[c77d859] | 1 | |
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| 2 | |
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[5062bbf] | 3 | ################################################################################ |
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| 4 | #This software was developed by the University of Tennessee as part of the |
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| 5 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 6 | #project funded by the US National Science Foundation. |
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| 7 | # |
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| 8 | #See the license text in license.txt |
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| 9 | # |
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| 10 | #copyright 2009, University of Tennessee |
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| 11 | ################################################################################ |
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| 12 | |
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[11a7e11] | 13 | import time |
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| 14 | import os |
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| 15 | import sys |
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[6f023e8] | 16 | import copy |
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[11a7e11] | 17 | import logging |
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[df7ed14] | 18 | import numpy |
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[c77d859] | 19 | |
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[35b556d] | 20 | import xml.dom.minidom |
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[11a7e11] | 21 | from xml.dom.minidom import parse |
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| 22 | from lxml import etree |
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| 23 | |
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[c21e87b] | 24 | import sans.dataloader |
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| 25 | from sans.dataloader.readers.cansas_reader import Reader as CansasReader |
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| 26 | from sans.dataloader.readers.cansas_reader import get_content, write_node |
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| 27 | from sans.dataloader.data_info import Data2D, Detector |
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[61cada5] | 28 | |
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[11a7e11] | 29 | #Information to read/write state as xml |
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[61cada5] | 30 | FITTING_NODE_NAME = 'fitting_plug_in' |
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| 31 | CANSAS_NS = "cansas1d/1.0" |
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| 32 | |
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[26f3dd5] | 33 | list_of_data_attributes = [["is_data", "is_data", "bool"], |
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[61cada5] | 34 | ["group_id", "data_group_id", "string"], |
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| 35 | ["data_name", "data_name", "string"], |
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| 36 | ["data_id", "data_id", "string"], |
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| 37 | ["name", "name", "string"], |
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[26f3dd5] | 38 | ["data_name", "data_name", "string"]] |
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[e3d1423] | 39 | list_of_state_attributes = [["engine_type", "engine_type", "string"], |
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| 40 | ["qmin", "qmin", "float"], |
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[61cada5] | 41 | ["qmax", "qmax", "float"], |
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| 42 | ["npts", "npts", "float"], |
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| 43 | ["shape_rbutton", "shape_rbutton", "bool"], |
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| 44 | ["shape_indep_rbutton", "shape_indep_rbutton", "bool"], |
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| 45 | ["plugin_rbutton", "plugin_rbutton","bool"], |
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| 46 | ["struct_rbutton", "struct_rbutton", "bool"], |
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[d40038e] | 47 | ["formfactorcombobox", "formfactorcombobox", "string"], |
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| 48 | ["structurecombobox", "structurecombobox", "string"], |
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[c0ff8cc] | 49 | ["multi_factor","multi_factor","float"], |
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[26f3dd5] | 50 | ["enable_smearer","enable_smearer","bool"], |
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| 51 | ["disable_smearer","disable_smearer","bool"], |
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| 52 | ["pinhole_smearer","pinhole_smearer","bool"], |
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| 53 | ["slit_smearer","slit_smearer","bool"], |
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| 54 | ["enable_disp","enable_disp","bool"], |
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| 55 | ["disable_disp","disable_disp","bool"], |
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[55bb249c] | 56 | ["dI_noweight","dI_noweight","bool"], |
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| 57 | ["dI_didata","dI_didata","bool"], |
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| 58 | ["dI_sqrdata","dI_sqrdata","bool"], |
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| 59 | ["dI_idata","dI_idata","bool"], |
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[26f3dd5] | 60 | ["enable2D","enable2D","bool"], |
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| 61 | ["cb1","cb1","bool"], |
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[5cc7001] | 62 | ["tcChi","tcChi","float"], |
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[55bb249c] | 63 | ["smearer", "smearer", "float"], |
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| 64 | ["smear_type","smear_type", "string"], |
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| 65 | ["dq_l", "dq_l", "string"], |
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| 66 | ["dq_r","dq_r", "string"]] |
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[5cc7001] | 67 | |
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[11a7e11] | 68 | list_of_model_attributes = [["values", "values"], |
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| 69 | ["weights", "weights"]] |
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| 70 | |
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[2296316] | 71 | list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]] |
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| 72 | |
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[fb59ed9] | 73 | list_of_state_parameters = [["parameters", "parameters"] , |
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| 74 | ["str_parameters", "str_parameters"] , |
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[61cada5] | 75 | ["orientation_parameters", "orientation_params"], |
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| 76 | ["dispersity_parameters", "orientation_params_disp"], |
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| 77 | ["fixed_param", "fixed_param"], |
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| 78 | ["fittable_param","fittable_param"]] |
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[df7ed14] | 79 | list_of_data_2d_attr = [["xmin", "xmin","float"], |
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| 80 | ["xmax","xmax","float"], |
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| 81 | ["ymin","ymin","float"], |
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| 82 | ["ymax","ymax","float"], |
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| 83 | ["_xaxis","_xaxis", "string"], |
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| 84 | ["_xunit", "_xunit", "string"], |
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| 85 | ["_yaxis","_yaxis","string"], |
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| 86 | ["_yunit","_yunit","string"], |
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| 87 | ["_zaxis","_zaxis","string"], |
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| 88 | ["_zunit","_zunit","string"]] |
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| 89 | list_of_data2d_values = [["qx_data","qx_data","float"], |
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| 90 | ["qy_data","qy_data","float"], |
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| 91 | ["dqx_data","dqx_data","float"], |
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| 92 | ["dqy_data","dqy_data","float"], |
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| 93 | ["data","data","float"], |
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| 94 | ["q_data","q_data","float"], |
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| 95 | ["err_data","err_data","float"], |
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| 96 | ["mask","mask","bool"]] |
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[61cada5] | 97 | |
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[0b12abb5] | 98 | def parse_entry_helper( node, item): |
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| 99 | """ |
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| 100 | Create a numpy list from value extrated from the node |
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| 101 | |
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| 102 | :param node: node from each the value is stored |
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| 103 | :param item: list name of three strings.the two first are name of data |
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| 104 | attribute and the third one is the type of the value of that |
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| 105 | attribute. type can be string, float, bool, etc. |
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| 106 | |
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| 107 | : return: numpy array |
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| 108 | """ |
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| 109 | if node is not None: |
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| 110 | if item[2] == "string": |
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| 111 | return str(node.get(item[0]).strip()) |
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| 112 | elif item[2] == "bool": |
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| 113 | try: |
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[e3d1423] | 114 | return node.get(item[0]).strip() == "True" |
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| 115 | |
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[0b12abb5] | 116 | except: |
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| 117 | return None |
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| 118 | else: |
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| 119 | try: |
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| 120 | return float(node.get(item[0])) |
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| 121 | except: |
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| 122 | return None |
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| 123 | |
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| 124 | |
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[cfc0913] | 125 | class PageState(object): |
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[c77d859] | 126 | """ |
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[5062bbf] | 127 | Contains information to reconstruct a page of the fitpanel. |
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[c77d859] | 128 | """ |
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[61cada5] | 129 | def __init__(self, parent=None, model=None, data=None): |
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[c77d859] | 130 | |
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| 131 | """ |
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[5062bbf] | 132 | Initialize the current state |
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| 133 | |
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| 134 | :param model: a selected model within a page |
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| 135 | :param data: |
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| 136 | |
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[c77d859] | 137 | """ |
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[61cada5] | 138 | self.file = None |
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[11a7e11] | 139 | #Time of state creation |
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| 140 | self.timestamp = time.time() |
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[c77d859] | 141 | ## Data member to store the dispersion object created |
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| 142 | self._disp_obj_dict = {} |
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[61cada5] | 143 | #------------------------ |
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[c77d859] | 144 | #Data used for fitting |
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| 145 | self.data = data |
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[2296316] | 146 | # model data |
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| 147 | self.theory_data = None |
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| 148 | #Is 2D |
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| 149 | self.is_2D = False |
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| 150 | self.images = None |
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| 151 | |
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[61cada5] | 152 | #save additional information on data that dataloader.reader does not read |
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| 153 | self.is_data = None |
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| 154 | self.data_name = "" |
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[c0ff8cc] | 155 | |
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[61cada5] | 156 | if self.data is not None: |
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| 157 | self.data_name = self.data.name |
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| 158 | self.data_id = None |
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| 159 | if self.data is not None and hasattr(self.data, "id"): |
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| 160 | self.data_id = self.data.id |
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| 161 | self.data_group_id = None |
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| 162 | if self.data is not None and hasattr(self.data, "group_id"): |
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| 163 | self.data_group_id = self.data.group_id |
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[0b12abb5] | 164 | |
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[61cada5] | 165 | ## reset True change the state of exsiting button |
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| 166 | self.reset = False |
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| 167 | |
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[c99a6c5] | 168 | #engine type |
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| 169 | self.engine_type = None |
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[c77d859] | 170 | # flag to allow data2D plot |
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[cfc0913] | 171 | self.enable2D = False |
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[c77d859] | 172 | # model on which the fit would be performed |
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| 173 | self.model = model |
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[93f0a862] | 174 | self.m_name = None |
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[dce84c0] | 175 | #list of process done to model |
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| 176 | self.process = [] |
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[c77d859] | 177 | #fit page manager |
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| 178 | self.manager = None |
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| 179 | #Store the parent of this panel parent |
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| 180 | # For this application fitpanel is the parent |
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| 181 | self.parent = parent |
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| 182 | # Event_owner is the owner of model event |
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| 183 | self.event_owner = None |
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[c9a4377] | 184 | ##page name |
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[cfc0913] | 185 | self.page_name = "" |
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[c77d859] | 186 | # Contains link between model ,all its parameters, and panel organization |
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[61cada5] | 187 | self.parameters = [] |
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[fb59ed9] | 188 | # String parameter list that can not be fitted |
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| 189 | self.str_parameters = [] |
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[c77d859] | 190 | # Contains list of parameters that cannot be fitted and reference to |
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| 191 | #panel objects |
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[61cada5] | 192 | self.fixed_param = [] |
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[c77d859] | 193 | # Contains list of parameters with dispersity and reference to |
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| 194 | #panel objects |
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[61cada5] | 195 | self.fittable_param = [] |
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[60132ef] | 196 | ## orientation parameters |
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[61cada5] | 197 | self.orientation_params = [] |
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[fc6ea43] | 198 | ## orientation parmaters for gaussian dispersity |
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[61cada5] | 199 | self.orientation_params_disp = [] |
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[3370922] | 200 | ## smearer info |
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[61cada5] | 201 | self.smearer = None |
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[7609f1a] | 202 | self.smear_type = None |
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| 203 | self.dq_l = None |
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| 204 | self.dq_r = None |
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| 205 | |
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[c77d859] | 206 | #list of dispersion paramaters |
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[cfc0913] | 207 | self.disp_list =[] |
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[61cada5] | 208 | if self.model is not None: |
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[71f0373] | 209 | self.disp_list = self.model.getDispParamList() |
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[2296316] | 210 | |
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[61cada5] | 211 | self.disp_cb_dict = {} |
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[2296316] | 212 | self.values = {} |
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| 213 | self.weights = {} |
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[dad49a0] | 214 | |
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[c77d859] | 215 | #contains link between a model and selected parameters to fit |
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[61cada5] | 216 | self.param_toFit = [] |
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[a074145] | 217 | ##dictionary of model type and model class |
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[cfc0913] | 218 | self.model_list_box = None |
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[a074145] | 219 | ## save the state of the context menu |
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[61cada5] | 220 | self.saved_states = {} |
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[240b9966] | 221 | ## save selection of combobox |
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[3b9e023] | 222 | self.formfactorcombobox = None |
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| 223 | self.structurecombobox = None |
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[c0ff8cc] | 224 | |
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[240b9966] | 225 | ## radio box to select type of model |
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| 226 | self.shape_rbutton = False |
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| 227 | self.shape_indep_rbutton = False |
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| 228 | self.struct_rbutton = False |
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| 229 | self.plugin_rbutton = False |
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[b787e68c] | 230 | ## the indice of the current selection |
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| 231 | self.disp_box = 0 |
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[c77d859] | 232 | ## Qrange |
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[cfc0913] | 233 | ## Q range |
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[61cada5] | 234 | self.qmin = 0.001 |
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| 235 | self.qmax = 0.1 |
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[0b12abb5] | 236 | #reset data range |
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| 237 | self.qmax_x = None |
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| 238 | self.qmin_x = None |
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| 239 | |
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[cfc0913] | 240 | self.npts = None |
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[61cada5] | 241 | self.name = "" |
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[4523b68] | 242 | self.multi_factor = None |
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[cfc0913] | 243 | ## enable smearering state |
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| 244 | self.enable_smearer = False |
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[fc6ea43] | 245 | self.disable_smearer = True |
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[7609f1a] | 246 | self.pinhole_smearer = False |
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| 247 | self.slit_smearer = False |
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[55bb249c] | 248 | # weighting options |
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| 249 | self.dI_noweight = False |
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| 250 | self.dI_didata = True |
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| 251 | self.dI_sqrdata = False |
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| 252 | self.dI_idata = False |
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[cfc0913] | 253 | ## disperity selection |
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[61cada5] | 254 | self.enable_disp = False |
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| 255 | self.disable_disp = True |
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[11a7e11] | 256 | |
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[cfc0913] | 257 | ## state of selected all check button |
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| 258 | self.cb1 = False |
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[0aeabc6] | 259 | ## store value of chisqr |
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[61cada5] | 260 | self.tcChi = None |
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[240b9966] | 261 | |
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[6f023e8] | 262 | def clone(self): |
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[61cada5] | 263 | """ |
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[5062bbf] | 264 | Create a new copy of the current object |
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[61cada5] | 265 | """ |
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| 266 | model = None |
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| 267 | if self.model is not None: |
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[6f023e8] | 268 | model = self.model.clone() |
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[bb70474] | 269 | model.name = self.model.name |
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[61cada5] | 270 | obj = PageState(self.parent, model=model) |
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| 271 | obj.file = copy.deepcopy(self.file) |
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[6f023e8] | 272 | obj.data = copy.deepcopy(self.data) |
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[61cada5] | 273 | if self.data is not None: |
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| 274 | self.data_name = self.data.name |
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| 275 | obj.data_name = self.data_name |
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| 276 | obj.is_data = self.is_data |
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[dcf29d7] | 277 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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[c99a6c5] | 278 | obj.engine_type = copy.deepcopy(self.engine_type) |
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[240b9966] | 279 | |
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[61cada5] | 280 | obj.formfactorcombobox = self.formfactorcombobox |
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| 281 | obj.structurecombobox = self.structurecombobox |
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[240b9966] | 282 | |
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| 283 | obj.shape_rbutton = self.shape_rbutton |
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| 284 | obj.shape_indep_rbutton = self.shape_indep_rbutton |
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| 285 | obj.struct_rbutton = self.struct_rbutton |
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| 286 | obj.plugin_rbutton = self.plugin_rbutton |
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| 287 | |
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[dcf29d7] | 288 | obj.manager = self.manager |
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| 289 | obj.event_owner = self.event_owner |
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[71f0373] | 290 | obj.disp_list = copy.deepcopy(self.disp_list) |
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[fc6ea43] | 291 | |
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[c477b31] | 292 | obj.enable2D = copy.deepcopy(self.enable2D) |
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[cfc0913] | 293 | obj.parameters = copy.deepcopy(self.parameters) |
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[fb59ed9] | 294 | obj.str_parameters = copy.deepcopy(self.str_parameters) |
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[cfc0913] | 295 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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| 296 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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[60132ef] | 297 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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[fc6ea43] | 298 | obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp) |
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[b787e68c] | 299 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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[fc6ea43] | 300 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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[0aeabc6] | 301 | obj.tcChi = self.tcChi |
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| 302 | |
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[c477b31] | 303 | if len(self._disp_obj_dict)>0: |
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| 304 | for k , v in self._disp_obj_dict.iteritems(): |
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| 305 | obj._disp_obj_dict[k]= v |
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[dad49a0] | 306 | if len(self.disp_cb_dict)>0: |
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| 307 | for k , v in self.disp_cb_dict.iteritems(): |
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| 308 | obj.disp_cb_dict[k]= v |
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[2296316] | 309 | if len(self.values)>0: |
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| 310 | for k , v in self.values.iteritems(): |
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| 311 | obj.values[k] = v |
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| 312 | if len(self.weights)>0: |
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| 313 | for k , v in self.weights.iteritems(): |
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| 314 | obj.weights[k] = v |
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[b787e68c] | 315 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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[fc6ea43] | 316 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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[7609f1a] | 317 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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| 318 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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| 319 | obj.smear_type = copy.deepcopy(self.smear_type) |
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[55bb249c] | 320 | obj.dI_noweight = copy.deepcopy(self.dI_noweight) |
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| 321 | obj.dI_didata = copy.deepcopy(self.dI_didata) |
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| 322 | obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata) |
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| 323 | obj.dI_idata = copy.deepcopy(self.dI_idata) |
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[7609f1a] | 324 | obj.dq_l = copy.deepcopy(self.dq_l) |
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| 325 | obj.dq_r = copy.deepcopy(self.dq_r) |
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| 326 | |
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[b787e68c] | 327 | obj.disp_box = copy.deepcopy(self.disp_box) |
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| 328 | obj.qmin = copy.deepcopy(self.qmin) |
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| 329 | obj.qmax = copy.deepcopy(self.qmax) |
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[c0ff8cc] | 330 | obj.multi_factor = self.multi_factor |
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[b787e68c] | 331 | obj.npts = copy.deepcopy(self.npts ) |
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| 332 | obj.cb1 = copy.deepcopy(self.cb1) |
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[3370922] | 333 | obj.smearer = copy.deepcopy(self.smearer) |
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| 334 | |
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[a074145] | 335 | for name, state in self.saved_states.iteritems(): |
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| 336 | copy_name = copy.deepcopy(name) |
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| 337 | copy_state = state.clone() |
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| 338 | obj.saved_states[copy_name]= copy_state |
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[6f023e8] | 339 | return obj |
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[61cada5] | 340 | |
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| 341 | def _repr_helper(self, list, rep): |
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| 342 | """ |
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[5062bbf] | 343 | Helper method to print a state |
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[61cada5] | 344 | """ |
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| 345 | for item in list: |
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[240b9966] | 346 | rep += "parameter name: %s \n"%str(item[1]) |
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| 347 | rep += "value: %s\n"%str(item[2]) |
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| 348 | rep += "selected: %s\n"%str(item[0]) |
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| 349 | rep += "error displayed : %s \n"%str(item[4][0]) |
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| 350 | rep += "error value:%s \n"%str(item[4][1]) |
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| 351 | rep += "minimum displayed : %s \n"%str(item[5][0]) |
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| 352 | rep += "minimum value : %s \n"%str(item[5][1]) |
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| 353 | rep += "maximum displayed : %s \n"%str(item[6][0]) |
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| 354 | rep += "maximum value : %s \n"%str(item[6][1]) |
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| 355 | rep += "parameter unit: %s\n\n"%str(item[7]) |
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| 356 | return rep |
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[c0ff8cc] | 357 | |
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[61cada5] | 358 | def __repr__(self): |
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[11a7e11] | 359 | """ |
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[5062bbf] | 360 | output string for printing |
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[11a7e11] | 361 | """ |
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| 362 | rep = "\nState name: %s\n"%self.file |
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| 363 | t = time.localtime(self.timestamp) |
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[deff488] | 364 | time_str = time.strftime("%b %d %Y %H;%M;%S ", t) |
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[c0ff8cc] | 365 | |
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[b7c6a4a] | 366 | rep += "State created: %s\n"%time_str |
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[11a7e11] | 367 | rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox |
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| 368 | rep += "State structure factor combobox selection: %s\n"%self.structurecombobox |
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| 369 | rep += "is data : %s\n"%self.is_data |
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| 370 | rep += "data's name : %s\n"%self.data_name |
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| 371 | rep += "data's id : %s\n"%self.data_id |
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[74dc0a4] | 372 | if self.model != None: |
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[93f0a862] | 373 | m_name = self.model.__class__.__name__ |
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| 374 | if m_name == 'Model': |
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| 375 | m_name = self.m_name |
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| 376 | rep += "model name : %s\n"% m_name |
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[74dc0a4] | 377 | else: |
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| 378 | rep += "model name : None\n" |
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[11a7e11] | 379 | rep += "model type (form factor) selected: %s\n"%self.shape_rbutton |
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[c0ff8cc] | 380 | rep += "multi_factor : %s\n"% str(self.multi_factor) |
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[11a7e11] | 381 | rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton |
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| 382 | rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton |
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| 383 | rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton |
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| 384 | rep += "data : %s\n"% str(self.data) |
---|
| 385 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin), |
---|
| 386 | str(self.qmax),str(self.npts)) |
---|
[0b12abb5] | 387 | rep += "Dispersion selection : %s\n"%str(self.disp_box) |
---|
| 388 | rep += "Smearing enable : %s\n"%str(self.enable_smearer) |
---|
| 389 | rep += "Smearing disable : %s\n"%str(self.disable_smearer) |
---|
| 390 | rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer) |
---|
| 391 | rep += "Slit smearer enable : %s\n"%str(self.slit_smearer) |
---|
| 392 | rep += "Dispersity enable : %s\n"%str(self.enable_disp) |
---|
| 393 | rep += "Dispersity disable : %s\n"%str(self.disable_disp) |
---|
| 394 | rep += "Slit smearer enable: %s\n"%str(self.slit_smearer) |
---|
[55bb249c] | 395 | |
---|
| 396 | rep += "dI_noweight : %s\n"%str(self.dI_noweight) |
---|
| 397 | rep += "dI_didata : %s\n"%str(self.dI_didata) |
---|
| 398 | rep += "dI_sqrdata : %s\n"%str(self.dI_sqrdata) |
---|
| 399 | rep += "dI_idata : %s\n"%str(self.dI_idata) |
---|
| 400 | |
---|
| 401 | |
---|
[0b12abb5] | 402 | rep += "2D enable : %s\n"%str(self.enable2D) |
---|
| 403 | rep += "All parameters checkbox selected: %s\n"%(self.cb1) |
---|
| 404 | rep += "Value of Chisqr : %s\n"%str(self.tcChi) |
---|
| 405 | rep += "Smear object : %s\n"%str(self.smearer) |
---|
| 406 | rep += "Smear type : %s\n"%(self.smear_type) |
---|
| 407 | rep += "dq_l : %s\n"%self.dq_l |
---|
| 408 | rep += "dq_r : %s\n"%self.dq_r |
---|
| 409 | |
---|
[11a7e11] | 410 | rep += "model : %s\n\n"% str(self.model) |
---|
[2296316] | 411 | temp_parameters = [] |
---|
| 412 | temp_fittable_param = [] |
---|
| 413 | if self.data.__class__.__name__ == "Data2D": |
---|
| 414 | self.is_2D = True |
---|
| 415 | else: |
---|
| 416 | self.is_2D = False |
---|
| 417 | if self.data is not None: |
---|
| 418 | if not self.is_2D: |
---|
| 419 | for item in self.parameters: |
---|
| 420 | if not item in self.orientation_params: |
---|
| 421 | temp_parameters.append(item) |
---|
| 422 | for item in self.fittable_param: |
---|
| 423 | if not item in self.orientation_params_disp: |
---|
| 424 | temp_fittable_param.append(item) |
---|
| 425 | else: |
---|
| 426 | temp_parameters = self.parameters |
---|
| 427 | temp_fittable_param = self.fittable_param |
---|
| 428 | |
---|
| 429 | rep += "number parameters(self.parameters): %s\n"%len(temp_parameters) |
---|
| 430 | rep = self._repr_helper( list=temp_parameters, rep=rep) |
---|
| 431 | rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters) |
---|
| 432 | rep = self._repr_helper( list=self.str_parameters, rep=rep) |
---|
| 433 | rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param) |
---|
| 434 | rep = self._repr_helper( list=temp_fittable_param, rep=rep) |
---|
| 435 | """ |
---|
| 436 | if is_2D: |
---|
| 437 | rep += "number orientation parameters" |
---|
| 438 | rep += "(self.orientation_params): %s\n"%len(self.orientation_params) |
---|
| 439 | rep = self._repr_helper( list=self.orientation_params, rep=rep) |
---|
| 440 | rep += "number dispersity parameters" |
---|
| 441 | rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp) |
---|
| 442 | rep = self._repr_helper( list=self.orientation_params_disp, rep=rep) |
---|
| 443 | """ |
---|
[61cada5] | 444 | return rep |
---|
[2296316] | 445 | |
---|
| 446 | def set_report_string(self): |
---|
| 447 | """ |
---|
| 448 | Get the values (strings) from __str__ for report |
---|
| 449 | """ |
---|
| 450 | # Dictionary of teh report strings |
---|
| 451 | repo_time = "" |
---|
| 452 | model_name = "" |
---|
| 453 | title = "" |
---|
| 454 | title_name = "" |
---|
| 455 | file_name = "" |
---|
| 456 | param_string = "" |
---|
| 457 | paramval_string = "" |
---|
| 458 | chi2_string = "" |
---|
[c0ff8cc] | 459 | multi_factor_string = "" |
---|
[2296316] | 460 | q_range = "" |
---|
| 461 | strings = self.__repr__() |
---|
| 462 | lines = strings.split('\n') |
---|
| 463 | |
---|
| 464 | # get all string values from __str__() |
---|
| 465 | for line in lines: |
---|
| 466 | value = "" |
---|
| 467 | content = line.split(":") |
---|
| 468 | name = content[0] |
---|
| 469 | try: |
---|
| 470 | value = content[1] |
---|
| 471 | except: |
---|
| 472 | pass |
---|
[b7c6a4a] | 473 | if name.count("State created"): |
---|
| 474 | repo_time = "" + value |
---|
[2296316] | 475 | if name.count("parameter name"): |
---|
| 476 | val_name = value.split(".") |
---|
| 477 | if len(val_name) > 1: |
---|
| 478 | if val_name[1].count("width"): |
---|
| 479 | param_string += value + ',' |
---|
| 480 | else: |
---|
| 481 | continue |
---|
| 482 | else: |
---|
| 483 | param_string += value + ',' |
---|
| 484 | if name == "value": |
---|
| 485 | param_string += value + ',' |
---|
| 486 | if name == "error value": |
---|
| 487 | param_string += value + ',' |
---|
| 488 | if name == "parameter unit": |
---|
| 489 | param_string += value + ':' |
---|
| 490 | if name == "Value of Chisqr ": |
---|
| 491 | chi2 = ("Chi2/Npts = " + value) |
---|
| 492 | chi2_string = CENTRE % chi2 |
---|
[c0ff8cc] | 493 | if name == "multi_factor ": |
---|
| 494 | muti_factor = ("muti_factor = " + value) |
---|
| 495 | muti_factor_string = CENTRE % muti_factor |
---|
[2296316] | 496 | if name == "Title": |
---|
| 497 | if len(value.strip()) == 0: |
---|
| 498 | continue |
---|
| 499 | title = value + " [" + repo_time + "]" |
---|
| 500 | title_name = HEADER % title |
---|
| 501 | if name == "data ": |
---|
| 502 | try: |
---|
| 503 | file = ("File name:" + content[2]) |
---|
| 504 | file_name = CENTRE % file |
---|
| 505 | if len(title) == 0: |
---|
| 506 | title = content[2] + " [" + repo_time + "]" |
---|
| 507 | title_name = HEADER % title |
---|
| 508 | except: |
---|
| 509 | pass |
---|
[74dc0a4] | 510 | if name == "model name ": |
---|
| 511 | try: |
---|
| 512 | modelname = "Model name:" + content[1] |
---|
| 513 | except: |
---|
| 514 | modelname = "Model name:" + " NAN" |
---|
| 515 | model_name = CENTRE % modelname |
---|
| 516 | |
---|
[2296316] | 517 | if name == "Plotting Range": |
---|
| 518 | try: |
---|
| 519 | q_range = content[1] + " = " + content[2] \ |
---|
| 520 | + " = " + content[3].split(",")[0] |
---|
| 521 | q_name = ("Q Range: " + q_range) |
---|
| 522 | q_range = CENTRE % q_name |
---|
| 523 | except: |
---|
| 524 | pass |
---|
| 525 | paramval = "" |
---|
| 526 | for lines in param_string.split(":"): |
---|
| 527 | line = lines.split(",") |
---|
| 528 | if len(lines) > 0: |
---|
| 529 | param = line[0] |
---|
| 530 | param += " = " + line[1] |
---|
| 531 | if len(line[2].split()) > 0 and not line[2].count("None"): |
---|
| 532 | param += " +- " + line[2] |
---|
| 533 | if len(line[3].split()) > 0 and not line[3].count("None"): |
---|
| 534 | param += " " + line[3] |
---|
| 535 | if not paramval.count(param): |
---|
| 536 | paramval += param + "\n" |
---|
| 537 | paramval_string += CENTRE % param + "\n" |
---|
[3a3dd9c] | 538 | |
---|
[f5bdb4a] | 539 | text_string = "\n\n\n" + title + "\n\n" + file + \ |
---|
| 540 | "\n" + q_name + \ |
---|
| 541 | "\n" + chi2 + \ |
---|
| 542 | "\n\n" + paramval |
---|
| 543 | |
---|
| 544 | title_name = self._check_html_format(title_name) |
---|
| 545 | file_name = self._check_html_format(file_name) |
---|
| 546 | title = self._check_html_format(title) |
---|
| 547 | |
---|
[2296316] | 548 | html_string = title_name + "\n" + file_name + \ |
---|
[74dc0a4] | 549 | "\n" + model_name +\ |
---|
[2296316] | 550 | "\n" + q_range + \ |
---|
| 551 | "\n" + chi2_string + \ |
---|
| 552 | "\n" + ELINE + \ |
---|
| 553 | "\n" + paramval_string + \ |
---|
| 554 | "\n" + ELINE + \ |
---|
| 555 | "\n" + FEET_1 % title + \ |
---|
| 556 | "\n" + FEET_2 |
---|
[f5bdb4a] | 557 | |
---|
[2296316] | 558 | return html_string, text_string, title |
---|
| 559 | |
---|
[f5bdb4a] | 560 | def _check_html_format(self, name): |
---|
| 561 | """ |
---|
| 562 | Check string '%' for html format |
---|
| 563 | """ |
---|
| 564 | if name.count('%'): |
---|
| 565 | name = name.replace('%', '%') |
---|
| 566 | |
---|
| 567 | return name |
---|
| 568 | |
---|
| 569 | |
---|
[2296316] | 570 | def report(self, figs=None, canvases=None): |
---|
| 571 | """ |
---|
| 572 | Invoke report dialog panel |
---|
| 573 | |
---|
| 574 | : param figs: list of pylab figures [list] |
---|
| 575 | """ |
---|
| 576 | from report_dialog import ReportDialog |
---|
| 577 | # get the strings for report |
---|
| 578 | html_str, text_str, title = self.set_report_string() |
---|
| 579 | # Allow 2 figures to append |
---|
| 580 | if len(figs) == 1: |
---|
| 581 | add_str = FEET_3 |
---|
| 582 | elif len(figs) == 2: |
---|
| 583 | add_str = ELINE |
---|
| 584 | add_str += FEET_2 % ("%s") |
---|
| 585 | add_str += ELINE |
---|
| 586 | add_str += FEET_3 |
---|
| 587 | elif len(figs) > 2: |
---|
| 588 | add_str = ELINE |
---|
| 589 | add_str += FEET_2 % ("%s") |
---|
| 590 | add_str += ELINE |
---|
| 591 | add_str += FEET_2 % ("%s") |
---|
| 592 | add_str += ELINE |
---|
| 593 | add_str += FEET_3 |
---|
| 594 | else: |
---|
| 595 | add_str = "" |
---|
[c0ff8cc] | 596 | |
---|
[2296316] | 597 | # final report html strings |
---|
| 598 | report_str = html_str % ("%s") + add_str |
---|
| 599 | |
---|
| 600 | # make plot image |
---|
| 601 | images = self.set_plot_state(figs, canvases) |
---|
| 602 | report_list = [report_str, text_str, images ] |
---|
| 603 | dialog = ReportDialog(report_list, None, -1, "") |
---|
| 604 | dialog.ShowModal() |
---|
[c0ff8cc] | 605 | |
---|
| 606 | |
---|
[61cada5] | 607 | def _toXML_helper(self, list, element, newdoc): |
---|
| 608 | """ |
---|
[5062bbf] | 609 | Helper method to create xml file for saving state |
---|
[61cada5] | 610 | """ |
---|
| 611 | for item in list: |
---|
| 612 | sub_element = newdoc.createElement('parameter') |
---|
| 613 | sub_element.setAttribute('name', str(item[1])) |
---|
| 614 | sub_element.setAttribute('value', str(item[2])) |
---|
| 615 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
---|
| 616 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
---|
| 617 | sub_element.setAttribute('error_value', str(item[4][1])) |
---|
| 618 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
---|
| 619 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
---|
| 620 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
---|
| 621 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
---|
| 622 | sub_element.setAttribute('unit', str(item[7])) |
---|
| 623 | element.appendChild(sub_element) |
---|
| 624 | |
---|
| 625 | def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None): |
---|
| 626 | """ |
---|
[5062bbf] | 627 | Writes the state of the InversionControl panel to file, as XML. |
---|
| 628 | |
---|
| 629 | Compatible with standalone writing, or appending to an |
---|
| 630 | already existing XML document. In that case, the XML document |
---|
| 631 | is required. An optional entry node in the XML document may also be given. |
---|
| 632 | |
---|
| 633 | :param file: file to write to |
---|
| 634 | :param doc: XML document object [optional] |
---|
| 635 | :param entry_node: XML node within the XML document at which we will append the data [optional] |
---|
| 636 | |
---|
[61cada5] | 637 | """ |
---|
| 638 | from xml.dom.minidom import getDOMImplementation |
---|
[71f0373] | 639 | |
---|
[61cada5] | 640 | # Check whether we have to write a standalone XML file |
---|
| 641 | if doc is None: |
---|
| 642 | impl = getDOMImplementation() |
---|
| 643 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
---|
| 644 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
---|
| 645 | top_element = newdoc.documentElement |
---|
| 646 | else: |
---|
| 647 | # We are appending to an existing document |
---|
| 648 | newdoc = doc |
---|
| 649 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
| 650 | if entry_node is None: |
---|
| 651 | newdoc.documentElement.appendChild(top_element) |
---|
| 652 | else: |
---|
| 653 | entry_node.appendChild(top_element) |
---|
| 654 | |
---|
| 655 | attr = newdoc.createAttribute("version") |
---|
| 656 | attr.nodeValue = '1.0' |
---|
| 657 | top_element.setAttributeNode(attr) |
---|
[cfc0913] | 658 | |
---|
[61cada5] | 659 | # File name |
---|
| 660 | element = newdoc.createElement("filename") |
---|
| 661 | if self.file is not None: |
---|
| 662 | element.appendChild(newdoc.createTextNode(str(self.file))) |
---|
| 663 | else: |
---|
| 664 | element.appendChild(newdoc.createTextNode(str(file))) |
---|
| 665 | top_element.appendChild(element) |
---|
[11a7e11] | 666 | |
---|
| 667 | element = newdoc.createElement("timestamp") |
---|
| 668 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
---|
| 669 | attr = newdoc.createAttribute("epoch") |
---|
| 670 | attr.nodeValue = str(self.timestamp) |
---|
| 671 | element.setAttributeNode(attr) |
---|
| 672 | top_element.appendChild(element) |
---|
[61cada5] | 673 | # Inputs |
---|
| 674 | inputs = newdoc.createElement("Attributes") |
---|
| 675 | top_element.appendChild(inputs) |
---|
| 676 | |
---|
[0b12abb5] | 677 | |
---|
[61cada5] | 678 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 679 | self.data_group_id = self.data.group_id |
---|
| 680 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
| 681 | self.is_data = self.data.is_data |
---|
| 682 | if self.data is not None: |
---|
| 683 | self.data_name = self.data.name |
---|
| 684 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 685 | self.data_id = self.data.id |
---|
| 686 | |
---|
[26f3dd5] | 687 | for item in list_of_data_attributes: |
---|
[0b12abb5] | 688 | element = newdoc.createElement(item[0]) |
---|
[2296316] | 689 | exec "element.setAttribute(item[0], str(self.%s))" % (item[1]) |
---|
[0b12abb5] | 690 | inputs.appendChild(element) |
---|
[26f3dd5] | 691 | |
---|
| 692 | for item in list_of_state_attributes: |
---|
| 693 | element = newdoc.createElement(item[0]) |
---|
[2296316] | 694 | exec "element.setAttribute(item[0], str(self.%s))" % (item[1]) |
---|
[26f3dd5] | 695 | inputs.appendChild(element) |
---|
[c0ff8cc] | 696 | |
---|
[2296316] | 697 | # For self.values ={ disp_param_name: [vals,...],...} |
---|
[c0ff8cc] | 698 | # and for self.weights ={ disp_param_name: [weights,...],...} |
---|
[11a7e11] | 699 | for item in list_of_model_attributes: |
---|
| 700 | element = newdoc.createElement(item[0]) |
---|
[2296316] | 701 | exec "list = self.%s" % item[1] |
---|
| 702 | for key, value in list.iteritems(): |
---|
| 703 | sub_element = newdoc.createElement(key) |
---|
| 704 | sub_element.setAttribute('name', str(key)) |
---|
| 705 | for val in value: |
---|
| 706 | com = "sub_element.appendChild" |
---|
| 707 | com += "(newdoc.createTextNode(str(%s)))" |
---|
| 708 | exec com % val |
---|
| 709 | |
---|
| 710 | element.appendChild(sub_element) |
---|
[11a7e11] | 711 | inputs.appendChild(element) |
---|
[2296316] | 712 | |
---|
| 713 | # Create doc for the dictionary of self._disp_obj_dic |
---|
| 714 | for item in list_of_obj_dic: |
---|
| 715 | element = newdoc.createElement(item[0]) |
---|
| 716 | exec "list = self.%s" % item[1] |
---|
| 717 | for key, val in list.iteritems(): |
---|
| 718 | value = repr(val) |
---|
| 719 | sub_element = newdoc.createElement(key) |
---|
| 720 | sub_element.setAttribute('name', str(key)) |
---|
| 721 | sub_element.setAttribute('value', str(value)) |
---|
| 722 | element.appendChild(sub_element) |
---|
| 723 | inputs.appendChild(element) |
---|
| 724 | |
---|
[61cada5] | 725 | for item in list_of_state_parameters: |
---|
| 726 | element = newdoc.createElement(item[0]) |
---|
[2296316] | 727 | com = "self._toXML_helper(list=self.%s," |
---|
| 728 | com += " element=element, newdoc=newdoc)" |
---|
| 729 | exec com % item[1] |
---|
[61cada5] | 730 | inputs.appendChild(element) |
---|
[c0ff8cc] | 731 | |
---|
[61cada5] | 732 | # Save the file |
---|
| 733 | if doc is None: |
---|
| 734 | fd = open(file, 'w') |
---|
| 735 | fd.write(newdoc.toprettyxml()) |
---|
| 736 | fd.close() |
---|
| 737 | return None |
---|
| 738 | else: |
---|
| 739 | return newdoc.toprettyxml() |
---|
| 740 | |
---|
| 741 | def _fromXML_helper(self, node, list): |
---|
| 742 | """ |
---|
[5062bbf] | 743 | Helper function to write state to xml |
---|
[61cada5] | 744 | """ |
---|
| 745 | for item in node: |
---|
[0b12abb5] | 746 | try: |
---|
| 747 | name = item.get('name') |
---|
| 748 | except: |
---|
| 749 | name = None |
---|
| 750 | try: |
---|
| 751 | value = item.get('value') |
---|
| 752 | except: |
---|
| 753 | value = None |
---|
| 754 | try: |
---|
[3ad91de] | 755 | selected_to_fit = (item.get('selected_to_fit') == "True") |
---|
[0b12abb5] | 756 | except: |
---|
| 757 | selected_to_fit = None |
---|
| 758 | try: |
---|
[3ad91de] | 759 | error_displayed = (item.get('error_displayed') == "True") |
---|
[0b12abb5] | 760 | except: |
---|
| 761 | error_displayed = None |
---|
| 762 | try: |
---|
| 763 | error_value = item.get('error_value') |
---|
| 764 | except: |
---|
| 765 | error_value = None |
---|
| 766 | try: |
---|
[3ad91de] | 767 | minimum_displayed = (item.get('minimum_displayed')== "True") |
---|
[0b12abb5] | 768 | except: |
---|
| 769 | minimum_displayed = None |
---|
| 770 | try: |
---|
| 771 | minimum_value = item.get('minimum_value') |
---|
| 772 | except: |
---|
| 773 | minimum_value = None |
---|
| 774 | try: |
---|
[3ad91de] | 775 | maximum_displayed = (item.get('maximum_displayed') == "True") |
---|
[0b12abb5] | 776 | except: |
---|
| 777 | maximum_displayed = None |
---|
| 778 | try: |
---|
| 779 | maximum_value = item.get('maximum_value') |
---|
| 780 | except: |
---|
| 781 | maximum_value = None |
---|
| 782 | try: |
---|
| 783 | unit = item.get('unit') |
---|
| 784 | except: |
---|
| 785 | unit = None |
---|
[2296316] | 786 | list.append([selected_to_fit, name, value, "+/-", |
---|
| 787 | [error_displayed, error_value], |
---|
| 788 | [minimum_displayed,minimum_value], |
---|
| 789 | [maximum_displayed,maximum_value], unit]) |
---|
[cfc0913] | 790 | |
---|
[61cada5] | 791 | def fromXML(self, file=None, node=None): |
---|
| 792 | """ |
---|
[5062bbf] | 793 | Load fitting state from a file |
---|
| 794 | |
---|
| 795 | :param file: .fitv file |
---|
| 796 | :param node: node of a XML document to read from |
---|
| 797 | |
---|
[61cada5] | 798 | """ |
---|
| 799 | if file is not None: |
---|
[11a7e11] | 800 | msg = "PageState no longer supports non-CanSAS" |
---|
| 801 | msg += " format for fitting files" |
---|
| 802 | raise RuntimeError, msg |
---|
[61cada5] | 803 | |
---|
[11a7e11] | 804 | if node.get('version')and node.get('version') == '1.0': |
---|
[61cada5] | 805 | |
---|
| 806 | # Get file name |
---|
| 807 | entry = get_content('ns:filename', node) |
---|
| 808 | if entry is not None: |
---|
| 809 | self.file = entry.text.strip() |
---|
[11a7e11] | 810 | |
---|
| 811 | # Get time stamp |
---|
| 812 | entry = get_content('ns:timestamp', node) |
---|
| 813 | if entry is not None and entry.get('epoch'): |
---|
| 814 | try: |
---|
| 815 | self.timestamp = float(entry.get('epoch')) |
---|
| 816 | except: |
---|
| 817 | msg = "PageState.fromXML: Could not" |
---|
| 818 | msg += " read timestamp\n %s" % sys.exc_value |
---|
| 819 | logging.error(msg) |
---|
| 820 | |
---|
[61cada5] | 821 | # Parse fitting attributes |
---|
| 822 | entry = get_content('ns:Attributes', node) |
---|
[0b12abb5] | 823 | for item in list_of_data_attributes: |
---|
| 824 | node = get_content('ns:%s'%item[0], entry) |
---|
| 825 | try: |
---|
[2296316] | 826 | exec "self.%s = parse_entry_helper(node, item)" % item[0] |
---|
[0b12abb5] | 827 | |
---|
| 828 | except: |
---|
| 829 | raise |
---|
[2296316] | 830 | |
---|
[61cada5] | 831 | if entry is not None: |
---|
[0b12abb5] | 832 | |
---|
[61cada5] | 833 | for item in list_of_state_attributes: |
---|
[2296316] | 834 | node = get_content('ns:%s' % item[0], entry) |
---|
[0b12abb5] | 835 | try: |
---|
[2296316] | 836 | exec "self.%s = parse_entry_helper(node, item)" % \ |
---|
| 837 | str(item[0]) |
---|
[0b12abb5] | 838 | except: |
---|
| 839 | raise |
---|
| 840 | |
---|
[2296316] | 841 | for item in list_of_state_parameters: |
---|
| 842 | node = get_content("ns:%s" % item[0], entry) |
---|
| 843 | exec "self._fromXML_helper(node=node, list=self.%s)" % \ |
---|
| 844 | item[1] |
---|
| 845 | |
---|
| 846 | # Recover _disp_obj_dict from xml file |
---|
| 847 | self._disp_obj_dict = {} |
---|
| 848 | for item in list_of_obj_dic: |
---|
| 849 | # Get node |
---|
| 850 | node = get_content("ns:%s" % item[0], entry) |
---|
| 851 | for attr in node: |
---|
| 852 | name = attr.get('name') |
---|
| 853 | val = attr.get('value') |
---|
| 854 | value = val.split(" instance")[0] |
---|
| 855 | disp_name = value.split("<")[1] |
---|
[11a7e11] | 856 | try: |
---|
[2296316] | 857 | # Try to recover disp_model object from strings |
---|
| 858 | com = "from sans.models.dispersion_models " |
---|
| 859 | com += "import %s as disp" |
---|
| 860 | com_name = disp_name.split(".")[3] |
---|
| 861 | exec com % com_name |
---|
| 862 | disp_model = disp() |
---|
| 863 | exec "self.%s['%s'] = com_name" % (item[1], name) |
---|
[11a7e11] | 864 | except: |
---|
[2296316] | 865 | pass |
---|
| 866 | |
---|
| 867 | # get self.values and self.weights dic. if exists |
---|
| 868 | for item in list_of_model_attributes: |
---|
| 869 | node = get_content("ns:%s" % item[0], entry) |
---|
| 870 | dic = {} |
---|
| 871 | list = [] |
---|
| 872 | for par in node: |
---|
| 873 | name = par.get('name') |
---|
| 874 | values = par.text.split('\n') |
---|
| 875 | # Get lines only with numbers |
---|
| 876 | for line in values: |
---|
| 877 | try: |
---|
| 878 | val= float(line) |
---|
| 879 | list.append(val) |
---|
| 880 | except: |
---|
| 881 | # pass if line is empty (it happens) |
---|
| 882 | pass |
---|
| 883 | dic[name] = numpy.array(list) |
---|
| 884 | exec "self.%s = dic" % item[1] |
---|
| 885 | |
---|
| 886 | def set_plot_state(self, figs, canvases): |
---|
| 887 | """ |
---|
| 888 | Build image state that wx.html understand |
---|
| 889 | by plotting, putting it into wx.FileSystem image object |
---|
| 890 | |
---|
| 891 | """ |
---|
| 892 | images = [] |
---|
| 893 | # some imports |
---|
| 894 | import wx |
---|
| 895 | |
---|
| 896 | # Reset memory |
---|
| 897 | self.imgRAM = None |
---|
| 898 | wx.MemoryFSHandler() |
---|
| 899 | |
---|
| 900 | # For no figures in the list, prepare empty plot |
---|
| 901 | if figs == None or len(figs) == 0: |
---|
| 902 | figs = [None] |
---|
| 903 | |
---|
| 904 | # Loop over the list of figures |
---|
| 905 | # use wx.MemoryFSHandler |
---|
| 906 | self.imgRAM = wx.MemoryFSHandler() |
---|
| 907 | for fig in figs: |
---|
| 908 | if figs != None: |
---|
| 909 | #fig.set_facecolor('w') |
---|
| 910 | ind = figs.index(fig) |
---|
| 911 | canvas = canvases[ind] |
---|
[0b12abb5] | 912 | |
---|
[2296316] | 913 | #bmp = wx.BitmapDataObject() |
---|
| 914 | #bmp.SetBitmap(canvas.bitmap) |
---|
| 915 | #store the image in wx.FileSystem Object |
---|
| 916 | wx.FileSystem.AddHandler(wx.MemoryFSHandler()) |
---|
| 917 | |
---|
| 918 | # index of the fig |
---|
| 919 | ind = figs.index(fig) |
---|
| 920 | |
---|
| 921 | #AddFile, image can be retrieved with 'memory:filename' |
---|
| 922 | self.imgRAM.AddFile('img_fit%s.png' % ind , |
---|
| 923 | canvas.bitmap, wx.BITMAP_TYPE_PNG) |
---|
| 924 | |
---|
| 925 | #append figs |
---|
| 926 | images.append(fig) |
---|
| 927 | |
---|
[c0ff8cc] | 928 | return images |
---|
[61cada5] | 929 | |
---|
| 930 | class Reader(CansasReader): |
---|
| 931 | """ |
---|
[5062bbf] | 932 | Class to load a .fitv fitting file |
---|
[61cada5] | 933 | """ |
---|
| 934 | ## File type |
---|
| 935 | type_name = "Fitting" |
---|
| 936 | |
---|
| 937 | ## Wildcards |
---|
[b35d3d1] | 938 | type = ["Fitting files (*.fitv)|*.fitv" |
---|
| 939 | "SANSView file (*.svs)|*.svs"] |
---|
[61cada5] | 940 | ## List of allowed extensions |
---|
[b35d3d1] | 941 | ext=['.fitv', '.FITV', '.svs', 'SVS'] |
---|
[61cada5] | 942 | |
---|
| 943 | def __init__(self, call_back=None, cansas=True): |
---|
[df7ed14] | 944 | CansasReader.__init__(self) |
---|
[61cada5] | 945 | """ |
---|
[5062bbf] | 946 | Initialize the call-back method to be called |
---|
| 947 | after we load a file |
---|
| 948 | |
---|
| 949 | :param call_back: call-back method |
---|
| 950 | :param cansas: True = files will be written/read in CanSAS format |
---|
| 951 | False = write CanSAS format |
---|
[61cada5] | 952 | |
---|
| 953 | """ |
---|
| 954 | ## Call back method to be executed after a file is read |
---|
| 955 | self.call_back = call_back |
---|
| 956 | ## CanSAS format flag |
---|
| 957 | self.cansas = cansas |
---|
[75fbd17] | 958 | self.state = None |
---|
| 959 | def get_state(self): |
---|
| 960 | return self.state |
---|
[61cada5] | 961 | |
---|
| 962 | def read(self, path): |
---|
| 963 | """ |
---|
[5062bbf] | 964 | Load a new P(r) inversion state from file |
---|
| 965 | |
---|
| 966 | :param path: file path |
---|
| 967 | |
---|
[61cada5] | 968 | """ |
---|
[e9b12eaf] | 969 | if self.cansas == True: |
---|
[61cada5] | 970 | return self._read_cansas(path) |
---|
[e9b12eaf] | 971 | |
---|
| 972 | def _data2d_to_xml_doc(self, datainfo): |
---|
[61cada5] | 973 | """ |
---|
[5062bbf] | 974 | Create an XML document to contain the content of a Data2D |
---|
| 975 | |
---|
| 976 | :param datainfo: Data2D object |
---|
| 977 | |
---|
[61cada5] | 978 | """ |
---|
| 979 | if not issubclass(datainfo.__class__, Data2D): |
---|
| 980 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
---|
| 981 | |
---|
| 982 | doc = xml.dom.minidom.Document() |
---|
| 983 | main_node = doc.createElement("SASroot") |
---|
| 984 | main_node.setAttribute("version", self.version) |
---|
[df7ed14] | 985 | main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) |
---|
| 986 | main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance") |
---|
| 987 | main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version) |
---|
| 988 | |
---|
[61cada5] | 989 | doc.appendChild(main_node) |
---|
| 990 | |
---|
| 991 | entry_node = doc.createElement("SASentry") |
---|
| 992 | main_node.appendChild(entry_node) |
---|
[df7ed14] | 993 | |
---|
[61cada5] | 994 | write_node(doc, entry_node, "Title", datainfo.title) |
---|
[df7ed14] | 995 | if datainfo is not None: |
---|
| 996 | write_node(doc, entry_node, "data_class", datainfo.__class__.__name__) |
---|
[61cada5] | 997 | for item in datainfo.run: |
---|
| 998 | runname = {} |
---|
| 999 | if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1: |
---|
| 1000 | runname = {'name': datainfo.run_name[item] } |
---|
| 1001 | write_node(doc, entry_node, "Run", item, runname) |
---|
| 1002 | # Data info |
---|
[df7ed14] | 1003 | new_node = doc.createElement("SASdata") |
---|
| 1004 | entry_node.appendChild(new_node) |
---|
[e9b12eaf] | 1005 | for item in list_of_data_2d_attr: |
---|
| 1006 | element = doc.createElement(item[0]) |
---|
| 1007 | exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1]) |
---|
[df7ed14] | 1008 | new_node.appendChild(element) |
---|
| 1009 | |
---|
[e9b12eaf] | 1010 | for item in list_of_data2d_values: |
---|
[df7ed14] | 1011 | root_node = doc.createElement(item[0]) |
---|
| 1012 | new_node.appendChild(root_node) |
---|
| 1013 | |
---|
[35b556d] | 1014 | exec "temp_list = datainfo.%s"%item[1] |
---|
[df7ed14] | 1015 | |
---|
[35b556d] | 1016 | if temp_list is None or len(temp_list)== 0: |
---|
[df7ed14] | 1017 | element = doc.createElement(item[0]) |
---|
[35b556d] | 1018 | exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list |
---|
[df7ed14] | 1019 | root_node.appendChild(element) |
---|
[35b556d] | 1020 | else: |
---|
| 1021 | for value in temp_list: |
---|
[df7ed14] | 1022 | element = doc.createElement(item[0]) |
---|
| 1023 | exec "element.setAttribute(item[0], str(%s))"%value |
---|
| 1024 | root_node.appendChild(element) |
---|
| 1025 | |
---|
[61cada5] | 1026 | # Sample info |
---|
| 1027 | sample = doc.createElement("SASsample") |
---|
| 1028 | if datainfo.sample.name is not None: |
---|
| 1029 | sample.setAttribute("name", str(datainfo.sample.name)) |
---|
| 1030 | entry_node.appendChild(sample) |
---|
| 1031 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
---|
| 1032 | write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit}) |
---|
| 1033 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
---|
| 1034 | write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit}) |
---|
| 1035 | |
---|
| 1036 | for item in datainfo.sample.details: |
---|
| 1037 | write_node(doc, sample, "details", item) |
---|
| 1038 | |
---|
| 1039 | pos = doc.createElement("position") |
---|
| 1040 | written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit}) |
---|
| 1041 | written = written | write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit}) |
---|
| 1042 | written = written | write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit}) |
---|
| 1043 | if written == True: |
---|
| 1044 | sample.appendChild(pos) |
---|
| 1045 | |
---|
| 1046 | ori = doc.createElement("orientation") |
---|
| 1047 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit}) |
---|
| 1048 | written = written | write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit}) |
---|
| 1049 | written = written | write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit}) |
---|
| 1050 | if written == True: |
---|
| 1051 | sample.appendChild(ori) |
---|
| 1052 | |
---|
| 1053 | # Instrument info |
---|
| 1054 | instr = doc.createElement("SASinstrument") |
---|
| 1055 | entry_node.appendChild(instr) |
---|
| 1056 | |
---|
| 1057 | write_node(doc, instr, "name", datainfo.instrument) |
---|
| 1058 | |
---|
| 1059 | # Source |
---|
| 1060 | source = doc.createElement("SASsource") |
---|
| 1061 | if datainfo.source.name is not None: |
---|
| 1062 | source.setAttribute("name", str(datainfo.source.name)) |
---|
| 1063 | instr.appendChild(source) |
---|
| 1064 | |
---|
| 1065 | write_node(doc, source, "radiation", datainfo.source.radiation) |
---|
| 1066 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
---|
| 1067 | size = doc.createElement("beam_size") |
---|
| 1068 | if datainfo.source.beam_size_name is not None: |
---|
| 1069 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
---|
| 1070 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit}) |
---|
| 1071 | written = written | write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit}) |
---|
| 1072 | written = written | write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit}) |
---|
| 1073 | if written == True: |
---|
| 1074 | source.appendChild(size) |
---|
| 1075 | |
---|
| 1076 | write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit}) |
---|
| 1077 | write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit}) |
---|
| 1078 | write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit}) |
---|
| 1079 | write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit}) |
---|
| 1080 | |
---|
| 1081 | # Collimation |
---|
| 1082 | for item in datainfo.collimation: |
---|
| 1083 | coll = doc.createElement("SAScollimation") |
---|
| 1084 | if item.name is not None: |
---|
| 1085 | coll.setAttribute("name", str(item.name)) |
---|
| 1086 | instr.appendChild(coll) |
---|
| 1087 | |
---|
| 1088 | write_node(doc, coll, "length", item.length, {"unit":item.length_unit}) |
---|
| 1089 | |
---|
| 1090 | for apert in item.aperture: |
---|
| 1091 | ap = doc.createElement("aperture") |
---|
| 1092 | if apert.name is not None: |
---|
| 1093 | ap.setAttribute("name", str(apert.name)) |
---|
| 1094 | if apert.type is not None: |
---|
| 1095 | ap.setAttribute("type", str(apert.type)) |
---|
| 1096 | coll.appendChild(ap) |
---|
| 1097 | |
---|
| 1098 | write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit}) |
---|
| 1099 | |
---|
| 1100 | size = doc.createElement("size") |
---|
| 1101 | if apert.size_name is not None: |
---|
| 1102 | size.setAttribute("name", str(apert.size_name)) |
---|
| 1103 | written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit}) |
---|
| 1104 | written = written | write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit}) |
---|
| 1105 | written = written | write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit}) |
---|
| 1106 | if written == True: |
---|
| 1107 | ap.appendChild(size) |
---|
| 1108 | |
---|
| 1109 | # Detectors |
---|
| 1110 | for item in datainfo.detector: |
---|
| 1111 | det = doc.createElement("SASdetector") |
---|
| 1112 | written = write_node(doc, det, "name", item.name) |
---|
| 1113 | written = written | write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit}) |
---|
| 1114 | written = written | write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit}) |
---|
| 1115 | if written == True: |
---|
| 1116 | instr.appendChild(det) |
---|
| 1117 | |
---|
| 1118 | off = doc.createElement("offset") |
---|
| 1119 | written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit}) |
---|
| 1120 | written = written | write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit}) |
---|
| 1121 | written = written | write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit}) |
---|
| 1122 | if written == True: |
---|
| 1123 | det.appendChild(off) |
---|
| 1124 | |
---|
| 1125 | center = doc.createElement("beam_center") |
---|
| 1126 | written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit}) |
---|
| 1127 | written = written | write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit}) |
---|
| 1128 | written = written | write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit}) |
---|
| 1129 | if written == True: |
---|
| 1130 | det.appendChild(center) |
---|
| 1131 | |
---|
| 1132 | pix = doc.createElement("pixel_size") |
---|
| 1133 | written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit}) |
---|
| 1134 | written = written | write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit}) |
---|
| 1135 | written = written | write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit}) |
---|
| 1136 | if written == True: |
---|
| 1137 | det.appendChild(pix) |
---|
| 1138 | |
---|
| 1139 | ori = doc.createElement("orientation") |
---|
| 1140 | written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit}) |
---|
| 1141 | written = written | write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit}) |
---|
| 1142 | written = written | write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit}) |
---|
| 1143 | if written == True: |
---|
| 1144 | det.appendChild(ori) |
---|
| 1145 | |
---|
| 1146 | # Processes info |
---|
| 1147 | for item in datainfo.process: |
---|
| 1148 | node = doc.createElement("SASprocess") |
---|
| 1149 | entry_node.appendChild(node) |
---|
| 1150 | |
---|
| 1151 | write_node(doc, node, "name", item.name) |
---|
| 1152 | write_node(doc, node, "date", item.date) |
---|
| 1153 | write_node(doc, node, "description", item.description) |
---|
| 1154 | for term in item.term: |
---|
| 1155 | value = term['value'] |
---|
| 1156 | del term['value'] |
---|
| 1157 | write_node(doc, node, "term", value, term) |
---|
| 1158 | for note in item.notes: |
---|
| 1159 | write_node(doc, node, "SASprocessnote", note) |
---|
| 1160 | # Return the document, and the SASentry node associated with |
---|
| 1161 | # the data we just wrote |
---|
| 1162 | return doc, entry_node |
---|
[e9b12eaf] | 1163 | |
---|
[61cada5] | 1164 | def _parse_state(self, entry): |
---|
| 1165 | """ |
---|
[5062bbf] | 1166 | Read a fit result from an XML node |
---|
| 1167 | |
---|
| 1168 | :param entry: XML node to read from |
---|
| 1169 | |
---|
| 1170 | :return: PageState object |
---|
[61cada5] | 1171 | """ |
---|
| 1172 | # Create an empty state |
---|
[b35d3d1] | 1173 | state = None |
---|
[61cada5] | 1174 | # Locate the P(r) node |
---|
| 1175 | try: |
---|
| 1176 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS}) |
---|
[b35d3d1] | 1177 | if nodes !=[]: |
---|
| 1178 | # Create an empty state |
---|
| 1179 | state = PageState() |
---|
| 1180 | state.fromXML(node=nodes[0]) |
---|
[61cada5] | 1181 | except: |
---|
| 1182 | logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value) |
---|
| 1183 | |
---|
| 1184 | return state |
---|
| 1185 | |
---|
[0b12abb5] | 1186 | |
---|
[df7ed14] | 1187 | |
---|
| 1188 | def _parse_entry(self, dom): |
---|
[e9b12eaf] | 1189 | """ |
---|
[5062bbf] | 1190 | Parse a SASentry |
---|
| 1191 | |
---|
| 1192 | :param node: SASentry node |
---|
| 1193 | |
---|
[df7ed14] | 1194 | :return: Data1D/Data2D object |
---|
[5062bbf] | 1195 | |
---|
[e9b12eaf] | 1196 | """ |
---|
[df7ed14] | 1197 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
---|
| 1198 | if not node or node[0].text.lstrip().rstrip() != "Data2D": |
---|
| 1199 | return CansasReader._parse_entry(self, dom) |
---|
| 1200 | |
---|
| 1201 | #Parse 2D |
---|
[e9b12eaf] | 1202 | data_info = Data2D() |
---|
| 1203 | |
---|
| 1204 | # Look up title |
---|
| 1205 | self._store_content('ns:Title', dom, 'title', data_info) |
---|
| 1206 | |
---|
| 1207 | # Look up run number |
---|
| 1208 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
---|
| 1209 | for item in nodes: |
---|
| 1210 | if item.text is not None: |
---|
| 1211 | value = item.text.strip() |
---|
| 1212 | if len(value) > 0: |
---|
| 1213 | data_info.run.append(value) |
---|
| 1214 | if item.get('name') is not None: |
---|
| 1215 | data_info.run_name[value] = item.get('name') |
---|
| 1216 | |
---|
| 1217 | # Look up instrument name |
---|
| 1218 | self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info) |
---|
| 1219 | |
---|
| 1220 | # Notes |
---|
| 1221 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
---|
| 1222 | for note in note_list: |
---|
| 1223 | try: |
---|
| 1224 | if note.text is not None: |
---|
| 1225 | note_value = note.text.strip() |
---|
| 1226 | if len(note_value) > 0: |
---|
| 1227 | data_info.notes.append(note_value) |
---|
| 1228 | except: |
---|
| 1229 | err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value |
---|
| 1230 | self.errors.append(err_mess) |
---|
| 1231 | logging.error(err_mess) |
---|
| 1232 | |
---|
| 1233 | # Sample info ################### |
---|
| 1234 | entry = get_content('ns:SASsample', dom) |
---|
| 1235 | if entry is not None: |
---|
| 1236 | data_info.sample.name = entry.get('name') |
---|
| 1237 | |
---|
| 1238 | self._store_content('ns:SASsample/ns:ID', |
---|
| 1239 | dom, 'ID', data_info.sample) |
---|
| 1240 | self._store_float('ns:SASsample/ns:thickness', |
---|
| 1241 | dom, 'thickness', data_info.sample) |
---|
| 1242 | self._store_float('ns:SASsample/ns:transmission', |
---|
| 1243 | dom, 'transmission', data_info.sample) |
---|
| 1244 | self._store_float('ns:SASsample/ns:temperature', |
---|
| 1245 | dom, 'temperature', data_info.sample) |
---|
| 1246 | |
---|
| 1247 | nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS}) |
---|
| 1248 | for item in nodes: |
---|
| 1249 | try: |
---|
| 1250 | if item.text is not None: |
---|
| 1251 | detail_value = item.text.strip() |
---|
| 1252 | if len(detail_value) > 0: |
---|
| 1253 | data_info.sample.details.append(detail_value) |
---|
| 1254 | except: |
---|
| 1255 | err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value |
---|
| 1256 | self.errors.append(err_mess) |
---|
| 1257 | logging.error(err_mess) |
---|
| 1258 | |
---|
| 1259 | # Position (as a vector) |
---|
| 1260 | self._store_float('ns:SASsample/ns:position/ns:x', |
---|
| 1261 | dom, 'position.x', data_info.sample) |
---|
| 1262 | self._store_float('ns:SASsample/ns:position/ns:y', |
---|
| 1263 | dom, 'position.y', data_info.sample) |
---|
| 1264 | self._store_float('ns:SASsample/ns:position/ns:z', |
---|
| 1265 | dom, 'position.z', data_info.sample) |
---|
| 1266 | |
---|
| 1267 | # Orientation (as a vector) |
---|
| 1268 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
---|
| 1269 | dom, 'orientation.x', data_info.sample) |
---|
| 1270 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
---|
| 1271 | dom, 'orientation.y', data_info.sample) |
---|
| 1272 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
---|
| 1273 | dom, 'orientation.z', data_info.sample) |
---|
| 1274 | |
---|
| 1275 | # Source info ################### |
---|
| 1276 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
---|
| 1277 | if entry is not None: |
---|
| 1278 | data_info.source.name = entry.get('name') |
---|
| 1279 | |
---|
| 1280 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
---|
| 1281 | dom, 'radiation', data_info.source) |
---|
| 1282 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
---|
| 1283 | dom, 'beam_shape', data_info.source) |
---|
| 1284 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
---|
| 1285 | dom, 'wavelength', data_info.source) |
---|
| 1286 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
---|
| 1287 | dom, 'wavelength_min', data_info.source) |
---|
| 1288 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
---|
| 1289 | dom, 'wavelength_max', data_info.source) |
---|
| 1290 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
---|
| 1291 | dom, 'wavelength_spread', data_info.source) |
---|
| 1292 | |
---|
| 1293 | # Beam size (as a vector) |
---|
| 1294 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
---|
| 1295 | if entry is not None: |
---|
| 1296 | data_info.source.beam_size_name = entry.get('name') |
---|
| 1297 | |
---|
| 1298 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
---|
| 1299 | dom, 'beam_size.x', data_info.source) |
---|
| 1300 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
---|
| 1301 | dom, 'beam_size.y', data_info.source) |
---|
| 1302 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
---|
| 1303 | dom, 'beam_size.z', data_info.source) |
---|
| 1304 | |
---|
| 1305 | # Collimation info ################### |
---|
| 1306 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS}) |
---|
| 1307 | for item in nodes: |
---|
| 1308 | collim = Collimation() |
---|
| 1309 | if item.get('name') is not None: |
---|
| 1310 | collim.name = item.get('name') |
---|
| 1311 | self._store_float('ns:length', item, 'length', collim) |
---|
| 1312 | |
---|
| 1313 | # Look for apertures |
---|
| 1314 | apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS}) |
---|
| 1315 | for apert in apert_list: |
---|
| 1316 | aperture = Aperture() |
---|
| 1317 | |
---|
| 1318 | # Get the name and type of the aperture |
---|
| 1319 | aperture.name = apert.get('name') |
---|
| 1320 | aperture.type = apert.get('type') |
---|
| 1321 | |
---|
| 1322 | self._store_float('ns:distance', apert, 'distance', aperture) |
---|
| 1323 | |
---|
| 1324 | entry = get_content('ns:size', apert) |
---|
| 1325 | if entry is not None: |
---|
| 1326 | aperture.size_name = entry.get('name') |
---|
| 1327 | |
---|
| 1328 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
---|
| 1329 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
---|
| 1330 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
---|
| 1331 | |
---|
| 1332 | collim.aperture.append(aperture) |
---|
| 1333 | |
---|
| 1334 | data_info.collimation.append(collim) |
---|
| 1335 | |
---|
| 1336 | # Detector info ###################### |
---|
| 1337 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS}) |
---|
| 1338 | for item in nodes: |
---|
| 1339 | |
---|
| 1340 | detector = Detector() |
---|
| 1341 | |
---|
| 1342 | self._store_content('ns:name', item, 'name', detector) |
---|
| 1343 | self._store_float('ns:SDD', item, 'distance', detector) |
---|
| 1344 | |
---|
| 1345 | # Detector offset (as a vector) |
---|
| 1346 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
---|
| 1347 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
---|
| 1348 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
---|
| 1349 | |
---|
| 1350 | # Detector orientation (as a vector) |
---|
| 1351 | self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector) |
---|
| 1352 | self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector) |
---|
| 1353 | self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector) |
---|
| 1354 | |
---|
| 1355 | # Beam center (as a vector) |
---|
| 1356 | self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector) |
---|
| 1357 | self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector) |
---|
| 1358 | self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector) |
---|
| 1359 | |
---|
| 1360 | # Pixel size (as a vector) |
---|
| 1361 | self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector) |
---|
| 1362 | self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector) |
---|
| 1363 | self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector) |
---|
| 1364 | |
---|
| 1365 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
---|
| 1366 | |
---|
| 1367 | data_info.detector.append(detector) |
---|
| 1368 | |
---|
| 1369 | # Processes info ###################### |
---|
| 1370 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
---|
| 1371 | for item in nodes: |
---|
| 1372 | process = Process() |
---|
| 1373 | self._store_content('ns:name', item, 'name', process) |
---|
| 1374 | self._store_content('ns:date', item, 'date', process) |
---|
| 1375 | self._store_content('ns:description', item, 'description', process) |
---|
| 1376 | |
---|
| 1377 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
---|
| 1378 | for term in term_list: |
---|
| 1379 | try: |
---|
| 1380 | term_attr = {} |
---|
| 1381 | for attr in term.keys(): |
---|
| 1382 | term_attr[attr] = term.get(attr).strip() |
---|
| 1383 | if term.text is not None: |
---|
| 1384 | term_attr['value'] = term.text.strip() |
---|
| 1385 | process.term.append(term_attr) |
---|
| 1386 | except: |
---|
| 1387 | err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value |
---|
| 1388 | self.errors.append(err_mess) |
---|
| 1389 | logging.error(err_mess) |
---|
| 1390 | |
---|
| 1391 | note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS}) |
---|
| 1392 | for note in note_list: |
---|
| 1393 | if note.text is not None: |
---|
| 1394 | process.notes.append(note.text.strip()) |
---|
| 1395 | |
---|
| 1396 | data_info.process.append(process) |
---|
| 1397 | |
---|
| 1398 | |
---|
| 1399 | # Data info ###################### |
---|
| 1400 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
---|
| 1401 | if len(nodes)>1: |
---|
| 1402 | raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries" |
---|
[df7ed14] | 1403 | |
---|
| 1404 | for entry in nodes: |
---|
| 1405 | for item in list_of_data_2d_attr: |
---|
| 1406 | #get node |
---|
| 1407 | node = get_content('ns:%s'%item[0], entry) |
---|
[0b12abb5] | 1408 | exec "data_info.%s = parse_entry_helper(node, item)"%(item[1]) |
---|
[e9b12eaf] | 1409 | |
---|
[df7ed14] | 1410 | for item in list_of_data2d_values: |
---|
| 1411 | field = get_content('ns:%s'%item[0], entry) |
---|
| 1412 | list = [] |
---|
| 1413 | if field is not None: |
---|
[0b12abb5] | 1414 | list = [parse_entry_helper(node, item) for node in field] |
---|
[df7ed14] | 1415 | exec "data_info.%s = numpy.array(list)"%item[0] |
---|
[e9b12eaf] | 1416 | |
---|
| 1417 | return data_info |
---|
| 1418 | |
---|
[61cada5] | 1419 | def _read_cansas(self, path): |
---|
| 1420 | """ |
---|
[5062bbf] | 1421 | Load data and P(r) information from a CanSAS XML file. |
---|
| 1422 | |
---|
| 1423 | :param path: file path |
---|
| 1424 | |
---|
| 1425 | :return: Data1D object if a single SASentry was found, |
---|
| 1426 | or a list of Data1D objects if multiple entries were found, |
---|
| 1427 | or None of nothing was found |
---|
| 1428 | |
---|
| 1429 | :raise RuntimeError: when the file can't be opened |
---|
| 1430 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
| 1431 | |
---|
[61cada5] | 1432 | """ |
---|
| 1433 | output = [] |
---|
[b63dc6e] | 1434 | basename = os.path.basename(path) |
---|
| 1435 | root, extension = os.path.splitext(basename) |
---|
| 1436 | ext = extension.lower() |
---|
[61cada5] | 1437 | try: |
---|
| 1438 | if os.path.isfile(path): |
---|
[b63dc6e] | 1439 | |
---|
[61cada5] | 1440 | #TODO: eventually remove the check for .xml once |
---|
| 1441 | # the P(r) writer/reader is truly complete. |
---|
[b63dc6e] | 1442 | if ext in self.ext or \ |
---|
| 1443 | ext == '.xml': |
---|
[61cada5] | 1444 | |
---|
| 1445 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
| 1446 | # Check the format version number |
---|
| 1447 | # Specifying the namespace will take care of the file format version |
---|
| 1448 | root = tree.getroot() |
---|
[df7ed14] | 1449 | entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS}) |
---|
[b35d3d1] | 1450 | for entry in entry_list: |
---|
[e9b12eaf] | 1451 | try: |
---|
| 1452 | sas_entry = self._parse_entry(entry) |
---|
| 1453 | except: |
---|
[df7ed14] | 1454 | raise |
---|
[61cada5] | 1455 | fitstate = self._parse_state(entry) |
---|
[b35d3d1] | 1456 | |
---|
| 1457 | #state could be None when .svs file is loaded |
---|
| 1458 | #in this case, skip appending to output |
---|
| 1459 | if fitstate != None: |
---|
| 1460 | sas_entry.meta_data['fitstate'] = fitstate |
---|
| 1461 | sas_entry.filename = fitstate.file |
---|
| 1462 | output.append(sas_entry) |
---|
[61cada5] | 1463 | else: |
---|
[b63dc6e] | 1464 | self.call_back(format=ext) |
---|
[61cada5] | 1465 | raise RuntimeError, "%s is not a file" % path |
---|
[b35d3d1] | 1466 | |
---|
[61cada5] | 1467 | # Return output consistent with the loader's api |
---|
| 1468 | if len(output)==0: |
---|
[b63dc6e] | 1469 | self.call_back(state=None, datainfo=None,format=ext) |
---|
[61cada5] | 1470 | return None |
---|
| 1471 | else: |
---|
[b35d3d1] | 1472 | for ind in range(len(output)): |
---|
| 1473 | # Call back to post the new state |
---|
| 1474 | state = output[ind].meta_data['fitstate'] |
---|
| 1475 | t = time.localtime(state.timestamp) |
---|
| 1476 | time_str = time.strftime("%b %d %H:%M", t) |
---|
| 1477 | # Check that no time stamp is already appended |
---|
| 1478 | max_char = state.file.find("[") |
---|
| 1479 | if max_char < 0: |
---|
| 1480 | max_char = len(state.file) |
---|
[ef16f59] | 1481 | original_fname = state.file[0:max_char] |
---|
| 1482 | state.file = original_fname +' [' + time_str + ']' |
---|
[b35d3d1] | 1483 | |
---|
| 1484 | |
---|
| 1485 | if state is not None and state.is_data is not None: |
---|
| 1486 | exec 'output[%d].is_data = state.is_data'% ind |
---|
| 1487 | |
---|
| 1488 | output[ind].filename = state.file |
---|
| 1489 | state.data = output[ind] |
---|
| 1490 | state.data.name = output[ind].filename #state.data_name |
---|
| 1491 | state.data.id = state.data_id |
---|
| 1492 | if state.is_data is not None: |
---|
| 1493 | state.data.is_data = state.is_data |
---|
[ef16f59] | 1494 | if output[ind].run_name is not None and len(output[ind].run_name) != 0 : |
---|
| 1495 | name = output[ind].run_name |
---|
| 1496 | else: |
---|
| 1497 | name=original_fname |
---|
| 1498 | state.data.group_id = name |
---|
| 1499 | #store state in fitting |
---|
[90a7bbd] | 1500 | self.call_back(state=state, datainfo=output[ind],format=ext) |
---|
[75fbd17] | 1501 | self.state= state |
---|
[ef16f59] | 1502 | return output |
---|
[b35d3d1] | 1503 | |
---|
[61cada5] | 1504 | except: |
---|
[4bee68d] | 1505 | self.call_back(format=ext) |
---|
| 1506 | #self.state= state |
---|
[61cada5] | 1507 | raise |
---|
| 1508 | |
---|
| 1509 | def write(self, filename, datainfo=None, fitstate=None): |
---|
| 1510 | """ |
---|
[b35d3d1] | 1511 | Write the content of a Data1D as a CanSAS XML file only for standalone |
---|
[5062bbf] | 1512 | |
---|
| 1513 | :param filename: name of the file to write |
---|
| 1514 | :param datainfo: Data1D object |
---|
| 1515 | :param fitstate: PageState object |
---|
| 1516 | |
---|
[61cada5] | 1517 | """ |
---|
| 1518 | # Sanity check |
---|
| 1519 | if self.cansas == True: |
---|
| 1520 | |
---|
| 1521 | # Add fitting information to the XML document |
---|
[ef16f59] | 1522 | doc = self.write_toXML(datainfo, fitstate) |
---|
[61cada5] | 1523 | # Write the XML document |
---|
| 1524 | fd = open(filename, 'w') |
---|
| 1525 | fd.write(doc.toprettyxml()) |
---|
| 1526 | fd.close() |
---|
| 1527 | else: |
---|
| 1528 | fitstate.toXML(file=filename) |
---|
| 1529 | |
---|
[b35d3d1] | 1530 | def write_toXML(self, datainfo=None, state=None): |
---|
| 1531 | """ |
---|
| 1532 | Write toXML, a helper for write() , could be used by guimanager._on_save() |
---|
| 1533 | |
---|
| 1534 | : return: xml doc |
---|
| 1535 | """ |
---|
[3c44c66] | 1536 | |
---|
[b35d3d1] | 1537 | if state.data is None: |
---|
[c21e87b] | 1538 | data = sans.dataloader.data_info.Data1D(x=[], y=[]) |
---|
[b35d3d1] | 1539 | else: |
---|
| 1540 | #make sure title and data run is filled up. |
---|
[028a0e8] | 1541 | if state.data.title == None or state.data.title=='': state.data.title = state.data.name |
---|
| 1542 | if state.data.run_name == None or state.data.run_name=={}: |
---|
| 1543 | state.data.run = [str(state.data.name)] |
---|
| 1544 | state.data.run_name[0] = state.data.name |
---|
[b35d3d1] | 1545 | |
---|
[c21e87b] | 1546 | if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D): |
---|
[028a0e8] | 1547 | |
---|
[b35d3d1] | 1548 | data = state.data |
---|
| 1549 | doc, sasentry = self._to_xml_doc(data) |
---|
| 1550 | else: |
---|
| 1551 | data = state.data |
---|
| 1552 | doc, sasentry = self._data2d_to_xml_doc(data) |
---|
| 1553 | |
---|
| 1554 | |
---|
| 1555 | if state is not None: |
---|
| 1556 | state.toXML(doc=doc, file=data.name, entry_node=sasentry) |
---|
| 1557 | |
---|
| 1558 | return doc |
---|
[2296316] | 1559 | |
---|
| 1560 | # Simple html report templet |
---|
| 1561 | HEADER = "<html>\n" |
---|
| 1562 | HEADER += "<head>\n" |
---|
| 1563 | HEADER += "<meta http-equiv=Content-Type content='text/html; " |
---|
| 1564 | HEADER += "charset=windows-1252'> \n" |
---|
| 1565 | HEADER += "<meta name=Generator >\n" |
---|
| 1566 | HEADER += "</head>\n" |
---|
| 1567 | HEADER += "<body lang=EN-US>\n" |
---|
| 1568 | HEADER += "<div class=WordSection1>\n" |
---|
| 1569 | HEADER += "<p class=MsoNormal><b><span ><center>" |
---|
| 1570 | HEADER += "%s</center></span></center></b></p>" |
---|
| 1571 | HEADER += "<p class=MsoNormal> </p>" |
---|
| 1572 | PARA = "<p class=MsoNormal> %s \n" |
---|
| 1573 | PARA += "</p>" |
---|
[3a3dd9c] | 1574 | CENTRE = "<p class=MsoNormal><center> %s \n" |
---|
| 1575 | CENTRE += "</center></p>" |
---|
[2296316] | 1576 | FEET_1 = \ |
---|
| 1577 | """ |
---|
[3a3dd9c] | 1578 | <p class=MsoNormal> </p> |
---|
[2296316] | 1579 | <p class=MsoNormal><b><span ><center> Graph</span></center></b></p> |
---|
[3a3dd9c] | 1580 | <p class=MsoNormal> </p> |
---|
[2296316] | 1581 | <center> |
---|
| 1582 | <br>Model Computation<br> |
---|
| 1583 | <br>Data: "%s"<br> |
---|
| 1584 | """ |
---|
| 1585 | FEET_2 = \ |
---|
| 1586 | """ |
---|
[0483fd48] | 1587 | <img src="%s" > |
---|
[2296316] | 1588 | </img> |
---|
| 1589 | """ |
---|
| 1590 | FEET_3 = \ |
---|
| 1591 | """ |
---|
| 1592 | </center> |
---|
| 1593 | </div> |
---|
| 1594 | </body> |
---|
| 1595 | </html> |
---|
| 1596 | """ |
---|
| 1597 | ELINE = "<p class=MsoNormal> </p>" |
---|
| 1598 | |
---|
[3c44c66] | 1599 | if __name__ == "__main__": |
---|
| 1600 | state = PageState(parent=None) |
---|
| 1601 | #state.toXML() |
---|
| 1602 | """ |
---|
[5062bbf] | 1603 | |
---|
[3c44c66] | 1604 | file = open("test_state", "w") |
---|
| 1605 | pickle.dump(state, file) |
---|
| 1606 | print pickle.dumps(state) |
---|
| 1607 | state.data_name = "hello---->" |
---|
| 1608 | pickle.dump(state, file) |
---|
| 1609 | file = open("test_state", "r") |
---|
| 1610 | new_state= pickle.load(file) |
---|
| 1611 | print "new state", new_state |
---|
| 1612 | new_state= pickle.load(file) |
---|
| 1613 | print "new state", new_state |
---|
| 1614 | #print "state", state |
---|
| 1615 | """ |
---|
| 1616 | import bsddb |
---|
| 1617 | import pickle |
---|
| 1618 | db= bsddb.btopen('file_state.db', 'c') |
---|
| 1619 | val = (pickle.dumps(state), "hello", "hi") |
---|
| 1620 | db['state1']= pickle.dumps(val) |
---|
| 1621 | print pickle.loads(db['state1']) |
---|
| 1622 | state.data_name = "hello---->22" |
---|
| 1623 | db['state2']= pickle.dumps(state) |
---|
| 1624 | state.data_name = "hello---->2" |
---|
| 1625 | db['state3']= pickle.dumps(state) |
---|
| 1626 | del db['state3'] |
---|
| 1627 | state.data_name = "hello---->3" |
---|
| 1628 | db['state4']= pickle.dumps(state) |
---|
| 1629 | new_state = pickle.loads(db['state1']) |
---|
| 1630 | #print db.last() |
---|
| 1631 | db.set_location('state2') |
---|
| 1632 | state.data_name = "hello---->5" |
---|
| 1633 | db['aastate5']= pickle.dumps(state) |
---|
| 1634 | db.keys().sort() |
---|
| 1635 | print pickle.loads(db['state2']) |
---|
| 1636 | |
---|
| 1637 | db.close() |
---|