[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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| 24 | import DataLoader |
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[61cada5] | 25 | from DataLoader.readers.cansas_reader import Reader as CansasReader |
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[e9b12eaf] | 26 | from DataLoader.readers.cansas_reader import get_content, write_node |
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[df7ed14] | 27 | from 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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[0b12abb5] | 47 | ["formfactorcombobox", "formfactorcombobox", "float"], |
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| 48 | ["structurecombobox", "structurecombobox", "float"], |
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| 49 | ["disp_box", "disp_box", "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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| 56 | ["slit_smearer","slit_smearer","bool"], |
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| 57 | ["enable2D","enable2D","bool"], |
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| 58 | ["cb1","cb1","bool"], |
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[5cc7001] | 59 | ["tcChi","tcChi","float"], |
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| 60 | ["smearer", "smearer", "float"], |
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| 61 | ["smear_type","smear_type", "string"], |
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| 62 | ["dq_l", "dq_l", "string"], |
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| 63 | ["dq_r","dq_r", "string"]] |
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| 64 | |
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[11a7e11] | 65 | list_of_model_attributes = [["values", "values"], |
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| 66 | ["weights", "weights"]] |
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| 67 | |
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[61cada5] | 68 | list_of_state_parameters = [["parameters", "parameters"] , |
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| 69 | ["orientation_parameters", "orientation_params"], |
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| 70 | ["dispersity_parameters", "orientation_params_disp"], |
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| 71 | ["fixed_param", "fixed_param"], |
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| 72 | ["fittable_param","fittable_param"]] |
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[df7ed14] | 73 | list_of_data_2d_attr = [["xmin", "xmin","float"], |
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| 74 | ["xmax","xmax","float"], |
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| 75 | ["ymin","ymin","float"], |
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| 76 | ["ymax","ymax","float"], |
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| 77 | ["_xaxis","_xaxis", "string"], |
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| 78 | ["_xunit", "_xunit", "string"], |
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| 79 | ["_yaxis","_yaxis","string"], |
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| 80 | ["_yunit","_yunit","string"], |
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| 81 | ["_zaxis","_zaxis","string"], |
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| 82 | ["_zunit","_zunit","string"]] |
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| 83 | list_of_data2d_values = [["qx_data","qx_data","float"], |
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| 84 | ["qy_data","qy_data","float"], |
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| 85 | ["dqx_data","dqx_data","float"], |
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| 86 | ["dqy_data","dqy_data","float"], |
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| 87 | ["data","data","float"], |
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| 88 | ["q_data","q_data","float"], |
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| 89 | ["err_data","err_data","float"], |
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| 90 | ["mask","mask","bool"]] |
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[61cada5] | 91 | |
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[0b12abb5] | 92 | def parse_entry_helper( node, item): |
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| 93 | """ |
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| 94 | Create a numpy list from value extrated from the node |
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| 95 | |
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| 96 | :param node: node from each the value is stored |
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| 97 | :param item: list name of three strings.the two first are name of data |
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| 98 | attribute and the third one is the type of the value of that |
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| 99 | attribute. type can be string, float, bool, etc. |
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| 100 | |
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| 101 | : return: numpy array |
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| 102 | """ |
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| 103 | if node is not None: |
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| 104 | if item[2] == "string": |
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| 105 | return str(node.get(item[0]).strip()) |
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| 106 | elif item[2] == "bool": |
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| 107 | try: |
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[e3d1423] | 108 | return node.get(item[0]).strip() == "True" |
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| 109 | |
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[0b12abb5] | 110 | except: |
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| 111 | return None |
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| 112 | else: |
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| 113 | try: |
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| 114 | return float(node.get(item[0])) |
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| 115 | except: |
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| 116 | return None |
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| 117 | |
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| 118 | |
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[cfc0913] | 119 | class PageState(object): |
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[c77d859] | 120 | """ |
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[5062bbf] | 121 | Contains information to reconstruct a page of the fitpanel. |
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[c77d859] | 122 | """ |
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[61cada5] | 123 | def __init__(self, parent=None, model=None, data=None): |
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[c77d859] | 124 | |
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| 125 | """ |
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[5062bbf] | 126 | Initialize the current state |
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| 127 | |
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| 128 | :param model: a selected model within a page |
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| 129 | :param data: |
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| 130 | |
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[c77d859] | 131 | """ |
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[61cada5] | 132 | self.file = None |
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[11a7e11] | 133 | #Time of state creation |
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| 134 | self.timestamp = time.time() |
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[c77d859] | 135 | ## Data member to store the dispersion object created |
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| 136 | self._disp_obj_dict = {} |
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[61cada5] | 137 | #------------------------ |
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[c77d859] | 138 | #Data used for fitting |
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| 139 | self.data = data |
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[61cada5] | 140 | #save additional information on data that dataloader.reader does not read |
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| 141 | self.is_data = None |
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| 142 | self.data_name = "" |
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| 143 | |
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| 144 | if self.data is not None: |
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| 145 | self.data_name = self.data.name |
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| 146 | self.data_id = None |
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| 147 | if self.data is not None and hasattr(self.data, "id"): |
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| 148 | self.data_id = self.data.id |
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| 149 | self.data_group_id = None |
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| 150 | if self.data is not None and hasattr(self.data, "group_id"): |
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| 151 | self.data_group_id = self.data.group_id |
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[0b12abb5] | 152 | |
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[61cada5] | 153 | ## reset True change the state of exsiting button |
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| 154 | self.reset = False |
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| 155 | |
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[c99a6c5] | 156 | #engine type |
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| 157 | self.engine_type = None |
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[c77d859] | 158 | # flag to allow data2D plot |
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[cfc0913] | 159 | self.enable2D = False |
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[c77d859] | 160 | # model on which the fit would be performed |
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| 161 | self.model = model |
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[61cada5] | 162 | |
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[c77d859] | 163 | #fit page manager |
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| 164 | self.manager = None |
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| 165 | #Store the parent of this panel parent |
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| 166 | # For this application fitpanel is the parent |
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| 167 | self.parent = parent |
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| 168 | # Event_owner is the owner of model event |
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| 169 | self.event_owner = None |
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[c9a4377] | 170 | ##page name |
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[cfc0913] | 171 | self.page_name = "" |
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[c77d859] | 172 | # Contains link between model ,all its parameters, and panel organization |
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[61cada5] | 173 | self.parameters = [] |
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[c77d859] | 174 | # Contains list of parameters that cannot be fitted and reference to |
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| 175 | #panel objects |
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[61cada5] | 176 | self.fixed_param = [] |
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[c77d859] | 177 | # Contains list of parameters with dispersity and reference to |
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| 178 | #panel objects |
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[61cada5] | 179 | self.fittable_param = [] |
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[60132ef] | 180 | ## orientation parameters |
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[61cada5] | 181 | self.orientation_params = [] |
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[fc6ea43] | 182 | ## orientation parmaters for gaussian dispersity |
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[61cada5] | 183 | self.orientation_params_disp = [] |
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[3370922] | 184 | ## smearer info |
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[61cada5] | 185 | self.smearer = None |
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[7609f1a] | 186 | self.smear_type = None |
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| 187 | self.dq_l = None |
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| 188 | self.dq_r = None |
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| 189 | |
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[c77d859] | 190 | #list of dispersion paramaters |
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[cfc0913] | 191 | self.disp_list =[] |
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[61cada5] | 192 | if self.model is not None: |
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[71f0373] | 193 | self.disp_list = self.model.getDispParamList() |
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[61cada5] | 194 | self._disp_obj_dict = {} |
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| 195 | self.disp_cb_dict = {} |
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| 196 | self.values = [] |
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| 197 | self.weights = [] |
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[dad49a0] | 198 | |
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[c77d859] | 199 | #contains link between a model and selected parameters to fit |
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[61cada5] | 200 | self.param_toFit = [] |
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[a074145] | 201 | ##dictionary of model type and model class |
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[cfc0913] | 202 | self.model_list_box = None |
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[a074145] | 203 | ## save the state of the context menu |
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[61cada5] | 204 | self.saved_states = {} |
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[240b9966] | 205 | ## save selection of combobox |
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[3b9e023] | 206 | self.formfactorcombobox = None |
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| 207 | self.structurecombobox = None |
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[240b9966] | 208 | ## radio box to select type of model |
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| 209 | self.shape_rbutton = False |
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| 210 | self.shape_indep_rbutton = False |
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| 211 | self.struct_rbutton = False |
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| 212 | self.plugin_rbutton = False |
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[b787e68c] | 213 | ## the indice of the current selection |
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| 214 | self.disp_box = 0 |
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[c77d859] | 215 | ## Qrange |
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[cfc0913] | 216 | ## Q range |
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[61cada5] | 217 | self.qmin = 0.001 |
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| 218 | self.qmax = 0.1 |
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[0b12abb5] | 219 | #reset data range |
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| 220 | self.qmax_x = None |
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| 221 | self.qmin_x = None |
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| 222 | |
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[cfc0913] | 223 | self.npts = None |
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[61cada5] | 224 | self.name = "" |
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[4523b68] | 225 | self.multi_factor = None |
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[cfc0913] | 226 | ## enable smearering state |
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| 227 | self.enable_smearer = False |
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[fc6ea43] | 228 | self.disable_smearer = True |
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[7609f1a] | 229 | self.pinhole_smearer = False |
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| 230 | self.slit_smearer = False |
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[cfc0913] | 231 | ## disperity selection |
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[61cada5] | 232 | self.enable_disp = False |
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| 233 | self.disable_disp = True |
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[11a7e11] | 234 | |
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[cfc0913] | 235 | ## state of selected all check button |
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| 236 | self.cb1 = False |
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[0aeabc6] | 237 | ## store value of chisqr |
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[61cada5] | 238 | self.tcChi = None |
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[240b9966] | 239 | |
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[6f023e8] | 240 | def clone(self): |
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[61cada5] | 241 | """ |
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[5062bbf] | 242 | Create a new copy of the current object |
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[61cada5] | 243 | """ |
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| 244 | model = None |
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| 245 | if self.model is not None: |
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[6f023e8] | 246 | model = self.model.clone() |
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[bb70474] | 247 | model.name = self.model.name |
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[61cada5] | 248 | obj = PageState(self.parent, model=model) |
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| 249 | obj.file = copy.deepcopy(self.file) |
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[6f023e8] | 250 | obj.data = copy.deepcopy(self.data) |
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[61cada5] | 251 | if self.data is not None: |
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| 252 | self.data_name = self.data.name |
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| 253 | obj.data_name = self.data_name |
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| 254 | obj.is_data = self.is_data |
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[dcf29d7] | 255 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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[c99a6c5] | 256 | obj.engine_type = copy.deepcopy(self.engine_type) |
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[240b9966] | 257 | |
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[61cada5] | 258 | obj.formfactorcombobox = self.formfactorcombobox |
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| 259 | obj.structurecombobox = self.structurecombobox |
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[240b9966] | 260 | |
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| 261 | obj.shape_rbutton = self.shape_rbutton |
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| 262 | obj.shape_indep_rbutton = self.shape_indep_rbutton |
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| 263 | obj.struct_rbutton = self.struct_rbutton |
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| 264 | obj.plugin_rbutton = self.plugin_rbutton |
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| 265 | |
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[dcf29d7] | 266 | obj.manager = self.manager |
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| 267 | obj.event_owner = self.event_owner |
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[71f0373] | 268 | obj.disp_list = copy.deepcopy(self.disp_list) |
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[fc6ea43] | 269 | |
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[c477b31] | 270 | obj.enable2D = copy.deepcopy(self.enable2D) |
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[cfc0913] | 271 | obj.parameters = copy.deepcopy(self.parameters) |
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| 272 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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| 273 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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[60132ef] | 274 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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[fc6ea43] | 275 | obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp) |
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[b787e68c] | 276 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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[fc6ea43] | 277 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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[0aeabc6] | 278 | obj.tcChi = self.tcChi |
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| 279 | |
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[c477b31] | 280 | if len(self._disp_obj_dict)>0: |
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| 281 | for k , v in self._disp_obj_dict.iteritems(): |
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| 282 | obj._disp_obj_dict[k]= v |
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[dad49a0] | 283 | if len(self.disp_cb_dict)>0: |
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| 284 | for k , v in self.disp_cb_dict.iteritems(): |
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| 285 | obj.disp_cb_dict[k]= v |
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[b421b1a] | 286 | |
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[dad49a0] | 287 | obj.values = copy.deepcopy(self.values) |
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| 288 | obj.weights = copy.deepcopy(self.weights) |
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[b787e68c] | 289 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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[fc6ea43] | 290 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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[7609f1a] | 291 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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| 292 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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| 293 | obj.smear_type = copy.deepcopy(self.smear_type) |
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| 294 | obj.dq_l = copy.deepcopy(self.dq_l) |
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| 295 | obj.dq_r = copy.deepcopy(self.dq_r) |
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| 296 | |
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[b787e68c] | 297 | obj.disp_box = copy.deepcopy(self.disp_box) |
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| 298 | obj.qmin = copy.deepcopy(self.qmin) |
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| 299 | obj.qmax = copy.deepcopy(self.qmax) |
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[4523b68] | 300 | obj.multi_factor = copy.deepcopy(self.multi_factor) |
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[b787e68c] | 301 | obj.npts = copy.deepcopy(self.npts ) |
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| 302 | obj.cb1 = copy.deepcopy(self.cb1) |
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[3370922] | 303 | obj.smearer = copy.deepcopy(self.smearer) |
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| 304 | |
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[a074145] | 305 | for name, state in self.saved_states.iteritems(): |
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| 306 | copy_name = copy.deepcopy(name) |
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| 307 | copy_state = state.clone() |
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| 308 | obj.saved_states[copy_name]= copy_state |
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[6f023e8] | 309 | return obj |
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[61cada5] | 310 | |
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| 311 | def _repr_helper(self, list, rep): |
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| 312 | """ |
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[5062bbf] | 313 | Helper method to print a state |
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[61cada5] | 314 | """ |
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| 315 | for item in list: |
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[240b9966] | 316 | rep += "parameter name: %s \n"%str(item[1]) |
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| 317 | rep += "value: %s\n"%str(item[2]) |
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| 318 | rep += "selected: %s\n"%str(item[0]) |
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| 319 | rep += "error displayed : %s \n"%str(item[4][0]) |
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| 320 | rep += "error value:%s \n"%str(item[4][1]) |
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| 321 | rep += "minimum displayed : %s \n"%str(item[5][0]) |
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| 322 | rep += "minimum value : %s \n"%str(item[5][1]) |
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| 323 | rep += "maximum displayed : %s \n"%str(item[6][0]) |
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| 324 | rep += "maximum value : %s \n"%str(item[6][1]) |
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| 325 | rep += "parameter unit: %s\n\n"%str(item[7]) |
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| 326 | return rep |
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[61cada5] | 327 | |
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| 328 | def __repr__(self): |
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[11a7e11] | 329 | """ |
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[5062bbf] | 330 | output string for printing |
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[11a7e11] | 331 | """ |
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| 332 | rep = "\nState name: %s\n"%self.file |
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| 333 | t = time.localtime(self.timestamp) |
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| 334 | time_str = time.strftime("%b %d %H:%M", t) |
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| 335 | rep += "State created on : %s\n"%time_str |
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| 336 | rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox |
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| 337 | rep += "State structure factor combobox selection: %s\n"%self.structurecombobox |
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| 338 | rep += "is data : %s\n"%self.is_data |
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| 339 | rep += "data's name : %s\n"%self.data_name |
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| 340 | rep += "data's id : %s\n"%self.data_id |
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| 341 | rep += "model type (form factor) selected: %s\n"%self.shape_rbutton |
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| 342 | rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton |
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| 343 | rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton |
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| 344 | rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton |
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| 345 | rep += "data : %s\n"% str(self.data) |
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| 346 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin), |
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| 347 | str(self.qmax),str(self.npts)) |
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[0b12abb5] | 348 | rep += "Dispersion selection : %s\n"%str(self.disp_box) |
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| 349 | rep += "Smearing enable : %s\n"%str(self.enable_smearer) |
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| 350 | rep += "Smearing disable : %s\n"%str(self.disable_smearer) |
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| 351 | rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer) |
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| 352 | rep += "Slit smearer enable : %s\n"%str(self.slit_smearer) |
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| 353 | rep += "Dispersity enable : %s\n"%str(self.enable_disp) |
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| 354 | rep += "Dispersity disable : %s\n"%str(self.disable_disp) |
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| 355 | rep += "Slit smearer enable: %s\n"%str(self.slit_smearer) |
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| 356 | rep += "2D enable : %s\n"%str(self.enable2D) |
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| 357 | rep += "All parameters checkbox selected: %s\n"%(self.cb1) |
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| 358 | rep += "Value of Chisqr : %s\n"%str(self.tcChi) |
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| 359 | rep += "Smear object : %s\n"%str(self.smearer) |
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| 360 | rep += "Smear type : %s\n"%(self.smear_type) |
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| 361 | rep += "dq_l : %s\n"%self.dq_l |
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| 362 | rep += "dq_r : %s\n"%self.dq_r |
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| 363 | |
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[11a7e11] | 364 | rep += "model : %s\n\n"% str(self.model) |
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| 365 | rep += "number parameters(self.parameters): %s\n"%len(self.parameters) |
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[3c44c66] | 366 | rep = self._repr_helper( list=self.parameters, rep=rep) |
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[11a7e11] | 367 | rep += "number orientation parameters" |
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| 368 | rep += "(self.orientation_params): %s\n"%len(self.orientation_params) |
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[3c44c66] | 369 | rep = self._repr_helper( list=self.orientation_params, rep=rep) |
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[11a7e11] | 370 | rep += "number dispersity parameters" |
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| 371 | rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp) |
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[3c44c66] | 372 | rep = self._repr_helper( list=self.orientation_params_disp, rep=rep) |
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[0b12abb5] | 373 | |
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[61cada5] | 374 | return rep |
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| 375 | |
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| 376 | def _toXML_helper(self, list, element, newdoc): |
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| 377 | """ |
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[5062bbf] | 378 | Helper method to create xml file for saving state |
---|
[61cada5] | 379 | """ |
---|
| 380 | for item in list: |
---|
| 381 | sub_element = newdoc.createElement('parameter') |
---|
| 382 | sub_element.setAttribute('name', str(item[1])) |
---|
| 383 | sub_element.setAttribute('value', str(item[2])) |
---|
| 384 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
---|
| 385 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
---|
| 386 | sub_element.setAttribute('error_value', str(item[4][1])) |
---|
| 387 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
---|
| 388 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
---|
| 389 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
---|
| 390 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
---|
| 391 | sub_element.setAttribute('unit', str(item[7])) |
---|
| 392 | element.appendChild(sub_element) |
---|
| 393 | |
---|
| 394 | def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None): |
---|
| 395 | """ |
---|
[5062bbf] | 396 | Writes the state of the InversionControl panel to file, as XML. |
---|
| 397 | |
---|
| 398 | Compatible with standalone writing, or appending to an |
---|
| 399 | already existing XML document. In that case, the XML document |
---|
| 400 | is required. An optional entry node in the XML document may also be given. |
---|
| 401 | |
---|
| 402 | :param file: file to write to |
---|
| 403 | :param doc: XML document object [optional] |
---|
| 404 | :param entry_node: XML node within the XML document at which we will append the data [optional] |
---|
| 405 | |
---|
[61cada5] | 406 | """ |
---|
| 407 | from xml.dom.minidom import getDOMImplementation |
---|
[71f0373] | 408 | |
---|
[61cada5] | 409 | # Check whether we have to write a standalone XML file |
---|
| 410 | if doc is None: |
---|
| 411 | impl = getDOMImplementation() |
---|
| 412 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
---|
| 413 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
---|
| 414 | top_element = newdoc.documentElement |
---|
| 415 | else: |
---|
| 416 | # We are appending to an existing document |
---|
| 417 | newdoc = doc |
---|
| 418 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
| 419 | if entry_node is None: |
---|
| 420 | newdoc.documentElement.appendChild(top_element) |
---|
| 421 | else: |
---|
| 422 | entry_node.appendChild(top_element) |
---|
| 423 | |
---|
| 424 | attr = newdoc.createAttribute("version") |
---|
| 425 | attr.nodeValue = '1.0' |
---|
| 426 | top_element.setAttributeNode(attr) |
---|
[cfc0913] | 427 | |
---|
[61cada5] | 428 | # File name |
---|
| 429 | element = newdoc.createElement("filename") |
---|
| 430 | if self.file is not None: |
---|
| 431 | element.appendChild(newdoc.createTextNode(str(self.file))) |
---|
| 432 | else: |
---|
| 433 | element.appendChild(newdoc.createTextNode(str(file))) |
---|
| 434 | top_element.appendChild(element) |
---|
[11a7e11] | 435 | |
---|
| 436 | element = newdoc.createElement("timestamp") |
---|
| 437 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
---|
| 438 | attr = newdoc.createAttribute("epoch") |
---|
| 439 | attr.nodeValue = str(self.timestamp) |
---|
| 440 | element.setAttributeNode(attr) |
---|
| 441 | top_element.appendChild(element) |
---|
[61cada5] | 442 | # Inputs |
---|
| 443 | inputs = newdoc.createElement("Attributes") |
---|
| 444 | top_element.appendChild(inputs) |
---|
| 445 | |
---|
[0b12abb5] | 446 | |
---|
[61cada5] | 447 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 448 | self.data_group_id = self.data.group_id |
---|
| 449 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
| 450 | self.is_data = self.data.is_data |
---|
| 451 | if self.data is not None: |
---|
| 452 | self.data_name = self.data.name |
---|
| 453 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 454 | self.data_id = self.data.id |
---|
| 455 | |
---|
[26f3dd5] | 456 | for item in list_of_data_attributes: |
---|
[0b12abb5] | 457 | element = newdoc.createElement(item[0]) |
---|
[61cada5] | 458 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
[0b12abb5] | 459 | inputs.appendChild(element) |
---|
[26f3dd5] | 460 | |
---|
| 461 | for item in list_of_state_attributes: |
---|
| 462 | element = newdoc.createElement(item[0]) |
---|
| 463 | exec "element.setAttribute(item[0], str(self.%s))"%(item[1]) |
---|
| 464 | inputs.appendChild(element) |
---|
[11a7e11] | 465 | |
---|
| 466 | for item in list_of_model_attributes: |
---|
| 467 | element = newdoc.createElement(item[0]) |
---|
| 468 | exec "list = self.%s"%item[1] |
---|
[e9b12eaf] | 469 | for value in list: |
---|
[0b12abb5] | 470 | exec "element.appendChild(newdoc.createTextNode(str(%s)))"%value |
---|
[11a7e11] | 471 | inputs.appendChild(element) |
---|
| 472 | |
---|
[61cada5] | 473 | for item in list_of_state_parameters: |
---|
| 474 | element = newdoc.createElement(item[0]) |
---|
| 475 | exec "self._toXML_helper(list=self.%s, element=element, newdoc=newdoc)"%item[1] |
---|
| 476 | inputs.appendChild(element) |
---|
| 477 | |
---|
| 478 | # Save the file |
---|
| 479 | if doc is None: |
---|
| 480 | fd = open(file, 'w') |
---|
| 481 | fd.write(newdoc.toprettyxml()) |
---|
| 482 | fd.close() |
---|
| 483 | return None |
---|
| 484 | else: |
---|
| 485 | return newdoc.toprettyxml() |
---|
| 486 | |
---|
| 487 | def _fromXML_helper(self, node, list): |
---|
| 488 | """ |
---|
[5062bbf] | 489 | Helper function to write state to xml |
---|
[61cada5] | 490 | """ |
---|
| 491 | for item in node: |
---|
[0b12abb5] | 492 | try: |
---|
| 493 | name = item.get('name') |
---|
| 494 | except: |
---|
| 495 | name = None |
---|
| 496 | try: |
---|
| 497 | value = item.get('value') |
---|
| 498 | except: |
---|
| 499 | value = None |
---|
| 500 | try: |
---|
[3ad91de] | 501 | selected_to_fit = (item.get('selected_to_fit') == "True") |
---|
[0b12abb5] | 502 | except: |
---|
| 503 | selected_to_fit = None |
---|
| 504 | try: |
---|
[3ad91de] | 505 | error_displayed = (item.get('error_displayed') == "True") |
---|
[0b12abb5] | 506 | except: |
---|
| 507 | error_displayed = None |
---|
| 508 | try: |
---|
| 509 | error_value = item.get('error_value') |
---|
| 510 | except: |
---|
| 511 | error_value = None |
---|
| 512 | try: |
---|
[3ad91de] | 513 | minimum_displayed = (item.get('minimum_displayed')== "True") |
---|
[0b12abb5] | 514 | except: |
---|
| 515 | minimum_displayed = None |
---|
| 516 | try: |
---|
| 517 | minimum_value = item.get('minimum_value') |
---|
| 518 | except: |
---|
| 519 | minimum_value = None |
---|
| 520 | try: |
---|
[3ad91de] | 521 | maximum_displayed = (item.get('maximum_displayed') == "True") |
---|
[0b12abb5] | 522 | except: |
---|
| 523 | maximum_displayed = None |
---|
| 524 | try: |
---|
| 525 | maximum_value = item.get('maximum_value') |
---|
| 526 | except: |
---|
| 527 | maximum_value = None |
---|
| 528 | try: |
---|
| 529 | unit = item.get('unit') |
---|
| 530 | except: |
---|
| 531 | unit = None |
---|
[61cada5] | 532 | list.append([selected_to_fit, name, value, "+/-",[error_displayed, error_value], |
---|
| 533 | [minimum_displayed,minimum_value],[maximum_displayed,maximum_value], unit]) |
---|
[cfc0913] | 534 | |
---|
[61cada5] | 535 | def fromXML(self, file=None, node=None): |
---|
| 536 | """ |
---|
[5062bbf] | 537 | Load fitting state from a file |
---|
| 538 | |
---|
| 539 | :param file: .fitv file |
---|
| 540 | :param node: node of a XML document to read from |
---|
| 541 | |
---|
[61cada5] | 542 | """ |
---|
| 543 | if file is not None: |
---|
[11a7e11] | 544 | msg = "PageState no longer supports non-CanSAS" |
---|
| 545 | msg += " format for fitting files" |
---|
| 546 | raise RuntimeError, msg |
---|
[61cada5] | 547 | |
---|
[11a7e11] | 548 | if node.get('version')and node.get('version') == '1.0': |
---|
[61cada5] | 549 | |
---|
| 550 | # Get file name |
---|
| 551 | entry = get_content('ns:filename', node) |
---|
| 552 | if entry is not None: |
---|
| 553 | self.file = entry.text.strip() |
---|
[11a7e11] | 554 | |
---|
| 555 | # Get time stamp |
---|
| 556 | entry = get_content('ns:timestamp', node) |
---|
| 557 | if entry is not None and entry.get('epoch'): |
---|
| 558 | try: |
---|
| 559 | self.timestamp = float(entry.get('epoch')) |
---|
| 560 | except: |
---|
| 561 | msg = "PageState.fromXML: Could not" |
---|
| 562 | msg += " read timestamp\n %s" % sys.exc_value |
---|
| 563 | logging.error(msg) |
---|
| 564 | |
---|
[61cada5] | 565 | # Parse fitting attributes |
---|
| 566 | entry = get_content('ns:Attributes', node) |
---|
[0b12abb5] | 567 | for item in list_of_data_attributes: |
---|
| 568 | node = get_content('ns:%s'%item[0], entry) |
---|
| 569 | try: |
---|
| 570 | exec "self.%s = parse_entry_helper(node, item)"%item[0] |
---|
| 571 | |
---|
| 572 | except: |
---|
| 573 | raise |
---|
| 574 | |
---|
[61cada5] | 575 | if entry is not None: |
---|
[0b12abb5] | 576 | |
---|
[61cada5] | 577 | for item in list_of_state_attributes: |
---|
[0b12abb5] | 578 | node = get_content('ns:%s'%item[0], entry) |
---|
| 579 | try: |
---|
| 580 | exec "self.%s = parse_entry_helper(node, item)"%str(item[0]) |
---|
| 581 | except: |
---|
| 582 | raise |
---|
| 583 | |
---|
[11a7e11] | 584 | for item in list_of_model_attributes: |
---|
| 585 | node = get_content("ns:%s"%item[0], entry) |
---|
| 586 | list = [] |
---|
| 587 | for value in node: |
---|
| 588 | try: |
---|
| 589 | list.append(float(value)) |
---|
| 590 | except: |
---|
| 591 | list.append(None) |
---|
| 592 | exec "self.%s = list"%item[1] |
---|
[0b12abb5] | 593 | |
---|
[61cada5] | 594 | for item in list_of_state_parameters: |
---|
[11a7e11] | 595 | node = get_content("ns:%s"%item[0], entry) |
---|
[0b12abb5] | 596 | exec "self._fromXML_helper(node=node, list=self.%s)"%item[1] |
---|
| 597 | |
---|
[61cada5] | 598 | |
---|
| 599 | class Reader(CansasReader): |
---|
| 600 | """ |
---|
[5062bbf] | 601 | Class to load a .fitv fitting file |
---|
[61cada5] | 602 | """ |
---|
| 603 | ## File type |
---|
| 604 | type_name = "Fitting" |
---|
| 605 | |
---|
| 606 | ## Wildcards |
---|
[b35d3d1] | 607 | type = ["Fitting files (*.fitv)|*.fitv" |
---|
| 608 | "SANSView file (*.svs)|*.svs"] |
---|
[61cada5] | 609 | ## List of allowed extensions |
---|
[b35d3d1] | 610 | ext=['.fitv', '.FITV', '.svs', 'SVS'] |
---|
[61cada5] | 611 | |
---|
| 612 | def __init__(self, call_back=None, cansas=True): |
---|
[df7ed14] | 613 | CansasReader.__init__(self) |
---|
[61cada5] | 614 | """ |
---|
[5062bbf] | 615 | Initialize the call-back method to be called |
---|
| 616 | after we load a file |
---|
| 617 | |
---|
| 618 | :param call_back: call-back method |
---|
| 619 | :param cansas: True = files will be written/read in CanSAS format |
---|
| 620 | False = write CanSAS format |
---|
[61cada5] | 621 | |
---|
| 622 | """ |
---|
| 623 | ## Call back method to be executed after a file is read |
---|
| 624 | self.call_back = call_back |
---|
| 625 | ## CanSAS format flag |
---|
| 626 | self.cansas = cansas |
---|
| 627 | |
---|
| 628 | def read(self, path): |
---|
| 629 | """ |
---|
[5062bbf] | 630 | Load a new P(r) inversion state from file |
---|
| 631 | |
---|
| 632 | :param path: file path |
---|
| 633 | |
---|
[61cada5] | 634 | """ |
---|
[e9b12eaf] | 635 | if self.cansas == True: |
---|
[61cada5] | 636 | return self._read_cansas(path) |
---|
[e9b12eaf] | 637 | |
---|
| 638 | def _data2d_to_xml_doc(self, datainfo): |
---|
[61cada5] | 639 | """ |
---|
[5062bbf] | 640 | Create an XML document to contain the content of a Data2D |
---|
| 641 | |
---|
| 642 | :param datainfo: Data2D object |
---|
| 643 | |
---|
[61cada5] | 644 | """ |
---|
| 645 | if not issubclass(datainfo.__class__, Data2D): |
---|
| 646 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
---|
| 647 | |
---|
| 648 | doc = xml.dom.minidom.Document() |
---|
| 649 | main_node = doc.createElement("SASroot") |
---|
| 650 | main_node.setAttribute("version", self.version) |
---|
[df7ed14] | 651 | main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) |
---|
| 652 | main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance") |
---|
| 653 | main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version) |
---|
| 654 | |
---|
[61cada5] | 655 | doc.appendChild(main_node) |
---|
| 656 | |
---|
| 657 | entry_node = doc.createElement("SASentry") |
---|
| 658 | main_node.appendChild(entry_node) |
---|
[df7ed14] | 659 | |
---|
[61cada5] | 660 | write_node(doc, entry_node, "Title", datainfo.title) |
---|
[df7ed14] | 661 | if datainfo is not None: |
---|
| 662 | write_node(doc, entry_node, "data_class", datainfo.__class__.__name__) |
---|
[61cada5] | 663 | for item in datainfo.run: |
---|
| 664 | runname = {} |
---|
| 665 | if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1: |
---|
| 666 | runname = {'name': datainfo.run_name[item] } |
---|
| 667 | write_node(doc, entry_node, "Run", item, runname) |
---|
| 668 | # Data info |
---|
[df7ed14] | 669 | new_node = doc.createElement("SASdata") |
---|
| 670 | entry_node.appendChild(new_node) |
---|
[e9b12eaf] | 671 | for item in list_of_data_2d_attr: |
---|
| 672 | element = doc.createElement(item[0]) |
---|
| 673 | exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1]) |
---|
[df7ed14] | 674 | new_node.appendChild(element) |
---|
| 675 | |
---|
[e9b12eaf] | 676 | for item in list_of_data2d_values: |
---|
[df7ed14] | 677 | root_node = doc.createElement(item[0]) |
---|
| 678 | new_node.appendChild(root_node) |
---|
| 679 | |
---|
[35b556d] | 680 | exec "temp_list = datainfo.%s"%item[1] |
---|
[df7ed14] | 681 | |
---|
[35b556d] | 682 | if temp_list is None or len(temp_list)== 0: |
---|
[df7ed14] | 683 | element = doc.createElement(item[0]) |
---|
[35b556d] | 684 | exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list |
---|
[df7ed14] | 685 | root_node.appendChild(element) |
---|
[35b556d] | 686 | else: |
---|
| 687 | for value in temp_list: |
---|
[df7ed14] | 688 | element = doc.createElement(item[0]) |
---|
| 689 | exec "element.setAttribute(item[0], str(%s))"%value |
---|
| 690 | root_node.appendChild(element) |
---|
| 691 | |
---|
[61cada5] | 692 | # Sample info |
---|
| 693 | sample = doc.createElement("SASsample") |
---|
| 694 | if datainfo.sample.name is not None: |
---|
| 695 | sample.setAttribute("name", str(datainfo.sample.name)) |
---|
| 696 | entry_node.appendChild(sample) |
---|
| 697 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
---|
| 698 | write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit}) |
---|
| 699 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
---|
| 700 | write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit}) |
---|
| 701 | |
---|
| 702 | for item in datainfo.sample.details: |
---|
| 703 | write_node(doc, sample, "details", item) |
---|
| 704 | |
---|
| 705 | pos = doc.createElement("position") |
---|
| 706 | written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit}) |
---|
| 707 | written = written | write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit}) |
---|
| 708 | written = written | write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit}) |
---|
| 709 | if written == True: |
---|
| 710 | sample.appendChild(pos) |
---|
| 711 | |
---|
| 712 | ori = doc.createElement("orientation") |
---|
| 713 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit}) |
---|
| 714 | written = written | write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit}) |
---|
| 715 | written = written | write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit}) |
---|
| 716 | if written == True: |
---|
| 717 | sample.appendChild(ori) |
---|
| 718 | |
---|
| 719 | # Instrument info |
---|
| 720 | instr = doc.createElement("SASinstrument") |
---|
| 721 | entry_node.appendChild(instr) |
---|
| 722 | |
---|
| 723 | write_node(doc, instr, "name", datainfo.instrument) |
---|
| 724 | |
---|
| 725 | # Source |
---|
| 726 | source = doc.createElement("SASsource") |
---|
| 727 | if datainfo.source.name is not None: |
---|
| 728 | source.setAttribute("name", str(datainfo.source.name)) |
---|
| 729 | instr.appendChild(source) |
---|
| 730 | |
---|
| 731 | write_node(doc, source, "radiation", datainfo.source.radiation) |
---|
| 732 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
---|
| 733 | size = doc.createElement("beam_size") |
---|
| 734 | if datainfo.source.beam_size_name is not None: |
---|
| 735 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
---|
| 736 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit}) |
---|
| 737 | written = written | write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit}) |
---|
| 738 | written = written | write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit}) |
---|
| 739 | if written == True: |
---|
| 740 | source.appendChild(size) |
---|
| 741 | |
---|
| 742 | write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit}) |
---|
| 743 | write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit}) |
---|
| 744 | write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit}) |
---|
| 745 | write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit}) |
---|
| 746 | |
---|
| 747 | # Collimation |
---|
| 748 | for item in datainfo.collimation: |
---|
| 749 | coll = doc.createElement("SAScollimation") |
---|
| 750 | if item.name is not None: |
---|
| 751 | coll.setAttribute("name", str(item.name)) |
---|
| 752 | instr.appendChild(coll) |
---|
| 753 | |
---|
| 754 | write_node(doc, coll, "length", item.length, {"unit":item.length_unit}) |
---|
| 755 | |
---|
| 756 | for apert in item.aperture: |
---|
| 757 | ap = doc.createElement("aperture") |
---|
| 758 | if apert.name is not None: |
---|
| 759 | ap.setAttribute("name", str(apert.name)) |
---|
| 760 | if apert.type is not None: |
---|
| 761 | ap.setAttribute("type", str(apert.type)) |
---|
| 762 | coll.appendChild(ap) |
---|
| 763 | |
---|
| 764 | write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit}) |
---|
| 765 | |
---|
| 766 | size = doc.createElement("size") |
---|
| 767 | if apert.size_name is not None: |
---|
| 768 | size.setAttribute("name", str(apert.size_name)) |
---|
| 769 | written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit}) |
---|
| 770 | written = written | write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit}) |
---|
| 771 | written = written | write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit}) |
---|
| 772 | if written == True: |
---|
| 773 | ap.appendChild(size) |
---|
| 774 | |
---|
| 775 | # Detectors |
---|
| 776 | for item in datainfo.detector: |
---|
| 777 | det = doc.createElement("SASdetector") |
---|
| 778 | written = write_node(doc, det, "name", item.name) |
---|
| 779 | written = written | write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit}) |
---|
| 780 | written = written | write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit}) |
---|
| 781 | if written == True: |
---|
| 782 | instr.appendChild(det) |
---|
| 783 | |
---|
| 784 | off = doc.createElement("offset") |
---|
| 785 | written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit}) |
---|
| 786 | written = written | write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit}) |
---|
| 787 | written = written | write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit}) |
---|
| 788 | if written == True: |
---|
| 789 | det.appendChild(off) |
---|
| 790 | |
---|
| 791 | center = doc.createElement("beam_center") |
---|
| 792 | written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit}) |
---|
| 793 | written = written | write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit}) |
---|
| 794 | written = written | write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit}) |
---|
| 795 | if written == True: |
---|
| 796 | det.appendChild(center) |
---|
| 797 | |
---|
| 798 | pix = doc.createElement("pixel_size") |
---|
| 799 | written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit}) |
---|
| 800 | written = written | write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit}) |
---|
| 801 | written = written | write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit}) |
---|
| 802 | if written == True: |
---|
| 803 | det.appendChild(pix) |
---|
| 804 | |
---|
| 805 | ori = doc.createElement("orientation") |
---|
| 806 | written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit}) |
---|
| 807 | written = written | write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit}) |
---|
| 808 | written = written | write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit}) |
---|
| 809 | if written == True: |
---|
| 810 | det.appendChild(ori) |
---|
| 811 | |
---|
| 812 | # Processes info |
---|
| 813 | for item in datainfo.process: |
---|
| 814 | node = doc.createElement("SASprocess") |
---|
| 815 | entry_node.appendChild(node) |
---|
| 816 | |
---|
| 817 | write_node(doc, node, "name", item.name) |
---|
| 818 | write_node(doc, node, "date", item.date) |
---|
| 819 | write_node(doc, node, "description", item.description) |
---|
| 820 | for term in item.term: |
---|
| 821 | value = term['value'] |
---|
| 822 | del term['value'] |
---|
| 823 | write_node(doc, node, "term", value, term) |
---|
| 824 | for note in item.notes: |
---|
| 825 | write_node(doc, node, "SASprocessnote", note) |
---|
| 826 | # Return the document, and the SASentry node associated with |
---|
| 827 | # the data we just wrote |
---|
| 828 | return doc, entry_node |
---|
[e9b12eaf] | 829 | |
---|
[61cada5] | 830 | def _parse_state(self, entry): |
---|
| 831 | """ |
---|
[5062bbf] | 832 | Read a fit result from an XML node |
---|
| 833 | |
---|
| 834 | :param entry: XML node to read from |
---|
| 835 | |
---|
| 836 | :return: PageState object |
---|
[61cada5] | 837 | """ |
---|
| 838 | # Create an empty state |
---|
[b35d3d1] | 839 | state = None |
---|
[61cada5] | 840 | # Locate the P(r) node |
---|
| 841 | try: |
---|
| 842 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS}) |
---|
[b35d3d1] | 843 | if nodes !=[]: |
---|
| 844 | # Create an empty state |
---|
| 845 | state = PageState() |
---|
| 846 | state.fromXML(node=nodes[0]) |
---|
[61cada5] | 847 | except: |
---|
| 848 | logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value) |
---|
| 849 | |
---|
| 850 | return state |
---|
| 851 | |
---|
[0b12abb5] | 852 | |
---|
[df7ed14] | 853 | |
---|
| 854 | def _parse_entry(self, dom): |
---|
[e9b12eaf] | 855 | """ |
---|
[5062bbf] | 856 | Parse a SASentry |
---|
| 857 | |
---|
| 858 | :param node: SASentry node |
---|
| 859 | |
---|
[df7ed14] | 860 | :return: Data1D/Data2D object |
---|
[5062bbf] | 861 | |
---|
[e9b12eaf] | 862 | """ |
---|
[df7ed14] | 863 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
---|
| 864 | if not node or node[0].text.lstrip().rstrip() != "Data2D": |
---|
| 865 | return CansasReader._parse_entry(self, dom) |
---|
| 866 | |
---|
| 867 | #Parse 2D |
---|
[e9b12eaf] | 868 | data_info = Data2D() |
---|
| 869 | |
---|
| 870 | # Look up title |
---|
| 871 | self._store_content('ns:Title', dom, 'title', data_info) |
---|
| 872 | |
---|
| 873 | # Look up run number |
---|
| 874 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
---|
| 875 | for item in nodes: |
---|
| 876 | if item.text is not None: |
---|
| 877 | value = item.text.strip() |
---|
| 878 | if len(value) > 0: |
---|
| 879 | data_info.run.append(value) |
---|
| 880 | if item.get('name') is not None: |
---|
| 881 | data_info.run_name[value] = item.get('name') |
---|
| 882 | |
---|
| 883 | # Look up instrument name |
---|
| 884 | self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info) |
---|
| 885 | |
---|
| 886 | # Notes |
---|
| 887 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
---|
| 888 | for note in note_list: |
---|
| 889 | try: |
---|
| 890 | if note.text is not None: |
---|
| 891 | note_value = note.text.strip() |
---|
| 892 | if len(note_value) > 0: |
---|
| 893 | data_info.notes.append(note_value) |
---|
| 894 | except: |
---|
| 895 | err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value |
---|
| 896 | self.errors.append(err_mess) |
---|
| 897 | logging.error(err_mess) |
---|
| 898 | |
---|
| 899 | # Sample info ################### |
---|
| 900 | entry = get_content('ns:SASsample', dom) |
---|
| 901 | if entry is not None: |
---|
| 902 | data_info.sample.name = entry.get('name') |
---|
| 903 | |
---|
| 904 | self._store_content('ns:SASsample/ns:ID', |
---|
| 905 | dom, 'ID', data_info.sample) |
---|
| 906 | self._store_float('ns:SASsample/ns:thickness', |
---|
| 907 | dom, 'thickness', data_info.sample) |
---|
| 908 | self._store_float('ns:SASsample/ns:transmission', |
---|
| 909 | dom, 'transmission', data_info.sample) |
---|
| 910 | self._store_float('ns:SASsample/ns:temperature', |
---|
| 911 | dom, 'temperature', data_info.sample) |
---|
| 912 | |
---|
| 913 | nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS}) |
---|
| 914 | for item in nodes: |
---|
| 915 | try: |
---|
| 916 | if item.text is not None: |
---|
| 917 | detail_value = item.text.strip() |
---|
| 918 | if len(detail_value) > 0: |
---|
| 919 | data_info.sample.details.append(detail_value) |
---|
| 920 | except: |
---|
| 921 | err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value |
---|
| 922 | self.errors.append(err_mess) |
---|
| 923 | logging.error(err_mess) |
---|
| 924 | |
---|
| 925 | # Position (as a vector) |
---|
| 926 | self._store_float('ns:SASsample/ns:position/ns:x', |
---|
| 927 | dom, 'position.x', data_info.sample) |
---|
| 928 | self._store_float('ns:SASsample/ns:position/ns:y', |
---|
| 929 | dom, 'position.y', data_info.sample) |
---|
| 930 | self._store_float('ns:SASsample/ns:position/ns:z', |
---|
| 931 | dom, 'position.z', data_info.sample) |
---|
| 932 | |
---|
| 933 | # Orientation (as a vector) |
---|
| 934 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
---|
| 935 | dom, 'orientation.x', data_info.sample) |
---|
| 936 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
---|
| 937 | dom, 'orientation.y', data_info.sample) |
---|
| 938 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
---|
| 939 | dom, 'orientation.z', data_info.sample) |
---|
| 940 | |
---|
| 941 | # Source info ################### |
---|
| 942 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
---|
| 943 | if entry is not None: |
---|
| 944 | data_info.source.name = entry.get('name') |
---|
| 945 | |
---|
| 946 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
---|
| 947 | dom, 'radiation', data_info.source) |
---|
| 948 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
---|
| 949 | dom, 'beam_shape', data_info.source) |
---|
| 950 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
---|
| 951 | dom, 'wavelength', data_info.source) |
---|
| 952 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
---|
| 953 | dom, 'wavelength_min', data_info.source) |
---|
| 954 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
---|
| 955 | dom, 'wavelength_max', data_info.source) |
---|
| 956 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
---|
| 957 | dom, 'wavelength_spread', data_info.source) |
---|
| 958 | |
---|
| 959 | # Beam size (as a vector) |
---|
| 960 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
---|
| 961 | if entry is not None: |
---|
| 962 | data_info.source.beam_size_name = entry.get('name') |
---|
| 963 | |
---|
| 964 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
---|
| 965 | dom, 'beam_size.x', data_info.source) |
---|
| 966 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
---|
| 967 | dom, 'beam_size.y', data_info.source) |
---|
| 968 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
---|
| 969 | dom, 'beam_size.z', data_info.source) |
---|
| 970 | |
---|
| 971 | # Collimation info ################### |
---|
| 972 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS}) |
---|
| 973 | for item in nodes: |
---|
| 974 | collim = Collimation() |
---|
| 975 | if item.get('name') is not None: |
---|
| 976 | collim.name = item.get('name') |
---|
| 977 | self._store_float('ns:length', item, 'length', collim) |
---|
| 978 | |
---|
| 979 | # Look for apertures |
---|
| 980 | apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS}) |
---|
| 981 | for apert in apert_list: |
---|
| 982 | aperture = Aperture() |
---|
| 983 | |
---|
| 984 | # Get the name and type of the aperture |
---|
| 985 | aperture.name = apert.get('name') |
---|
| 986 | aperture.type = apert.get('type') |
---|
| 987 | |
---|
| 988 | self._store_float('ns:distance', apert, 'distance', aperture) |
---|
| 989 | |
---|
| 990 | entry = get_content('ns:size', apert) |
---|
| 991 | if entry is not None: |
---|
| 992 | aperture.size_name = entry.get('name') |
---|
| 993 | |
---|
| 994 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
---|
| 995 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
---|
| 996 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
---|
| 997 | |
---|
| 998 | collim.aperture.append(aperture) |
---|
| 999 | |
---|
| 1000 | data_info.collimation.append(collim) |
---|
| 1001 | |
---|
| 1002 | # Detector info ###################### |
---|
| 1003 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS}) |
---|
| 1004 | for item in nodes: |
---|
| 1005 | |
---|
| 1006 | detector = Detector() |
---|
| 1007 | |
---|
| 1008 | self._store_content('ns:name', item, 'name', detector) |
---|
| 1009 | self._store_float('ns:SDD', item, 'distance', detector) |
---|
| 1010 | |
---|
| 1011 | # Detector offset (as a vector) |
---|
| 1012 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
---|
| 1013 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
---|
| 1014 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
---|
| 1015 | |
---|
| 1016 | # Detector orientation (as a vector) |
---|
| 1017 | self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector) |
---|
| 1018 | self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector) |
---|
| 1019 | self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector) |
---|
| 1020 | |
---|
| 1021 | # Beam center (as a vector) |
---|
| 1022 | self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector) |
---|
| 1023 | self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector) |
---|
| 1024 | self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector) |
---|
| 1025 | |
---|
| 1026 | # Pixel size (as a vector) |
---|
| 1027 | self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector) |
---|
| 1028 | self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector) |
---|
| 1029 | self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector) |
---|
| 1030 | |
---|
| 1031 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
---|
| 1032 | |
---|
| 1033 | data_info.detector.append(detector) |
---|
| 1034 | |
---|
| 1035 | # Processes info ###################### |
---|
| 1036 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
---|
| 1037 | for item in nodes: |
---|
| 1038 | process = Process() |
---|
| 1039 | self._store_content('ns:name', item, 'name', process) |
---|
| 1040 | self._store_content('ns:date', item, 'date', process) |
---|
| 1041 | self._store_content('ns:description', item, 'description', process) |
---|
| 1042 | |
---|
| 1043 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
---|
| 1044 | for term in term_list: |
---|
| 1045 | try: |
---|
| 1046 | term_attr = {} |
---|
| 1047 | for attr in term.keys(): |
---|
| 1048 | term_attr[attr] = term.get(attr).strip() |
---|
| 1049 | if term.text is not None: |
---|
| 1050 | term_attr['value'] = term.text.strip() |
---|
| 1051 | process.term.append(term_attr) |
---|
| 1052 | except: |
---|
| 1053 | err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value |
---|
| 1054 | self.errors.append(err_mess) |
---|
| 1055 | logging.error(err_mess) |
---|
| 1056 | |
---|
| 1057 | note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS}) |
---|
| 1058 | for note in note_list: |
---|
| 1059 | if note.text is not None: |
---|
| 1060 | process.notes.append(note.text.strip()) |
---|
| 1061 | |
---|
| 1062 | data_info.process.append(process) |
---|
| 1063 | |
---|
| 1064 | |
---|
| 1065 | # Data info ###################### |
---|
| 1066 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
---|
| 1067 | if len(nodes)>1: |
---|
| 1068 | raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries" |
---|
[df7ed14] | 1069 | |
---|
| 1070 | for entry in nodes: |
---|
| 1071 | for item in list_of_data_2d_attr: |
---|
| 1072 | #get node |
---|
| 1073 | node = get_content('ns:%s'%item[0], entry) |
---|
[0b12abb5] | 1074 | exec "data_info.%s = parse_entry_helper(node, item)"%(item[1]) |
---|
[e9b12eaf] | 1075 | |
---|
[df7ed14] | 1076 | for item in list_of_data2d_values: |
---|
| 1077 | field = get_content('ns:%s'%item[0], entry) |
---|
| 1078 | list = [] |
---|
| 1079 | if field is not None: |
---|
[0b12abb5] | 1080 | list = [parse_entry_helper(node, item) for node in field] |
---|
[df7ed14] | 1081 | exec "data_info.%s = numpy.array(list)"%item[0] |
---|
[e9b12eaf] | 1082 | |
---|
| 1083 | return data_info |
---|
| 1084 | |
---|
[61cada5] | 1085 | def _read_cansas(self, path): |
---|
| 1086 | """ |
---|
[5062bbf] | 1087 | Load data and P(r) information from a CanSAS XML file. |
---|
| 1088 | |
---|
| 1089 | :param path: file path |
---|
| 1090 | |
---|
| 1091 | :return: Data1D object if a single SASentry was found, |
---|
| 1092 | or a list of Data1D objects if multiple entries were found, |
---|
| 1093 | or None of nothing was found |
---|
| 1094 | |
---|
| 1095 | :raise RuntimeError: when the file can't be opened |
---|
| 1096 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
| 1097 | |
---|
[61cada5] | 1098 | """ |
---|
| 1099 | output = [] |
---|
[b63dc6e] | 1100 | basename = os.path.basename(path) |
---|
| 1101 | root, extension = os.path.splitext(basename) |
---|
| 1102 | ext = extension.lower() |
---|
[61cada5] | 1103 | try: |
---|
| 1104 | if os.path.isfile(path): |
---|
[b63dc6e] | 1105 | |
---|
[61cada5] | 1106 | #TODO: eventually remove the check for .xml once |
---|
| 1107 | # the P(r) writer/reader is truly complete. |
---|
[b63dc6e] | 1108 | if ext in self.ext or \ |
---|
| 1109 | ext == '.xml': |
---|
[61cada5] | 1110 | |
---|
| 1111 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
| 1112 | # Check the format version number |
---|
| 1113 | # Specifying the namespace will take care of the file format version |
---|
| 1114 | root = tree.getroot() |
---|
[df7ed14] | 1115 | entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS}) |
---|
[b35d3d1] | 1116 | for entry in entry_list: |
---|
[e9b12eaf] | 1117 | try: |
---|
| 1118 | sas_entry = self._parse_entry(entry) |
---|
| 1119 | except: |
---|
[df7ed14] | 1120 | raise |
---|
[61cada5] | 1121 | fitstate = self._parse_state(entry) |
---|
[b35d3d1] | 1122 | |
---|
| 1123 | #state could be None when .svs file is loaded |
---|
| 1124 | #in this case, skip appending to output |
---|
| 1125 | if fitstate != None: |
---|
| 1126 | sas_entry.meta_data['fitstate'] = fitstate |
---|
| 1127 | sas_entry.filename = fitstate.file |
---|
| 1128 | output.append(sas_entry) |
---|
[61cada5] | 1129 | else: |
---|
[b63dc6e] | 1130 | self.call_back(format=ext) |
---|
[61cada5] | 1131 | raise RuntimeError, "%s is not a file" % path |
---|
[b35d3d1] | 1132 | |
---|
[61cada5] | 1133 | # Return output consistent with the loader's api |
---|
| 1134 | if len(output)==0: |
---|
[b63dc6e] | 1135 | self.call_back(state=None, datainfo=None,format=ext) |
---|
[61cada5] | 1136 | return None |
---|
| 1137 | else: |
---|
[b35d3d1] | 1138 | for ind in range(len(output)): |
---|
| 1139 | # Call back to post the new state |
---|
| 1140 | state = output[ind].meta_data['fitstate'] |
---|
| 1141 | t = time.localtime(state.timestamp) |
---|
| 1142 | time_str = time.strftime("%b %d %H:%M", t) |
---|
| 1143 | # Check that no time stamp is already appended |
---|
| 1144 | max_char = state.file.find("[") |
---|
| 1145 | if max_char < 0: |
---|
| 1146 | max_char = len(state.file) |
---|
[ef16f59] | 1147 | original_fname = state.file[0:max_char] |
---|
| 1148 | state.file = original_fname +' [' + time_str + ']' |
---|
[b35d3d1] | 1149 | |
---|
| 1150 | |
---|
| 1151 | if state is not None and state.is_data is not None: |
---|
| 1152 | exec 'output[%d].is_data = state.is_data'% ind |
---|
| 1153 | |
---|
| 1154 | output[ind].filename = state.file |
---|
| 1155 | state.data = output[ind] |
---|
| 1156 | state.data.name = output[ind].filename #state.data_name |
---|
| 1157 | state.data.id = state.data_id |
---|
| 1158 | if state.is_data is not None: |
---|
| 1159 | state.data.is_data = state.is_data |
---|
[ef16f59] | 1160 | if output[ind].run_name is not None and len(output[ind].run_name) != 0 : |
---|
| 1161 | name = output[ind].run_name |
---|
| 1162 | else: |
---|
| 1163 | name=original_fname |
---|
| 1164 | state.data.group_id = name |
---|
| 1165 | #store state in fitting |
---|
[b63dc6e] | 1166 | self.call_back(state=state, datainfo=output[ind],format=ext) |
---|
[ef16f59] | 1167 | return output |
---|
[b35d3d1] | 1168 | |
---|
[61cada5] | 1169 | except: |
---|
[b63dc6e] | 1170 | self.call_back(format=ext) |
---|
[61cada5] | 1171 | raise |
---|
| 1172 | |
---|
| 1173 | def write(self, filename, datainfo=None, fitstate=None): |
---|
| 1174 | """ |
---|
[b35d3d1] | 1175 | Write the content of a Data1D as a CanSAS XML file only for standalone |
---|
[5062bbf] | 1176 | |
---|
| 1177 | :param filename: name of the file to write |
---|
| 1178 | :param datainfo: Data1D object |
---|
| 1179 | :param fitstate: PageState object |
---|
| 1180 | |
---|
[61cada5] | 1181 | """ |
---|
| 1182 | # Sanity check |
---|
| 1183 | if self.cansas == True: |
---|
| 1184 | |
---|
| 1185 | # Add fitting information to the XML document |
---|
[ef16f59] | 1186 | doc = self.write_toXML(datainfo, fitstate) |
---|
[61cada5] | 1187 | # Write the XML document |
---|
| 1188 | fd = open(filename, 'w') |
---|
| 1189 | fd.write(doc.toprettyxml()) |
---|
| 1190 | fd.close() |
---|
| 1191 | else: |
---|
| 1192 | fitstate.toXML(file=filename) |
---|
| 1193 | |
---|
[b35d3d1] | 1194 | def write_toXML(self, datainfo=None, state=None): |
---|
| 1195 | """ |
---|
| 1196 | Write toXML, a helper for write() , could be used by guimanager._on_save() |
---|
| 1197 | |
---|
| 1198 | : return: xml doc |
---|
| 1199 | """ |
---|
[3c44c66] | 1200 | |
---|
[b35d3d1] | 1201 | if state.data is None: |
---|
| 1202 | data = DataLoader.data_info.Data1D(x=[], y=[]) |
---|
| 1203 | else: |
---|
| 1204 | #make sure title and data run is filled up. |
---|
[028a0e8] | 1205 | if state.data.title == None or state.data.title=='': state.data.title = state.data.name |
---|
| 1206 | if state.data.run_name == None or state.data.run_name=={}: |
---|
| 1207 | state.data.run = [str(state.data.name)] |
---|
| 1208 | state.data.run_name[0] = state.data.name |
---|
[b35d3d1] | 1209 | |
---|
| 1210 | if issubclass(state.data.__class__, DataLoader.data_info.Data1D): |
---|
[028a0e8] | 1211 | |
---|
[b35d3d1] | 1212 | data = state.data |
---|
| 1213 | doc, sasentry = self._to_xml_doc(data) |
---|
| 1214 | else: |
---|
| 1215 | data = state.data |
---|
| 1216 | doc, sasentry = self._data2d_to_xml_doc(data) |
---|
| 1217 | |
---|
| 1218 | |
---|
| 1219 | if state is not None: |
---|
| 1220 | state.toXML(doc=doc, file=data.name, entry_node=sasentry) |
---|
| 1221 | |
---|
| 1222 | return doc |
---|
[5062bbf] | 1223 | |
---|
[3c44c66] | 1224 | if __name__ == "__main__": |
---|
| 1225 | state = PageState(parent=None) |
---|
| 1226 | #state.toXML() |
---|
| 1227 | """ |
---|
[5062bbf] | 1228 | |
---|
[3c44c66] | 1229 | file = open("test_state", "w") |
---|
| 1230 | pickle.dump(state, file) |
---|
| 1231 | print pickle.dumps(state) |
---|
| 1232 | state.data_name = "hello---->" |
---|
| 1233 | pickle.dump(state, file) |
---|
| 1234 | file = open("test_state", "r") |
---|
| 1235 | new_state= pickle.load(file) |
---|
| 1236 | print "new state", new_state |
---|
| 1237 | new_state= pickle.load(file) |
---|
| 1238 | print "new state", new_state |
---|
| 1239 | #print "state", state |
---|
| 1240 | """ |
---|
| 1241 | import bsddb |
---|
| 1242 | import pickle |
---|
| 1243 | db= bsddb.btopen('file_state.db', 'c') |
---|
| 1244 | val = (pickle.dumps(state), "hello", "hi") |
---|
| 1245 | db['state1']= pickle.dumps(val) |
---|
| 1246 | print pickle.loads(db['state1']) |
---|
| 1247 | state.data_name = "hello---->22" |
---|
| 1248 | db['state2']= pickle.dumps(state) |
---|
| 1249 | state.data_name = "hello---->2" |
---|
| 1250 | db['state3']= pickle.dumps(state) |
---|
| 1251 | del db['state3'] |
---|
| 1252 | state.data_name = "hello---->3" |
---|
| 1253 | db['state4']= pickle.dumps(state) |
---|
| 1254 | new_state = pickle.loads(db['state1']) |
---|
| 1255 | #print db.last() |
---|
| 1256 | db.set_location('state2') |
---|
| 1257 | state.data_name = "hello---->5" |
---|
| 1258 | db['aastate5']= pickle.dumps(state) |
---|
| 1259 | db.keys().sort() |
---|
| 1260 | print pickle.loads(db['state2']) |
---|
| 1261 | |
---|
| 1262 | db.close() |
---|