[11a7e11] | 1 | """ |
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| 2 | This software was developed by the University of Tennessee as part of the |
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| 3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 4 | project funded by the US National Science Foundation. |
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[c77d859] | 5 | |
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[11a7e11] | 6 | See the license text in license.txt |
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[c77d859] | 7 | |
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[11a7e11] | 8 | copyright 2009, University of Tennessee |
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| 9 | """ |
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| 10 | import time |
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| 11 | import os |
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| 12 | import sys |
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[6f023e8] | 13 | import copy |
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[11a7e11] | 14 | import logging |
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[c77d859] | 15 | |
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[35b556d] | 16 | import xml.dom.minidom |
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[11a7e11] | 17 | from xml.dom.minidom import parse |
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| 18 | from lxml import etree |
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| 19 | |
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| 20 | import DataLoader |
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[61cada5] | 21 | from DataLoader.readers.cansas_reader import Reader as CansasReader |
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[e9b12eaf] | 22 | from DataLoader.readers.cansas_reader import get_content, write_node |
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[35b556d] | 23 | from DataLoader.data_info import Data2D |
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[61cada5] | 24 | |
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[11a7e11] | 25 | #Information to read/write state as xml |
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[61cada5] | 26 | FITTING_NODE_NAME = 'fitting_plug_in' |
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| 27 | CANSAS_NS = "cansas1d/1.0" |
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| 28 | |
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[26f3dd5] | 29 | list_of_data_attributes = [["is_data", "is_data", "bool"], |
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[61cada5] | 30 | ["group_id", "data_group_id", "string"], |
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| 31 | ["data_name", "data_name", "string"], |
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| 32 | ["data_id", "data_id", "string"], |
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| 33 | ["name", "name", "string"], |
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[26f3dd5] | 34 | ["data_name", "data_name", "string"]] |
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| 35 | list_of_state_attributes = [["qmin", "qmin", "float"], |
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[61cada5] | 36 | ["qmax", "qmax", "float"], |
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| 37 | ["npts", "npts", "float"], |
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| 38 | ["shape_rbutton", "shape_rbutton", "bool"], |
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| 39 | ["shape_indep_rbutton", "shape_indep_rbutton", "bool"], |
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| 40 | ["plugin_rbutton", "plugin_rbutton","bool"], |
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| 41 | ["struct_rbutton", "struct_rbutton", "bool"], |
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| 42 | ["formfactorcombobox", "formfactorcombobox", "bool"], |
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| 43 | ["structurecombobox", "structurecombobox", "bool"], |
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[26f3dd5] | 44 | ["disp_box", "disp_box"], |
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| 45 | ["enable_smearer","enable_smearer","bool"], |
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| 46 | ["disable_smearer","disable_smearer","bool"], |
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| 47 | ["pinhole_smearer","pinhole_smearer","bool"], |
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| 48 | ["slit_smearer","slit_smearer","bool"], |
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| 49 | ["enable_disp","enable_disp","bool"], |
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| 50 | ["disable_disp","disable_disp","bool"], |
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| 51 | ["slit_smearer","slit_smearer","bool"], |
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| 52 | ["enable2D","enable2D","bool"], |
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| 53 | ["cb1","cb1","bool"], |
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[5cc7001] | 54 | ["tcChi","tcChi","float"], |
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| 55 | ["smearer", "smearer", "float"], |
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| 56 | ["smear_type","smear_type", "string"], |
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| 57 | ["dq_l", "dq_l", "string"], |
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| 58 | ["dq_r","dq_r", "string"]] |
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| 59 | |
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[11a7e11] | 60 | list_of_model_attributes = [["values", "values"], |
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| 61 | ["weights", "weights"]] |
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| 62 | |
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[61cada5] | 63 | list_of_state_parameters = [["parameters", "parameters"] , |
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| 64 | ["orientation_parameters", "orientation_params"], |
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| 65 | ["dispersity_parameters", "orientation_params_disp"], |
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| 66 | ["fixed_param", "fixed_param"], |
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| 67 | ["fittable_param","fittable_param"]] |
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[e9b12eaf] | 68 | list_of_data_2d_attr = [["xmin", "xmin"], |
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| 69 | ["xmax","xmax"], |
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| 70 | ["ymin","ymin"], |
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| 71 | ["ymax","ymax"], |
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| 72 | ["_xaxis","_xaxis"], |
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| 73 | ["_xunit", "_xunit"], |
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| 74 | ["_yaxis","_yaxis"], |
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| 75 | ["_yunit","_yunit"], |
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| 76 | ["_zaxis","_zaxis"], |
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| 77 | ["_zunit","_zunit"]] |
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| 78 | list_of_data2d_values = [["qx_data","qx_data"], |
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| 79 | ["qy_data","qy_data"], |
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[35b556d] | 80 | ["dqx_data","dqx_data"], |
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| 81 | ["dqy_data","dqy_data"], |
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[e9b12eaf] | 82 | ["data","data"], |
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| 83 | ["q_data","q_data"], |
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| 84 | ["err_data","err_data"], |
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| 85 | ["mask","mask"],] |
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[61cada5] | 86 | |
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[cfc0913] | 87 | class PageState(object): |
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[c77d859] | 88 | """ |
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[11a7e11] | 89 | Contains information to reconstruct a page of the fitpanel. |
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[c77d859] | 90 | """ |
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[61cada5] | 91 | def __init__(self, parent=None, model=None, data=None): |
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[c77d859] | 92 | |
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| 93 | """ |
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[61cada5] | 94 | Initialize the current state |
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[11a7e11] | 95 | @param model: a selected model within a page |
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| 96 | @param data: |
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[c77d859] | 97 | """ |
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[61cada5] | 98 | self.file = None |
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[11a7e11] | 99 | #Time of state creation |
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| 100 | self.timestamp = time.time() |
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[c77d859] | 101 | ## Data member to store the dispersion object created |
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| 102 | self._disp_obj_dict = {} |
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[61cada5] | 103 | #------------------------ |
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[c77d859] | 104 | #Data used for fitting |
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| 105 | self.data = data |
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[61cada5] | 106 | #save additional information on data that dataloader.reader does not read |
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| 107 | self.is_data = None |
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| 108 | self.data_name = "" |
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| 109 | |
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| 110 | if self.data is not None: |
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| 111 | self.data_name = self.data.name |
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| 112 | self.data_id = None |
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| 113 | if self.data is not None and hasattr(self.data, "id"): |
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| 114 | self.data_id = self.data.id |
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| 115 | self.data_group_id = None |
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| 116 | if self.data is not None and hasattr(self.data, "group_id"): |
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| 117 | self.data_group_id = self.data.group_id |
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| 118 | #------------------------- |
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| 119 | ## reset True change the state of exsiting button |
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| 120 | self.reset = False |
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| 121 | |
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[c99a6c5] | 122 | #engine type |
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| 123 | self.engine_type = None |
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[c77d859] | 124 | # flag to allow data2D plot |
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[cfc0913] | 125 | self.enable2D = False |
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[c77d859] | 126 | # model on which the fit would be performed |
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| 127 | self.model = model |
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[61cada5] | 128 | |
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[c77d859] | 129 | #fit page manager |
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| 130 | self.manager = None |
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| 131 | #Store the parent of this panel parent |
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| 132 | # For this application fitpanel is the parent |
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| 133 | self.parent = parent |
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| 134 | # Event_owner is the owner of model event |
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| 135 | self.event_owner = None |
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[c9a4377] | 136 | ##page name |
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[cfc0913] | 137 | self.page_name = "" |
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[c77d859] | 138 | # Contains link between model ,all its parameters, and panel organization |
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[61cada5] | 139 | self.parameters = [] |
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[c77d859] | 140 | # Contains list of parameters that cannot be fitted and reference to |
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| 141 | #panel objects |
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[61cada5] | 142 | self.fixed_param = [] |
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[c77d859] | 143 | # Contains list of parameters with dispersity and reference to |
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| 144 | #panel objects |
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[61cada5] | 145 | self.fittable_param = [] |
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[60132ef] | 146 | ## orientation parameters |
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[61cada5] | 147 | self.orientation_params = [] |
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[fc6ea43] | 148 | ## orientation parmaters for gaussian dispersity |
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[61cada5] | 149 | self.orientation_params_disp = [] |
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[3370922] | 150 | ## smearer info |
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[61cada5] | 151 | self.smearer = None |
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[7609f1a] | 152 | self.smear_type = None |
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| 153 | self.dq_l = None |
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| 154 | self.dq_r = None |
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| 155 | |
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[c77d859] | 156 | #list of dispersion paramaters |
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[cfc0913] | 157 | self.disp_list =[] |
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[61cada5] | 158 | if self.model is not None: |
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[71f0373] | 159 | self.disp_list = self.model.getDispParamList() |
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[61cada5] | 160 | self._disp_obj_dict = {} |
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| 161 | self.disp_cb_dict = {} |
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| 162 | self.values = [] |
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| 163 | self.weights = [] |
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[dad49a0] | 164 | |
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[c77d859] | 165 | #contains link between a model and selected parameters to fit |
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[61cada5] | 166 | self.param_toFit = [] |
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[a074145] | 167 | ##dictionary of model type and model class |
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[cfc0913] | 168 | self.model_list_box = None |
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[a074145] | 169 | ## save the state of the context menu |
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[61cada5] | 170 | self.saved_states = {} |
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[240b9966] | 171 | ## save selection of combobox |
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[3b9e023] | 172 | self.formfactorcombobox = None |
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| 173 | self.structurecombobox = None |
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[240b9966] | 174 | ## radio box to select type of model |
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| 175 | self.shape_rbutton = False |
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| 176 | self.shape_indep_rbutton = False |
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| 177 | self.struct_rbutton = False |
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| 178 | self.plugin_rbutton = False |
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[b787e68c] | 179 | ## the indice of the current selection |
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| 180 | self.disp_box = 0 |
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[c77d859] | 181 | ## Qrange |
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[cfc0913] | 182 | ## Q range |
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[61cada5] | 183 | self.qmin = 0.001 |
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| 184 | self.qmax = 0.1 |
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[cfc0913] | 185 | self.npts = None |
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[61cada5] | 186 | self.name = "" |
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[cfc0913] | 187 | ## enable smearering state |
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| 188 | self.enable_smearer = False |
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[fc6ea43] | 189 | self.disable_smearer = True |
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[7609f1a] | 190 | self.pinhole_smearer = False |
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| 191 | self.slit_smearer = False |
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[cfc0913] | 192 | ## disperity selection |
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[61cada5] | 193 | self.enable_disp = False |
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| 194 | self.disable_disp = True |
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[11a7e11] | 195 | |
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[cfc0913] | 196 | ## state of selected all check button |
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| 197 | self.cb1 = False |
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[0aeabc6] | 198 | ## store value of chisqr |
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[61cada5] | 199 | self.tcChi = None |
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[240b9966] | 200 | |
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[6f023e8] | 201 | def clone(self): |
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[61cada5] | 202 | """ |
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| 203 | Create a new copy of the current object |
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| 204 | """ |
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| 205 | model = None |
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| 206 | if self.model is not None: |
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[6f023e8] | 207 | model = self.model.clone() |
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[bb70474] | 208 | model.name = self.model.name |
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[61cada5] | 209 | obj = PageState(self.parent, model=model) |
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| 210 | obj.file = copy.deepcopy(self.file) |
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[6f023e8] | 211 | obj.data = copy.deepcopy(self.data) |
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[61cada5] | 212 | if self.data is not None: |
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| 213 | self.data_name = self.data.name |
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| 214 | obj.data_name = self.data_name |
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| 215 | obj.is_data = self.is_data |
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[dcf29d7] | 216 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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[c99a6c5] | 217 | obj.engine_type = copy.deepcopy(self.engine_type) |
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[240b9966] | 218 | |
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[61cada5] | 219 | obj.formfactorcombobox = self.formfactorcombobox |
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| 220 | obj.structurecombobox = self.structurecombobox |
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[240b9966] | 221 | |
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| 222 | obj.shape_rbutton = self.shape_rbutton |
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| 223 | obj.shape_indep_rbutton = self.shape_indep_rbutton |
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| 224 | obj.struct_rbutton = self.struct_rbutton |
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| 225 | obj.plugin_rbutton = self.plugin_rbutton |
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| 226 | |
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[dcf29d7] | 227 | obj.manager = self.manager |
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| 228 | obj.event_owner = self.event_owner |
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[71f0373] | 229 | obj.disp_list = copy.deepcopy(self.disp_list) |
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[fc6ea43] | 230 | |
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[c477b31] | 231 | obj.enable2D = copy.deepcopy(self.enable2D) |
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[cfc0913] | 232 | obj.parameters = copy.deepcopy(self.parameters) |
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| 233 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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| 234 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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[60132ef] | 235 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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[fc6ea43] | 236 | obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp) |
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[b787e68c] | 237 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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[fc6ea43] | 238 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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[0aeabc6] | 239 | obj.tcChi = self.tcChi |
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| 240 | |
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[c477b31] | 241 | if len(self._disp_obj_dict)>0: |
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| 242 | for k , v in self._disp_obj_dict.iteritems(): |
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| 243 | obj._disp_obj_dict[k]= v |
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[dad49a0] | 244 | if len(self.disp_cb_dict)>0: |
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| 245 | for k , v in self.disp_cb_dict.iteritems(): |
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| 246 | obj.disp_cb_dict[k]= v |
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[b421b1a] | 247 | |
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[dad49a0] | 248 | obj.values = copy.deepcopy(self.values) |
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| 249 | obj.weights = copy.deepcopy(self.weights) |
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[b787e68c] | 250 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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[fc6ea43] | 251 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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[7609f1a] | 252 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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| 253 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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| 254 | obj.smear_type = copy.deepcopy(self.smear_type) |
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| 255 | obj.dq_l = copy.deepcopy(self.dq_l) |
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| 256 | obj.dq_r = copy.deepcopy(self.dq_r) |
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| 257 | |
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[b787e68c] | 258 | obj.disp_box = copy.deepcopy(self.disp_box) |
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| 259 | obj.qmin = copy.deepcopy(self.qmin) |
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| 260 | obj.qmax = copy.deepcopy(self.qmax) |
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| 261 | obj.npts = copy.deepcopy(self.npts ) |
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| 262 | obj.cb1 = copy.deepcopy(self.cb1) |
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[3370922] | 263 | obj.smearer = copy.deepcopy(self.smearer) |
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| 264 | |
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[a074145] | 265 | for name, state in self.saved_states.iteritems(): |
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| 266 | copy_name = copy.deepcopy(name) |
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| 267 | copy_state = state.clone() |
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| 268 | obj.saved_states[copy_name]= copy_state |
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[6f023e8] | 269 | return obj |
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[61cada5] | 270 | |
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| 271 | def _repr_helper(self, list, rep): |
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| 272 | """ |
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[11a7e11] | 273 | Helper method to print a state |
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[61cada5] | 274 | """ |
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| 275 | for item in list: |
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[240b9966] | 276 | rep += "parameter name: %s \n"%str(item[1]) |
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| 277 | rep += "value: %s\n"%str(item[2]) |
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| 278 | rep += "selected: %s\n"%str(item[0]) |
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| 279 | rep += "error displayed : %s \n"%str(item[4][0]) |
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| 280 | rep += "error value:%s \n"%str(item[4][1]) |
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| 281 | rep += "minimum displayed : %s \n"%str(item[5][0]) |
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| 282 | rep += "minimum value : %s \n"%str(item[5][1]) |
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| 283 | rep += "maximum displayed : %s \n"%str(item[6][0]) |
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| 284 | rep += "maximum value : %s \n"%str(item[6][1]) |
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| 285 | rep += "parameter unit: %s\n\n"%str(item[7]) |
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| 286 | return rep |
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[61cada5] | 287 | |
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| 288 | def __repr__(self): |
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[11a7e11] | 289 | """ |
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| 290 | output string for printing |
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| 291 | """ |
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| 292 | rep = "\nState name: %s\n"%self.file |
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| 293 | t = time.localtime(self.timestamp) |
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| 294 | time_str = time.strftime("%b %d %H:%M", t) |
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| 295 | rep += "State created on : %s\n"%time_str |
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| 296 | rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox |
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| 297 | rep += "State structure factor combobox selection: %s\n"%self.structurecombobox |
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| 298 | rep += "is data : %s\n"%self.is_data |
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| 299 | rep += "data's name : %s\n"%self.data_name |
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| 300 | rep += "data's id : %s\n"%self.data_id |
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| 301 | rep += "model type (form factor) selected: %s\n"%self.shape_rbutton |
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| 302 | rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton |
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| 303 | rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton |
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| 304 | rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton |
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| 305 | rep += "data : %s\n"% str(self.data) |
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| 306 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin), |
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| 307 | str(self.qmax),str(self.npts)) |
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| 308 | """ |
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| 309 | rep += "model : %s\n\n"% str(self.model) |
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| 310 | rep += "number parameters(self.parameters): %s\n"%len(self.parameters) |
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| 311 | rep += self._repr_helper( list=self.parameters, rep=rep) |
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| 312 | rep += "number orientation parameters" |
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| 313 | rep += "(self.orientation_params): %s\n"%len(self.orientation_params) |
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| 314 | rep += self._repr_helper( list=self.orientation_params, rep=rep) |
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| 315 | rep += "number dispersity parameters" |
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| 316 | rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp) |
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| 317 | rep += self._repr_helper( list=self.orientation_params_disp, rep=rep) |
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| 318 | """ |
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[61cada5] | 319 | return rep |
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| 320 | |
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| 321 | def _toXML_helper(self, list, element, newdoc): |
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| 322 | """ |
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[11a7e11] | 323 | Helper method to create xml file for saving state |
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[61cada5] | 324 | """ |
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| 325 | for item in list: |
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| 326 | sub_element = newdoc.createElement('parameter') |
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| 327 | sub_element.setAttribute('name', str(item[1])) |
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| 328 | sub_element.setAttribute('value', str(item[2])) |
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| 329 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
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| 330 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
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| 331 | sub_element.setAttribute('error_value', str(item[4][1])) |
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| 332 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
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| 333 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
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| 334 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
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| 335 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
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| 336 | sub_element.setAttribute('unit', str(item[7])) |
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| 337 | element.appendChild(sub_element) |
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| 338 | |
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| 339 | def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None): |
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| 340 | """ |
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| 341 | Writes the state of the InversionControl panel to file, as XML. |
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| 342 | |
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| 343 | Compatible with standalone writing, or appending to an |
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| 344 | already existing XML document. In that case, the XML document |
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| 345 | is required. An optional entry node in the XML document may also be given. |
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| 346 | |
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| 347 | @param file: file to write to |
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| 348 | @param doc: XML document object [optional] |
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| 349 | @param entry_node: XML node within the XML document at which we will append the data [optional] |
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| 350 | """ |
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| 351 | from xml.dom.minidom import getDOMImplementation |
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[71f0373] | 352 | |
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[61cada5] | 353 | # Check whether we have to write a standalone XML file |
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| 354 | if doc is None: |
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| 355 | impl = getDOMImplementation() |
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| 356 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
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| 357 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
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| 358 | top_element = newdoc.documentElement |
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| 359 | else: |
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| 360 | # We are appending to an existing document |
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| 361 | newdoc = doc |
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| 362 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
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| 363 | if entry_node is None: |
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| 364 | newdoc.documentElement.appendChild(top_element) |
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| 365 | else: |
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| 366 | entry_node.appendChild(top_element) |
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| 367 | |
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| 368 | attr = newdoc.createAttribute("version") |
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| 369 | attr.nodeValue = '1.0' |
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| 370 | top_element.setAttributeNode(attr) |
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[cfc0913] | 371 | |
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[61cada5] | 372 | # File name |
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| 373 | element = newdoc.createElement("filename") |
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| 374 | if self.file is not None: |
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| 375 | element.appendChild(newdoc.createTextNode(str(self.file))) |
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| 376 | else: |
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| 377 | element.appendChild(newdoc.createTextNode(str(file))) |
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| 378 | top_element.appendChild(element) |
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[11a7e11] | 379 | |
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| 380 | element = newdoc.createElement("timestamp") |
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| 381 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
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| 382 | attr = newdoc.createAttribute("epoch") |
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| 383 | attr.nodeValue = str(self.timestamp) |
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| 384 | element.setAttributeNode(attr) |
---|
| 385 | top_element.appendChild(element) |
---|
[61cada5] | 386 | # Inputs |
---|
| 387 | inputs = newdoc.createElement("Attributes") |
---|
| 388 | top_element.appendChild(inputs) |
---|
| 389 | |
---|
| 390 | element = newdoc.createElement('data_attributes') |
---|
| 391 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 392 | self.data_group_id = self.data.group_id |
---|
| 393 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
| 394 | self.is_data = self.data.is_data |
---|
| 395 | if self.data is not None: |
---|
| 396 | self.data_name = self.data.name |
---|
| 397 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 398 | self.data_id = self.data.id |
---|
| 399 | |
---|
[26f3dd5] | 400 | for item in list_of_data_attributes: |
---|
[61cada5] | 401 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
| 402 | inputs.appendChild(element) |
---|
[26f3dd5] | 403 | |
---|
| 404 | for item in list_of_state_attributes: |
---|
| 405 | element = newdoc.createElement(item[0]) |
---|
| 406 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
| 407 | inputs.appendChild(element) |
---|
[11a7e11] | 408 | |
---|
| 409 | for item in list_of_model_attributes: |
---|
| 410 | element = newdoc.createElement(item[0]) |
---|
| 411 | exec "list = self.%s"%item[1] |
---|
[e9b12eaf] | 412 | for value in list: |
---|
| 413 | exec "element.appendChild(newdoc.createTextNode(str(%s)))" % value |
---|
[11a7e11] | 414 | inputs.appendChild(element) |
---|
| 415 | |
---|
[61cada5] | 416 | for item in list_of_state_parameters: |
---|
| 417 | element = newdoc.createElement(item[0]) |
---|
| 418 | exec "self._toXML_helper(list=self.%s, element=element, newdoc=newdoc)"%item[1] |
---|
| 419 | inputs.appendChild(element) |
---|
| 420 | |
---|
| 421 | # Save the file |
---|
| 422 | if doc is None: |
---|
| 423 | fd = open(file, 'w') |
---|
| 424 | fd.write(newdoc.toprettyxml()) |
---|
| 425 | fd.close() |
---|
| 426 | return None |
---|
| 427 | else: |
---|
| 428 | return newdoc.toprettyxml() |
---|
| 429 | |
---|
| 430 | def _fromXML_helper(self, node, list): |
---|
| 431 | """ |
---|
[11a7e11] | 432 | Helper function to write state to xml |
---|
[61cada5] | 433 | """ |
---|
| 434 | for item in node: |
---|
| 435 | name = item.get('name') |
---|
| 436 | value = item.get('value') |
---|
| 437 | selected_to_fit = item.get('selected_to_fit') |
---|
| 438 | error_displayed = item.get('error_displayed') |
---|
| 439 | error_value = item.get('error_value') |
---|
| 440 | minimum_displayed = item.get('minimum_displayed') |
---|
| 441 | minimum_value = item.get('minimum_value') |
---|
| 442 | maximum_displayed = item.get('maximum_displayed') |
---|
| 443 | maximum_value = item.get('maximum_value') |
---|
| 444 | unit = item.get('unit') |
---|
| 445 | list.append([selected_to_fit, name, value, "+/-",[error_displayed, error_value], |
---|
| 446 | [minimum_displayed,minimum_value],[maximum_displayed,maximum_value], unit]) |
---|
[cfc0913] | 447 | |
---|
[61cada5] | 448 | def fromXML(self, file=None, node=None): |
---|
| 449 | """ |
---|
| 450 | Load fitting state from a file |
---|
| 451 | |
---|
| 452 | @param file: .fitv file |
---|
| 453 | @param node: node of a XML document to read from |
---|
| 454 | """ |
---|
| 455 | |
---|
| 456 | if file is not None: |
---|
[11a7e11] | 457 | msg = "PageState no longer supports non-CanSAS" |
---|
| 458 | msg += " format for fitting files" |
---|
| 459 | raise RuntimeError, msg |
---|
[61cada5] | 460 | |
---|
[11a7e11] | 461 | if node.get('version')and node.get('version') == '1.0': |
---|
[61cada5] | 462 | |
---|
| 463 | # Get file name |
---|
| 464 | entry = get_content('ns:filename', node) |
---|
| 465 | if entry is not None: |
---|
| 466 | self.file = entry.text.strip() |
---|
[11a7e11] | 467 | |
---|
| 468 | # Get time stamp |
---|
| 469 | entry = get_content('ns:timestamp', node) |
---|
| 470 | if entry is not None and entry.get('epoch'): |
---|
| 471 | try: |
---|
| 472 | self.timestamp = float(entry.get('epoch')) |
---|
| 473 | except: |
---|
| 474 | msg = "PageState.fromXML: Could not" |
---|
| 475 | msg += " read timestamp\n %s" % sys.exc_value |
---|
| 476 | logging.error(msg) |
---|
| 477 | |
---|
[61cada5] | 478 | # Parse fitting attributes |
---|
| 479 | entry = get_content('ns:Attributes', node) |
---|
| 480 | if entry is not None: |
---|
| 481 | for item in list_of_state_attributes: |
---|
| 482 | field = get_content('ns:%s'%item[0], entry) |
---|
| 483 | if field is not None: |
---|
| 484 | if item[2] == "string": |
---|
| 485 | exec "self.%s= str(field.text)"%item[1] |
---|
| 486 | elif item[2] == "bool": |
---|
| 487 | try: |
---|
| 488 | exec "self.%s= field.get(str(%s))"%(item[1], item[0]) |
---|
| 489 | except: |
---|
| 490 | exec "self.%s = None"%item[1] |
---|
| 491 | else: |
---|
| 492 | try: |
---|
| 493 | exec "self.%s = float(field.get(%s))"%(item[1], item[0]) |
---|
| 494 | except: |
---|
| 495 | exec "self.%s = None"%item[1] |
---|
[11a7e11] | 496 | for item in list_of_model_attributes: |
---|
| 497 | node = get_content("ns:%s"%item[0], entry) |
---|
| 498 | list = [] |
---|
| 499 | for value in node: |
---|
| 500 | try: |
---|
| 501 | list.append(float(value)) |
---|
| 502 | except: |
---|
| 503 | list.append(None) |
---|
| 504 | |
---|
| 505 | exec "self.%s = list"%item[1] |
---|
| 506 | |
---|
[61cada5] | 507 | for item in list_of_state_parameters: |
---|
[11a7e11] | 508 | node = get_content("ns:%s"%item[0], entry) |
---|
| 509 | self._fromXML_helper(node=node, list=self.parameters) |
---|
[61cada5] | 510 | |
---|
| 511 | |
---|
| 512 | class Reader(CansasReader): |
---|
| 513 | """ |
---|
| 514 | Class to load a .fitv fitting file |
---|
| 515 | """ |
---|
| 516 | ## File type |
---|
| 517 | type_name = "Fitting" |
---|
| 518 | |
---|
| 519 | ## Wildcards |
---|
| 520 | type = ["Fitting files (*.fitv)|*.fitv"] |
---|
| 521 | ## List of allowed extensions |
---|
| 522 | ext=['.fitv', '.FITV'] |
---|
| 523 | |
---|
| 524 | def __init__(self, call_back=None, cansas=True): |
---|
| 525 | """ |
---|
| 526 | Initialize the call-back method to be called |
---|
| 527 | after we load a file |
---|
| 528 | @param call_back: call-back method |
---|
| 529 | @param cansas: True = files will be written/read in CanSAS format |
---|
| 530 | False = write CanSAS format |
---|
| 531 | |
---|
| 532 | """ |
---|
| 533 | ## Call back method to be executed after a file is read |
---|
| 534 | self.call_back = call_back |
---|
| 535 | ## CanSAS format flag |
---|
| 536 | self.cansas = cansas |
---|
| 537 | |
---|
| 538 | def read(self, path): |
---|
| 539 | """ |
---|
| 540 | Load a new P(r) inversion state from file |
---|
| 541 | |
---|
| 542 | @param path: file path |
---|
| 543 | @return: None |
---|
| 544 | """ |
---|
[e9b12eaf] | 545 | if self.cansas == True: |
---|
[61cada5] | 546 | return self._read_cansas(path) |
---|
[e9b12eaf] | 547 | |
---|
| 548 | def _data2d_to_xml_doc(self, datainfo): |
---|
[61cada5] | 549 | """ |
---|
| 550 | Create an XML document to contain the content of a Data2D |
---|
| 551 | |
---|
| 552 | @param datainfo: Data2D object |
---|
| 553 | """ |
---|
| 554 | if not issubclass(datainfo.__class__, Data2D): |
---|
| 555 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
---|
| 556 | |
---|
| 557 | doc = xml.dom.minidom.Document() |
---|
| 558 | main_node = doc.createElement("SASroot") |
---|
| 559 | main_node.setAttribute("version", self.version) |
---|
| 560 | |
---|
| 561 | doc.appendChild(main_node) |
---|
| 562 | |
---|
| 563 | entry_node = doc.createElement("SASentry") |
---|
| 564 | main_node.appendChild(entry_node) |
---|
| 565 | |
---|
| 566 | write_node(doc, entry_node, "Title", datainfo.title) |
---|
| 567 | |
---|
| 568 | for item in datainfo.run: |
---|
| 569 | runname = {} |
---|
| 570 | if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1: |
---|
| 571 | runname = {'name': datainfo.run_name[item] } |
---|
| 572 | write_node(doc, entry_node, "Run", item, runname) |
---|
| 573 | # Data info |
---|
| 574 | node = doc.createElement("SASdata") |
---|
| 575 | entry_node.appendChild(node) |
---|
[e9b12eaf] | 576 | for item in list_of_data_2d_attr: |
---|
| 577 | element = doc.createElement(item[0]) |
---|
| 578 | exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1]) |
---|
| 579 | entry_node.appendChild(element) |
---|
| 580 | for item in list_of_data2d_values: |
---|
| 581 | element = doc.createElement(item[0]) |
---|
[35b556d] | 582 | exec "temp_list = datainfo.%s"%item[1] |
---|
| 583 | if temp_list is None or len(temp_list)== 0: |
---|
| 584 | exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list |
---|
| 585 | else: |
---|
| 586 | for value in temp_list: |
---|
| 587 | exec "element.appendChild(doc.createTextNode(str(%s)))"%value |
---|
[e9b12eaf] | 588 | entry_node.appendChild(element) |
---|
| 589 | |
---|
[61cada5] | 590 | # Sample info |
---|
| 591 | sample = doc.createElement("SASsample") |
---|
| 592 | if datainfo.sample.name is not None: |
---|
| 593 | sample.setAttribute("name", str(datainfo.sample.name)) |
---|
| 594 | entry_node.appendChild(sample) |
---|
| 595 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
---|
| 596 | write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit}) |
---|
| 597 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
---|
| 598 | write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit}) |
---|
| 599 | |
---|
| 600 | for item in datainfo.sample.details: |
---|
| 601 | write_node(doc, sample, "details", item) |
---|
| 602 | |
---|
| 603 | pos = doc.createElement("position") |
---|
| 604 | written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit}) |
---|
| 605 | written = written | write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit}) |
---|
| 606 | written = written | write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit}) |
---|
| 607 | if written == True: |
---|
| 608 | sample.appendChild(pos) |
---|
| 609 | |
---|
| 610 | ori = doc.createElement("orientation") |
---|
| 611 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit}) |
---|
| 612 | written = written | write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit}) |
---|
| 613 | written = written | write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit}) |
---|
| 614 | if written == True: |
---|
| 615 | sample.appendChild(ori) |
---|
| 616 | |
---|
| 617 | # Instrument info |
---|
| 618 | instr = doc.createElement("SASinstrument") |
---|
| 619 | entry_node.appendChild(instr) |
---|
| 620 | |
---|
| 621 | write_node(doc, instr, "name", datainfo.instrument) |
---|
| 622 | |
---|
| 623 | # Source |
---|
| 624 | source = doc.createElement("SASsource") |
---|
| 625 | if datainfo.source.name is not None: |
---|
| 626 | source.setAttribute("name", str(datainfo.source.name)) |
---|
| 627 | instr.appendChild(source) |
---|
| 628 | |
---|
| 629 | write_node(doc, source, "radiation", datainfo.source.radiation) |
---|
| 630 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
---|
| 631 | size = doc.createElement("beam_size") |
---|
| 632 | if datainfo.source.beam_size_name is not None: |
---|
| 633 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
---|
| 634 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit}) |
---|
| 635 | written = written | write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit}) |
---|
| 636 | written = written | write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit}) |
---|
| 637 | if written == True: |
---|
| 638 | source.appendChild(size) |
---|
| 639 | |
---|
| 640 | write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit}) |
---|
| 641 | write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit}) |
---|
| 642 | write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit}) |
---|
| 643 | write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit}) |
---|
| 644 | |
---|
| 645 | # Collimation |
---|
| 646 | for item in datainfo.collimation: |
---|
| 647 | coll = doc.createElement("SAScollimation") |
---|
| 648 | if item.name is not None: |
---|
| 649 | coll.setAttribute("name", str(item.name)) |
---|
| 650 | instr.appendChild(coll) |
---|
| 651 | |
---|
| 652 | write_node(doc, coll, "length", item.length, {"unit":item.length_unit}) |
---|
| 653 | |
---|
| 654 | for apert in item.aperture: |
---|
| 655 | ap = doc.createElement("aperture") |
---|
| 656 | if apert.name is not None: |
---|
| 657 | ap.setAttribute("name", str(apert.name)) |
---|
| 658 | if apert.type is not None: |
---|
| 659 | ap.setAttribute("type", str(apert.type)) |
---|
| 660 | coll.appendChild(ap) |
---|
| 661 | |
---|
| 662 | write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit}) |
---|
| 663 | |
---|
| 664 | size = doc.createElement("size") |
---|
| 665 | if apert.size_name is not None: |
---|
| 666 | size.setAttribute("name", str(apert.size_name)) |
---|
| 667 | written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit}) |
---|
| 668 | written = written | write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit}) |
---|
| 669 | written = written | write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit}) |
---|
| 670 | if written == True: |
---|
| 671 | ap.appendChild(size) |
---|
| 672 | |
---|
| 673 | # Detectors |
---|
| 674 | for item in datainfo.detector: |
---|
| 675 | det = doc.createElement("SASdetector") |
---|
| 676 | written = write_node(doc, det, "name", item.name) |
---|
| 677 | written = written | write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit}) |
---|
| 678 | written = written | write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit}) |
---|
| 679 | if written == True: |
---|
| 680 | instr.appendChild(det) |
---|
| 681 | |
---|
| 682 | off = doc.createElement("offset") |
---|
| 683 | written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit}) |
---|
| 684 | written = written | write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit}) |
---|
| 685 | written = written | write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit}) |
---|
| 686 | if written == True: |
---|
| 687 | det.appendChild(off) |
---|
| 688 | |
---|
| 689 | center = doc.createElement("beam_center") |
---|
| 690 | written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit}) |
---|
| 691 | written = written | write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit}) |
---|
| 692 | written = written | write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit}) |
---|
| 693 | if written == True: |
---|
| 694 | det.appendChild(center) |
---|
| 695 | |
---|
| 696 | pix = doc.createElement("pixel_size") |
---|
| 697 | written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit}) |
---|
| 698 | written = written | write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit}) |
---|
| 699 | written = written | write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit}) |
---|
| 700 | if written == True: |
---|
| 701 | det.appendChild(pix) |
---|
| 702 | |
---|
| 703 | ori = doc.createElement("orientation") |
---|
| 704 | written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit}) |
---|
| 705 | written = written | write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit}) |
---|
| 706 | written = written | write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit}) |
---|
| 707 | if written == True: |
---|
| 708 | det.appendChild(ori) |
---|
| 709 | |
---|
| 710 | # Processes info |
---|
| 711 | for item in datainfo.process: |
---|
| 712 | node = doc.createElement("SASprocess") |
---|
| 713 | entry_node.appendChild(node) |
---|
| 714 | |
---|
| 715 | write_node(doc, node, "name", item.name) |
---|
| 716 | write_node(doc, node, "date", item.date) |
---|
| 717 | write_node(doc, node, "description", item.description) |
---|
| 718 | for term in item.term: |
---|
| 719 | value = term['value'] |
---|
| 720 | del term['value'] |
---|
| 721 | write_node(doc, node, "term", value, term) |
---|
| 722 | for note in item.notes: |
---|
| 723 | write_node(doc, node, "SASprocessnote", note) |
---|
| 724 | |
---|
| 725 | # Return the document, and the SASentry node associated with |
---|
| 726 | # the data we just wrote |
---|
| 727 | return doc, entry_node |
---|
[e9b12eaf] | 728 | |
---|
[61cada5] | 729 | |
---|
| 730 | def _parse_state(self, entry): |
---|
| 731 | """ |
---|
| 732 | Read a fit result from an XML node |
---|
| 733 | @param entry: XML node to read from |
---|
| 734 | @return: PageState object |
---|
| 735 | """ |
---|
| 736 | # Create an empty state |
---|
| 737 | state = PageState() |
---|
| 738 | # Locate the P(r) node |
---|
| 739 | try: |
---|
| 740 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS}) |
---|
| 741 | state.fromXML(node=nodes[0]) |
---|
| 742 | except: |
---|
| 743 | logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value) |
---|
| 744 | |
---|
| 745 | return state |
---|
| 746 | |
---|
[e9b12eaf] | 747 | def _parse_entry_2d(self, dom): |
---|
| 748 | """ |
---|
| 749 | Parse a SASentry |
---|
| 750 | |
---|
| 751 | @param node: SASentry node |
---|
| 752 | @return: Data2D object |
---|
| 753 | """ |
---|
| 754 | |
---|
| 755 | data_info = Data2D() |
---|
| 756 | |
---|
| 757 | # Look up title |
---|
| 758 | self._store_content('ns:Title', dom, 'title', data_info) |
---|
| 759 | |
---|
| 760 | # Look up run number |
---|
| 761 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
---|
| 762 | for item in nodes: |
---|
| 763 | if item.text is not None: |
---|
| 764 | value = item.text.strip() |
---|
| 765 | if len(value) > 0: |
---|
| 766 | data_info.run.append(value) |
---|
| 767 | if item.get('name') is not None: |
---|
| 768 | data_info.run_name[value] = item.get('name') |
---|
| 769 | |
---|
| 770 | # Look up instrument name |
---|
| 771 | self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info) |
---|
| 772 | |
---|
| 773 | # Notes |
---|
| 774 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
---|
| 775 | for note in note_list: |
---|
| 776 | try: |
---|
| 777 | if note.text is not None: |
---|
| 778 | note_value = note.text.strip() |
---|
| 779 | if len(note_value) > 0: |
---|
| 780 | data_info.notes.append(note_value) |
---|
| 781 | except: |
---|
| 782 | err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value |
---|
| 783 | self.errors.append(err_mess) |
---|
| 784 | logging.error(err_mess) |
---|
| 785 | |
---|
| 786 | # Sample info ################### |
---|
| 787 | entry = get_content('ns:SASsample', dom) |
---|
| 788 | if entry is not None: |
---|
| 789 | data_info.sample.name = entry.get('name') |
---|
| 790 | |
---|
| 791 | self._store_content('ns:SASsample/ns:ID', |
---|
| 792 | dom, 'ID', data_info.sample) |
---|
| 793 | self._store_float('ns:SASsample/ns:thickness', |
---|
| 794 | dom, 'thickness', data_info.sample) |
---|
| 795 | self._store_float('ns:SASsample/ns:transmission', |
---|
| 796 | dom, 'transmission', data_info.sample) |
---|
| 797 | self._store_float('ns:SASsample/ns:temperature', |
---|
| 798 | dom, 'temperature', data_info.sample) |
---|
| 799 | |
---|
| 800 | nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS}) |
---|
| 801 | for item in nodes: |
---|
| 802 | try: |
---|
| 803 | if item.text is not None: |
---|
| 804 | detail_value = item.text.strip() |
---|
| 805 | if len(detail_value) > 0: |
---|
| 806 | data_info.sample.details.append(detail_value) |
---|
| 807 | except: |
---|
| 808 | err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value |
---|
| 809 | self.errors.append(err_mess) |
---|
| 810 | logging.error(err_mess) |
---|
| 811 | |
---|
| 812 | # Position (as a vector) |
---|
| 813 | self._store_float('ns:SASsample/ns:position/ns:x', |
---|
| 814 | dom, 'position.x', data_info.sample) |
---|
| 815 | self._store_float('ns:SASsample/ns:position/ns:y', |
---|
| 816 | dom, 'position.y', data_info.sample) |
---|
| 817 | self._store_float('ns:SASsample/ns:position/ns:z', |
---|
| 818 | dom, 'position.z', data_info.sample) |
---|
| 819 | |
---|
| 820 | # Orientation (as a vector) |
---|
| 821 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
---|
| 822 | dom, 'orientation.x', data_info.sample) |
---|
| 823 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
---|
| 824 | dom, 'orientation.y', data_info.sample) |
---|
| 825 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
---|
| 826 | dom, 'orientation.z', data_info.sample) |
---|
| 827 | |
---|
| 828 | # Source info ################### |
---|
| 829 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
---|
| 830 | if entry is not None: |
---|
| 831 | data_info.source.name = entry.get('name') |
---|
| 832 | |
---|
| 833 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
---|
| 834 | dom, 'radiation', data_info.source) |
---|
| 835 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
---|
| 836 | dom, 'beam_shape', data_info.source) |
---|
| 837 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
---|
| 838 | dom, 'wavelength', data_info.source) |
---|
| 839 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
---|
| 840 | dom, 'wavelength_min', data_info.source) |
---|
| 841 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
---|
| 842 | dom, 'wavelength_max', data_info.source) |
---|
| 843 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
---|
| 844 | dom, 'wavelength_spread', data_info.source) |
---|
| 845 | |
---|
| 846 | # Beam size (as a vector) |
---|
| 847 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
---|
| 848 | if entry is not None: |
---|
| 849 | data_info.source.beam_size_name = entry.get('name') |
---|
| 850 | |
---|
| 851 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
---|
| 852 | dom, 'beam_size.x', data_info.source) |
---|
| 853 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
---|
| 854 | dom, 'beam_size.y', data_info.source) |
---|
| 855 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
---|
| 856 | dom, 'beam_size.z', data_info.source) |
---|
| 857 | |
---|
| 858 | # Collimation info ################### |
---|
| 859 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS}) |
---|
| 860 | for item in nodes: |
---|
| 861 | collim = Collimation() |
---|
| 862 | if item.get('name') is not None: |
---|
| 863 | collim.name = item.get('name') |
---|
| 864 | self._store_float('ns:length', item, 'length', collim) |
---|
| 865 | |
---|
| 866 | # Look for apertures |
---|
| 867 | apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS}) |
---|
| 868 | for apert in apert_list: |
---|
| 869 | aperture = Aperture() |
---|
| 870 | |
---|
| 871 | # Get the name and type of the aperture |
---|
| 872 | aperture.name = apert.get('name') |
---|
| 873 | aperture.type = apert.get('type') |
---|
| 874 | |
---|
| 875 | self._store_float('ns:distance', apert, 'distance', aperture) |
---|
| 876 | |
---|
| 877 | entry = get_content('ns:size', apert) |
---|
| 878 | if entry is not None: |
---|
| 879 | aperture.size_name = entry.get('name') |
---|
| 880 | |
---|
| 881 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
---|
| 882 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
---|
| 883 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
---|
| 884 | |
---|
| 885 | collim.aperture.append(aperture) |
---|
| 886 | |
---|
| 887 | data_info.collimation.append(collim) |
---|
| 888 | |
---|
| 889 | # Detector info ###################### |
---|
| 890 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS}) |
---|
| 891 | for item in nodes: |
---|
| 892 | |
---|
| 893 | detector = Detector() |
---|
| 894 | |
---|
| 895 | self._store_content('ns:name', item, 'name', detector) |
---|
| 896 | self._store_float('ns:SDD', item, 'distance', detector) |
---|
| 897 | |
---|
| 898 | # Detector offset (as a vector) |
---|
| 899 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
---|
| 900 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
---|
| 901 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
---|
| 902 | |
---|
| 903 | # Detector orientation (as a vector) |
---|
| 904 | self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector) |
---|
| 905 | self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector) |
---|
| 906 | self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector) |
---|
| 907 | |
---|
| 908 | # Beam center (as a vector) |
---|
| 909 | self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector) |
---|
| 910 | self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector) |
---|
| 911 | self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector) |
---|
| 912 | |
---|
| 913 | # Pixel size (as a vector) |
---|
| 914 | self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector) |
---|
| 915 | self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector) |
---|
| 916 | self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector) |
---|
| 917 | |
---|
| 918 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
---|
| 919 | |
---|
| 920 | data_info.detector.append(detector) |
---|
| 921 | |
---|
| 922 | # Processes info ###################### |
---|
| 923 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
---|
| 924 | for item in nodes: |
---|
| 925 | process = Process() |
---|
| 926 | self._store_content('ns:name', item, 'name', process) |
---|
| 927 | self._store_content('ns:date', item, 'date', process) |
---|
| 928 | self._store_content('ns:description', item, 'description', process) |
---|
| 929 | |
---|
| 930 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
---|
| 931 | for term in term_list: |
---|
| 932 | try: |
---|
| 933 | term_attr = {} |
---|
| 934 | for attr in term.keys(): |
---|
| 935 | term_attr[attr] = term.get(attr).strip() |
---|
| 936 | if term.text is not None: |
---|
| 937 | term_attr['value'] = term.text.strip() |
---|
| 938 | process.term.append(term_attr) |
---|
| 939 | except: |
---|
| 940 | err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value |
---|
| 941 | self.errors.append(err_mess) |
---|
| 942 | logging.error(err_mess) |
---|
| 943 | |
---|
| 944 | note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS}) |
---|
| 945 | for note in note_list: |
---|
| 946 | if note.text is not None: |
---|
| 947 | process.notes.append(note.text.strip()) |
---|
| 948 | |
---|
| 949 | data_info.process.append(process) |
---|
| 950 | |
---|
| 951 | |
---|
| 952 | # Data info ###################### |
---|
| 953 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
---|
| 954 | if len(nodes)>1: |
---|
| 955 | raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries" |
---|
| 956 | |
---|
| 957 | nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS}) |
---|
| 958 | |
---|
| 959 | for item in nodes: |
---|
| 960 | _x, attr = get_float('ns:Q', item) |
---|
| 961 | _dx, attr_d = get_float('ns:Qdev', item) |
---|
| 962 | _dxl, attr_l = get_float('ns:dQl', item) |
---|
| 963 | _dxw, attr_w = get_float('ns:dQw', item) |
---|
| 964 | if _dx == None: |
---|
| 965 | _dx = 0.0 |
---|
| 966 | if _dxl == None: |
---|
| 967 | _dxl = 0.0 |
---|
| 968 | if _dxw == None: |
---|
| 969 | _dxw = 0.0 |
---|
| 970 | |
---|
| 971 | if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower(): |
---|
| 972 | if has_converter==True: |
---|
| 973 | try: |
---|
| 974 | data_conv_q = Converter(attr['unit']) |
---|
| 975 | _x = data_conv_q(_x, units=data_info.x_unit) |
---|
| 976 | except: |
---|
| 977 | raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \ |
---|
| 978 | % (attr['unit'], data_info.x_unit, sys.exc_value) |
---|
| 979 | else: |
---|
| 980 | raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \ |
---|
| 981 | % (attr['unit'], data_info.x_unit) |
---|
| 982 | # Error in Q |
---|
| 983 | if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower(): |
---|
| 984 | if has_converter==True: |
---|
| 985 | try: |
---|
| 986 | data_conv_q = Converter(attr_d['unit']) |
---|
| 987 | _dx = data_conv_q(_dx, units=data_info.x_unit) |
---|
| 988 | except: |
---|
| 989 | raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \ |
---|
| 990 | % (attr['unit'], data_info.x_unit, sys.exc_value) |
---|
| 991 | else: |
---|
| 992 | raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \ |
---|
| 993 | % (attr['unit'], data_info.x_unit) |
---|
| 994 | # Slit length |
---|
| 995 | if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower(): |
---|
| 996 | if has_converter==True: |
---|
| 997 | try: |
---|
| 998 | data_conv_q = Converter(attr_l['unit']) |
---|
| 999 | _dxl = data_conv_q(_dxl, units=data_info.x_unit) |
---|
| 1000 | except: |
---|
| 1001 | raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \ |
---|
| 1002 | % (attr['unit'], data_info.x_unit, sys.exc_value) |
---|
| 1003 | else: |
---|
| 1004 | raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \ |
---|
| 1005 | % (attr['unit'], data_info.x_unit) |
---|
| 1006 | # Slit width |
---|
| 1007 | if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower(): |
---|
| 1008 | if has_converter==True: |
---|
| 1009 | try: |
---|
| 1010 | data_conv_q = Converter(attr_w['unit']) |
---|
| 1011 | _dxw = data_conv_q(_dxw, units=data_info.x_unit) |
---|
| 1012 | except: |
---|
| 1013 | raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \ |
---|
| 1014 | % (attr['unit'], data_info.x_unit, sys.exc_value) |
---|
| 1015 | else: |
---|
| 1016 | raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \ |
---|
| 1017 | % (attr['unit'], data_info.x_unit) |
---|
| 1018 | |
---|
| 1019 | _y, attr = get_float('ns:I', item) |
---|
| 1020 | _dy, attr_d = get_float('ns:Idev', item) |
---|
| 1021 | if _dy == None: |
---|
| 1022 | _dy = 0.0 |
---|
| 1023 | if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower(): |
---|
| 1024 | if has_converter==True: |
---|
| 1025 | try: |
---|
| 1026 | data_conv_i = Converter(attr['unit']) |
---|
| 1027 | _y = data_conv_i(_y, units=data_info.y_unit) |
---|
| 1028 | except: |
---|
| 1029 | raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \ |
---|
| 1030 | % (attr['unit'], data_info.y_unit, sys.exc_value) |
---|
| 1031 | else: |
---|
| 1032 | raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \ |
---|
| 1033 | % (attr['unit'], data_info.y_unit) |
---|
| 1034 | if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower(): |
---|
| 1035 | if has_converter==True: |
---|
| 1036 | try: |
---|
| 1037 | data_conv_i = Converter(attr_d['unit']) |
---|
| 1038 | _dy = data_conv_i(_dy, units=data_info.y_unit) |
---|
| 1039 | except: |
---|
| 1040 | raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \ |
---|
| 1041 | % (attr_d['unit'], data_info.y_unit, sys.exc_value) |
---|
| 1042 | else: |
---|
| 1043 | raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \ |
---|
| 1044 | % (attr_d['unit'], data_info.y_unit) |
---|
| 1045 | |
---|
| 1046 | if _x is not None and _y is not None: |
---|
| 1047 | exec "item = numpy.append(x, _x)" |
---|
| 1048 | |
---|
| 1049 | for item in list_of_model_attributes: |
---|
| 1050 | node = get_content("ns:%s"%item[0], entry) |
---|
| 1051 | list = [] |
---|
| 1052 | for value in node: |
---|
| 1053 | try: |
---|
| 1054 | list.append(float(value)) |
---|
| 1055 | except: |
---|
| 1056 | list.append(None) |
---|
| 1057 | |
---|
| 1058 | exec "self.%s = list"%item[1] |
---|
| 1059 | data_conv_q = None |
---|
| 1060 | data_conv_i = None |
---|
| 1061 | |
---|
| 1062 | if has_converter == True and data_info.x_unit != '1/A': |
---|
| 1063 | data_conv_q = Converter('1/A') |
---|
| 1064 | # Test it |
---|
| 1065 | data_conv_q(1.0, output.Q_unit) |
---|
| 1066 | |
---|
| 1067 | if has_converter == True and data_info.y_unit != '1/cm': |
---|
| 1068 | data_conv_i = Converter('1/cm') |
---|
| 1069 | # Test it |
---|
| 1070 | data_conv_i(1.0, output.I_unit) |
---|
| 1071 | |
---|
| 1072 | if data_conv_q is not None: |
---|
| 1073 | data_info.xaxis("\\rm{%s}"%str(_xaxis), data_info.x_unit) |
---|
| 1074 | else: |
---|
| 1075 | data_info.xaxis("\\rm{%s}"%str(_xaxis), 'A^{-1}') |
---|
| 1076 | if data_conv_i is not None: |
---|
| 1077 | data_info.yaxis("\\rm{%s}"%str(_yaxis), data_info.y_unit) |
---|
| 1078 | else: |
---|
| 1079 | data_info.yaxis("\\rm{%s}"%str(_yaxis),"cm^{-1}") |
---|
| 1080 | |
---|
| 1081 | return data_info |
---|
| 1082 | |
---|
[61cada5] | 1083 | def _read_cansas(self, path): |
---|
| 1084 | """ |
---|
| 1085 | Load data and P(r) information from a CanSAS XML file. |
---|
| 1086 | |
---|
| 1087 | @param path: file path |
---|
| 1088 | @return: Data1D object if a single SASentry was found, |
---|
| 1089 | or a list of Data1D objects if multiple entries were found, |
---|
| 1090 | or None of nothing was found |
---|
| 1091 | @raise RuntimeError: when the file can't be opened |
---|
| 1092 | @raise ValueError: when the length of the data vectors are inconsistent |
---|
| 1093 | """ |
---|
| 1094 | output = [] |
---|
| 1095 | try: |
---|
| 1096 | if os.path.isfile(path): |
---|
| 1097 | basename = os.path.basename(path) |
---|
| 1098 | root, extension = os.path.splitext(basename) |
---|
| 1099 | #TODO: eventually remove the check for .xml once |
---|
| 1100 | # the P(r) writer/reader is truly complete. |
---|
| 1101 | if extension.lower() in self.ext or \ |
---|
| 1102 | extension.lower() == '.xml': |
---|
| 1103 | |
---|
| 1104 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
| 1105 | # Check the format version number |
---|
| 1106 | # Specifying the namespace will take care of the file format version |
---|
| 1107 | root = tree.getroot() |
---|
| 1108 | entry_list = root.xpath('/ns:SASroot/ns:SASentry', namespaces={'ns': CANSAS_NS}) |
---|
| 1109 | for entry in entry_list: |
---|
[e9b12eaf] | 1110 | try: |
---|
| 1111 | sas_entry = self._parse_entry(entry) |
---|
| 1112 | except: |
---|
| 1113 | sas_entry = self._parse_entry_2d(entry) |
---|
[61cada5] | 1114 | fitstate = self._parse_state(entry) |
---|
| 1115 | sas_entry.meta_data['fitstate'] = fitstate |
---|
| 1116 | sas_entry.filename = fitstate.file |
---|
| 1117 | output.append(sas_entry) |
---|
| 1118 | |
---|
| 1119 | else: |
---|
| 1120 | raise RuntimeError, "%s is not a file" % path |
---|
| 1121 | |
---|
| 1122 | # Return output consistent with the loader's api |
---|
| 1123 | if len(output)==0: |
---|
| 1124 | return None |
---|
| 1125 | elif len(output)==1: |
---|
| 1126 | # Call back to post the new state |
---|
| 1127 | state = output[0].meta_data['fitstate'] |
---|
[11a7e11] | 1128 | t = time.localtime(state.timestamp) |
---|
| 1129 | time_str = time.strftime("%b %d %H:%M", t) |
---|
| 1130 | # Check that no time stamp is already appended |
---|
| 1131 | max_char = state.file.find("[") |
---|
| 1132 | if max_char < 0: |
---|
| 1133 | max_char = len(state.file) |
---|
| 1134 | state.file = state.file[0:max_char] +' [' + time_str + ']' |
---|
| 1135 | |
---|
| 1136 | |
---|
[61cada5] | 1137 | if state is not None and state.is_data is not None: |
---|
| 1138 | exec 'output[0].is_data = state.is_data' |
---|
| 1139 | |
---|
[11a7e11] | 1140 | output[0].filename = state.file |
---|
| 1141 | #output[0].filename = state.data_name |
---|
[61cada5] | 1142 | state.data = output[0] |
---|
| 1143 | state.data.name = state.data_name |
---|
| 1144 | state.data.id = state.data_id |
---|
[11a7e11] | 1145 | #state.data.group_id = state.data_group_id |
---|
| 1146 | state.data.group_id = output[0].filename |
---|
| 1147 | |
---|
[61cada5] | 1148 | self.call_back(state=state, datainfo=output[0]) |
---|
| 1149 | return output[0] |
---|
| 1150 | else: |
---|
| 1151 | return output |
---|
| 1152 | except: |
---|
| 1153 | raise |
---|
| 1154 | |
---|
| 1155 | def write(self, filename, datainfo=None, fitstate=None): |
---|
| 1156 | """ |
---|
| 1157 | Write the content of a Data1D as a CanSAS XML file |
---|
| 1158 | |
---|
| 1159 | @param filename: name of the file to write |
---|
| 1160 | @param datainfo: Data1D object |
---|
| 1161 | @param fitstate: PageState object |
---|
| 1162 | """ |
---|
| 1163 | # Sanity check |
---|
| 1164 | if self.cansas == True: |
---|
| 1165 | |
---|
| 1166 | # Add fitting information to the XML document |
---|
| 1167 | if fitstate is not None: |
---|
| 1168 | if fitstate.data is None: |
---|
| 1169 | data = DataLoader.data_info.Data1D(x=[], y=[]) |
---|
| 1170 | elif issubclass(fitstate.data.__class__, DataLoader.data_info.Data1D): |
---|
| 1171 | data = fitstate.data |
---|
| 1172 | doc, sasentry = self._to_xml_doc(data) |
---|
| 1173 | else: |
---|
| 1174 | data = fitstate.data |
---|
| 1175 | doc, sasentry = self._data2d_to_xml_doc(data) |
---|
[e9b12eaf] | 1176 | fitstate.toXML(doc=doc, file=data.name, entry_node=sasentry) |
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[61cada5] | 1177 | # Write the XML document |
---|
| 1178 | fd = open(filename, 'w') |
---|
| 1179 | fd.write(doc.toprettyxml()) |
---|
| 1180 | fd.close() |
---|
| 1181 | else: |
---|
| 1182 | fitstate.toXML(file=filename) |
---|
| 1183 | |
---|
| 1184 | |
---|
| 1185 | if __name__ == "__main__": |
---|
| 1186 | state = PageState(parent=None) |
---|
| 1187 | state.toXML() |
---|
[11a7e11] | 1188 | print "state", state |
---|