
[2f4b430] | 1027 | |
---|
[61cada5] | 1028 | # Get file name |
---|
| 1029 | entry = get_content('ns:filename', node) |
---|
| 1030 | if entry is not None: |
---|
| 1031 | self.file = entry.text.strip() |
---|
[2f4b430] | 1032 | |
---|
[11a7e11] | 1033 | # Get time stamp |
---|
| 1034 | entry = get_content('ns:timestamp', node) |
---|
| 1035 | if entry is not None and entry.get('epoch'): |
---|
| 1036 | try: |
---|
| 1037 | self.timestamp = float(entry.get('epoch')) |
---|
| 1038 | except: |
---|
| 1039 | msg = "PageState.fromXML: Could not" |
---|
| 1040 | msg += " read timestamp\n %s" % sys.exc_value |
---|
[c155a16] | 1041 | logger.error(msg) |
---|
[2f4b430] | 1042 | |
---|
[61cada5] | 1043 | if entry is not None: |
---|
[c8e1996] | 1044 | # Parse fitting attributes |
---|
| 1045 | entry = get_content('ns:Attributes', node) |
---|
| 1046 | for item in LIST_OF_DATA_ATTRIBUTES: |
---|
| 1047 | node = get_content('ns:%s' % item[0], entry) |
---|
| 1048 | setattr(self, item[0], parse_entry_helper(node, item)) |
---|
| 1049 | |
---|
[d5aff7f] | 1050 | dx_old_node = get_content('ns:%s' % 'dx_min', entry) |
---|
[b1e609c] | 1051 | for item in LIST_OF_STATE_ATTRIBUTES: |
---|
[d5aff7f] | 1052 | if item[0] == "dx_percent" and dx_old_node is not None: |
---|
| 1053 | dxmin = ["dx_min", "dx_min", "float"] |
---|
| 1054 | setattr(self, item[0], parse_entry_helper(dx_old_node, |
---|
| 1055 | dxmin)) |
---|
[096181d] | 1056 | self.dx_old = True |
---|
| 1057 | else: |
---|
[d85f1d8a] | 1058 | node = get_content('ns:%s' % item[0], entry) |
---|
[096181d] | 1059 | setattr(self, item[0], parse_entry_helper(node, item)) |
---|
[2f4b430] | 1060 | |
---|
[b1e609c] | 1061 | for item in LIST_OF_STATE_PARAMETERS: |
---|
[2296316] | 1062 | node = get_content("ns:%s" % item[0], entry) |
---|
[c8e1996] | 1063 | self._from_xml_helper(node=node, |
---|
| 1064 | list=getattr(self, item[1])) |
---|
[2f4b430] | 1065 | |
---|
[f32d144] | 1066 | # Recover _disp_obj_dict from xml file |
---|
| 1067 | self._disp_obj_dict = {} |
---|
[6c382da] | 1068 | for tagname, varname, tagtype in DISPERSION_LIST: |
---|
| 1069 | node = get_content("ns:%s" % tagname, entry) |
---|
[2296316] | 1070 | for attr in node: |
---|
[6c382da] | 1071 | parameter = str(attr.get('name')) |
---|
| 1072 | value = attr.get('value') |
---|
| 1073 | if value.startswith("<"): |
---|
| 1074 | try: |
---|
| 1075 | # <path.to.NamedDistribution object/instance...> |
---|
| 1076 | cls_name = value[1:].split()[0].split('.')[-1] |
---|
| 1077 | cls = getattr(sasmodels.weights, cls_name) |
---|
| 1078 | value = cls.type |
---|
| 1079 | except Exception: |
---|
[998ca90] | 1080 | base = "unable to load distribution %r for %s" |
---|
[c155a16] | 1081 | logger.error(base % (value, parameter)) |
---|
[6c382da] | 1082 | continue |
---|
| 1083 | _disp_obj_dict = getattr(self, varname) |
---|
| 1084 | _disp_obj_dict[parameter] = value |
---|
[2f4b430] | 1085 | |
---|
[f32d144] | 1086 | # get self.values and self.weights dic. if exists |
---|
[6c382da] | 1087 | for tagname, varname in LIST_OF_MODEL_ATTRIBUTES: |
---|
| 1088 | node = get_content("ns:%s" % tagname, entry) |
---|
[2296316] | 1089 | dic = {} |
---|
[b1e609c] | 1090 | value_list = [] |
---|
[2296316] | 1091 | for par in node: |
---|
| 1092 | name = par.get('name') |
---|
[6c382da] | 1093 | values = par.text.split() |
---|
[2296316] | 1094 | # Get lines only with numbers |
---|
| 1095 | for line in values: |
---|
| 1096 | try: |
---|
[f32d144] | 1097 | val = float(line) |
---|
[b1e609c] | 1098 | value_list.append(val) |
---|
[7673ecd] | 1099 | except Exception: |
---|
[2296316] | 1100 | # pass if line is empty (it happens) |
---|
[6c382da] | 1101 | msg = ("Error reading %r from %s %s\n" |
---|
| 1102 | % (line, tagname, name)) |
---|
[c155a16] | 1103 | logger.error(msg + traceback.format_exc()) |
---|
[9a5097c] | 1104 | dic[name] = np.array(value_list) |
---|
[6c382da] | 1105 | setattr(self, varname, dic) |
---|
[2f4b430] | 1106 | |
---|
[2296316] | 1107 | def set_plot_state(self, figs, canvases): |
---|
| 1108 | """ |
---|
| 1109 | Build image state that wx.html understand |
---|
| 1110 | by plotting, putting it into wx.FileSystem image object |
---|
| 1111 | |
---|
| 1112 | """ |
---|
| 1113 | images = [] |
---|
| 1114 | |
---|
| 1115 | # Reset memory |
---|
| 1116 | self.imgRAM = None |
---|
| 1117 | wx.MemoryFSHandler() |
---|
[2f4b430] | 1118 | |
---|
[2296316] | 1119 | # For no figures in the list, prepare empty plot |
---|
[c8e1996] | 1120 | if figs is None or len(figs) == 0: |
---|
[2296316] | 1121 | figs = [None] |
---|
[2f4b430] | 1122 | |
---|
[f32d144] | 1123 | # Loop over the list of figures |
---|
[2296316] | 1124 | # use wx.MemoryFSHandler |
---|
[f32d144] | 1125 | self.imgRAM = wx.MemoryFSHandler() |
---|
[2296316] | 1126 | for fig in figs: |
---|
[c8e1996] | 1127 | if fig is not None: |
---|
[2296316] | 1128 | ind = figs.index(fig) |
---|
| 1129 | canvas = canvases[ind] |
---|
[2f4b430] | 1130 | |
---|
[c8e1996] | 1131 | # store the image in wx.FileSystem Object |
---|
[2296316] | 1132 | wx.FileSystem.AddHandler(wx.MemoryFSHandler()) |
---|
[2f4b430] | 1133 | |
---|
[2296316] | 1134 | # index of the fig |
---|
| 1135 | ind = figs.index(fig) |
---|
[2f4b430] | 1136 | |
---|
[c8e1996] | 1137 | # AddFile, image can be retrieved with 'memory:filename' |
---|
[f32d144] | 1138 | self.imgRAM.AddFile('img_fit%s.png' % ind, |
---|
[2296316] | 1139 | canvas.bitmap, wx.BITMAP_TYPE_PNG) |
---|
[2f4b430] | 1140 | |
---|
[c8e1996] | 1141 | # append figs |
---|
[2296316] | 1142 | images.append(fig) |
---|
[2f4b430] | 1143 | |
---|
[c0ff8cc] | 1144 | return images |
---|
[61cada5] | 1145 | |
---|
[f32d144] | 1146 | |
---|
[61cada5] | 1147 | class Reader(CansasReader): |
---|
| 1148 | """ |
---|
[5062bbf] | 1149 | Class to load a .fitv fitting file |
---|
[61cada5] | 1150 | """ |
---|
[c8e1996] | 1151 | # File type |
---|
[61cada5] | 1152 | type_name = "Fitting" |
---|
[2f4b430] | 1153 | |
---|
[c8e1996] | 1154 | # Wildcards |
---|
[b35d3d1] | 1155 | type = ["Fitting files (*.fitv)|*.fitv" |
---|
[b9a5f0e] | 1156 | "SASView file (*.svs)|*.svs"] |
---|
[c8e1996] | 1157 | # List of allowed extensions |
---|
[f32d144] | 1158 | ext = ['.fitv', '.FITV', '.svs', 'SVS'] |
---|
[2f4b430] | 1159 | |
---|
[61cada5] | 1160 | def __init__(self, call_back=None, cansas=True): |
---|
[df7ed14] | 1161 | CansasReader.__init__(self) |
---|
[61cada5] | 1162 | """ |
---|
[5062bbf] | 1163 | Initialize the call-back method to be called |
---|
| 1164 | after we load a file |
---|
[2f4b430] | 1165 | |
---|
[5062bbf] | 1166 | :param call_back: call-back method |
---|
| 1167 | :param cansas: True = files will be written/read in CanSAS format |
---|
| 1168 | False = write CanSAS format |
---|
[2f4b430] | 1169 | |
---|
[61cada5] | 1170 | """ |
---|
[c8e1996] | 1171 | # Call back method to be executed after a file is read |
---|
[61cada5] | 1172 | self.call_back = call_back |
---|
[c8e1996] | 1173 | # CanSAS format flag |
---|
[61cada5] | 1174 | self.cansas = cansas |
---|
[75fbd17] | 1175 | self.state = None |
---|
[a95ae9a] | 1176 | # batch fitting params for saving |
---|
| 1177 | self.batchfit_params = [] |
---|
[2f4b430] | 1178 | |
---|
[75fbd17] | 1179 | def get_state(self): |
---|
| 1180 | return self.state |
---|
[2f4b430] | 1181 | |
---|
[61cada5] | 1182 | def read(self, path): |
---|
[f32d144] | 1183 | """ |
---|
[5062bbf] | 1184 | Load a new P(r) inversion state from file |
---|
[2f4b430] | 1185 | |
---|
[5062bbf] | 1186 | :param path: file path |
---|
[2f4b430] | 1187 | |
---|
[61cada5] | 1188 | """ |
---|
[c8e1996] | 1189 | if self.cansas: |
---|
[61cada5] | 1190 | return self._read_cansas(path) |
---|
[2f4b430] | 1191 | |
---|
[61cada5] | 1192 | def _parse_state(self, entry): |
---|
| 1193 | """ |
---|
[5062bbf] | 1194 | Read a fit result from an XML node |
---|
[2f4b430] | 1195 | |
---|
[f32d144] | 1196 | :param entry: XML node to read from |
---|
[5062bbf] | 1197 | :return: PageState object |
---|
[61cada5] | 1198 | """ |
---|
| 1199 | # Create an empty state |
---|
[2f4b430] | 1200 | state = None |
---|
[61cada5] | 1201 | # Locate the P(r) node |
---|
| 1202 | try: |
---|
[f32d144] | 1203 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
---|
| 1204 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1205 | if nodes: |
---|
[b35d3d1] | 1206 | # Create an empty state |
---|
[f32d144] | 1207 | state = PageState() |
---|
[c8e1996] | 1208 | state.from_xml(node=nodes[0]) |
---|
[2f4b430] | 1209 | |
---|
[61cada5] | 1210 | except: |
---|
[c155a16] | 1211 | logger.info("XML document does not contain fitting information.\n" |
---|
[6c382da] | 1212 | + traceback.format_exc()) |
---|
[2f4b430] | 1213 | |
---|
[61cada5] | 1214 | return state |
---|
[2f4b430] | 1215 | |
---|
[e89aed5] | 1216 | def _parse_simfit_state(self, entry): |
---|
| 1217 | """ |
---|
| 1218 | Parses the saved data for a simultaneous fit |
---|
| 1219 | :param entry: XML object to read from |
---|
| 1220 | :return: XML object for a simultaneous fit or None |
---|
| 1221 | """ |
---|
| 1222 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
---|
| 1223 | namespaces={'ns': CANSAS_NS}) |
---|
| 1224 | if nodes: |
---|
| 1225 | simfitstate = nodes[0].xpath('ns:simultaneous_fit', |
---|
| 1226 | namespaces={'ns': CANSAS_NS}) |
---|
| 1227 | if simfitstate: |
---|
| 1228 | from simfitpage import SimFitPageState |
---|
| 1229 | sim_fit_state = SimFitPageState() |
---|
| 1230 | simfitstate_0 = simfitstate[0] |
---|
| 1231 | all = simfitstate_0.xpath('ns:select_all', |
---|
[c8e1996] | 1232 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1233 | atts = all[0].attrib |
---|
| 1234 | checked = atts.get('checked') |
---|
| 1235 | sim_fit_state.select_all = bool(checked) |
---|
| 1236 | model_list = simfitstate_0.xpath('ns:model_list', |
---|
[c8e1996] | 1237 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1238 | model_list_items = model_list[0].xpath('ns:model_list_item', |
---|
[c8e1996] | 1239 | namespaces={'ns': |
---|
| 1240 | CANSAS_NS}) |
---|
[e89aed5] | 1241 | for model in model_list_items: |
---|
| 1242 | attrs = model.attrib |
---|
| 1243 | sim_fit_state.model_list.append(attrs) |
---|
[998ca90] | 1244 | |
---|
[e89aed5] | 1245 | constraints = simfitstate_0.xpath('ns:constraints', |
---|
| 1246 | namespaces={'ns': CANSAS_NS}) |
---|
| 1247 | constraint_list = constraints[0].xpath('ns:constraint', |
---|
[998ca90] | 1248 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1249 | for constraint in constraint_list: |
---|
| 1250 | attrs = constraint.attrib |
---|
| 1251 | sim_fit_state.constraints_list.append(attrs) |
---|
| 1252 | |
---|
| 1253 | return sim_fit_state |
---|
| 1254 | else: |
---|
| 1255 | return None |
---|
| 1256 | |
---|
[ac5b69d] | 1257 | def _parse_save_state_entry(self, dom): |
---|
[e9b12eaf] | 1258 | """ |
---|
[5062bbf] | 1259 | Parse a SASentry |
---|
[2f4b430] | 1260 | |
---|
[5062bbf] | 1261 | :param node: SASentry node |
---|
[2f4b430] | 1262 | |
---|
[df7ed14] | 1263 | :return: Data1D/Data2D object |
---|
[2f4b430] | 1264 | |
---|
[e9b12eaf] | 1265 | """ |
---|
[df7ed14] | 1266 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
---|
[af08e55] | 1267 | return_value, _ = self._parse_entry(dom) |
---|
| 1268 | return return_value, _ |
---|
[e9b12eaf] | 1269 | |
---|
[61cada5] | 1270 | def _read_cansas(self, path): |
---|
[f32d144] | 1271 | """ |
---|
[e89aed5] | 1272 | Load data and fitting information from a CanSAS XML file. |
---|
[2f4b430] | 1273 | |
---|
[5062bbf] | 1274 | :param path: file path |
---|
[f32d144] | 1275 | :return: Data1D object if a single SASentry was found, |
---|
[5062bbf] | 1276 | or a list of Data1D objects if multiple entries were found, |
---|
| 1277 | or None of nothing was found |
---|
| 1278 | :raise RuntimeError: when the file can't be opened |
---|
| 1279 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
[61cada5] | 1280 | """ |
---|
| 1281 | output = [] |
---|
[e89aed5] | 1282 | simfitstate = None |
---|
[f32d144] | 1283 | basename = os.path.basename(path) |
---|
[b63dc6e] | 1284 | root, extension = os.path.splitext(basename) |
---|
| 1285 | ext = extension.lower() |
---|
[61cada5] | 1286 | try: |
---|
| 1287 | if os.path.isfile(path): |
---|
[a95ae9a] | 1288 | if ext in self.ext or ext == '.xml': |
---|
[61cada5] | 1289 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
| 1290 | # Check the format version number |
---|
[a95ae9a] | 1291 | # Specifying the namespace will take care of the file |
---|
| 1292 | # format version |
---|
[61cada5] | 1293 | root = tree.getroot() |
---|
[f32d144] | 1294 | entry_list = root.xpath('ns:SASentry', |
---|
| 1295 | namespaces={'ns': CANSAS_NS}) |
---|
| 1296 | for entry in entry_list: |
---|
[e9b12eaf] | 1297 | try: |
---|
[ac5b69d] | 1298 | sas_entry, _ = self._parse_save_state_entry(entry) |
---|
[e9b12eaf] | 1299 | except: |
---|
[df7ed14] | 1300 | raise |
---|
[61cada5] | 1301 | fitstate = self._parse_state(entry) |
---|
[2f4b430] | 1302 | |
---|
[a95ae9a] | 1303 | # state could be None when .svs file is loaded |
---|
| 1304 | # in this case, skip appending to output |
---|
| 1305 | if fitstate is not None: |
---|
[b35d3d1] | 1306 | sas_entry.meta_data['fitstate'] = fitstate |
---|
| 1307 | sas_entry.filename = fitstate.file |
---|
| 1308 | output.append(sas_entry) |
---|
[e89aed5] | 1309 | |
---|
[61cada5] | 1310 | else: |
---|
[b63dc6e] | 1311 | self.call_back(format=ext) |
---|
[61cada5] | 1312 | raise RuntimeError, "%s is not a file" % path |
---|
[b35d3d1] | 1313 | |
---|
[61cada5] | 1314 | # Return output consistent with the loader's api |
---|
[f32d144] | 1315 | if len(output) == 0: |
---|
| 1316 | self.call_back(state=None, datainfo=None, format=ext) |
---|
[61cada5] | 1317 | return None |
---|
| 1318 | else: |
---|
[b35d3d1] | 1319 | for ind in range(len(output)): |
---|
| 1320 | # Call back to post the new state |
---|
| 1321 | state = output[ind].meta_data['fitstate'] |
---|
| 1322 | t = time.localtime(state.timestamp) |
---|
| 1323 | time_str = time.strftime("%b %d %H:%M", t) |
---|
| 1324 | # Check that no time stamp is already appended |
---|
| 1325 | max_char = state.file.find("[") |
---|
| 1326 | if max_char < 0: |
---|
| 1327 | max_char = len(state.file) |
---|
[ef16f59] | 1328 | original_fname = state.file[0:max_char] |
---|
[f32d144] | 1329 | state.file = original_fname + ' [' + time_str + ']' |
---|
[2f4b430] | 1330 | |
---|
[b35d3d1] | 1331 | if state is not None and state.is_data is not None: |
---|
[b1e609c] | 1332 | output[ind].is_data = state.is_data |
---|
[2f4b430] | 1333 | |
---|
[b35d3d1] | 1334 | output[ind].filename = state.file |
---|
| 1335 | state.data = output[ind] |
---|
[f32d144] | 1336 | state.data.name = output[ind].filename # state.data_name |
---|
[b35d3d1] | 1337 | state.data.id = state.data_id |
---|
| 1338 | if state.is_data is not None: |
---|
| 1339 | state.data.is_data = state.is_data |
---|
[f32d144] | 1340 | if output[ind].run_name is not None\ |
---|
[c8e1996] | 1341 | and len(output[ind].run_name) != 0: |
---|
[654e8e0] | 1342 | if isinstance(output[ind].run_name, dict): |
---|
| 1343 | name = output[ind].run_name.keys()[0] |
---|
| 1344 | else: |
---|
| 1345 | name = output[ind].run_name |
---|
[f32d144] | 1346 | else: |
---|
| 1347 | name = original_fname |
---|
[ef16f59] | 1348 | state.data.group_id = name |
---|
[fa487d93] | 1349 | state.version = fitstate.version |
---|
[a95ae9a] | 1350 | # store state in fitting |
---|
[f32d144] | 1351 | self.call_back(state=state, |
---|
| 1352 | datainfo=output[ind], format=ext) |
---|
| 1353 | self.state = state |
---|
[e6de6b8] | 1354 | simfitstate = self._parse_simfit_state(entry) |
---|
[e89aed5] | 1355 | if simfitstate is not None: |
---|
| 1356 | self.call_back(state=simfitstate) |
---|
| 1357 | |
---|
[ef16f59] | 1358 | return output |
---|
[61cada5] | 1359 | except: |
---|
[4bee68d] | 1360 | self.call_back(format=ext) |
---|
[61cada5] | 1361 | raise |
---|
[2f4b430] | 1362 | |
---|
[61cada5] | 1363 | def write(self, filename, datainfo=None, fitstate=None): |
---|
| 1364 | """ |
---|
[b35d3d1] | 1365 | Write the content of a Data1D as a CanSAS XML file only for standalone |
---|
[2f4b430] | 1366 | |
---|
[5062bbf] | 1367 | :param filename: name of the file to write |
---|
| 1368 | :param datainfo: Data1D object |
---|
| 1369 | :param fitstate: PageState object |
---|
[2f4b430] | 1370 | |
---|
[61cada5] | 1371 | """ |
---|
| 1372 | # Sanity check |
---|
[a95ae9a] | 1373 | if self.cansas: |
---|
[61cada5] | 1374 | # Add fitting information to the XML document |
---|
[ef16f59] | 1375 | doc = self.write_toXML(datainfo, fitstate) |
---|
[61cada5] | 1376 | # Write the XML document |
---|
| 1377 | else: |
---|
[c8e1996] | 1378 | doc = fitstate.to_xml(file=filename) |
---|
[2f4b430] | 1379 | |
---|
[ac5b69d] | 1380 | # Save the document no matter the type |
---|
| 1381 | fd = open(filename, 'w') |
---|
| 1382 | fd.write(doc.toprettyxml()) |
---|
| 1383 | fd.close() |
---|
[2f4b430] | 1384 | |
---|
[a95ae9a] | 1385 | def write_toXML(self, datainfo=None, state=None, batchfit=None): |
---|
[b35d3d1] | 1386 | """ |
---|
[f32d144] | 1387 | Write toXML, a helper for write(), |
---|
| 1388 | could be used by guimanager._on_save() |
---|
[2f4b430] | 1389 | |
---|
[b35d3d1] | 1390 | : return: xml doc |
---|
| 1391 | """ |
---|
[3c44c66] | 1392 | |
---|
[a95ae9a] | 1393 | self.batchfit_params = batchfit |
---|
| 1394 | if state.data is None or not state.data.is_data: |
---|
[3b148c3] | 1395 | return None |
---|
[a95ae9a] | 1396 | # make sure title and data run are filled. |
---|
| 1397 | if state.data.title is None or state.data.title == '': |
---|
| 1398 | state.data.title = state.data.name |
---|
| 1399 | if state.data.run_name is None or state.data.run_name == {}: |
---|
| 1400 | state.data.run = [str(state.data.name)] |
---|
| 1401 | state.data.run_name[0] = state.data.name |
---|
| 1402 | |
---|
[83c09af] | 1403 | data = state.data |
---|
| 1404 | doc, sasentry = self._to_xml_doc(data) |
---|
[2f4b430] | 1405 | |
---|
[b35d3d1] | 1406 | if state is not None: |
---|
[c8e1996] | 1407 | doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry, |
---|
| 1408 | batch_fit_state=self.batchfit_params) |
---|
[2f4b430] | 1409 | |
---|
[f32d144] | 1410 | return doc |
---|
[467202f] | 1411 | |
---|
| 1412 | # Simple html report templet |
---|
| 1413 | HEADER = "<html>\n" |
---|
| 1414 | HEADER += "<head>\n" |
---|
| 1415 | HEADER += "<meta http-equiv=Content-Type content='text/html; " |
---|
| 1416 | HEADER += "charset=windows-1252'> \n" |
---|
| 1417 | HEADER += "<meta name=Generator >\n" |
---|
| 1418 | HEADER += "</head>\n" |
---|
| 1419 | HEADER += "<body lang=EN-US>\n" |
---|
| 1420 | HEADER += "<div class=WordSection1>\n" |
---|
| 1421 | HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >" |
---|
| 1422 | HEADER += "%s</font></center></span></center></b></p>" |
---|
| 1423 | HEADER += "<p class=MsoNormal> </p>" |
---|
| 1424 | PARA = "<p class=MsoNormal><font size='4' > %s \n" |
---|
| 1425 | PARA += "</font></p>" |
---|
| 1426 | CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n" |
---|
| 1427 | CENTRE += "</font></center></p>" |
---|
| 1428 | FEET_1 = \ |
---|
| 1429 | """ |
---|
| 1430 | <p class=MsoNormal> </p> |
---|
| 1431 | <br> |
---|
| 1432 | <p class=MsoNormal><b><span ><center> <font size='4' > Graph |
---|
| 1433 | </font></span></center></b></p> |
---|
| 1434 | <p class=MsoNormal> </p> |
---|
| 1435 | <center> |
---|
| 1436 | <br><font size='4' >Model Computation</font> |
---|
| 1437 | <br><font size='4' >Data: "%s"</font><br> |
---|
| 1438 | """ |
---|
| 1439 | FEET_2 = \ |
---|
| 1440 | """ |
---|
| 1441 | <img src="%s" > |
---|
| 1442 | </img> |
---|
| 1443 | """ |
---|
| 1444 | FEET_3 = \ |
---|
| 1445 | """ |
---|
| 1446 | </center> |
---|
| 1447 | </div> |
---|
| 1448 | </body> |
---|
| 1449 | </html> |
---|
| 1450 | """ |
---|
[c8e1996] | 1451 | ELINE = "<p class=MsoNormal> </p>" |
---|